PLoS Computational Biology, Volume 15

Volume 15, Number 1, January 2019

Editorials

• 
  Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist:
  Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.
• 
  Fran Lewitter, Philip E. Bourne, Teresa K. Attwood:
  Ten Simple Rules for avoiding and resolving conflicts with your colleagues.
• 
  Christopher J. Lortie:
  Ten simple rules for writing statistical book reviews.

Education

• 
  Fatma Z. Guerfali, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia:
  Designing and running an advanced Bioinformatics and genome analyses course in Tunisia.

Research Articles

• 
  Joel Ostblom, Emanuel J. P. Nazareth, Mukul Tewary, Peter W. Zandstra:
  Context-explorer: Analysis of spatially organized protein expression in high-throughput screens.
• 
  Song-Yao Zhang, Shaowu Zhang, Xiaonan Fan, Jia Meng, Yidong Chen, Shou-Jiang Gao, Yufei Huang:
  Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods.
• 
  Mehrdad Salmasi, Alex Loebel, Stefan Glasauer, Martin Stemmler:
  Short-term synaptic depression can increase the rate of information transfer at a release site.
• 
  Anna C. Sales, Karl J. Friston, Matthew W. Jones, Anthony E. Pickering, Rosalyn J. Moran:
  Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model.
• 
  Jignesh H. Parmar, Pedro Mendes:
  A computational model to understand mouse iron physiology and disease.
• 
  Fabien Vinckier, Lionel Rigoux, Irma T. Kurniawan, Chen Hu, Sacha Bourgeois-Gironde, Jean Daunizeau, Mathias Pessiglione:
  Sour grapes and sweet victories: How actions shape preferences.
• 
  Tomasz Wojdyla, Hrishikesh Mehta, Taly Glaubach, Roberto Bertolusso, Marta Iwanaszko, Rosemary Braun, Seth J. Corey, Marek Kimmel:
  Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia.
• 
  Raji Viswanathan, J. Eduardo Fajardo, Gabriel Steinberg, Matthew Haller, András Fiser:
  Protein - protein binding supersites.
• 
  Sathyavani Malyala, Yizhu Zhang, Jasiel O. Strubbe, Jason N. Bazil:
  Calcium phosphate precipitation inhibits mitochondrial energy metabolism.
• 
  Matías Fuentealba, Handan Melike Dönertas, Rhianna Williams, Johnathan Labbadia, Janet M. Thornton, Linda Partridge:
  Using the drug-protein interactome to identify anti-ageing compounds for humans.
• 
  Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared Broddrick, Karsten Zengler, Bernhard O. Palsson:
  A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.
• 
  Douglas K. Brubaker, Elizabeth A. Proctor, Kevin M. Haigis, Douglas A. Lauffenburger:
  Computational translation of genomic responses from experimental model systems to humans.
• 
  Deena M. A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Ping-Jiang Cao, Lincoln D. Stein, Julie M. Wilson, John M. S. Bartlett, Ming-Sound Tsao, Neesha Dhani, David Hedley, Steven Gallinger, Benjamin Haibe-Kains:
  Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.
• 
  Guohua Shen, Tomoyasu Horikawa, Kei Majima, Yukiyasu Kamitani:
  Deep image reconstruction from human brain activity.
• 
  Yuan-Hao Hsu, Claire Churchhouse, Tune H. Pers, Josep M. Mercader, Andres Metspalu, Krista Fischer, Kristen Fortney, Eric K. Morgen, Clicerio Gonzalez, Maria E. Gonzalez, Tõnu Esko, Joel Hirschhorn:
  PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data.
• 
  Zachary R. Fox, Brian Munsky:
  The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments.
• 
  Dheeraj Dube, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal, Surajit Sengupta:
  On identifying collective displacements in apo-proteins that reveal eventual binding pathways.
• 
  Ada W. C. Yan, Sophie G. Zaloumis, Julie A. Simpson, James M. McCaw:
  Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection.
• 
  Abdul-Saboor Sheikh, Nicol S. Harper, Jakob Drefs, Yosef Singer, Zhenwen Dai, Richard E. Turner, Jörg Lücke:
  STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds.
• 
  Keesha E. Erickson, Oleksii S. Rukhlenko, MD Shahinuzzaman, Kalina P. Slavkova, Yen Ting Lin, Ryan Suderman, Edward C. Stites, Marian Anghel, Richard G. Posner, Dipak Barua, Boris N. Kholodenko, William S. Hlavacek:
  Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor.
• 
  Alejandra Gonzalez, Shadi Jafari, Alberto Zenere, Mattias Alenius, Claudio Altafini:
  Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila.
• 
  Carlos Alquezar-Baeta, Silvia Gimeno-Martos, Sara Miguel-Jiménez, Pilar Santolaria, Jesús Yániz, Inmaculada Palacín, Adriana Casao, José Álvaro Cebrián-Pérez, Teresa Muiño-Blanco, Rosaura Pérez-Pé:
  OpenCASA: A new open-source and scalable tool for sperm quality analysis.
• 
  David J. Haw, Derek A. T. Cummings, Justin Lessler, Henrik Salje, Jonathan M. Read, Steven Riley:
  Differential mobility and local variation in infection attack rate.
• 
  Wayne Adams, James N. Graham, Xuchen Han, Hermann Riecke:
  Top-down inputs drive neuronal network rewiring and context-enhanced sensory processing in olfaction.
• 
  Rafael D'Andrea, Maria A. Riolo, Annette Ostling:
  Generalizing clusters of similar species as a signature of coexistence under competition.
• 
  Debmalya Chakrabarty, Mounya Elhilali:
  A Gestalt inference model for auditory scene segregation.
• 
  Carmen Lía Murall, Robert Jackson, Ingeborg Zehbe, Nathalie Boulle, Michel Segondy, Samuel Alizon:
  Epithelial stratification shapes infection dynamics.
• 
  Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau:
  Multi-study inference of regulatory networks for more accurate models of gene regulation.
• 
  David Hodgson, Andrew D. Rowan, Francesco Falciani, Carole J. Proctor:
  Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli.
• 
  Anika Küken, Jeanne M. O. Eloundou-Mbebi, Georg Basler, Zoran Nikoloski:
  Cellular determinants of metabolite concentration ranges.
• 
  Xiaohu Hu, Yibo Wang, Amanda Hunkele, Davide Provasi, Gavril W. Pasternak, Marta Filizola:
  Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis.
• 
  Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas:
  A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism.
• 
  Joseph D. Monaco, Rose M. De Guzman, Hugh T. Blair, Kechen Zhang:
  Spatial synchronization codes from coupled rate-phase neurons.
• 
  Timothy Majarian, Robert F. Murphy, Seema S. Lakdawala:
  Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization.
• 
  Margot C. Bjoring, C. Daniel Meliza:
  A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex.
• 
  Jordan J. Clark, Mark L. Benson, Richard D. Smith, Heather A. Carlson:
  Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures.
• 
  Alessandro Di Stefano, Marialisa Scatà, Supreeta Vijayakumar, Claudio Angione, Aurelio La Corte, Pietro Liò:
  Social dynamics modeling of chrono-nutrition.
• 
  Sulav Duwal, Laura Dickinson, Saye Khoo, Max von Kleist:
  Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis.
• 
  Itay Katzir, Murat Cokol, Bree B. Aldridge, Uri Alon:
  Prediction of ultra-high-order antibiotic combinations based on pairwise interactions.
• 
  Laurent Mombaerts, Alberto Carignano, Fiona C. Robertson, Timothy J. Hearn, Jin Junyang, David P. Hayden, Zoe Rutterford, Carlos T. Hotta, Katherine E. Hubbard, Marti Ruiz C. Maria, Ye Yuan, Matthew A. Hannah, Jorge M. Gonçalves, Alex Webb:
  Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator.
• 
  Dimitrije Markovic, Andrea M. F. Reiter, Stefan J. Kiebel:
  Predicting change: Approximate inference under explicit representation of temporal structure in changing environments.

Corrections

• 
  Correction: clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.
• 
  Notice of Republication: Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects.

Volume 15, Number 2, February 2019

Editorial

• 
  PLOS Computational Biology 2018 Reviewer and Editorial Board Thank You.

Education

• 
  Ana Julia Velez Rueda, Guillermo I. Benítez, Julia Marchetti, Marcia Anahi Hasenahuer, María Silvina Fornasari, Nicolas Palopoli, Gustavo D. Parisi:
  Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools.

Research Articles

• 
  Dave Osthus, Ashlynn R. Daughton, Reid Priedhorsky:
  Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited.
• 
  Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt:
  RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion.
• 
  Stephanie L. Barnes, Nathan M. Belliveau, William T. Ireland, Justin B. Kinney, Rob Phillips:
  Mapping DNA sequence to transcription factor binding energy in vivo.
• 
  Honda Naoki, Ryutaro Akiyama, Dini Wahyu Kartika Sari, Shin Ishii, Yasumasa Bessho, Takaaki Matsui:
  Noise-resistant developmental reproducibility in vertebrate somite formation.
• 
  Ahmed A. Metwally, Philip S. Yu, Derek Reiman, Yang Dai, Patricia W. Finn, David L. Perkins:
  Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks.
• 
  Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine, Hsiao-Chun Wu, Michal Brylinski:
  DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network.
• 
  David V. McLeod, Troy Day:
  Social evolution under demographic stochasticity.
• 
  Wan Yang, Juan Li, Jeffrey Shaman:
  Characteristics of measles epidemics in China (1951-2004) and implications for elimination: A case study of three key locations.
• 
  Robert Marsland III, Cui Wenping, Joshua Goldford, Alvaro Sanchez, Kirill S. Korolev, Pankaj Mehta:
  Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.
• 
  Amin Allahyar, Joske Ubels, Jeroen de Ridder:
  A data-driven interactome of synergistic genes improves network-based cancer outcome prediction.
• 
  Nathan A. Dunn, Deepak R. Unni, Colin M. Diesh, Monica C. Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis:
  Apollo: Democratizing genome annotation.
• 
  Lior Tiroshi, Joshua A. Goldberg:
  Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors.
• 
  Simon N. Weber, Henning Sprekeler:
  A local measure of symmetry and orientation for individual spikes of grid cells.
• 
  Daniel Toker, Friedrich T. Sommer:
  Information integration in large brain networks.
• 
  Aleix Lafita, Spencer Bliven, Andreas Prlic, Dmytro Guzenko, Peter W. Rose, Anthony R. Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael L. Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte:
  BioJava 5: A community driven open-source bioinformatics library.
• 
  Abhishek Niroula, Mauno Vihinen:
  How good are pathogenicity predictors in detecting benign variants?
• 
  Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph:
  Network-guided prediction of aromatase inhibitor response in breast cancer.
• 
  Qingtian Zhang, Xiaolin Hu, Bo Hong, Bo Zhang:
  A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex.
• 
  Nicholas Rogers, John Hermiz, Mehran Ganji, Erik J. Kaestner, Kivilcim Kiliç, Lorraine Hossain, Martin Thunemann, Daniel R. Cleary, Bob S. Carter, David Barba, Anna Devor, Eric Halgren, Shadi A. Dayeh, Vikash Gilja:
  Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components.
• 
  Julien Moukhtar, Alain Trubuil, Katia Belcram, David Legland, Zhor Khadir, Aurélie Urbain, Jean-Christophe Palauqui, Philippe Andrey:
  Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos.
• 
  Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind M. Eggo, W. John Edmunds:
  Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.
• 
  Damien G. Hicks, Terence P. Speed, Mohammed Yassin, Sarah M. Russell:
  Maps of variability in cell lineage trees.
• 
  Yangchun Frank Chen, Yu Xia:
  Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes.
• 
  Nitzan Shahar, Tobias U. Hauser, Michael Moutoussis, Rani Moran, Mehdi Keramati, Raymond J. Dolan:
  Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling.
• 
  Giuseppe Passucci, Megan E. Brasch, James H. Henderson, Vasily Zaburdaev, M. Lisa Manning:
  Identifying the mechanism for superdiffusivity in mouse fibroblast motility.
• 
  Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma:
  IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.
• 
  Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Shizhuo Yu, Bertram Ludäscher:
  Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.
• 
  Ardi Tampuu, Tambet Matiisen, H. Freyja Ólafsdóttir, Caswell Barry, Raul Vicente:
  Efficient neural decoding of self-location with a deep recurrent network.
• 
  Rachel Marceau West, Wenbin Lu, Daniel M. Rotroff, Mélaine A. Kuenemann, Sheng-Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger-Reif, Denis Fourches, Jung-Ying Tzeng:
  Identifying individual risk rare variants using protein structure guided local tests (POINT).
• 
  Ivar Grytten, Knut D. Rand, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve:
  Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.
• 
  Masayuki Maeda, Hideaki Yamashita:
  A numerical approach for a discrete Markov model for progressing drug resistance of cancer.
• 
  He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng:
  A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.
• 
  Muhammad Ali Al-Radhawi, Domitilla Del Vecchio, Eduardo D. Sontag:
  Multi-modality in gene regulatory networks with slow promoter kinetics.
• 
  Koichiro Uriu, Hajime Tei:
  A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks.
• 
  Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao:
  Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.
• 
  Daniel Rüdiger, Sascha Young Kupke, Tanja Laske, Pawel Zmora, Udo Reichl:
  Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions.
• 
  David G. P. van IJzendoorn, Karoly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V. M. G. Bovée:
  Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas.
• 
  David Aagten-Murphy, Paul M. Bays:
  Independent working memory resources for egocentric and allocentric spatial information.
• 
  Tyler Funnell, Allen W. Zhang, Diljot Grewal, Steven McKinney, Ali Bashashati, Yi Kan Wang, Sohrab P. Shah:
  Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models.
• 
  Nir Even-Chen, Blue Sheffer, Saurabh Vyas, Stephen I. Ryu, Krishna V. Shenoy:
  Structure and variability of delay activity in premotor cortex.
• 
  Anita T. Layton, Harold E. Layton:
  A computational model of epithelial solute and water transport along a human nephron.
• 
  Tuan Pham, Julie S. Haas:
  Electrical synapses regulate both subthreshold integration and population activity of principal cells in response to transient inputs within canonical feedforward circuits.
• 
  Simona Olmi, Spase Petkoski, Maxime Guye, Fabrice Bartolomei, Viktor K. Jirsa:
  Controlling seizure propagation in large-scale brain networks.
• 
  Stephen Woloszynek, Zhengqiao Zhao, Jian Chen, Gail L. Rosen:
  16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses.
• 
  Cornelia Metzig, Oliver Ratmann, Daniela Bezemer, Caroline Colijn:
  Phylogenies from dynamic networks.
• 
  Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance:
  CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis.
• 
  Sarah C. Kramer, Jeffrey Shaman:
  Development and validation of influenza forecasting for 64 temperate and tropical countries.
• 
  Jorge Fernandez-de-Cossío-Diaz, Roberto Mulet:
  Maximum entropy and population heterogeneity in continuous cell cultures.
• 
  Gao Wang, Bo Peng:
  Script of Scripts: A pragmatic workflow system for daily computational research.
• 
  Moritz Möller, Rafal Bogacz:
  Learning the payoffs and costs of actions.
• 
  Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans V. Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri:
  Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.
• 
  Sen Pei, Mark A. Cane, Jeffrey Shaman:
  Predictability in process-based ensemble forecast of influenza.
• 
  Shayne M. Plourde, Prativa Amom, Michelle Tan, Adriana T. Dawes, Anna A. Dobritsa:
  Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana.
• 
  Alejandro Tabas, Martin Andermann, Valeria Schuberth, Helmut Riedel, Emili Balaguer-Ballester, André Rupp:
  Modeling and MEG evidence of early consonance processing in auditory cortex.
• 
  Moritz Hoffmann, Christoph Fröhner, Frank Noé:
  ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics.

Correction

• 
  Dariusz Matlak, Ewa Szczurek:
  Correction: Epistasis in genomic and survival data of cancer patients.

Volume 15, Number 3, March 2019

Education

• 
  Tomasz Miksa, Stephanie Renee Simms, Daniel Mietchen, Sarah Jones:
  Ten principles for machine-actionable data management plans.

Reviews

• 
  Chad M. Glen, Melissa L. Kemp, Eberhard O. Voit:
  Agent-based modeling of morphogenetic systems: Advantages and challenges.
• 
  Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng:
  Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.

Research Articles

• 
  Colton J. Lloyd, Zachary A. King, Troy E. Sandberg, Ying Hefner, Connor A. Olson, Patrick V. Phaneuf, Edward J. O'Brien, Jon G. Sanders, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Rob Knight, Adam M. Feist:
  The genetic basis for adaptation of model-designed syntrophic co-cultures.
• 
  Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing:
  Spatial clustering and common regulatory elements correlate with coordinated gene expression.
• 
  Joshua H. Goldwyn, Michiel W. H. Remme, John Rinzel:
  Soma-axon coupling configurations that enhance neuronal coincidence detection.
• 
  Marc de Kamps, Mikkel E. Lepperød, Yi Ming Lai:
  Computational geometry for modeling neural populations: From visualization to simulation.
• 
  Joshua G. A. Cashaback, Christopher K. Lao, Dimitrios J. Palidis, Susan K. Coltman, Heather R. McGregor, Paul L. Gribble:
  The gradient of the reinforcement landscape influences sensorimotor learning.
• 
  Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora:
  Genesis of the αβ T-cell receptor.
• 
  Marieke Rohde, Kenichi Narioka, Jochen J. Steil, Lina K. Klein, Marc O. Ernst:
  Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition.
• 
  Mohamed Mounir, Marta Lucchetta, Tiago Chedraoui Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo:
  New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.
• 
  Karin Münch, Richard Münch, Rebekka Biedendieck, Dieter Jahn, Johannes Müller:
  Evolutionary model for the unequal segregation of high copy plasmids.
• 
  David R. Berg, Chetan Offord, Iris Kemler, Matthew K. Ennis, Lawrence Chang, George F. Paulik, Zeljko Bajzer, Claudia Neuhauser, David Dingli:
  In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics.
• 
  Maor Grinberg, Tomer Orevi, Nadav Kashtan:
  Bacterial surface colonization, preferential attachment and fitness under periodic stress.
• 
  Songting Li, Nan Liu, Li Yao, Xiaohui Zhang, Douglas Zhou, David Cai:
  Determination of effective synaptic conductances using somatic voltage clamp.
• 
  Florian Eberhardt, Andreas V. M. Herz, Stefan Häusler:
  Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits.
• 
  Yuri Kheifetz, Markus Scholz:
  Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy.
• 
  Jonathan B. Dingwell, Joseph P. Cusumano:
  Humans use multi-objective control to regulate lateral foot placement when walking.
• 
  Robert John Holash, Brian MacIntosh:
  A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell.
• 
  Maxim V. Shapovalov, Slobodan Vucetic, Roland L. Dunbrack Jr.:
  A new clustering and nomenclature for beta turns derived from high-resolution protein structures.
• 
  Enrico Riccardi, Eva C. van Mastbergen, William Wiley Navarre, Jocelyne Vreede:
  Predicting the mechanism and rate of H-NS binding to AT-rich DNA.
• 
  Joanne K. Liu, Colton J. Lloyd, Mahmoud M. Al-Bassam, Ali Ebrahim, Ji-Nu Kim, Connor A. Olson, Alexander Aksenov, Pieter C. Dorrestein, Karsten Zengler:
  Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen.
• 
  Yujie Ye, Xin Kang, Jordan Bailey, Chunhe Li, Tian Hong:
  An enriched network motif family regulates multistep cell fate transitions with restricted reversibility.
• 
  Solveig Engebretsen, Kenth Engø-Monsen, Arnoldo Frigessi, Birgitte Freiesleben de Blasio:
  A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions.
• 
  Ramu Anandakrishnan, Robin T. Varghese, Nicholas Kinney, Harold R. Garner:
  Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations.
• 
  Alfredo Rago, Kostas Kouvaris, Tobias Uller, Richard A. Watson:
  How adaptive plasticity evolves when selected against.
• 
  Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Kevin Alessandri, Pierre Nassoy, Dirk Drasdo:
  Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines.
• 
  Agustin Lage-Castellanos, Giancarlo Valente, Elia Formisano, Federico De Martino:
  Methods for computing the maximum performance of computational models of fMRI responses.
• 
  Lilith K. Whittles, Peter J. White, Xavier Didelot:
  A dynamic power-law sexual network model of gonorrhoea outbreaks.
• 
  Giovanni Marini, Giorgio Guzzetta, Cecilia Marques-Toledo, Mauro Teixeira, Roberto Rosà, Stefano Merler:
  Effectiveness of Ultra-Low Volume insecticide spraying to prevent dengue in a non-endemic metropolitan area of Brazil.
• 
  Andrea Avena-Koenigsberger, Xiaoran Yan, Artemy Kolchinsky, Martijn P. van den Heuvel, Patric Hagmann, Olaf Sporns:
  A spectrum of routing strategies for brain networks.
• 
  Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D. Price, Chenguang Liu, Zhuo Wang:
  OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.
• 
  Pei-Chi Yang, Shweta Purawat, Pek U. Ieong, Mao-Tsuen Jeng, Kevin R. DeMarco, Igor Vorobyov, Andrew D. McCulloch, Ilkay Altintas, Rommie E. Amaro, Colleen E. Clancy:
  A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.
• 
  Rodoniki Athanasiadou, Benjamin Neymotin, Nathan Brandt, Wei Wang, Lionel A. Christiaen, David Gresham, Daniel Tranchina:
  A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory.
• 
  Bernardo P. de Almeida, André F. Vieira, Joana Paredes, Mónica Bettencourt-Dias, Nuno L. Barbosa-Morais:
  Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome.
• 
  Margaret P. Chapman, Tyler T. Risom, Anil Aswani, Ellen M. Langer, Rosalie C. Sears, Claire J. Tomlin:
  Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer.
• 
  David Hocker, Il Memming Park:
  Myopic control of neural dynamics.
• 
  Daan H. de Groot, Coco van Boxtel, Robert Planqué, Frank J. Bruggeman, Bas Teusink:
  The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates.
• 
  Shariq N. Iqbal, Lun Yin, Caroline B. Drucker, Qian Kuang, Jean-François Gariépy, Michael L. Platt, John M. Pearson:
  Latent goal models for dynamic strategic interaction.
• 
  Niceto R. Luque, Francisco Naveros, Richard R. Carrillo, Eduardo Ros, Angelo Arleo:
  Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation.
• 
  Can Eren Sezener, Amir Dezfouli, Mohammad Mehdi Keramati:
  Optimizing the depth and the direction of prospective planning using information values.
• 
  Jacopo Bono, Claudia Clopath:
  Synaptic plasticity onto inhibitory neurons as a mechanism for ocular dominance plasticity.
• 
  Sifat Afroj Moon, Lee W. Cohnstaedt, D. Scott McVey, Caterina M. Scoglio:
  A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus.
• 
  Manh Cuong Ngô, Mads Peter Heide-Jørgensen, Susanne Ditlevsen:
  Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence.
• 
  Andrey V. Dmitriev, Alexander A. Dmitriev, Robert A. Linsenmeier:
  The logic of ionic homeostasis: Cations are for voltage, but not for volume.
• 
  Herbert Sizek, Andrew Hamel, Dávid Deritei, Sarah Campbell, Erzsébet Ravasz Regan:
  Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K.
• 
  Nina Kudryashova, Aygul Nizamieva, Valeriya Tsvelaya, Alexander V. Panfilov, Konstantin I. Agladze:
  Self-organization of conducting pathways explains electrical wave propagation in cardiac tissues with high fraction of non-conducting cells.
• 
  Paul C. Bressloff:
  Stochastic neural field model of stimulus-dependent variability in cortical neurons.
• 
  Christopher DiMattina, Curtis L. Baker Jr.:
  Modeling second-order boundary perception: A machine learning approach.
• 
  Eugenio Valdano, Susanna Manrubia, Sergio Gómez, Alex Arenas:
  Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission.
• 
  Mphatso Kalemera, Dilyana Mincheva, Joe Grove, Christopher J. R. Illingworth:
  Building a mechanistic mathematical model of hepatitis C virus entry.
• 
  T. Alex Perkins, Robert C. Reiner Jr., Guido España, Quirine A. ten Bosch, Amit Verma, Kelly A. Liebman, Valerie A. Paz-Soldan, John P. Elder, Amy C. Morrison, Steven T. Stoddard, Uriel Kitron, Gonzalo M. Vazquez-Prokopec, Thomas W. Scott, David L. Smith:
  An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections.
• 
  Sheng Wang, Edward W. Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha:
  Identification of pathways associated with chemosensitivity through network embedding.
• 
  Yarden Golan, Raphael Alhadeff, Arieh Warshel, Yehuda G. Assaraf:
  ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion.
• 
  Manuel Beiran, Srdjan Ostojic:
  Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks.
• 
  Vishaka Datta, Sridhar Hannenhalli, Rahul Siddharthan:
  ChIPulate: A comprehensive ChIP-seq simulation pipeline.
• 
  Marie Weiel, Ines Reinartz, Alexander Schug:
  Rapid interpretation of small-angle X-ray scattering data.
• 
  Sungho Shin, Ophelia S. Venturelli, Victor M. Zavala:
  Scalable nonlinear programming framework for parameter estimation in dynamic biological system models.
• 
  Christophe Noroy, Thierry Lefrançois, Damien F. Meyer:
  Searching algorithm for Type IV effector proteins (S4TE) 2.0: Improved tools for Type IV effector prediction, analysis and comparison in proteobacteria.
• 
  Andrea Bizzego, Nicole Bussola, Marco Chierici, Valerio Maggio, Margherita Francescatto, Luca Cima, Marco Cristoforetti, Giuseppe Jurman, Cesare Furlanello:
  Evaluating reproducibility of AI algorithms in digital pathology with DAPPER.
• 
  Nicholas I. Brodie, Konstantin I. Popov, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers:
  Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.
• 
  Lei Wang, Zhu-Hong You, Xing Chen, Yang-Ming Li, Ya-Nan Dong, Li-Ping Li, Kai Zheng:
  LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities.
• 
  Weiling Li, Lin Lin, Raunaq Malhotra, Lei Yang, Raj Acharya, Mary Poss:
  A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations.
• 
  Lawrence W. Sheppard, Emma J. Defriez, Philip C. Reid, Daniel C. Reuman:
  Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas.
• 
  Daniel B. Larremore:
  Bayes-optimal estimation of overlap between populations of fixed size.
• 
  Finlay Campbell, Anne Cori, Neil M. Ferguson, Thibaut Jombart:
  Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data.

Correction

• 
  Vasileios Vavourakis, Triantafyllos Stylianopoulos, Peter A. Wijeratne:
  Correction: In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability.

Volume 15, Number 4, April 2019

Editorials

• 
  Faisal M. Fadlelmola, Sumir Panji, Azza E. Ahmed, Amel Ghouila, Wisdom A. Akurugu, Jean-Baka Domelevo Entfellner, Oussema Souiai, Nicola J. Mulder, H3ABioNet Consortium:
  Ten simple rules for organizing a webinar series.
• 
  Fernando T. Maestre:
  Ten simple rules towards healthier research labs.
• 
  Emily A. Lescak, Kate M. O'Neill, Giovanna M. Collu, Subhamoy Das:
  Ten simple rules for providing a meaningful research experience to high school students.

Education Articles

• 
  Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica C. Munoz-Torres, Mirella Flores, Lukas A. Mueller, Helen Wiersma-Koch, Tom D'Elia, Susan J. Brown, Surya Saha:
  A quick guide for student-driven community genome annotation.
• 
  Greg Wilson:
  Ten quick tips for creating an effective lesson.

Perspective

• 
  Lewi Stone, Daniel Simberloff, Yael Artzy-Randrup:
  Network motifs and their origins.

Research Articles

• 
  Arumay Pal, Yaakov Levy:
  Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.
• 
  Philip Gerlee, Mia Johansson:
  Inferring rates of metastatic dissemination using stochastic network models.
• 
  Cheng Liang, Shengpeng Yu, Jiawei Luo:
  Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs.
• 
  Qi Su, Lei Zhou, Long Wang:
  Evolutionary multiplayer games on graphs with edge diversity.
• 
  Craig A. Magaret, David C. Benkeser, Brian D. Williamson, Bhavesh Borate, Lindsay N. Carpp, Ivelin S. Georgiev, Ian Setliff, Adam S. Dingens, Noah Simon, Marco Carone, Christopher Simpkins, David C. Montefiori, Galit Alter, Wen-Han Yu, Michal Juraska, Paul Thatcher Edlefsen, Shelly Karuna, Nyaradzo M. Mgodi, Srilatha Edugupanti, Peter B. Gilbert:
  Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.
• 
  Hailong Meng, Gur Yaari, Christopher R. Bolen, Stefan Avey, Steven H. Kleinstein:
  Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).
• 
  Yifan Gu, Yang Qi, Pulin Gong:
  Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits.
• 
  Giovanni Minervini, Federica Quaglia, Francesco Tabaro, Silvio C. E. Tosatto:
  Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors.
• 
  Natalie Ng, Handuo Shi, Alexandre Colavin, Kerwyn Casey Huang:
  Conservation of conformational dynamics across prokaryotic actins.
• 
  Minki Hwang, Jaehyuk Kim, Byounghyun Lim, Jun-Seop Song, Boyoung Joung, Eun Bo Shim, Hui-Nam Pak:
  Multiple factors influence the morphology of the bipolar electrogram: An in silico modeling study.
• 
  Leonardo Dalla Porta, Mauro Copelli:
  Modeling neuronal avalanches and long-range temporal correlations at the emergence of collective oscillations: Continuously varying exponents mimic M/EEG results.
• 
  Max S. Y. Lau, Bryan T. Grenfell, Colin J. Worby, Gavin J. Gibson:
  Model diagnostics and refinement for phylodynamic models.
• 
  Kyriaki Kalimeri, Matteo Delfino, Ciro Cattuto, Daniela Perrotta, Vittoria Colizza, Caroline Guerrisi, Clément Turbelin, Jim Duggan, John Edmunds, Chinelo Obi, Richard Pebody, Ana O. Franco, Yamir Moreno, Sandro Meloni, Carl Koppeschaar, Charlotte Kjelsø, Ricardo Mexia, Daniela Paolotti:
  Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms.
• 
  Remco R. Bouckaert, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David A. Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond:
  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
• 
  Andrea Malandrino, Xavier Trepat, Roger D. Kamm, Michael Mak:
  Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3D extracellular matrices.
• 
  Vilim Stih, Luigi Petrucco, Andreas M. Kist, Ruben Portugues:
  Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments.
• 
  Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio:
  The intrinsic dimension of protein sequence evolution.
• 
  Jose Manuel Martí:
  Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.
• 
  Maël Lebreton, Karin Bacily, Stefano Palminteri, Jan B. Engelmann:
  Contextual influence on confidence judgments in human reinforcement learning.
• 
  Micha Heilbron, Florent Meyniel:
  Confidence resets reveal hierarchical adaptive learning in humans.
• 
  Simone Conti, Martin Karplus:
  Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning.
• 
  Julien Varennes, Hye-ran Moon, Soutick Saha, Andrew Mugler, Bumsoo Han:
  Physical constraints on accuracy and persistence during breast cancer cell chemotaxis.
• 
  Anna S. Blazier, Jason A. Papin:
  Reconciling high-throughput gene essentiality data with metabolic network reconstructions.
• 
  Abrar E. Al-Shaer, George R. Flentke, Mark E. Berres, Ana Garic, Susan M. Smith:
  Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder.
• 
  Tanja Laske, Mandy Bachmann, Melanie Dostert, Alexander Karlas, Dagmar Wirth, Timo Frensing, Thomas F. Meyer, Hansjörg Hauser, Udo Reichl:
  Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth.
• 
  Bahadir Kasap, A. John van Opstal:
  Microstimulation in a spiking neural network model of the midbrain superior colliculus.
• 
  Daniel I. S. Rosenbloom, Peter Bacchetti, Mars Stone, Xutao Deng, Ronald J. Bosch, Douglas D. Richman, Janet D. Siliciano, John W. Mellors, Steven G. Deeks, Roger G. Ptak, Rebecca Hoh, Sheila M. Keating, Melanie Dimapasoc, Marta Massanella, Jun Lai, Michele D. Sobolewski, Deanna A. Kulpa, Michael P. Busch:
  Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size.
• 
  Ana Radonjic, Nicolas P. Cottaris, David H. Brainard:
  The relative contribution of color and material in object selection.
• 
  Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, Daisuke Kihara:
  A global map of the protein shape universe.
• 
  Michael D. Nicholson, Tibor Antal:
  Competing evolutionary paths in growing populations with applications to multidrug resistance.
• 
  Anne Richelle, Austin W. T. Chiang, Chih-Chung Kuo, Nathan E. Lewis:
  Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions.
• 
  Lex E. Flagel, Benjamin Blackman, Lila Fishman, Patrick J. Monnahan, Andrea Sweigart, John K. Kelly:
  GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity.
• 
  Marina Salvadores, David Mas-Ponte, Fran Supek:
  Passenger mutations accurately classify human tumors.
• 
  Ivan Juric, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yan-Xiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Ming Hu:
  MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.
• 
  Scott L. Nuismer, Bob Week:
  Approximate Bayesian estimation of coevolutionary arms races.
• 
  Alexis Pietak, Johanna Bischof, Joshua LaPalme, Junji Morokuma, Michael Levin:
  Neural control of body-plan axis in regenerating planaria.
• 
  Vincent Moens, Alexandre Zenon:
  Learning and forgetting using reinforced Bayesian change detection.
• 
  Graeme Benstead-Hume, Xiangrong Chen, Suzanna R. Hopkins, Karen A. Lane, Jessica A. Downs, Frances M. G. Pearl:
  Predicting synthetic lethal interactions using conserved patterns in protein interaction networks.
• 
  Elina Stengård, Ronald Van den Berg:
  Imperfect Bayesian inference in visual perception.
• 
  Paula Villa Martín, Miguel A. Muñoz, Simone Pigolotti:
  Bet-hedging strategies in expanding populations.
• 
  Félix P. Hartmann, Pierre Barbier De Reuille, Cris Kuhlemeier:
  Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism.
• 
  Ðorðe Miladinovic, Christine Muheim, Stefan Bauer, Andrea Spinnler, Daniela Noain, Mojtaba Bandarabadi, Benjamin Gallusser, Gabriel Krummenacher, Christian R. Baumann, Antoine Adamantidis, Steven A. Brown, Joachim M. Buhmann:
  SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species.
• 
  Rosangela Canino-Koning, Michael J. Wiser, Charles Ofria:
  Fluctuating environments select for short-term phenotypic variation leading to long-term exploration.
• 
  Vikash Pandey, Vassily Hatzimanikatis:
  Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data.
• 
  Takafumi Arakaki, Gregory Barello, Yashar Ahmadian:
  Inferring neural circuit structure from datasets of heterogeneous tuning curves.
• 
  Alexander Seeholzer, Moritz Deger, Wulfram Gerstner:
  Stability of working memory in continuous attractor networks under the control of short-term plasticity.
• 
  Thomas Sherman, Luciane T. Kagohara, Raymon Cao, Raymond Cheng, Matthew Satriano, Michael Considine, Gabriel Krigsfeld, Ruchira Ranaweera, Yong Tang, Sandra A. Jablonski, Genevieve L. Stein-O'Brien, Daria A. Gaykalova, Louis M. Weiner, Christine H. Chung, Elana J. Fertig:
  CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.
• 
  Marko Järvenpää, Mohamad R. Abdul Sater, Georgia K. Lagoudas, Paul C. Blainey, Loren G. Miller, James A. McKinnell, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen:
  A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation.
• 
  Lucas L. Dwiel, Jibran Y. Khokhar, Michael A. Connerney, Alan I. Green, Wilder T. Doucette:
  Finding the balance between model complexity and performance: Using ventral striatal oscillations to classify feeding behavior in rats.
• 
  Spencer E. Bliven, Aleix Lafita, Peter W. Rose, Guido Capitani, Andreas Prlic, Philip E. Bourne:
  Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.
• 
  Antoine D. Madar, Laura A. Ewell, Mathew V. Jones:
  Temporal pattern separation in hippocampal neurons through multiplexed neural codes.
• 
  Oveis Jamialahmadi, Sameereh Hashemi-Najafabadi, Ehsan Motamedian, Stefano Romeo, Fatemeh Bagheri:
  A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism.
• 
  Maria Kiskowski, Tilmann Glimm, Nickolas Moreno, Tony Gamble, Ylenia Chiari:
  Isolating and quantifying the role of developmental noise in generating phenotypic variation.
• 
  Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence Yang, Anand Sastry, Yara Seif, Bernhard O. Palsson, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre-Étienne Jacques:
  BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
• 
  Josef Ladenbauer, Klaus Obermayer:
  Weak electric fields promote resonance in neuronal spiking activity: Analytical results from two-compartment cell and network models.
• 
  András Szabó, Eric Theveneau, Melissa Turan, Roberto Mayor:
  Neural crest streaming as an emergent property of tissue interactions during morphogenesis.
• 
  Santiago A. Cadena, George H. Denfield, Edgar Y. Walker, Leon A. Gatys, Andreas S. Tolias, Matthias Bethge, Alexander S. Ecker:
  Deep convolutional models improve predictions of macaque V1 responses to natural images.
• 
  Hannah Choi, Stefan Mihalas:
  Synchronization dependent on spatial structures of a mesoscopic whole-brain network.
• 
  Sergio M. G. Solinas, Elke Edelmann, Volkmar Lessmann, Michele Migliore:
  A kinetic model for Brain-Derived Neurotrophic Factor mediated spike timing-dependent LTP.
• 
  Shou-Wen Wang, Anne-Florence Bitbol, Ned S. Wingreen:
  Revealing evolutionary constraints on proteins through sequence analysis.
• 
  Kai Liu, Brian Chu, Jay M. Newby, Elizabeth L. Read, John S. Lowengrub, Jun Allard:
  Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length.
• 
  Renato C. Duarte, Abigail Morrison:
  Leveraging heterogeneity for neural computation with fading memory in layer 2/3 cortical microcircuits.
• 
  Carmen C. Licon, Guillaume Bosc, Mohammed Sabri, Marylou Mantel, Arnaud P. Fournel, Caroline Bushdid, Jérôme Golebiowski, Céline Robardet, Marc Plantevit, Mehdi Kaytoue, Moustafa Bensafi:
  Chemical features mining provides new descriptive structure-odor relationships.
• 
  Hatice Akarsu, Patricia Bordes, Moise Mansour, Donna-Joe Bigot, Pierre Genevaux, Laurent Falquet:
  TASmania: A bacterial Toxin-Antitoxin Systems database.
• 
  Joshua Russell-Buckland, Christopher P. Barnes, Ilias Tachtsidis:
  A Bayesian framework for the analysis of systems biology models of the brain.
• 
  Peter M. U. Ung, Masahiro Sonoshita, Alex P. Scopton, Arvin C. Dar, Ross L. Cagan, Avner Schlessinger:
  Integrated computational and Drosophila cancer model platform captures previously unappreciated chemicals perturbing a kinase network.
• 
  Derek S. Park, Afua Abrafi Boakye, David E. Muench, H. Leighton Grimes, Pearlie K. Epling-Burnette, Philip K. Maini, Alexander R. A. Anderson, Michael B. Bonsall:
  Clonal hematopoiesis of indeterminate potential and its impact on patient trajectories after stem cell transplantation.
• 
  Malte Kähne, Sten Rüdiger, Alexandre H. Kihara, Benjamin Lindner:
  Gap junctions set the speed and nucleation rate of stage I retinal waves.
• 
  Anna-Leigh Brown, Minghui Li, Alexander Goncearenco, Anna R. Panchenko:
  Finding driver mutations in cancer: Elucidating the role of background mutational processes.
• 
  Qiwen Sun, Feng Jiao, Genghong Lin, Jianshe Yu, Moxun Tang:
  The nonlinear dynamics and fluctuations of mRNA levels in cell cycle coupled transcription.
• 
  Núria Folguera-Blasco, Ruben Perez-Carrasco, Elisabet Cuyàs, Javier A. Menéndez, Tomás Alarcón:
  A multiscale model of epigenetic heterogeneity-driven cell fate decision-making.
• 
  Laurel Fogarty, Nicole Creanza, Marcus W. Feldman:
  The life history of learning: Demographic structure changes cultural outcomes.
• 
  Stelios Pavlidis, Calixte Monast, Matthew J. Loza, Patrick Branigan, Kiang F. Chung, Ian M. Adcock, Yike Guo, Anthony Rowe, Frédéric Baribaud:
  I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment.

Formal Comment

• 
  Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou:
  Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang.

Volume 15, Number 5, May 2019

Editorials

• 
  Diego A. Forero, Sandra Lopez-Leon, Yeimy González-Giraldo, Pantelis G. Bagos:
  Ten simple rules for carrying out and writing meta-analyses.
• 
  Jason A. Papin, Feilim Mac Gabhann:
  Wisdom of crowds in computational biology.

Education Articles

• 
  Y. Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C. Munoz-Torres, Drashtti Vasant, Eleanor Williams, Melissa A. Haendel:
  Ten quick tips for biocuration.
• 
  Anthony C. Fletcher, Cameron Mura:
  Ten quick tips for using a Raspberry Pi.
• 
  Santiago Guerrero, Andrés López-Cortés, Jennyfer M. García-Cárdenas, Pablo Saa, Alberto Indacochea, Isaac Armendáriz-Castillo, Ana Karina Zambrano, Verónica Yumiceba, Andy Pérez-Villa, Patricia Guevara-Ramírez, Oswaldo Moscoso-Zea, Joel Paredes, Paola E. Leone, Cesar Paz-y-Miño:
  A quick guide for using Microsoft OneNote as an electronic laboratory notebook.
• 
  Phillip E. C. Compeau:
  Establishing a computational biology flipped classroom.

Perspectives

• 
  John M. Drake, Tobias S. Brett, Shiyang Chen, Bogdan I. Epureanu, Matthew J. Ferrari, Éric Marty, Paige B. Miller, Eamon B. O'Dea, Suzanne M. O'Regan, Andrew W. Park, Pejman Rohani:
  The statistics of epidemic transitions.
• 
  Joanna M. Leng, Massa Shoura, Tom C. B. McLeish, Alan N. Real, Mariann Hardey, James McCafferty, Neil A. Ranson, Sarah A. Harris:
  Securing the future of research computing in the biosciences.

Research Articles

• 
  Arjun Singh Yadaw, Mustafa M. Siddiq, Vera Rabinovich, Rosa Tolentino, Jens Hansen, Ravi Iyengar:
  Dynamic balance between vesicle transport and microtubule growth enables neurite outgrowth.
• 
  Assaf Almog, M. Renate Buijink, Ori Roethler, Stephan Michel, Johanna H. Meijer, Jos Rohling, Diego Garlaschelli:
  Uncovering functional signature in neural systems via random matrix theory.
• 
  Daniel A. Cannon, Lu Shan, Qun Du, Lena Shirinian, Keith W. Rickert, Kim L. Rosenthal, Martin Korade III, Lilian E. van Vlerken-Ysla, Andrew Buchanan, Tristan J. Vaughan, Melissa M. Damschroder, Bojana Popovic:
  Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design.
• 
  Jorge Escribano, Michelle B. Chen, Emad Moeendarbary, Xuan Cao, Vivek Shenoy, José Manuel García-Aznar, Roger D. Kamm, Fabian Spill:
  Balance of mechanical forces drives endothelial gap formation and may facilitate cancer and immune-cell extravasation.
• 
  Yaser Saffar Talori, Jing-Shan Zhao, Yun-Fei Liu, Wenxiu Lu, Zhi-Heng Li, Jingmai Kathleen O'Connor:
  Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis.
• 
  Yihao Zhang, Anastasios V. Tzingounis, George Lykotrafitis:
  Modeling of the axon plasma membrane structure and its effects on protein diffusion.
• 
  Xundong Wu, Gabriel C. Mel, DJ Strouse, Bartlett W. Mel:
  How Dendrites Affect Online Recognition Memory.
• 
  Anne Grimbs, David F. Klosik, Stefan Bornholdt, Marc-Thorsten Hütt:
  A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli.
• 
  Jakob Lund Dideriksen, Dario Farina:
  Amplitude cancellation influences the association between frequency components in the neural drive to muscle and the rectified EMG signal.
• 
  Florence Bansept, Kathrin Schumann-Moor, Médéric Diard, Wolf-Dietrich Hardt, Emma Slack, Claude Loverdo:
  Enchained growth and cluster dislocation: A possible mechanism for microbiota homeostasis.
• 
  Mario Negrello, Pascal Warnaar, Vincenzo Romano, Cullen B. Owens, Sander Lindeman, Elisabetta Iavarone, Jochen K. Spanke, Laurens W. J. Bosman, Chris I. De Zeeuw:
  Quasiperiodic rhythms of the inferior olive.
• 
  Monzilur Rahman, Ben D. B. Willmore, Andrew J. King, Nicol S. Harper:
  A dynamic network model of temporal receptive fields in primary auditory cortex.
• 
  Yuning Hao, Ming Yan, Blake R. Heath, Yu L. Lei, Yuying Xie:
  Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares.
• 
  Kyle Dunovan, Catalina Vich, Matthew Clapp, Timothy D. Verstynen, Jonathan E. Rubin:
  Reward-driven changes in striatal pathway competition shape evidence evaluation in decision-making.
• 
  Chi-Chou Liao, Liang-Jwu Chen, Shuen-Fang Lo, Chi-Wei Chen, Yen-Wei Chu:
  EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches.
• 
  Amitabha Bose, Áine Byrne, John Rinzel:
  A neuromechanistic model for rhythmic beat generation.
• 
  Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C. Denis, George Kollias, Christoforos Nikolaou:
  An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis.
• 
  Grégory Dumont, Boris S. Gutkin:
  Macroscopic phase resetting-curves determine oscillatory coherence and signal transfer in inter-coupled neural circuits.
• 
  Adrien Doerig, Alban Bornet, Ruth Rosenholtz, Gregory Francis, Aaron Michael Clarke, Michael H. Herzog:
  Beyond Bouma's window: How to explain global aspects of crowding?
• 
  Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee, Insuk Lee:
  Pathway-specific protein domains are predictive for human diseases.
• 
  Victor Kulikov, Syuan-Ming Guo, Matthew Stone, Allen Goodman, Anne E. Carpenter, Mark Bathe, Victor S. Lempitsky:
  DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images.
• 
  Vikash Pandey, Noushin Hadadi, Vassily Hatzimanikatis:
  Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models.
• 
  Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren:
  The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern.
• 
  Yuanxiao Gao, Arne Traulsen, Yuriy Pichugin:
  Interacting cells driving the evolution of multicellular life cycles.
• 
  Jingwei Sun, Jian Li, Hang Zhang:
  Human representation of multimodal distributions as clusters of samples.
• 
  Natalie Schaworonkow, Vadim V. Nikulin:
  Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG.
• 
  Karim Rajaei, Yalda Mohsenzadeh, Reza Ebrahimpour, Seyed-Mahdi Khaligh-Razavi:
  Beyond core object recognition: Recurrent processes account for object recognition under occlusion.
• 
  Jeongkyun Kim, Jung-Jae Kim, Hyunju Lee:
  DigChem: Identification of disease-gene-chemical relationships from Medline abstracts.
• 
  Elisabetta Iavarone, Jane Yi, Ying Shi, Bas-Jan Zandt, Christian O'Reilly, Werner Van Geit, Christian Rössert, Henry Markram, Sean L. Hill:
  Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons.
• 
  Loreen Hertäg, Henning Sprekeler:
  Amplifying the redistribution of somato-dendritic inhibition by the interplay of three interneuron types.
• 
  Piotr Bentkowski, Jacek Radwan:
  Evolution of major histocompatibility complex gene copy number.
• 
  Alina Malyutina, Muntasir Mamun Majumder, Wenyu Wang, Alberto Pessia, Caroline Heckman, Jing Tang:
  Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer.
• 
  Matti Javanainen, Giray Enkavi, Ramon Guixà-González, Waldemar Kulig, Hector Martinez-Seara, Ilya Levental, Ilpo Vattulainen:
  Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions.
• 
  Kumar Mainali, Sharon Bewick, Briana Vecchio-Pagan, David K. Karig, William F. Fagan:
  Detecting interaction networks in the human microbiome with conditional Granger causality.
• 
  Francesco Pinotti, Eric Fleury, Didier Guillemot, Pierre-Yves Boëlle, Chiara Poletto:
  Host contact dynamics shapes richness and dominance of pathogen strains.
• 
  Avichai Tendler, Anat Zimmer, Avi E. Mayo, Uri Alon:
  Noise-precision tradeoff in predicting combinations of mutations and drugs.
• 
  Rebecca Sarto Basso, Dorit S. Hochbaum, Fabio Vandin:
  Efficient algorithms to discover alterations with complementary functional association in cancer.
• 
  Anupama Sharma, Shakti N. Menon, V. Sasidevan, Sitabhra Sinha:
  Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes.
• 
  Michal Ben-Nun, Pete Riley, James Turtle, David P. Bacon, Steven Riley:
  Forecasting national and regional influenza-like illness for the USA.
• 
  Ajeet K. Sharma, Pietro Sormanni, Nabeel Ahmed, Prajwal Ciryam, Ulrike A. Friedrich, Günter Kramer, Edward P. O'Brien:
  A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.
• 
  Mingbo Cai, Nicolas W. Schuck, Jonathan W. Pillow, Yael Niv:
  Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias.
• 
  Eline R. Kupers, Marisa Carrasco, Jonathan Winawer:
  Modeling visual performance differences 'around' the visual field: A computational observer approach.
• 
  Sheng Qian, Siqi Liang, Haiyuan Yu:
  Leveraging genetic interactions for adverse drug-drug interaction prediction.
• 
  David A. Knowles, Gina Bouchard, Sylvia K. Plevritis:
  Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features.
• 
  Le Zhang, Wanyu Bai, Na Yuan, Zhenglin Du:
  Comprehensively benchmarking applications for detecting copy number variation.
• 
  Teemu J. Häkkinen, S. Susanna Sova, Ian J. Corfe, Leo Tjäderhane, Antti Hannukainen, Jukka Jernvall:
  Modeling enamel matrix secretion in mammalian teeth.
• 
  Audrey Duval, Thomas Obadia, Pierre-Yves Boëlle, Eric Fleury, Jean-Louis Herrmann, Didier Guillemot, Laura Temime, Lulla Opatowski:
  Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings.
• 
  Agus Hartoyo, Peter J. Cadusch, David T. J. Liley, Damien G. Hicks:
  Parameter estimation and identifiability in a neural population model for electro-cortical activity.
• 
  Anthony Stigliani, Brianna Jeska, Kalanit Grill-Spector:
  Differential sustained and transient temporal processing across visual streams.
• 
  Shilo Ohayon, Arik Girsault, Maisa Nasser, Shai Shen-Orr, Amit Meller:
  Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification.
• 
  Audrey J. Sederberg, Aurélie Pala, He J. V. Zheng, Biyu J. He, Garrett B. Stanley:
  State-aware detection of sensory stimuli in the cortex of the awake mouse.
• 
  Alessandro Pandini, Howard Schulman, Shahid Khan:
  Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II.
• 
  Karoline H. Jæger, Andrew G. Edwards, Andrew D. McCulloch, Aslak Tveito:
  Properties of cardiac conduction in a cell-based computational model.
• 
  Emil Wärnberg, Arvind Kumar:
  Perturbing low dimensional activity manifolds in spiking neuronal networks.
• 
  Gergely Boza, Sarah F. Worsley, Douglas W. Yu, István Scheuring:
  Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability.

Corrections

• 
  Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel, Yehuda G. Assaraf:
  Correction: Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter.
• 
  Correction: The role of the encapsulated cargo in microcompartment assembly.
• 
  Joanne C. Van Slooten, Sara Jahfari, Tomas Knapen, Jan Theeuwes:
  Correction: How pupil responses track value-based decision-making during and after reinforcement learning.
• 
  Notice of Republication: Ten simple rules for organizing a webinar series.
• 
  Correction: Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models.

Formal Comment

• 
  Chia-Ying Chen, Trees-Juen Chuang:
  Comment on "A comprehensive overview and evaluation of circular RNA detection tools".

Volume 15, Number 6, June 2019

Editorial

• 
  Kristine Briedis, Yi-Shiou Chen, Scott Markel:
  Ten simple rules for successfully hosting an intern at a scientific software company.

Education Articles

• 
  Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard C. Laubenbacher, Jeffrey H. Chuang:
  Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.
• 
  Lan H. Nguyen, Susan P. Holmes:
  Ten quick tips for effective dimensionality reduction.
• 
  Angela C. Davies, Diane Harris, Amanda Banks Gatenby, Andy Brass:
  Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?
• 
  Annette McGrath, Katherine Champ, Catherine A. Shang, Ellen van Dam, Cath Brooksbank, Sarah L. Morgan:
  From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training.

Perspective

• 
  Matthew J. Michalska-Smith, Stefano Allesina:
  Telling ecological networks apart by their structure: A computational challenge.

Reviews

• 
  Jay Ghurye, Mihai Pop:
  Modern technologies and algorithms for scaffolding assembled genomes.
• 
  Ruth Nussinov, Chung-Jung Tsai, Hyunbum Jang:
  Protein ensembles link genotype to phenotype.
• 
  Michael Beyeler, Emily L. Rounds, Kristofor D. Carlson, Nikil D. Dutt, Jeffrey L. Krichmar:
  Neural correlates of sparse coding and dimensionality reduction.

Research Articles

• 
  Alexander S. Leonard, Sebastian E. Ahnert:
  Evolution of interface binding strengths in simplified model of protein quaternary structure.
• 
  Monica Civera, Francesca Vasile, Donatella Potenza, Cinzia Colombo, Sara Parente, Chiara Vettraino, Tommaso Prosdocimi, Emilio Parisini, Laura Belvisi:
  Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies.
• 
  Marzena Mura, Céline Feillet, Roberto Bertolusso, Franck Delaunay, Marek Kimmel:
  Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells.
• 
  Chuankai Cheng, Edward J. O'Brien, Douglas McCloskey, Jose Utrilla, Connor A. Olson, Ryan A. LaCroix, Troy E. Sandberg, Adam M. Feist, Bernhard O. Palsson, Zachary A. King:
  Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism.
• 
  Duncan J. MacGregor, Gareth Leng:
  Emergent decision-making behaviour and rhythm generation in a computational model of the ventromedial nucleus of the hypothalamus.
• 
  Tamara Carla Bidone, Austin V. Skeeters, Patrick W. Oakes, Gregory A. Voth:
  Multiscale model of integrin adhesion assembly.
• 
  Yapeng Su, Marcus Bintz, Yezi Yang, Lidia Robert, Alphonsus H. C. Ng, Victoria Liu, Antoni Ribas, James R. Heath, Wei Wei:
  Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance.
• 
  Thomas M. Bury, Chris T. Bauch, Madhur Anand:
  Charting pathways to climate change mitigation in a coupled socio-climate model.
• 
  Takaaki Yonekura, Akitoshi Iwamoto, Hironori Fujita, Munetaka Sugiyama:
  Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis.
• 
  Hongjun Bai, Yifan Li, Nelson Michael, Merlin L. Robb, Morgane Rolland:
  The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes.
• 
  Daniel H. Baker, Bruno Richard:
  Dynamic properties of internal noise probed by modulating binocular rivalry.
• 
  Atsushi Kamimura, Yoshiya Matsubara, Kunihiko Kaneko, Nobuto Takeuchi:
  Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes.
• 
  Anna Song, Olivier D. Faugeras, Romain Veltz:
  A neural field model for color perception unifying assimilation and contrast.
• 
  Yifeng Qi, Bin Zhang:
  Predicting three-dimensional genome organization with chromatin states.
• 
  Samuel P. Muscinelli, Wulfram Gerstner, Tilo Schwalger:
  How single neuron properties shape chaotic dynamics and signal transmission in random neural networks.
• 
  Amir Dezfouli, Kristi Griffiths, Fabio Ramos, Peter Dayan, Bernard W. Balleine:
  Models that learn how humans learn: The case of decision-making and its disorders.
• 
  Mahua Roy, Stacey D. Finley:
  Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model.
• 
  Romain Ligneul:
  Sequential exploration in the Iowa gambling task: Validation of a new computational model in a large dataset of young and old healthy participants.
• 
  Hiroshi Momiji, Kirsty L. Hassall, Karen Featherstone, Anne V. McNamara, Amanda L. Patist, David G. Spiller, Helen C. Christian, Michael R. H. White, Julian R. E. Davis, Bärbel F. Finkenstädt, David A. Rand:
  Disentangling juxtacrine from paracrine signalling in dynamic tissue.
• 
  Laurens F. M. Verscheijden, Jan B. Koenderink, Saskia N. de Wildt, Frans G. M. Russel:
  Development of a physiologically-based pharmacokinetic pediatric brain model for prediction of cerebrospinal fluid drug concentrations and the influence of meningitis.
• 
  David S. Goodsell, Andrew Jewett, Arthur J. Olson, Stefano Forli:
  Integrative modeling of the HIV-1 ribonucleoprotein complex.
• 
  Kymberleigh A. Pagel, Danny Antaki, Aojie Lian, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac:
  Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome.
• 
  Ingoo Lee, Jongsoo Keum, Hojung Nam:
  DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences.
• 
  Hansaim Lim, Di He, Yue Qiu, Patrycja Krawczuk, Xiaoru Sun, Lei Xie:
  Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.
• 
  David Hasler, Pinelopi Anagnostopoulou, Sylvia Nyilas, Philipp Latzin, Johannes C. Schittny, Dominik Obrist:
  A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test.
• 
  Payam Piray, Amir Dezfouli, Tom Heskes, Michael J. Frank, Nathaniel D. Daw:
  Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies.
• 
  Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis:
  Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes.
• 
  Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis, Dani Or:
  Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH).
• 
  Ibrahim Cheddadi, Michel Génard, Nadia Bertin, Christophe Godin:
  Coupling water fluxes with cell wall mechanics in a multicellular model of plant development.
• 
  Paul W. Sweeney, Angela d'Esposito, Simon Walker-Samuel, Rebecca J. Shipley:
  Modelling the transport of fluid through heterogeneous, whole tumours in silico.
• 
  Sharmila Venugopal, Soju Seki, David H. Terman, Antonios Pantazis, Riccardo Olcese, Martina Wiedau-Pazos, Scott H. Chandler:
  Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons.
• 
  Anthony Hauser, Katharina Kusejko, Leigh F. Johnson, Gilles Wandeler, Julien Riou, Fardo Goldstein, Matthias Egger, Roger D. Kouyos:
  Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa.
• 
  Sanjeevan Ahilan, Rebecca B. Solomon, Yannick-André Breton, Kent L. Conover, Ritwik K. Niyogi, Peter Shizgal, Peter Dayan:
  Learning to use past evidence in a sophisticated world model.
• 
  Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter:
  Open collaborative writing with Manubot.
• 
  Kalinga Pavan T. Silva, James Q. Boedicker:
  A neural network model predicts community-level signaling states in a diverse microbial community.
• 
  Erlend Hodneland, Erik A. Hanson, Ove Sævareid, Geir Nævdal, Arvid Lundervold, Veronika Soltészová, Antonella Zanna Munthe-Kaas, Andreas Deistung, Jürgen R. Reichenbach, Jan M. Nordbotten:
  A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model.
• 
  Mikael F. Forsgren, Markus Karlsson, Olof Dahlqvist Leinhard, Nils Dahlström, Bengt Norén, Thobias Romu, Simone Ignatova, Mattias Ekstedt, Stergios Kechagias, Peter Lundberg, Gunnar Cedersund:
  Model-inferred mechanisms of liver function from magnetic resonance imaging data: Validation and variation across a clinically relevant cohort.
• 
  Hanne Hoitzing, Payam A. Gammage, Lindsey Van Haute, Michal Minczuk, Iain G. Johnston, Nick S. Jones:
  Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations.
• 
  Sora An, Fabrice Bartolomei, Maxime Guye, Viktor K. Jirsa:
  Optimization of surgical intervention outside the epileptogenic zone in the Virtual Epileptic Patient (VEP).
• 
  Marouen Ben Guebila, Ines Thiele:
  Predicting gastrointestinal drug effects using contextualized metabolic models.
• 
  Joshua M. Mueller, Primoz Ravbar, Julie H. Simpson, Jean M. Carlson:
  Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales.
• 
  Sid Kiblawi, Deborah Chasman, Amanda Henning, Eunju Park, Hoifung Poon, Michael Gould, Paul Ahlquist, Mark Craven:
  Augmenting subnetwork inference with information extracted from the scientific literature.
• 
  Liat Shenhav, Ori Furman, Leah Briscoe, Mike Thompson, Justin D. Silverman, Itzhak Mizrahi, Eran Halperin:
  Modeling the temporal dynamics of the gut microbial community in adults and infants.
• 
  Rohan V. Koodli, Benjamin Keep, Katherine R. Coppess, Fernando Portela, Rhiju Das:
  EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame.
• 
  Filip Gesiarz, Donal Cahill, Tali Sharot:
  Evidence accumulation is biased by motivation: A computational account.

Corrections

• 
  Notification of Republication: Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy.
• 
  Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng:
  Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.
• 
  Correction: A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana.
• 
  Correction: Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence.
• 
  Correction: Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria.
• 
  Correction: Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable.
• 
  Correction: Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection.
• 
  Correction: The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction.
• 
  Correction: Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
• 
  Correction: Ten Simple Rules for Taking Advantage of Git and GitHub.
• 
  Correction: Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics.
• 
  Wan Yang, Liang Wen, Shen-Long Li, Kai Chen, Wen-Yi Zhang, Jeffrey Shaman:
  Correction: Geospatial characteristics of measles transmission in China during 2005-2014.
• 
  Jose Manuel Martí:
  Correction: Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.
• 
  Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein:
  Correction: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.
• 
  Sven Zenker, Jonathan E. Rubin, Gilles Clermont:
  Correction: From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses.

Volume 15, Number 7, July 2019

Editorials

• 
  Adam Rule, Amanda Birmingham, Cristal Zuñiga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose:
  Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.
• 
  Shayna A. Sura, Lauren L. Smith, Monique Renee Ambrose, C. Eduardo Guerra Amorim, Annabel C. Beichman, Ana C. R. Gomez, Mark Juhn, Gaurav S. Kandlikar, Julie S. Miller, Jazlyn Mooney, Riley O. Mummah, Kirk E. Lohmueller, James O. Lloyd-Smith:
  Ten simple rules for giving an effective academic job talk.

Perspective

• 
  Christopher Brian Currin, Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P. Vogels, Joseph Valentino Raimondo:
  Think: Theory for Africa.

Review

• 
  Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske, Claudio Angione:
  Machine and deep learning meet genome-scale metabolic modeling.

Research Articles

• 
  Albert Tian Chen, Alexander Franks, Nikolai Slavov:
  DART-ID increases single-cell proteome coverage.
• 
  Da Zhou, Yue Luo, David Dingli, Arne Traulsen:
  The invasion of de-differentiating cancer cells into hierarchical tissues.
• 
  Jakob Ruess, Maros Pleska, Calin C. Guet, Gasper Tkacik:
  Molecular noise of innate immunity shapes bacteria-phage ecologies.
• 
  Andrea Komljenovic, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson-Rechavi:
  Cross-species functional modules link proteostasis to human normal aging.
• 
  Jane Loveless, Konstantinos Lagogiannis, Barbara Webb:
  Modelling the mechanics of exploration in larval Drosophila.
• 
  Juan J. Caceres, Alberto Paccanaro:
  Disease gene prediction for molecularly uncharacterized diseases.
• 
  Chunhui Cai, Gregory F. Cooper, Kevin N. Lu, Xiaojun Ma, Shuping Xu, Zhenlong Zhao, Xueer Chen, Yifan Xue, Adrian V. Lee, Nathan Clark, Vicky Chen, Songjian Lu, Lujia Chen, Liyue Yu, Harry Hochheiser, Xia Jiang, Q. Jane Wang, Xinghua Lu:
  Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference.
• 
  Peter Vincent, Thomas Parr, David Benrimoh, Karl J. Friston:
  With an eye on uncertainty: Modelling pupillary responses to environmental volatility.
• 
  Elyse H. Norton, Luigi Acerbi, Wei Ji Ma, Michael S. Landy:
  Human online adaptation to changes in prior probability.
• 
  Aravind Chandrasekaran, Arpita Upadhyaya, Garegin A. Papoian:
  Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling.
• 
  Chun Chan, Xiaoyun Pang, Yan Zhang, Tongxin Niu, Shengjiang Yang, Daohui Zhao, Jian Li, Lanyuan Lu, Victor W. Hsu, Jian Zhou, Fei Sun, Jun Fan:
  ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages.
• 
  Tsuyoshi Mikkaichi, Michael R. Yeaman, Alexander Hoffmann, MRSA Systems Immunobiology Group:
  Identifying determinants of persistent MRSA bacteremia using mathematical modeling.
• 
  Jennifer Crodelle, Sofia H. Piltz, Megan Hastings Hagenauer, Victoria Booth:
  Modeling the daily rhythm of human pain processing in the dorsal horn.
• 
  Emma D. Wilson, Sean R. Anderson, Paul Dean, John Porrill:
  Sensorimotor maps can be dynamically calibrated using an adaptive-filter model of the cerebellum.
• 
  Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, Jan Grau:
  PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting.
• 
  Stefano Recanatesi, Gabriel Koch Ocker, Michael A. Buice, Eric Shea-Brown:
  Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity.
• 
  Tomasz Jetka, Karol Nienaltowski, Tomasz Winarski, Slawomir Blonski, Michal Komorowski:
  Information-theoretic analysis of multivariate single-cell signaling responses.
• 
  Nicolas Cazin, Martin Llofriu Alonso, Pablo Scleidorovich, Tatiana Pelc, Bruce Harland, Alfredo Weitzenfeld, Jean-Marc Fellous, Peter Ford Dominey:
  Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with spatial reward propagation.
• 
  Víctor M. Pérez-García, Luis E. Ayala-Hernández, Juan Belmonte-Beitia, Philippe Schucht, Michael Murek, Andreas Raabe, Juan Sepúlveda:
  Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas.
• 
  Maarten H. G. Heusinkveld, Wouter Huberts, Joost Lumens, Theo Arts, Tammo Delhaas, Koen D. Reesink:
  Large vessels as a tree of transmission lines incorporated in the CircAdapt whole-heart model: A computational tool to examine heart-vessel interaction.
• 
  Tim Breitenbach, Chunguang Liang, Niklas Beyersdorf, Thomas Dandekar:
  Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks.
• 
  Aleksandra Karolak, Sharan Poonja, Katarzyna A. Rejniak:
  Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential.
• 
  Evripidis Gkanias, Benjamin Risse, Michael Mangan, Barbara Webb:
  From skylight input to behavioural output: A computational model of the insect polarised light compass.
• 
  Sergey Ivanov, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov:
  Assessment of the cardiovascular adverse effects of drug-drug interactions through a combined analysis of spontaneous reports and predicted drug-target interactions.
• 
  James J. Bull, Scott L. Nuismer, Rustom Antia:
  Recombinant vector vaccine evolution.
• 
  Benjamin Merkt, Friedrich Schüßler, Stefan Rotter:
  Propagation of orientation selectivity in a spiking network model of layered primary visual cortex.
• 
  Anne Richelle, Chintan J. Joshi, Nathan E. Lewis:
  Assessing key decisions for transcriptomic data integration in biochemical networks.
• 
  David Zwicker:
  Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned.
• 
  Elizabeth A. Proctor, David D. Mowrey, Nikolay V. Dokholyan:
  β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology.
• 
  Yun-Ching Chen, Laura Elnitski:
  Aberrant DNA methylation defines isoform usage in cancer, with functional implications.
• 
  Duncan K. Ralph, Frederick A. Matsen IV:
  Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data.
• 
  Walter Basile, Marco Salvatore, Claudio Bassot, Arne Elofsson:
  Why do eukaryotic proteins contain more intrinsically disordered regions?
• 
  Xing Chen, Chi-Chi Zhu, Jun Yin:
  Ensemble of decision tree reveals potential miRNA-disease associations.
• 
  Christopher Bates, Ilker Yildirim, Joshua B. Tenenbaum, Peter W. Battaglia:
  Modeling human intuitions about liquid flow with particle-based simulation.
• 
  Bhavin S. Khatri, Richard A. Goldstein:
  Biophysics and population size constrains speciation in an evolutionary model of developmental system drift.
• 
  Madhura R. Joglekar, Logan Chariker, Robert Shapley, Lai-Sang Young:
  A case study in the functional consequences of scaling the sizes of realistic cortical models.
• 
  Enrico Seiler, Kathrin Trappe, Bernhard Y. Renard:
  Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.
• 
  Paul A. Roberts, Ryan M. Huebinger, Emma Keen, Anne-Marie Krachler, Sara Jabbari:
  Mathematical model predicts anti-adhesion-antibiotic-debridement combination therapies can clear an antibiotic resistant infection.
• 
  Jacob D. Davidson, Ahmed El Hady:
  Foraging as an evidence accumulation process.
• 
  Eric Libby, Laurent Hébert-Dufresne, Sayed-Rzgar Hosseini, Andreas Wagner:
  Syntrophy emerges spontaneously in complex metabolic systems.
• 
  Jessica M. Conway, Alan S. Perelson, Jonathan Z. Li:
  Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers.
• 
  Joseph A. Lewnard, Benjamin A. Lopman, Umesh D. Parashar, Aisleen Bennett, Naor Bar-Zeev, Nigel A. Cunliffe, Prasanna Samuel, M. Lourdes Guerrero, Guillermo Ruiz-Palacios, Gagandeep Kang, Virginia E. Pitzer:
  Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications.
• 
  Jan R. Wessel, David E. Huber:
  Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism.
• 
  Shiva Rudraraju, Derek E. Moulton, Régis Chirat, Alain Goriely, Krishna C. Garikipati:
  A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth.
• 
  Lou Safra, Coralie Chevallier, Stefano Palminteri:
  Depressive symptoms are associated with blunted reward learning in social contexts.
• 
  Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J. Williams, Weini Huang, Giulio Caravagna, Trevor A. Graham, Andrea Sottoriva:
  Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data.
• 
  Majed Mohamed Magzoub, Marcos Prunello, Kevin Brennan, Olivier Gevaert:
  The impact of DNA methylation on the cancer proteome.
• 
  Gratia Nguyen, Alan W. Freeman:
  A model for the origin and development of visual orientation selectivity.
• 
  Jonathan E. Rubin, Jeffrey C. Smith:
  Robustness of respiratory rhythm generation across dynamic regimes.
• 
  Marcella Torres, Jing Wang, Paul J. Yannie, Shobha Ghosh, Rebecca A. Segal, Angela M. Reynolds:
  Identifying important parameters in the inflammatory process with a mathematical model of immune cell influx and macrophage polarization.

Corrections

• 
  Hendrik B. Tiedemann, Elida Schneltzer, Stefan Zeiser, Bastian Hoesel, Johannes Beckers, Gerhard K. H. Przemeck, Martin Hrabé de Angelis:
  Correction: From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm.
• 
  Yoram Zarai, Tamir Tuller:
  Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources.
• 
  Christian L. Vestergaard, Mathieu Génois:
  Correction: Temporal Gillespie algorithm: Fast simulation of contagion processes on time-varying networks.

Volume 15, Number 8, August 2019

Education

• 
  Francis Mairet, Olivier Bernard:
  Twelve quick tips for designing sound dynamical models for bioprocesses.

Research Articles

• 
  Sophia Rudorf:
  Efficiency of protein synthesis inhibition depends on tRNA and codon compositions.
• 
  Sasikiran Kandula, Jeffrey Shaman:
  Reappraising the utility of Google Flu Trends.
• 
  Luke E. Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler, Philipp Berens:
  Bayesian hypothesis testing and experimental design for two-photon imaging data.
• 
  Ramón Díaz-Uriarte, Claudia Vasallo:
  Every which way? On predicting tumor evolution using cancer progression models.
• 
  Efrat Greenwald, Jean-Pierre Eckmann, Ofer Feinerman:
  Colony entropy - Allocation of goods in ant colonies.
• 
  Huikun Zhang, Spencer S. Ericksen, Ching-pei Lee, Gene E. Ananiev, Nathan Wlodarchak, Peng Yu, Julie C. Mitchell, Anthony Gitter, Stephen J. Wright, F. Michael Hoffmann, Scott A. Wildman, Michael A. Newton:
  Predicting kinase inhibitors using bioactivity matrix derived informer sets.
• 
  Julia Jade Harris, Elisabeth Engl, David Attwell, Renaud Jolivet:
  Energy-efficient information transfer at thalamocortical synapses.
• 
  Francisco Herrerías-Azcué, Vicente Pérez-Muñuzuri, Tobias Galla:
  Motion, fixation probability and the choice of an evolutionary process.
• 
  Jason Chen, Scott L. Diamond:
  Reduced model to predict thrombin and fibrin during thrombosis on collagen/tissue factor under venous flow: Roles of γ'-fibrin and factor XIa.
• 
  Arup K. Bag, Sapan Mandloi, Saulius Jarmalavicius, Susmita Mondal, Krishna Kumar, Chhabinath Mandal, Peter Walden, Saikat Chakrabarti, Chitra Mandal:
  Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma.
• 
  Jing Yang, Nicola F. Müller, Remco R. Bouckaert, Bing Xu, Alexei J. Drummond:
  Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration.
• 
  Alexey Uvarovskii, Isabel S. Naarmann-de Vries, Christoph Dieterich:
  On the optimal design of metabolic RNA labeling experiments.
• 
  Felix Funk, Christoph Hauert:
  Directed migration shapes cooperation in spatial ecological public goods games.
• 
  Michael A. Colman:
  Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation.
• 
  Gihan Weerasinghe, Benoit Duchet, Hayriye Cagnan, Peter Brown, Christian Bick, Rafal Bogacz:
  Predicting the effects of deep brain stimulation using a reduced coupled oscillator model.
• 
  Carlos R. Cassanello, Florian Ostendorf, Martin Rolfs:
  A generative learning model for saccade adaptation.
• 
  Song Cui, Qiang Wu, James West, Jiangping Bai:
  Machine learning-based microarray analyses indicate low-expression genes might collectively influence PAH disease.
• 
  Jérémie Scire, Nathanaël Hozé, Hildegard Uecker:
  Aggressive or moderate drug therapy for infectious diseases? Trade-offs between different treatment goals at the individual and population levels.
• 
  Janne M. J. Huttunen, Leo Kärkkäinen, Harri Lindholm:
  Pulse transit time estimation of aortic pulse wave velocity and blood pressure using machine learning and simulated training data.
• 
  Alexander Klug, Su-Chan Park, Joachim Krug:
  Recombination and mutational robustness in neutral fitness landscapes.
• 
  Jacopo Marchi, Ezequiel A. Galpern, Rocío Espada, Diego U. Ferreiro, Aleksandra M. Walczak, Thierry Mora:
  Size and structure of the sequence space of repeat proteins.
• 
  Michael Gabel, Tobias Hohl, Andrea Imle, Oliver T. Fackler, Frederik Graw:
  FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics.
• 
  Jianan Lin, Yuping Zhang, Wayne N. Frankel, Zhengqing Ouyang:
  PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks.
• 
  Fabio C. P. Navarro, Jacob Hoops, Lauren Bellfy, Eliza Cerveira, Qihui Zhu, Chengsheng Zhang, Charles Lee, Mark B. Gerstein:
  TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
• 
  James A. Hay, Karen L. Laurie, Michael White, Steven Riley:
  Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets.
• 
  Audrey Denizot, Misa Arizono, U. Valentin Nägerl, Hédi Soula, Hugues Berry:
  Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity.
• 
  Pieter Verbeke, Tom Verguts:
  Learning to synchronize: How biological agents can couple neural task modules for dealing with the stability-plasticity dilemma.
• 
  Ljubisa Miskovic, Jonas Béal, Michael Moret, Vassily Hatzimanikatis:
  Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties.
• 
  Franca J. Bongers, Jacob C. Douma, Yoh Iwasa, Ronald Pierik, Jochem B. Evers, Niels P. R. Anten:
  Variation in plastic responses to light results from selection in different competitive environments - A game theoretical approach using virtual plants.
• 
  Georgia Koppe, Hazem Toutounji, Peter Kirsch, Stefanie Lis, Daniel Durstewitz:
  Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI.
• 
  Jay Ghurye, Arang Rhie, Brian Walenz, Anthony D. Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy, Sergey Koren:
  Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
• 
  Benjamin Walker, Dane Taylor, Josh Lawrimore, Caitlin Hult, David Adalsteinsson, Kerry Bloom, M. Gregory Forest:
  Transient crosslinking kinetics optimize gene cluster interactions.
• 
  Sanjay Dharmavaram, Selene Baochen She, Guillermo Lázaro, Michael F. Hagan, Robijn Bruinsma:
  Gaussian curvature and the budding kinetics of enveloped viruses.
• 
  Somnath Tagore, Alessandro Gorohovski, Lars Juhl Jensen, Milana Frenkel-Morgenstern:
  ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.
• 
  Jung Min Han, Vipul Periwal:
  A mathematical model of calcium dynamics: Obesity and mitochondria-associated ER membranes.
• 
  Geir Halnes, Simen Tennøe, Trude M. Haug, Gaute T. Einevoll, Finn-Arne Weltzien, Kjetil Hodne:
  A computational model for gonadotropin releasing cells in the teleost fish medaka.
• 
  Shira Warszawski, Aliza Borenstein Katz, Rosalie Lipsh, Lev Khmelnitsky, Gili Ben Nissan, Gabriel Javitt, Orly Dym, Tamar Unger, Orli Knop, Shira Albeck, Ron Diskin, Deborah Fass, Michal Sharon, Sarel Jacob Fleishman:
  Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces.
• 
  Morgan Craig, Kamran Kaveh, Alec Woosley, Andrew S. Brown, David Goldman, Elliot Eton, Ravindra M. Mehta, Andrew Dhawan, Kazuya Arai, M. Mamunur Rahman, Sidi Chen, Martin A. Nowak, Aaron Goldman:
  Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer.
• 
  Ge Tan, Dimitris Polychronopoulos, Boris Lenhard:
  CNEr: A toolkit for exploring extreme noncoding conservation.
• 
  Maxim Komarov, Paola Malerba, Ryan Golden, Paul Nunez, Eric Halgren, Maxim Bazhenov:
  Selective recruitment of cortical neurons by electrical stimulation.
• 
  Jonathan Yaacov Weinstein, Assaf Elazar, Sarel Jacob Fleishman:
  A lipophilicity-based energy function for membrane-protein modelling and design.
• 
  Eva S. Deutekom, Julian Vosseberg, Teunis J. P. van Dam, Berend Snel:
  Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences.
• 
  Thi Mui Pham, Mirjam E. Kretzschmar, Xavier Bertrand, Martin C. J. Bootsma:
  Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models.
• 
  Vincent Miele, Christian Guill, Rodrigo Ramos-Jiliberto, Sonia Kéfi:
  Non-trophic interactions strengthen the diversity - functioning relationship in an ecological bioenergetic network model.
• 
  Laura W. Pomeroy, Hyeyoung Kim, Ningchuan Xiao, Mark Moritz, Rebecca Garabed:
  Network analyses to quantify effects of host movement in multilevel disease transmission models using foot and mouth disease in Cameroon as a case study.
• 
  Moshe Glickman, Orian Sharoni, Dino J. Levy, Ernst Niebur, Veit Stuphorn, Marius Usher:
  The formation of preference in risky choice.
• 
  Jacob Bradford, Dimitri Perrin:
  A benchmark of computational CRISPR-Cas9 guide design methods.
• 
  Diego Pereira Botelho, Kathleen M. Curran, Madeleine M. Lowery:
  Anatomically accurate model of EMG during index finger flexion and abduction derived from diffusion tensor imaging.
• 
  Joel A. Paulson, Marc Martin-Casas, Ali Mesbah:
  Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions.
• 
  Ryan S. Phillips, Jonathan E. Rubin:
  Effects of persistent sodium current blockade in respiratory circuits depend on the pharmacological mechanism of action and network dynamics.
• 
  Vladimir A. Fedorov, Philipp S. Orekhov, Ekaterina G. Kholina, Artem A. Zhmurov, Fazoil I. Ataullakhanov, Ilya B. Kovalenko, Nikita B. Gudimchuk:
  Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability.
• 
  Ming-Wen Hu, Dong Won Kim, Sheng Liu, Donald J. Zack, Seth Blackshaw, Jiang Qian:
  PanoView: An iterative clustering method for single-cell RNA sequencing data.
• 
  Franca Schmid, Matthew J. P. Barrett, Dominik Obrist, Bruno Weber, Patrick Jenny:
  Red blood cells stabilize flow in brain microvascular networks.
• 
  Laxmi Parida, Claudia Haferlach, Kahn Rhrissorrakrai, Filippo Utro, Chaya Levovitz, Wolfgang Kern, Niroshan Nadarajah, Sven Twardziok, Stephan Hutter, Manja Meggendorfer, Wencke Walter, Constance Baer, Torsten Haferlach:
  Dark-matter matters: Discriminating subtle blood cancers using the darkest DNA.
• 
  Hilje M. Doekes, Rob J. De Boer, Rutger Hermsen:
  Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations.

Volume 15, Number 9, September 2019

Editorial

• 
  G. Elisabeta Marai, Bruno Pinaud, Katja Bühler, Alexander Lex, John H. Morris:
  Ten simple rules to create biological network figures for communication.

Education

• 
  Dan Sholler, Igor Steinmacher, Denae Ford, Mara Averick, Mike Hoye, Greg Wilson:
  Ten simple rules for helping newcomers become contributors to open projects.

Perspectives

• 
  Eberhard O. Voit:
  Perspective: Dimensions of the scientific method.
• 
  Qanita Bani Baker, Maryam S. Nuser:
  Bioinformatics in Jordan: Status, challenges, and future directions.

Research Articles

• 
  Sarah Anhala Cepeda-Humerez, Jakob Ruess, Gasper Tkacik:
  Estimating information in time-varying signals.
• 
  Alex X. Lu, Oren Z. Kraus, Sam Cooper, Alan M. Moses:
  Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting.
• 
  Benjamin Parrell, Vikram Ramanarayanan, Srikantan S. Nagarajan, John F. Houde:
  The FACTS model of speech motor control: Fusing state estimation and task-based control.
• 
  Sergio Picart-Armada, Steven J. Barrett, David R. Willé, Alexandre Perera-Lluna, Alex Gutteridge, Benoit H. Dessailly:
  Benchmarking network propagation methods for disease gene identification.
• 
  Qinwei Zhuang, Brandon Alexander Holt, Gabriel A. Kwong, Peng Qiu:
  Deconvolving multiplexed protease signatures with substrate reduction and activity clustering.
• 
  Allison L. Hicks, Nicole E. Wheeler, Leonor Sánchez-Busó, Jennifer L. Rakeman, Simon R. Harris, Yonatan H. Grad:
  Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.
• 
  Rohith Palli, Mukta G. Palshikar, Juilee Thakar:
  Executable pathway analysis using ensemble discrete-state modeling for large-scale data.
• 
  Yufeng Su, Yunan Luo, Xiaoming Zhao, Yang Liu, Jian Peng:
  Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction.
• 
  Tingyu Ming, Bowen Jin, Jialei Song, Haoxiang Luo, Ruxu Du, Yang Ding:
  3D computational models explain muscle activation patterns and energetic functions of internal structures in fish swimming.
• 
  Amir Dezfouli, Bernard W. Balleine:
  Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making.
• 
  Nura Sidarus, Stefano Palminteri, Valérian Chambon:
  Cost-benefit trade-offs in decision-making and learning.
• 
  Carles Foguet, Anusha Jayaraman, Silvia Marin, Vitaly A. Selivanov, Pablo A. Moreno, Ramon Messeguer, Pedro de Atauri, Marta Cascante:
  p13CMFA: Parsimonious 13C metabolic flux analysis.
• 
  Yin Zhang, Julie M. Huynh, Guan-Sheng Liu, Richard Ballweg, Kayenat S. Aryeh, Andrew L. Paek, Tongli Zhang:
  Designing combination therapies with modeling chaperoned machine learning.
• 
  Bernhard Knapp, P. Anton van der Merwe, Omer Dushek, Charlotte M. Deane:
  MHC binding affects the dynamics of different T-cell receptors in different ways.
• 
  Merijn Mestdagh, Stijn Verdonck, Kristof Meers, Tim Loossens, Francis Tuerlinckx:
  Prepaid parameter estimation without likelihoods.
• 
  Zhiwei Ji, Weiling Zhao, Hui-Kuan Lin, Xiaobo Zhou:
  Systematically understanding the immunity leading to CRPC progression.
• 
  Charles J. Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz, Costas D. Maranas:
  From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline.
• 
  Sungrim Seirin-Lee, Fumitaka Osakada, Junichi Takeda, Satoshi Tashiro, Ryo Kobayashi, Takashi Yamamoto, Hiroshi Ochiai:
  Role of dynamic nuclear deformation on genomic architecture reorganization.
• 
  Adam Conn, Arjun Chandrasekhar, Martin van Rongen, Ottoline Leyser, Joanne Chory, Saket Navlakha:
  Network trade-offs and homeostasis in Arabidopsis shoot architectures.
• 
  David F. Read, Kate Cook, Yang Young Lu, Karine G. Le Roch, William Stafford Noble:
  Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features.
• 
  Gabriel Cardona, Joan Carles Pons, Céline Scornavacca:
  Generation of Binary Tree-Child phylogenetic networks.
• 
  Alexander D. Becker, Amy Wesolowski, Ottar N. Bjørnstad, Bryan T. Grenfell:
  Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination.
• 
  Kaiser Niknam, Amir Akbarian, Kelsey L. Clark, Yasin Zamani, Behrad Noudoost, Neda Nategh:
  Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity.
• 
  Christoph Schmal, Daisuke Ono, Jihwan Myung, J. Patrick Pett, Sato Honma, Ken-ichi Honma, Hanspeter Herzel, Isao T. Tokuda:
  Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics.
• 
  Bruno Burlando, Franco Blanchini, Giulia Giordano:
  Loop analysis of blood pressure/volume homeostasis.
• 
  Francisco J. H. Heras, Francisco Romero-Ferrero, Robert Hinz, Gonzalo G. de Polavieja:
  Deep attention networks reveal the rules of collective motion in zebrafish.
• 
  Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Sandie Arnoux, Gaël Beaunée, Pauline Ezanno:
  EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology.
• 
  Yunming Xiao, Bin Wu:
  Close spatial arrangement of mutants favors and disfavors fixation.
• 
  Amy L. Cochran, Josh M. Cisler:
  A flexible and generalizable model of online latent-state learning.
• 
  Srinivasan Venkatramanan, Jiangzhuo Chen, Arindam Fadikar, Sandeep Gupta, Dave Higdon, Bryan L. Lewis, Madhav V. Marathe, Henning S. Mortveit, Anil Vullikanti:
  Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints.
• 
  Jesse A. Livezey, Kristofer E. Bouchard, Edward F. Chang:
  Deep learning as a tool for neural data analysis: Speech classification and cross-frequency coupling in human sensorimotor cortex.
• 
  Bijaya Adhikari, Bryan L. Lewis, Anil Vullikanti, José M. Jiménez, B. Aditya Prakash:
  Fast and near-optimal monitoring for healthcare acquired infection outbreaks.
• 
  Sanggeun Song, Gil-Suk Yang, Seong Jun Park, Sungguan Hong, Ji-Hyun Kim, Jaeyoung Sung:
  Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics.
• 
  Ryan S. McClure, Jason P. Wendler, Joshua N. Adkins, Jesica Swanstrom, Ralph S. Baric, Brooke L. Deatherage Kaiser, Kristie L. Oxford, Katrina M. Waters, Jason E. McDermott:
  Unified feature association networks through integration of transcriptomic and proteomic data.
• 
  Cansu Dincer, Tugba Turkoglu Kaya, Ozlem Keskin, Attila Gürsoy, Nurcan Tuncbag:
  3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients.
• 
  Monica Chagoyen, Juan F. Poyatos:
  Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program.
• 
  Yang Yang, Qingwei Fang, Hong-Bin Shen:
  Predicting gene regulatory interactions based on spatial gene expression data and deep learning.
• 
  Michaëlle N. Mayalu, Min-Cheol Kim, H. Harry Asada:
  Multi-cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space.
• 
  Mateusz Kogut, Cyprian Kleist, Jacek Czub:
  Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail.
• 
  Gregory J. Kimmel, Philip Gerlee, Philipp M. Altrock:
  Time scales and wave formation in non-linear spatial public goods games.
• 
  Katy A. M. Gaythorpe, Kévin Jean, Laurence Cibrelus, Tini Garske:
  Quantifying model evidence for yellow fever transmission routes in Africa.
• 
  Jordan P. Skittrall, Carin K. Ingemarsdotter, Julia R. Gog, Andrew M. L. Lever:
  A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.
• 
  Timothy H. Rumbell, James R. Kozloski:
  Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons.
• 
  Anna Matveeva, Michael Fichtner, Katherine S. L. McAllister, Christopher McCann, Marc Sturrock, Daniel B. Longley, Jochen H. M. Prehn:
  Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform.
• 
  Julie E. Elie, Frédéric E. Theunissen:
  Invariant neural responses for sensory categories revealed by the time-varying information for communication calls.
• 
  Ivana Bozic, Chay Paterson, Bartlomiej Waclaw:
  On measuring selection in cancer from subclonal mutation frequencies.
• 
  Matthew L. Bendall, Miguel de Mulder, Luis Pedro Iñiguez, Aarón Lecanda-Sánchez, Marcos Pérez-Losada, Mario A. Ostrowski, R. Brad Jones, Lubbertus C. F. Mulder, Gustavo Reyes-Terán, Keith A. Crandall, Christopher E. Ormsby, Douglas F. Nixon:
  Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.
• 
  Olivier Collier, Véronique Stoven, Jean-Philippe Vert:
  LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes.
• 
  Ivan Juric, Julian M. Hibberd, Mike Blatt, Nigel J. Burroughs:
  Computational modelling predicts substantial carbon assimilation gains for C3 plants with a single-celled C4 biochemical pump.

Corrections

• 
  Anton V. Chizhov, Artyom V. Zefirov, Dmitry V. Amakhin, Elena Yu. Smirnova, Aleksey V. Zaitsev:
  Correction: Minimal model of interictal and ictal discharges "Epileptor-2".
• 
  Le Zhang, Wanyu Bai, Na Yuan, Zhenglin Du:
  Correction: Comprehensively benchmarking applications for detecting copy number variation.

Volume 15, Number 10, October 2019

Editorials

• 
  Romina Garrido, Casandra A. Trowbridge, Nana Tamura:
  Ten simple rules for providing optimal administrative support to research teams.
• 
  Philip E. Bourne:
  Ten simple rules to aid in achieving a vision.

Education

• 
  Greg Wilson:
  Ten quick tips for delivering programming lessons.

Perspective

• 
  Miguel Vazquez, Alfonso Valencia:
  Patient Dossier: Healthcare queries over distributed resources.

Research Articles

• 
  Reid Priedhorsky, Ashlynn R. Daughton, Martha Barnard, Fiona O'Connell, Dave Osthus:
  Estimating influenza incidence using search query deceptiveness and generalized ridge regression.
• 
  Shenshen Wang, Lei Dai:
  Evolving generalists in switching rugged landscapes.
• 
  Katrina M. Kaur, Pierre-Jean G. Malé, Erik Spence, Crisanto Gomez, Megan E. Frederickson:
  Using text-mined trait data to test for cooperate-and-radiate co-evolution between ants and plants.
• 
  Shauna D. O'Donovan, Michael Lenz, Roel G. Vink, Nadia J. T. Roumans, Theo M. de Kok, Edwin C. M. Mariman, Ralf L. M. Peeters, Natal A. W. van Riel, Marleen A. van Baak, Ilja C. W. Arts:
  A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data.
• 
  Iaroslav Ispolatov, Evgeniia Alekseeva, Michael Doebeli:
  Competition-driven evolution of organismal complexity.
• 
  Federica Capparelli, Klaus Pawelzik, Udo Ernst:
  Constrained inference in sparse coding reproduces contextual effects and predicts laminar neural dynamics.
• 
  Avery Parr, Nicholas R. Anderson, Daniel A. Hammer:
  A simulation of the random and directed motion of dendritic cells in chemokine fields.
• 
  Bogdan Barz, Jennifer Loschwitz, Birgit Strodel:
  Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations.
• 
  Carmichael F. Ong, Thomas Geijtenbeek, Jennifer L. Hicks, Scott L. Delp:
  Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations.
• 
  Maurizio Mattia, Matteo Biggio, Andrea Galluzzi, Marco Storace:
  Dimensional reduction in networks of non-Markovian spiking neurons: Equivalence of synaptic filtering and heterogeneous propagation delays.
• 
  Jimmy Bell, Maureen Larson, Michelle Kutzler, Massimo Bionaz, Christiane V. Löhr, David A. Hendrix:
  miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs.
• 
  Toby Wise, Jochen Michely, Peter Dayan, Raymond J. Dolan:
  A computational account of threat-related attentional bias.
• 
  Andrew J. Monaghan, Rebecca J. Eisen, Lars Eisen, Janet McAllister, Harry M. Savage, John-Paul Mutebi, Michael A. Johansson:
  Consensus and uncertainty in the geographic range of Aedes aegypti and Aedes albopictus in the contiguous United States: Multi-model assessment and synthesis.
• 
  Nalin Harischandra, Anthony J. Clare, Jure Zakotnik, Laura M. L. Blackburn, Tom Matheson, Volker Dürr:
  Evaluation of linear and non-linear activation dynamics models for insect muscle.
• 
  Arno Onken, Jue Xie, Stefano Panzeri, Camillo Padoa-Schioppa:
  Categorical encoding of decision variables in orbitofrontal cortex.
• 
  Mehran Spitmaan, Oihane Horno, Emily Chu, Alireza Soltani:
  Combinations of low-level and high-level neural processes account for distinct patterns of context-dependent choice.
• 
  Guillaume Marmier, Martin Weigt, Anne-Florence Bitbol:
  Phylogenetic correlations can suffice to infer protein partners from sequences.
• 
  Alireza Tafazzol, Yong Duan:
  Key residues in TLR4-MD2 tetramer formation identified by free energy simulations.
• 
  Mike Li, Yinuo Han, Matthew J. Aburn, Michael Breakspear, Russell A. Poldrack, James M. Shine, Joseph T. Lizier:
  Transitions in information processing dynamics at the whole-brain network level are driven by alterations in neural gain.
• 
  Alexandre C. Xavier, Rodney J. Scott, Bente A. Talseth-Palmer:
  TAPES: A tool for assessment and prioritisation in exome studies.
• 
  Ole Adrian Heggli, Joana Cabral, Ivana Konvalinka, Peter Vuust, Morten L. Kringelbach:
  A Kuramoto model of self-other integration across interpersonal synchronization strategies.
• 
  Luis U. Aguilera, William Raymond, Zachary R. Fox, Michael May, Elliot Djokic, Tatsuya Morisaki, Timothy J. Stasevich, Brian Munsky:
  Computational design and interpretation of single-RNA translation experiments.
• 
  Wei Zheng, Qiqige Wuyun, Yang Li, S. M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang:
  Detecting distant-homology protein structures by aligning deep neural-network based contact maps.
• 
  Alireza Kazemi, Bruno Louis, Daniel Isabey, Gary F. Nieman, Louis A. Gatto, Joshua Satalin, Sarah Baker, James B. Grotberg, Marcel Filoche:
  Surfactant delivery in rat lungs: Comparing 3D geometrical simulation model with experimental instillation.
• 
  Helmut Schmidt, Thomas R. Knösche:
  Action potential propagation and synchronisation in myelinated axons.
• 
  Camille Breuil, Ben Jennings, Simon Barthelmé, Nathalie Guyader, Frederick A. A. Kingdom:
  Color improves edge classification in human vision.
• 
  Mateo Lopez Espejo, Zachary P. Schwartz, Stephen V. David:
  Spectral tuning of adaptation supports coding of sensory context in auditory cortex.
• 
  Ruchi Lohia, Reza Salari, Grace Brannigan:
  Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein.
• 
  Manuel Rausch, Michael Zehetleitner:
  The folded X-pattern is not necessarily a statistical signature of decision confidence.
• 
  Giancarlo Croce, Thomas Gueudré, Maria Ruiz-Cuevas, Victoria Keidel, Matteo Figliuzzi, Hendrik Szurmant, Martin Weigt:
  A multi-scale coevolutionary approach to predict interactions between protein domains.
• 
  Jeong-Mo Choi, Furqan Dar, Rohit V. Pappu:
  LASSI: A lattice model for simulating phase transitions of multivalent proteins.
• 
  Nicholas Franzese, Adam Groce, T. M. Murali, Anna M. Ritz:
  Hypergraph-based connectivity measures for signaling pathway topologies.
• 
  Elisa Salviato, Vera Djordjilovic, Monica Chiogna, Chiara Romualdi:
  SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways.
• 
  Sebastian Spreizer, Ad Aertsen, Arvind Kumar:
  From space to time: Spatial inhomogeneities lead to the emergence of spatiotemporal sequences in spiking neuronal networks.
• 
  Elod Méhes, Beáta Biri-Kovács, Dona G. Isai, Márton Gulyás, László Nyitray, András Czirók:
  Matrigel patterning reflects multicellular contractility.
• 
  Sean West, Sushil Kumar, Surinder K. Batra, Hesham Ali, Dario Ghersi:
  Uncovering and characterizing splice variants associated with survival in lung cancer patients.
• 
  Esther Wershof, Danielle Park, Robert P. Jenkins, David J. Barry, Erik Sahai, Paul A. Bates:
  Matrix feedback enables diverse higher-order patterning of the extracellular matrix.
• 
  James Negen, Linda Bou Ali, Brittney Chere, Hannah E. Roome, Yeachan Park, Marko Nardini:
  Coding Locations Relative to One or Many Landmarks in Childhood.
• 
  Boyang Zhao, Justin R. Pritchard:
  Evolution of the nonsense-mediated decay pathway is associated with decreased cytolytic immune infiltration.
• 
  Qiao Liu, Di He, Lei Xie:
  Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature.
• 
  Fang Wang, Shaoheng Liang, Tapsi Kumar, Nicholas Navin, Ken Chen:
  SCMarker: Ab initio marker selection for single cell transcriptome profiling.
• 
  Benjamin J. Liebeskind, Richard W. Aldrich, Edward M. Marcotte:
  Ancestral reconstruction of protein interaction networks.
• 
  Edward M. Hill, Stavros Petrou, Simon de Lusignan, Ivelina Yonova, Matt J. Keeling:
  Seasonal influenza: Modelling approaches to capture immunity propagation.
• 
  Gabriel Balaban, Brian Halliday, Wenjia Bai, Bradley Porter, Carlotta Malvuccio, Pablo Lamata, Christopher A. Rinaldi, Gernot Plank, Daniel Rueckert, Sanjay K. Prasad, Martin J. Bishop:
  Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort.
• 
  Mariana Gómez-Schiavon, Nicolas E. Buchler:
  Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise.
• 
  Siva Venkadesh, Alexander O. Komendantov, Diek W. Wheeler, David J. Hamilton, Giorgio A. Ascoli:
  Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity.
• 
  Parul Maheshwari, Hao Du, Jen Sheen, Sarah M. Assmann, Réka Albert:
  Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling.
• 
  Tianshun Gao, Jiang Qian:
  EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions.
• 
  Neil J. Bruce, Daniele Narzi, Daniel Trpevski, Siri Camee van Keulen, Anu G. Nair, Ursula Rothlisberger, Rebecca C. Wade, Paolo Carloni, Jeanette Hellgren Kotaleski:
  Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals.
• 
  Grgur Tokic, Dick K. P. Yue:
  Energetics of optimal undulatory swimming organisms.
• 
  Irán R. Román, Auriel Washburn, Edward W. Large, Chris Chafe, Takako Fujioka:
  Delayed feedback embedded in perception-action coordination cycles results in anticipation behavior during synchronized rhythmic action: A dynamical systems approach.
• 
  Guillermo Vidal-Diez de Ulzurrun, Tsung-Yu Huang, Ching-Wen Chang, Hung-Che Lin, Yen-Ping Hsueh:
  Fungal feature tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi.
• 
  David J. Wooten, Sarah M. Groves, Darren R. Tyson, Qi Liu, Jing S. Lim, Réka Albert, Carlos F. Lopez, Julien Sage, Vito Quaranta:
  Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers.
• 
  Giovanni Diana, Thomas T. J. Sainsbury, Martin P. Meyer:
  Bayesian inference of neuronal assemblies.

Corrections

• 
  Francesco Rigoli, Christoph Mathys, Karl J. Friston, Raymond J. Dolan:
  Correction: A unifying Bayesian account of contextual effects in value-based choice.
• 
  Correction: Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism.
• 
  Correction: A model for the origin and development of visual orientation selectivity.
• 
  Gabriel Cardona, Joan Carles Pons, Céline Scornavacca:
  Correction: Generation of Binary Tree-Child phylogenetic networks.
• 
  Margaret P. Chapman, Tyler T. Risom, Anil Aswani, Ellen M. Langer, Rosalie C. Sears, Claire J. Tomlin:
  Correction: Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer.
• 
  Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida:
  Correction: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.
• 
  Luke E. Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler, Philipp Berens:
  Correction: Bayesian hypothesis testing and experimental design for two-photon imaging data.
• 
  Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas G. Close, Daqing Guo, Mario Negrello, Erik De Schutter:
  Correction: Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer.

Volume 15, Number 11, November 2019

Research Articles

• 
  Mattia Miotto, Enzo Marinari, Andrea De Martino:
  Competing endogenous RNA crosstalk at system level.
• 
  Rachel Howard, Aaron Scheiner, Jessica J. Cunningham, Robert A. Gatenby:
  Cytoplasmic convection currents and intracellular temperature gradients.
• 
  Jiajun Zhang, Wenbo Zhu, Qianliang Wang, Jiayu Gu, L. Frank Huang, Xiaoqiang Sun:
  Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data.
• 
  Yu Zhang, Shaun Mahony:
  Direct prediction of regulatory elements from partial data without imputation.
• 
  M. S. Vijayabaskar, Debbie K. Goode, Nadine Obier, Monika Lichtinger, Amber M. L. Emmett, Fatin N. Zainul Abidin, Nisar Shar, Rebecca Hannah, Salam A. Assi, Michael Lie-A.-Ling, Berthold Göttgens, Georges Lacaud, Valerie Kouskoff, Constanze Bonifer, David R. Westhead:
  Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.
• 
  Marilia Menezes de Oliveira, James C. Pang, Peter A. Robinson, Xiaochen Liu, Mark M. Schira:
  Feasibility of functional magnetic resonance imaging of ocular dominance and orientation preference in primary visual cortex.
• 
  Michael Everett Rule, David Schnoerr, Matthias H. Hennig, Guido Sanguinetti:
  Neural field models for latent state inference: Application to large-scale neuronal recordings.
• 
  Camden Jansen, Ricardo N. Ramirez, Nicole C. El-Ali, David Gomez-Cabrero, Jesper Tegnér, Matthias Merkenschlager, Ana Conesa, Ali Mortazavi:
  Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.
• 
  Ilya Plyusnin, Liisa Holm, Petri Törönen:
  Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
• 
  Michael Seifert, Claudia Peitzsch, Ielizaveta Gorodetska, Caroline Börner, Barbara Klink, Anna Dubrovska:
  Network-based analysis of prostate cancer cell lines reveals novel marker gene candidates associated with radioresistance and patient relapse.
• 
  Peter C. St. John, Jonathan Strutz, Linda J. Broadbelt, Keith E. J. Tyo, Yannick J. Bomble:
  Bayesian inference of metabolic kinetics from genome-scale multiomics data.
• 
  Valerya V. Zheltkova, Jordi Argilaguet, Cristina Peligero, Gennady Bocharov, Andreas Meyerhans:
  Prediction of PD-L1 inhibition effects for HIV-infected individuals.
• 
  R. Becket Ebitz, Brianna J. Sleezer, Hank P. Jedema, Charles W. Bradberry, Benjamin Y. Hayden:
  Tonic exploration governs both flexibility and lapses.
• 
  Sahand Khakabimamaghani, Dujian Ding, Oliver Snow, Martin Ester:
  Uncovering the subtype-specific temporal order of cancer pathway dysregulation.
• 
  Yichen Zheng, Thomas Wiehe:
  Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.
• 
  Tarunendu Mapder, Samuel Clifford, John Aaskov, Kevin Burrage:
  A population of bang-bang switches of defective interfering particles makes within-host dynamics of dengue virus controllable.
• 
  Jifan Shi, Tiejun Li, Luonan Chen, Kazuyuki Aihara:
  Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process.
• 
  Jilin W. J. L. Wang, Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, Plamen Ch. Ivanov:
  Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture.
• 
  Elmar D. Grosskurth, Dominik R. Bach, Marcos Economides, Quentin J. M. Huys, Lisa Holper:
  No substantial change in the balance between model-free and model-based control via training on the two-step task.
• 
  Oliver W. Layton, Diederick Christian Niehorster:
  A model of how depth facilitates scene-relative object motion perception.
• 
  Julijana Gjorgjieva, Markus Meister, Haim Sompolinsky:
  Functional diversity among sensory neurons from efficient coding principles.
• 
  David M. Alexander, Tonio Ball, Andreas Schulze-Bonhage, Cees van Leeuwen:
  Large-scale cortical travelling waves predict localized future cortical signals.
• 
  Kenneth Barr, John Reinitz, Ovidiu Radulescu:
  An in silico analysis of robust but fragile gene regulation links enhancer length to robustness.
• 
  Chen Zhao, Adam C. Mirando, Richard J. Sové, Thalyta X. Medeiros, Brian H. Annex, Aleksander S. Popel:
  A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology.
• 
  Jani V. Anttila, Mikhail Shubin, Johannes Cairns, Florian Borse, Qingli Guo, Tommi Mononen, Ignacio Vázquez-García, Otto Pulkkinen, Ville Mustonen:
  Contrasting the impact of cytotoxic and cytostatic drug therapies on tumour progression.
• 
  Jingyang Zhou, Noah C. Benson, Kendrick N. Kay, Jonathan Winawer:
  Predicting neuronal dynamics with a delayed gain control model.
• 
  Stefano Avanzini, Tibor Antal:
  Cancer recurrence times from a branching process model.
• 
  Delyle T. Polet, John E. A. Bertram:
  An inelastic quadrupedal model discovers four-beat walking, two-beat running, and pseudo-elastic actuation as energetically optimal.
• 
  Prashant Rangarajan, Sandeep K. Mody, Madhav V. Marathe:
  Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data.
• 
  Charlotte Le Mouel, Romain Brette:
  Anticipatory coadaptation of ankle stiffness and sensorimotor gain for standing balance.
• 
  George S. Watts, James E. Thornton Jr., Ken Youens-Clark, Alise J. Ponsero, Marvin J. Slepian, Emmanuel Menashi, Charles Hu, Wuquan Deng, David G. Armstrong, Spenser Reed, Lee D. Cranmer, Bonnie L. Hurwitz:
  Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity.
• 
  Kiya W. Govek, Venkata S. Yamajala, Pablo G. Cámara:
  Clustering-independent analysis of genomic data using spectral simplicial theory.
• 
  Nicholas G. Reich, Craig J. McGowan, Teresa K. Yamana, Abhinav Tushar, Evan L. Ray, Dave Osthus, Sasikiran Kandula, Logan C. Brooks, Willow Crawford-Crudell, Graham Casey Gibson, Evan Moore, Rebecca Silva, Matthew Biggerstaff, Michael A. Johansson, Roni Rosenfeld, Jeffrey Shaman:
  Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S.
• 
  Yinyin Wang, Mohieddin Jafari, Yun Tang, Jing Tang:
  Predicting Meridian in Chinese traditional medicine using machine learning approaches.
• 
  Miranda D. Stobbe, Gian A. Thun, Andrea Diéguez-Docampo, Meritxell Oliva, Justin P. Whalley, Emanuele Raineri, Ivo Glynne Gut:
  Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer.
• 
  Weifeng Guo, Shao-Wu Zhang, Tao Zeng, Yan Li, Jianxi Gao, Luonan Chen:
  A novel network control model for identifying personalized driver genes in cancer.
• 
  Ewan Colman, Petter Holme, Hiroki Sayama, Carlos Gershenson:
  Efficient sentinel surveillance strategies for preventing epidemics on networks.
• 
  Shahriar Shadkhoo, Madhav Mani:
  The role of intracellular interactions in the collective polarization of tissues and its interplay with cellular geometry.
• 
  Tyler Cassidy, Morgan Craig:
  Determinants of combination GM-CSF immunotherapy and oncolytic virotherapy success identified through in silico treatment personalization.

Volume 15, Number 12, December 2019

Education

• 
  Vincent Miele, Catherine Matias, Stéphane Robin, Stéphane Dray:
  Nine quick tips for analyzing network data.

Perspective

• 
  Anastasia Chasapi, Michalis Aivaliotis, Lefteris Angelis, Anastasios Chanalaris, Ioannis Iliopoulos, Ilias Kappas, Christos Karapiperis, Nikos Kyrpides, Evangelos Pafilis, Eleftherios Panteris, Pantelis Topalis, George Tsiamis, Ioannis S. Vizirianakis, Metaxia Vlassi, Vasilis J. Promponas, Christos A. Ouzounis:
  Establishment of computational biology in Greece and Cyprus: Past, present, and future.

Research Articles

• 
  Xiaoling Zhai, Joseph W. Larkin, Kaito Kikuchi, Samuel E. Redford, Ushasi Roy, Gürol M. Süel, Andrew Mugler:
  Statistics of correlated percolation in a bacterial community.
• 
  Shelly Mahlab-Aviv, Nathan Linial, Michal Linial:
  A cell-based probabilistic approach unveils the concerted action of miRNAs.
• 
  Kai Kang, Qian Meng, Igor Shats, David M. Umbach, Melissa Li, Yuanyuan Li, Xiaoling Li, Leping Li:
  CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data.
• 
  Haoyang Lu, Li Yi, Hang Zhang:
  Autistic traits influence the strategic diversity of information sampling: Insights from two-stage decision models.
• 
  Vu Viet Hoang Pham, Lin Liu, Cameron Bracken, Gregory J. Goodall, Qi Long, Jiuyong Li, Thuc Duy Le:
  CBNA: A control theory based method for identifying coding and non-coding cancer drivers.
• 
  Tomas Barta, Lubomir Kostal:
  The effect of inhibition on rate code efficiency indicators.
• 
  Austin Tuttle, Jorge Riera Diaz, Yoichiro Mori:
  A computational study on the role of glutamate and NMDA receptors on cortical spreading depression using a multidomain electrodiffusion model.
• 
  Bin Du, Laurence Yang, Colton J. Lloyd, Xin Fang, Bernhard O. Palsson:
  Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.
• 
  Shu Wang, Jia-Ren Lin, Eduardo D. Sontag, Peter K. Sorger:
  Inferring reaction network structure from single-cell, multiplex data, using toric systems theory.
• 
  Chris Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John W. Steill, Scott Swanson, Brian E. McIntosh, Ron M. Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher:
  Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics.
• 
  Tuure Hameri, Marc-Olivier Boldi, Vassily Hatzimanikatis:
  Statistical inference in ensemble modeling of cellular metabolism.
• 
  Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard:
  Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.
• 
  Richard F. Betzel, Katherine C. Wood, Christopher Angeloni, Maria N. Geffen, Danielle S. Bassett:
  Stability of spontaneous, correlated activity in mouse auditory cortex.
• 
  Elisabeth G. Rens, Leah Edelstein-Keshet:
  From energy to cellular forces in the Cellular Potts Model: An algorithmic approach.
• 
  Simon Mathis Kønig, Vendela Rissler, Thilde Terkelsen, Matteo Lambrughi, Elena Papaleo:
  Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level.
• 
  Vinil T. Chackochan, Vittorio Sanguineti:
  Incomplete information about the partner affects the development of collaborative strategies in joint action.
• 
  Arjan Boonman, Brock Fenton, Yossi Yovel:
  The benefits of insect-swarm hunting to echolocating bats, and its influence on the evolution of bat echolocation signals.
• 
  Caroline Horn, Julia Salzman:
  Molecular sampling at logarithmic rates for next-generation sequencing.
• 
  Bowen Li, Denis Taniguchi, Pahala Gedara Jayathilake, Valentina Gogulancea, Rebeca Gonzalez-Cabaleiro, Jinju Chen, Andrew Stephen McGough, Irina Dana Ofiteru, Thomas P. Curtis, Paolo Zuliani:
  NUFEB: A massively parallel simulator for individual-based modelling of microbial communities.
• 
  Colette Mair, Sema Nickbakhsh, Richard E. Reeve, Jim McMenamin, Arlene Reynolds, Rory N. Gunson, Pablo R. Murcia, Louise Matthews:
  Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models.
• 
  Holger Finger, Richard Gast, Christian Gerloff, Andreas K. Engel, Peter König:
  Probing neural networks for dynamic switches of communication pathways.
• 
  John E. Mittler, James T. Murphy, Sarah E. Stansfield, Kathryn Peebles, Geoffrey S. Gottlieb, Neil F. Abernethy, Molly C. Reid, Steven M. Goodreau, Joshua T. Herbeck:
  Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model.
• 
  Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini:
  Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling.
• 
  Jiajin Li, Brandon Jew, Lingyu Zhan, Sungoo Hwang, Giovanni Coppola, Nelson B. Freimer, Jae Hoon Sul:
  ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest.
• 
  Tong Wang, Akshit Goyal, Veronika Dubinkina, Sergei Maslov:
  Evidence for a multi-level trophic organization of the human gut microbiome.
• 
  Markus Reischl, Mazin Jouda, Neil MacKinnon, Erwin Fuhrer, Natalia Bakhtina, Andreas Bartschat, Ralf Mikut, Jan G. Korvink:
  Motion prediction enables simulated MR-imaging of freely moving model organisms.
• 
  Agnese Codutti, Klaas Bente, Damien Faivre, Stefan Klumpp:
  Chemotaxis in external fields: Simulations for active magnetic biological matter.
• 
  Peter K. Koo, Sean R. Eddy:
  Representation learning of genomic sequence motifs with convolutional neural networks.
• 
  Carl Bou Mansour, Elijah Koreman, Jan Steckel, Herbert Peremans, Dieter Vanderelst:
  Avoidance of non-localizable obstacles in echolocating bats: A robotic model.
• 
  Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M. Monk, Rayees Rahman, Mini Kamboj, Bernhard O. Palsson, Weigang Qiu, João B. Xavier:
  Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection.
• 
  Matt Crum, Nikhil Ram-Mohan, Michelle M. Meyer:
  Regulatory context drives conservation of glycine riboswitch aptamers.
• 
  Camilla Pierella, Maura Casadio, Ferdinando A. Mussa-Ivaldi, Sara A. Solla:
  The dynamics of motor learning through the formation of internal models.
• 
  Abby Hill, Scott Gleim, Florian Kiefer, Frederic Sigoillot, Joseph Loureiro, Jeremy L. Jenkins, Melody K. Morris:
  Benchmarking network algorithms for contextualizing genes of interest.
• 
  Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Nick V. Grishin:
  Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways.
• 
  Marina A. Ferreira, Evangeline Despin-Guitard, Fernando Duarte, Pierre Degond, Eric Theveneau:
  Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation.
• 
  Razie Yousefi, Maga Rowicka:
  Stochasticity of replication forks' speeds plays a key role in the dynamics of DNA replication.
• 
  Apeksha Singh, Frank V. Marcoline, Salome Veshaguri, Aimee W. Kao, Marcel Bruchez, Joseph A. Mindell, Dimitrios G. Stamou, Michael Grabe:
  Protons in small spaces: Discrete simulations of vesicle acidification.
• 
  Matthew C. Pharris, Neal M. Patel, Tyler G. VanDyk, Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy, Melanie I. Stefan, Tamara Kinzer-Ursem:
  A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation.
• 
  Mengyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu, Jianxin Wang:
  Overlap matrix completion for predicting drug-associated indications.
• 
  Haishan Zhang, Ximing Shao, Yin Peng, Yanning Teng, Konda Mani Saravanan, Huiling Zhang, Hongchang Li, Yanjie Wei:
  A novel machine learning based approach for iPS progenitor cell identification.
• 
  Akira Endo, Mitsuo Uchida, Adam J. Kucharski, Sebastian Funk:
  Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15.
• 
  Yongcui Wang, Shilong Chen, Luonan Chen, Yong Wang:
  Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs.
• 
  Go Ashida, Helen T. Heinermann, Jutta Kretzberg:
  Neuronal population model of globular bushy cells covering unit-to-unit variability.