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ORCIDF1000Research, Volume 5
Volume 5, 2016
- Ulrich Dirnagl
, Ingo Przesdzing:
A pocket guide to electronic laboratory notebooks in the academic life sciences. 2 - Suzanne M. Paquette, Kalle Leinonen, William J. R. Longabaugh:
BioTapestry now provides a web application and improved drawing and layout tools. 39 - Xuejun Dong:
How to put plant root uptake into a soil water flow model. 43 - Bence Mátyás, Máté Szarka, Gábor Járvás, Gábor Kusper, István Argay:
A novel data storage logic in the cloud. 93 - Geoffrey Siwo, Andrew K. Rider, Asako Tan, Richard S. Pinapati, Scott J. Emrich, Nitesh V. Chawla, Michael T. Ferdig:
Prediction of fine-tuned promoter activity from DNA sequence. 158 - Simon Mitternacht:
FreeSASA: An open source C library for solvent accessible surface area calculations. 189 - Darawan Rinchai, Sabri Boughorbel, Scott R. Presnell, Charlie Quinn, Damien Chaussabel:
A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery. 291 - Jana Blazkova, Sabri Boughorbel, Scott R. Presnell, Charlie Quinn, Damien Chaussabel:
A curated transcriptome dataset collection to investigate the immunobiology of HIV infection. 327 - Tariq Daouda, Claude Perreault, Sébastien Lemieux:
pyGeno: A Python package for precision medicine and proteogenomics. 381 - José I. López, Jesús M. Cortés:
A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma. 385 - Elise Ruark, Anthony Renwick, Matthew Clarke, Katie Snape, Emma Ramsay, Anna Elliott, Sandra Hanks, Ann Strydom, Sheila Seal, Nazneen Rahman:
The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis. 386 - Swarit Jasial, Ye Hu, Martin Vogt, Jürgen Bajorath:
Activity-relevant similarity values for fingerprints and implications for similarity searching. 591 - Georgia B. McGaughey, W. Patrick Walters, Brian Goldman:
Understanding covariate shift in model performance. 597 - Maria Cecília D. Costa, Thijs Slijkhuis, Wilco Ligterink, Henk W. M. Hilhorst, Dick de Ridder, Harm Nijveen:
CyLineUp: A Cytoscape app for visualizing data in network small multiples. 635 - Richard J. Naftalin:
A computer model simulating human glucose absorption and metabolism in health and metabolic disease states. 647 - Ben Busby, Matthew Lesko, Lisa Federer:
Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping. 672 - Eric Moyer, Megan Hastings Hagenauer, Matthew Lesko, Felix Francis, Oscar Rodriguez, Vijayaraj Nagarajan, Vojtech Huser, Ben Busby:
MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. 674 - Bianca Kramer, Jeroen Bosman:
Innovations in scholarly communication - global survey on research tool usage. 692 - Richard Smith, Ian Roberts:
Time for sharing data to become routine: the seven excuses for not doing so are all invalid. 781 - Glenn Hyman, Elizabeth Barona, Chandrashekhar M. Biradar, Edward Guevara, John Dixon, Steve Beebe, Silvia Elena Castano, Tunrayo Alabi, Murali Krishna Gumma, Shoba Sivasankar, Ovidio Rivera, Herlin Espinosa, Jorge Cardona:
Priority regions for research on dryland cereals and legumes. 885 - Elizabeth Baskin, Peter De-Ford, Allison F. Dennis, Ian Misner, Frederick J. Tan, Ben Busby:
A cloud-based learning environment for comparing RNA-seq aligners. 888 - Lennart C. Karssen, Cornelia M. van Duijn, Yurii S. Aulchenko:
The GenABEL Project for statistical genomics. 914 - Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons:
Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments. 950 - Philip J. Chapman, Dominic I. James, Amanda J. Watson, Gemma V. Hopkins, Ian D. Waddell, Donald J. Ogilvie:
IncucyteDRC: An R package for the dose response analysis of live cell imaging data. 962 - Mohd Izzuddin Hairol, Qazi Mohamad Omair, Sharanjeet Kaur:
Effects of flanker type and position on foveal letter recognition. 1013 - Karina Salvatierra, Hector Florez:
Biomedical Mutation Analysis (BMA): A software tool for analyzing mutations associated with antiviral resistance. 1141 - Ye Hu, Jürgen Bajorath:
Analyzing compound activity records and promiscuity degrees in light of publication statistics. 1227 - Andy G. Lynch:
Decomposition of mutational context signatures using quadratic programming methods. 1253 - Jovana Maksimovic, Belinda Phipson, Alicia Oshlack:
A cross-package Bioconductor workflow for analysing methylation array data. 1281 - Rebecca C. Wilson, Oliver W. Butters, Tom Clark, Joel Minion, Andrew Turner, Madeleine J. Murtagh:
Digital methodology to implement the ECOUTER engagement process. 1307 - Alexandra Popa, Kevin Le Brigand, Agnes Paquet, Nicolas Nottet, Karine Robbe-Sermesant, Rainer Waldmann, Pascal Barbry:
RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing. 1309 - Achim Wolf:
Facebook and mental wellbeing: a crossover randomised controlled study. 1311 - Bernd Klaus:
An end to end workflow for differential gene expression using Affymetrix microarrays. 1384 - Dean A. Attali, Roza Bidshahri, Charles Haynes, Jennifer Bryan:
ddpcr: an R package and web application for analysis of droplet digital PCR data. 1411 - Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth:
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. 1438 - Upendra Kumar Devisetty, Kathleen Kennedy, Paul Sarando, Nirav C. Merchant, Eric Lyons:
Bringing your tools to CyVerse Discovery Environment using Docker. 1442 - M. Jonathan Vachon, Catherine W. Striley, Mollie R. Gordon, Miriam L. Schroeder, Emily C. Bihun, Jonathan M. Koller, Kevin J. Black:
VISIT-TS version 2: A multimedia tool for population studies on tic disorders. 1518 - Karoline Faust, Jeroen Raes:
CoNet app: inference of biological association networks using Cytoscape. 1519 - Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach:
Robust de novo pathway enrichment with KeyPathwayMiner 5. 1531 - Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr:
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. 1542 - Akila Subasinghe Arachchige, Jagath Samarabandu, YanXin Li, Ruth Wilkins, Farrah Flegal, Joan Knoll, Peter K. Rogan:
Centromere detection of human metaphase chromosome images using a candidate based method. 1565 - Jeffrey De Fauw, Pearse A. Keane, Nenad Tomasev, Daniel Visentin, George van den Driessche, Mike Johnson, Cían Hughes, Carlton Chu, Joseph R. Ledsam, Trevor Back, Tunde Peto, Geraint Rees, Hugh Montgomery, Rosalind Raine, Olaf Ronneberger, Julien Cornebise:
Automated analysis of retinal imaging using machine learning techniques for computer vision. 1573 - Zichen Wang, Avi Ma'ayan:
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. 1574 - Willem Siers, Michiel Bakker, Bob Rubbens, Ruben Haasjes, Jacco Brandt, Stefano Schivo:
webANIMO: Improving the accessibility of ANIMO. 1714 - Ganesh M. Babulal, Aaron Addison, Nupur Ghoshal, Sarah H. Stout, Elizabeth K. Vernon, Mark Sellan, Catherine M. Roe:
Development and interval testing of a naturalistic driving methodology to evaluate driving behavior in clinical research. 1716 - Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D. Bader:
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. 1717 - Matthias König:
cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK. 1736 - Oliver W. Butters, Shajid Issa, Jeff Lusted, Malcolm Newbury, Russ Parsloe, Nick Holden, Robert C. Free, Tim Beck, Rebecca C. Wilson, Paul R. Burton, Jonathan Tedds:
The Biomedical Research Infrastructure Software as a Service Kit (BRISSKit): technical description. 1905 - Gopal P. Sarma, Travis W. Jacobs, Mark D. Watts, S. Vahid Ghayoomie, Stephen D. Larson, Richard C. Gerkin:
Unit testing, model validation, and biological simulation. 1946 - Haydee Artaza, Neil P. Chue Hong, Manuel Corpas, Angel Corpuz, Rob W. W. Hooft, Rafael C. Jiménez, Brane Leskosek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vareková, Thomas Van Parys, Daniel Vaughan:
Top 10 metrics for life science software good practices. 2000 - Rosa Guarch, Jesús M. Cortés, Charles H. Lawrie, José I. López:
Multi-site tumor sampling (MSTS) improves the performance of histological detection of intratumor heterogeneity in clear cell renal cell carcinoma (CCRCC). 2020 - Carlton Chu, Jeffrey De Fauw, Nenad Tomasev, Bernardino Romera-Paredes, Cían Hughes, Joseph R. Ledsam, Trevor Back, Hugh Montgomery, Geraint Rees, Rosalind Raine, Kevin Sullivan, Syed Ali Moinuddin, Derek D'Souza, Olaf Ronneberger, Ruheena Mendes, Julien Cornebise:
Applying machine learning to automated segmentation of head and neck tumour volumes and organs at risk on radiotherapy planning CT and MRI scans. 2104 - Iman Rezaeian, Eliseos J. Mucaki, Katherina Baranova, Huy Quang Pham, Dimo Angelov, Alioune Ngom, Luis Rueda, Peter K. Rogan:
Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning. 2124 - Nicolas Torquet, Fabrice de Chaumont, Philippe Faure, Thomas Bourgeron, Elodie Ey:
mouseTube - a database to collaboratively unravel mouse ultrasonic communication. 2332 - Evert van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J. A. Fijneman, Sanne Abeln:
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. 2340 - Nirupama Benis, Dirkjan Schokker, Frank Kramer, Mari A. Smits, María Suárez-Diez:
Building pathway graphs from BioPAX data in R. 2414 - Martin Scharm, Dagmar Waltemath:
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. 2421 - Nomi L. Harris, Peter J. A. Cock, Brad Chapman, Christopher J. Fields, Karsten Hokamp, Hilmar Lapp, Monica C. Munoz-Torres, Heather Wiencko:
The 2016 Bioinformatics Open Source Conference (BOSC). 2464 - Jawoo Koo, Cindy M. Cox, Melanie Bacou, Carlo Azzarri, Zhe Guo, Ulrike Wood-Sichra, Queenie Gong, Liangzhi You:
CELL5M: A geospatial database of agricultural indicators for Africa South of the Sahara. 2490 - Dylan Collins, Joseph Lee, Niklas Bobrovitz, Constantinos Koshiaris, Alison Ward, Carl J. Heneghan:
Simple and adaptable R implementation of WHO/ISH cardiovascular risk charts for all epidemiological subregions of the world. 2522 - Gabriele Tosadori, Ivan Bestvina, Fausto Spoto, Carlo Laudanna, Giovanni Scardoni:
Creating, generating and comparing random network models with Network Randomizer. 2524 - Timothy Nugent, David Upton, Mihai Cimpoesu:
Improving data transparency in clinical trials using blockchain smart contracts. 2541 - Braxton Fitts, Ziran Zhang, Massoud Maher, Barry Demchak:
dot-app: a Graphviz-Cytoscape conversion plug-in. 2543 - Aprameya Mysore, Andreas Velten, Kevin W. Eliceiri:
Sonification of hyperspectral fluorescence microscopy datasets. 2572 - Thomas P. Quinn, Daniel Tylee, Stephen J. Glatt:
exprso: an R-package for the rapid implementation of machine learning algorithms. 2588 - Antonio de la Vega de León, Jürgen Bajorath:
Design of chemical space networks incorporating compound distance relationships. 2634 - Ivan Kondofersky, Michael Laimighofer, Christoph Kurz, Norbert Krautenbacher, Julia F. Söllner, Philip Dargatz, Hagen Scherb, Donna P. Ankerst, Christiane Fuchs:
Three general concepts to improve risk prediction: good data, wisdom of the crowd, recalibration. 2671 - Detian Deng, Yu Du, Zhicheng Ji, Karthik Rao, Zhenke Wu, Yuxin Zhu, R. Yates Coley:
Predicting survival time for metastatic castration resistant prostate cancer: An iterative imputation approach. 2672 - Daniel Kristiyanto, Kevin E. Anderson, Ling-Hong Hung, Ka Yee Yeung:
Predicting discontinuation of docetaxel treatment for metastatic castration-resistant prostate cancer (mCRPC) with random forest. 2673 - Mehrad Mahmoudian, Fatemeh Seyednasrollah, Liisa Koivu, Outi Hirvonen, Sirkku Jyrkkiö, Laura L. Elo:
A predictive model of overall survival in patients with metastatic castration-resistant prostate cancer. 2674 - Massimiliano Zanin:
Using complex networks for refining survival prognosis in prostate cancer patient. 2675 - Richard Meier, Stefan Graw, Joseph Usset, Rama Raghavan, Junqiang Dai, Prabhakar Chalise, Shellie Ellis, Brooke L. Fridley, Devin C. Koestler:
An ensemble-based Cox proportional hazards regression framework for predicting survival in metastatic castration-resistant prostate cancer (mCRPC) patients. 2677 - Miika Ahdesmäki, Simon R. Gray, Justin H. Johnson, Zhongwu Lai:
Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples. 2741 - Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic B. Bastian:
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests. 2748 - Nitesh Turaga, Mallory Ann Freeberg, Dannon Baker, John Chilton, The Galaxy Team, Anton Nekrutenko, James Taylor:
A guide and best practices for R/Bioconductor tool integration in Galaxy. 2757 - Ignacio Enrique Sanchez:
Optimal threshold estimation for binary classifiers using game theory. 2762 - Michael A. Carson, Nathan Basiliko:
Approaches to R education in Canadian universities. 2802 - Antoine Zambelli:
A data-driven approach to estimating the number of clusters in hierarchical clustering. 2809 - Daniel Chubb, Peter Broderick, Sara E. Dobbins, Richard S. Houlston:
CanVar: A resource for sharing germline variation in cancer patients. 2813 - Philip Ewels, Felix Krueger, Max Käller, Simon R. Andrews:
Cluster Flow: A user-friendly bioinformatics workflow tool. 2824 - Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia D. Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J. A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, J. Dylan Spalding, Sanne Abeln:
Integration of EGA secure data access into Galaxy. 2841 - Martin Ryberg:
Phylommand - a command line software package for phylogenetics. 2903 - Lisa M. Breckels, Claire M. Mulvey, Kathryn S. Lilley, Laurent Gatto:
A Bioconductor workflow for processing and analysing spatial proteomics data. 2926
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