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ORCIDBMC Bioinformatics, Volume 13 - Supplements
Volume 13, Number S-1, January 2012
- Albert Burger, Adrian Paschke, Paolo Romano
, M. Scott Marshall, Andrea Splendiani:
Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010. S1 - E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist language-neutral query composer. S2 - Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani, Martin Kuiper:
Gauging triple stores with actual biological data. S3 - Mohameth-François Sy, Sylvie Ranwez, Jacky Montmain, Armelle Regnault, Michel Crampes, Vincent Ranwez:
User centered and ontology based information retrieval system for life sciences. S4 - Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens:
Populous: a tool for building OWL ontologies from templates. S5 - Rafael Berlanga Llavori, Ernesto Jiménez-Ruiz, Victoria Nebot:
Exploring and linking biomedical resources through multidimensional semantic spaces. S6 - Abdelaali Briache, Kamar Marrakchi, Amine Kerzazi, Ismael Navas-Delgado, Badr Din Rossi Hassani, Khalid Lairini, José Francisco Aldana Montes:
Transparent mediation-based access to multiple yeast data sources using an ontology driven interface. S7 - Kenneth McLeod, Gus Ferguson, Albert Burger:
Argudas: lessons for argumentation in biology based on a gene expression use case. S8 - Alejandra N. González-Beltrán, Ben Tagger, Anthony Finkelstein:
Federated ontology-based queries over cancer data. S9 - Matthew Holford, Jamie P. McCusker, Kei-Hoi Cheung, Michael Krauthammer:
A semantic web framework to integrate cancer omics data with biological knowledge. S10
Volume 13, Number S-2, March 2012
- Robert A. Colvin, Jundong Liu:
Preface. I1 - Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, Jake Y. Chen:
Reordering based integrative expression profiling for microarray classification. S1 - Zhi Han, Lu Tian, Thierry Pécot, Tim Hui-Ming Huang, Raghu Machiraju, Kun Huang:
A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data. S2 - Jeremy W. Prokop, Thomas C. Leeper, Zhong-Hui Duan, Amy Milsted:
Amino acid function and docking site prediction through combining disease variants, structure alignments, sequence alignments, and molecular dynamics: a study of the HMG domain. S3 - Fernando Farfán, Jun Ma, Maureen A. Sartor, George Michailidis, H. V. Jagadish:
THINK Back: KNowledge-based Interpretation of High Throughput data. S4 - Franziska Jentzsch, Jennifer V. Hines:
Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery. S5 - Juan Esquivel-Rodríguez, Daisuke Kihara:
Evaluation of multiple protein docking structures using correctly predicted pairwise subunits. S6 - Lee Sael, Daisuke Kihara:
Constructing patch-based ligand-binding pocket database for predicting function of proteins. S7 - Richard C. McEachin, Keerthi S. Sannareddy, James D. Cavalcoli, Alla Karnovsky, Jacqueline M. Vink, Maureen A. Sartor:
Convergence of genetic influences in comorbidity. S8 - Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu, Geoffrey C. Fox:
Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. S9 - Ariful Azad, Saumyadipta Pyne, Alex Pothen:
Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry. S10 - Mark R. Dalman, Anthony Deeter, Gayathri Nimishakavi, Zhong-Hui Duan:
Fold change and p-value cutoffs significantly alter microarray interpretations. S11 - Yang Xiang, Cun-Quan Zhang, Kun Huang:
Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data. S12 - Lauren S. Mogil, Kamil Slowikowski, Howard M. Laten:
Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome. S13
Volume 13, Number S-3, March 2012
- Li An, Haibin Ling, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou:
Learning pair-wise gene functional similarity by multiplex gene expression maps. S1 - Ferhat Ay, Michael Dang, Tamer Kahveci:
Metabolic network alignment in large scale by network compression. S2 - Lu He, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for optimizing cross-overs in DNA shuffling. S3 - Richard Jang, Xin Gao, Ming Li:
Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY. S4 - Yuan Li, Shaojie Zhang:
Predicting folding pathways between RNA conformational structures guided by RNA stacks. S5 - Adriana Muñoz, David Sankoff:
Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution. S6 - R. Mitchell Parry, John H. Phan, May D. Wang:
Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems. S7 - Marco Pellegrini, Maria Elena Renda, Alessio Vecchio:
Ab initio detection of fuzzy amino acid tandem repeats in protein sequences. S8 - Corban G. Rivera, Brett M. Tyler, T. M. Murali:
Sensitive detection of pathway perturbations in cancers. S9 - Boon-Siew Seah, Sourav S. Bhowmick, C. Forbes Dewey Jr., Hanry Yu:
FUSE: a profit maximization approach for functional summarization of biological networks. S10 - Yu-Keng Shih, Srinivasan Parthasarathy:
Scalable global alignment for multiple biological networks. S11 - Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu:
Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy. S12 - Jeremy R. Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan:
Comparative analysis and visualization of multiple collinear genomes. S13 - Lei Yang, En Cheng, Z. Meral Özsoyoglu:
Efficient path-based computations on pedigree graphs with compact encodings. S14 - Youngik Yang, Kenneth P. Nephew, Sun Kim:
A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters. S15
Volume 13, Number S-4, March 2012
- Paolo Romano, Manuela Helmer-Citterich:
Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics. I1 - Jia-Ming Chang, Paolo Di Tommaso, Jean-François Taly, Cédric Notredame:
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. S1 - Emanuele Bramucci, Alessandro Paiardini, Francesco Bossa, Stefano Pascarella:
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL. S2 - Marco Pellegrini, Maria Elena Renda, Alessio Vecchio:
Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases. S3 - Paolo Pannarale, Domenico Catalano, Giorgio De Caro, Giorgio Grillo, Pietro Leo, Graziano Pappadà, Francesco Rubino, Gaetano Scioscia, Flavio Licciulli:
GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database. S4 - Daniele Segagni, Valentina Tibollo, Arianna Dagliati, Alberto Zambelli, Silvia G. Priori, Riccardo Bellazzi:
An ICT infrastructure to integrate clinical and molecular data in oncology research. S5 - Renato Umeton, Giuseppe Nicosia, C. Forbes Dewey Jr.:
OREMPdb: a semantic dictionary of computational pathway models. S6 - Achille Zappa, Andrea Splendiani, Paolo Romano:
Towards linked open gene mutations data. S7 - Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio:
Fine-tuning anti-tumor immunotherapies via stochastic simulations. S8 - Lorenzo Lazzerini-Ospri, Pasquale Stano, Pier Luigi Luisi, Roberto Marangoni:
Characterization of the emergent properties of a synthetic quasi-cellular system. S9 - Fabio Mavelli:
Stochastic simulations of minimal cells: the Ribocell model. S10 - Susanna Zucca, Lorenzo Pasotti, Giuliano Mazzini, Maria Gabriella Cusella De Angelis, Paolo Magni:
Characterization of an inducible promoter in different DNA copy number conditions. S11 - Domenico Catalano, Domenico Pignone, Gabriella Sonnante, Mariella M. Finetti-Sialer:
In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus. S12 - Andrea Cornero, Massimo Acquaviva, Paolo Fardin, Rogier Versteeg, Alexander Schramm, Alessandra Eva, Maria Bosco, Fabiola Blengio, Sara Barzaghi, Luigi Varesio:
Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome. S13 - Marco Falda, Stefano Toppo, Alessandro Pescarolo, Enrico Lavezzo, Barbara Di Camillo, Andrea Facchinetti, Elisa Cilia, Riccardo Velasco, Paolo Fontana:
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. S14 - Francesco Maria Calabrese, Domenico Simone, Marcella Attimonelli:
Primates and mouse NumtS in the UCSC Genome Browser. S15 - Raluca Mihaela Andrei, Marco Callieri, Maria Francesca Zini, Tiziana Loni, Giuseppe Maraziti, Mike Chen Pan, Monica Zoppè:
Intuitive representation of surface properties of biomolecules using BioBlender. S16 - Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich, Gabriele Ausiello:
Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. S17 - Federico Fogolari, Alessandra Corazza, Vijaylakshmi Yarra, Anusha Jalaru, Paolo Viglino, Gennaro Esposito:
Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii. S18 - Anna Vangone, Romina Oliva, Luigi Cavallo:
CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. S19 - Fabio Fioravanti, Manuela Helmer-Citterich, Enrico Nardelli:
Modeling gene regulatory network motifs using statecharts. S20 - Arianna Consiglio, Massimo Carella, Giorgio De Caro, Gianfranco Delle Foglie, Candida Giovannelli, Giorgio Grillo, Massimo Ianigro, Flavio Licciulli, Orazio Palumbo, Ada Piepoli, Elena Ranieri, Sabino Liuni:
BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments. S21 - Tiziana Sanavia, Fabio Aiolli, Giovanni Da San Martino, Andrea Bisognin, Barbara Di Camillo:
Improving biomarker list stability by integration of biological knowledge in the learning process. S22
Volume 13, Number S-5, April 2012
- Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying-Wai Li, Russell L. Malmberg, Liming Cai:
Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds. S1 - Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni:
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. S2 - Yuhong Zhang, Sanchit Misra, Ankit Agrawal, Md. Mostofa Ali Patwary, Wei-keng Liao, Zhiguang Qin, Alok N. Choudhary:
Accelerating pairwise statistical significance estimation for local alignment by harvesting GPU's power. S3 - Mayank Daga, Wu-chun Feng:
Multi-dimensional characterization of electrostatic surface potential computation on graphics processors. S4 - Hsiu J. Ho, Tsung-I Lin, Hannah H. Chang, Steven B. Haase, Sui Huang, Saumyadipta Pyne:
Parametric modeling of cellular state transitions as measured with flow cytometry. S5 - Peter Clote, Feng Lou, William Andrew Lorenz:
Maximum expected accuracy structural neighbors of an RNA secondary structure. S6 - Piotr Dittwald, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin:
Inferring serum proteolytic activity from LC-MS/MS data. S7 - Sumit Kumar Jha, Christopher James Langmead:
Exploring behaviors of stochastic differential equation models of biological systems using change of measures. S8
Volume 13, Number S-6, April 2012
- Chengxi Ye, Zhanshan (Sam) Ma, Charles H. Cannon, Mihai Pop, Douglas W. Yu:
Exploiting sparseness in de novo genome assembly. S1 - Roye Rozov, Eran Halperin, Ron Shamir:
MGMR: leveraging RNA-Seq population data to optimize expression estimation. S2 - Anatoly Efros, Eran Halperin:
Haplotype reconstruction using perfect phylogeny and sequence data. S3 - Ekaterina Khrameeva, Mikhail S. Gelfand:
Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. S4 - Gustavo Akio Tominaga Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix:
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. S5 - Jin Zhang, Jiayin Wang, Yufeng Wu:
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. S6 - Jón Sveinbjörnsson, Bjarni V. Halldórsson:
PAIR: polymorphic Alu insertion recognition. S7 - Matthew D. Edwards, David K. Gifford:
High-resolution genetic mapping with pooled sequencing. S8 - Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel:
A context-based approach to identify the most likely mapping for RNA-seq experiments. S9 - Layla Oesper, Anna M. Ritz, Sarah J. Aerni, Ryan Drebin, Benjamin J. Raphael:
Reconstructing cancer genomes from paired-end sequencing data. S10 - Boyko Kakaradov, Hui Yuan Xiong, Leo J. Lee, Nebojsa Jojic, Brendan J. Frey:
Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. S11
Volume 13, Number S-7, May 2012
- M. Michael Gromiha, De-Shuang Huang:
Introduction: advanced intelligent computing theories and their applications in bioinformatics. I1 - M. Michael Gromiha, K. Harini, R. Sowdhamini, Kazuhiko Fukui:
Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity. S1 - Jingyan Wang, Xin Gao, Quanquan Wang, Yongping Li:
ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval. S2 - Ying-Ke Lei, Zhuhong You, Zhen Ji, Lin Zhu, De-Shuang Huang:
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration. S3 - Xuesong Wang, Lijing Li, Yuhu Cheng:
An overlapping module identification method in protein-protein interaction networks. S4 - Guangyu Cui, Chao Fang, Kyungsook Han:
Prediction of protein-protein interactions between viruses and human by an SVM model. S5 - Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K. K. Leung, Xiang-Sun Zhang, Stephen Kwok-Wing Tsui, Luonan Chen:
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. S6 - Yin-Ying Wang, Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao:
Exploring drug combinations in genetic interaction network. S7 - Yu-Ting Hsiao, Wei-Po Lee:
Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method. S8 - Vitoantonio Bevilacqua, Paolo Pannarale, Mirko Abbrescia, Claudia Cava, Angelo Paradiso, Stefania Tommasi:
Comparison of data-merging methods with SVM attribute selection and classification in breast cancer gene expression. S9 - Byungkyu Park, Wook Lee, Kyungsook Han:
Modeling the interactions of Alzheimer-related genes from the whole brain microarray data and diffusion tensor images of human brain. S10 - Wassim Ayadi, Mourad Elloumi, Jin-Kao Hao:
Pattern-driven neighborhood search for biclustering of microarray data. S11 - Kwang Su Jung, Sanghoon Moon, Young Kim, Bong-Jo Kim, Kiejung Park:
Genovar: a detection and visualization tool for genomic variants. S12
Volume 13, Number S-8, May 2012
- Jessie Kennedy, Jos B. T. M. Roerdink:
Highlights of the 1st IEEE Symposium on Biological Data Visualization. S1 - Julian Heinrich, Corinna Vehlow, Florian Battke, Günter Jäger, Daniel Weiskopf, Kay Nieselt:
iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data. S2 - Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai:
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. S3 - Hendrik Strobelt, Enrico Bertini, Joachim Braun, Oliver Deussen, Ulrich Groth, Thomas U. Mayer, Dorit Merhof:
HiTSEE KNIME: a visualization tool for hit selection and analysis in high-throughput screening experiments for the KNIME platform. S4 - Trevor Paterson, Martin Graham, Jessie B. Kennedy, Andy Law:
VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees. S5 - Philip Livengood, Ross Maciejewski, Wei Chen, David S. Ebert:
OmicsVis: an interactive tool for visually analyzing metabolomics data. S6 - David Mayerich, Christopher Björnsson, Jonothan Taylor, Badrinath Roysam:
NetMets: software for quantifying and visualizing errors in biological network segmentation. S7 - Christopher W. Bartlett, Soo Yeon Cheong, Liping Hou, Jesse Paquette, Pek Yee Lum, Günter Jäger, Florian Battke, Corinna Vehlow, Julian Heinrich, Kay Nieselt, Ryo Sakai, Jan Aerts, William C. Ray:
An eQTL biological data visualization challenge and approaches from the visualization community. S8
Volume 13, Number S-9, June 2012
- Yann Christinat, Bernard M. E. Moret:
Inferring transcript phylogenies. S1 - Qinmin Hu, Jimmy X. Huang, Xiaohua Hu:
Modeling and mining term association for improving biomedical information retrieval performance. S2 - Xijun Liang, Zhonghang Xia, Li-Wei Zhang, Fang-Xiang Wu:
Inference of gene regulatory subnetworks from time course gene expression data. S3 - Weimin Luo, Keith C. C. Chan:
Discovering patterns in drug-protein interactions based on their fingerprints. S4 - Sohee Oh, Jaehoon Lee, Min-Seok Kwon, Bruce Weir, Kyooseob Ha, Taesung Park:
A novel method to identify high order gene-gene interactions in genome-wide association studies: Gene-based MDR. S5 - Kristopher L. Patton, David J. John, James L. Norris:
Bayesian probabilistic network modeling from multiple independent replicates. S6 - Jingchun Sun, Yonghui Wu, Hua Xu, Zhongming Zhao:
DTome: a web-based tool for drug-target interactome construction. S7 - Zhenyu Yang, David Sankoff:
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. S8
Volume 13, Number S-10, June 2012
- Jianer Chen, Ion I. Mandoiu, Raj Sunderraman, Jianxin Wang, Alexander Zelikovsky:
Guest Editors' Introduction. S1 - Fei Guo, Lusheng Wang:
Computing the protein binding sites. S2 - Andrea Szabóová, Ondrej Kuzelka, Filip Zelezný, Jakub Tolar:
Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search. S3 - Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu:
High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs. S4 - John D. Eblen, Charles A. Phillips, Gary L. Rogers, Michael A. Langston:
The maximum clique enumeration problem: algorithms, applications, and implementations. S5 - Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alex Zelikovsky, Yuri Khudyakov:
Efficient error correction for next-generation sequencing of viral amplicons. S6 - Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, Michael A. Langston:
A systematic comparison of genome-scale clustering algorithms. S7 - Zhan Zhou, Jianying Gu, Yong-Quan Li, Yufeng Wang:
Genome plasticity and systems evolution in Streptomyces. S8 - Chunfang Zheng, David Sankoff:
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes. S9 - Vadim Mozhayskiy, Ilias Tagkopoulos:
Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation. S10 - Ruchi Chaudhary, J. Gordon Burleigh, Oliver Eulenstein:
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. S11 - Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein:
Consensus properties for the deep coalescence problem and their application for scalable tree search. S12 - Vadim Mozhayskiy, Ilias Tagkopoulos:
Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution. S13 - Pawel Górecki, Oliver Eulenstein:
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. S14 - Matej Holec, Jirí Kléma, Filip Zelezný, Jakub Tolar:
Comparative evaluation of set-level techniques in predictive classification of gene expression samples. S15 - Wen-Chieh Chang, Sudheer Vakati, Roland Krause, Oliver Eulenstein:
Exploring biological interaction networks with tailored weighted quasi-bicliques. S16 - Pingzhao Hu, Shelley B. Bull, Hui Jiang:
Gene network modular-based classification of microarray samples. S17 - Pavol Jancura, Eleftheria Mavridou, Enrique Carrillo-de Santa Pau, Elena Marchiori:
A methodology for detecting the orthology signal in a PPI network at a functional complex level. S18 - Jieyue He, Chaojun Li, Baoliu Ye, Wei Zhong:
Efficient and accurate greedy search methods for mining functional modules in protein interaction networks. S19 - Jonathan Q. Jiang, Maoying Wu:
Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study. S20
Volume 13, Number S-11, June 2012
- Jin-Dong Kim, Ngan L. T. Nguyen, Yue Wang, Jun'ichi Tsujii, Toshihisa Takagi, Akinori Yonezawa:
The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011. S1 - Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou:
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. S2 - Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Érick Alphonse, Maarten van de Guchte, Philippe Bessières, Claire Nedellec:
BioNLP Shared Task - The Bacteria Track. S3 - Jari Björne, Filip Ginter, Tapio Salakoski:
University of Turku in the BioNLP'11 Shared Task. S4 - Andreas Vlachos, Mark Craven:
Biomedical event extraction from abstracts and full papers using search-based structured prediction. S5 - Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer:
Semantically linking molecular entities in literature through entity relationships. S6 - Halil Kilicoglu, Sabine Bergler:
Biological event composition. S7 - Zorana Ratkovic, Wiktoria Golik, Pierre Warnier:
Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach. S8 - David McClosky, Sebastian Riedel, Mihai Surdeanu, Andrew McCallum, Christopher D. Manning:
Combining joint models for biomedical event extraction. S9
Volume 13, Number S-12, July 2012
- Eric C. Rouchka, Robert M. Flight, Hunter N. B. Moseley:
Proceedings of the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2012. A1 - Alexander Kemper, Musa Hindi, Kenneth S. Ramos, Theodore S. Kalbfleisch:
Comprehensive characterization of an individual's LINE-1 insertion profile using next generation sequencing data. A2 - Gopinath Rajadinakaran, Huifang Sun, Claire Rinehart, Eric C. Rouchka, Michael E. Smith:
Regulation of cell proliferation and apoptosis by growth hormone during zebrafish auditory hair cell regeneration. A3 - Benjamin J. Harrison, Robert M. Flight, Abdallah Eteleeb, Eric C. Rouchka, Jeffrey C. Petruska:
RNASeq profiling of UTR expression during neuronal plasticity. A4 - Caroline Rempe, Charles R. Budinoff, T. Effler, Alison Buchan:
The influence of sample biases on estimations of marine microbial diversity. A5 - Nourtan Abdeltawab, Lu Lu, Robert W. Williams, Malak Kotb:
Meta-analysis of genes within QTLs of group A streptococcal sepsis and their expression QTLs reveal pathways modulating host differential response to streptococcal sepsis. A6 - Lishi Wang, Wenli Lu, Rachel Scheib, Yue Huang, Xiaoyun Liu, Linda Myers, Lu Lu, Robert W. Williams, Yan Jiao, Weikuan Gu:
QTLs for bone mineral density of femurs and tibias in recombinant inbred strains derived from C57BL/6J and DBA/2J inbred strains. A7 - Fusheng Zhao, Yonghui Ma, Yan Jiao, Lishi Wang, Yue Huang, Wei Wei, Weikuan Gu:
Identification of hearing loss relevant genes in QTL on mouse chromosome 16. A8 - Denise R. Koessler, Elizabeth G. Johnson, Jordan M. Utley, Harry A. Richards, Cynthia B. Peterson:
Building better interdisciplinary scientists: creating graduate level courses to address the communication gap in interdisciplinary research. A9 - Chandrajit Lahiri, Pawar Shrikant, Radhakrishnan Sabarinathan, M. Izhar Ashraf, Dipshikha Chakravortty:
Identifying indispensable proteins of the type III secretion systems of Salmonella enterica serovar Typhimurium strain LT2. A10 - Yonghui Ma, Yan Jiao, Fusheng Zhao, Weikuan Gu:
Evaluation of gene expression in muscle in mouse model lacking of vitamin C synthesis. A11 - Neil Moore, Jerzy W. Jaromczyk, Christopher L. Schardl:
Finding long protein products of alternatively spliced genes. A12 - Behrouz Madahian, Robert C. Klesges, Lisa Klesges, Ramin Homayouni:
System dynamics modeling of childhood obesity. A13 - Christopher Burton, Sujin Kim:
The development of a three-frame timeline for clinical concepts extracted from discharge summaries. A14 - Paul A. Harris:
Research Electronic Data Capture (REDCap) - planning, collecting and managing data for clinical and translational research. A15 - Wenyuan Zhao, Tieqian Zhao, Yuanjian Chen, Yao Sun:
Temporal and spatial relationship of gene expression in the infarcted rat heart. A16 - Yue Huang, Lishi Wang, Robert W. Williams, Weikuan Gu, Yan Jiao:
Evaluation of potential role of Atp5g3 in modulating alcohol preference and obesity. A17 - Yan Jiao, Yonghui Ma, Xiaoyun Liu, Weikuan Gu:
Evaluation of potential role of vitamin C in differential skeletal development between female and male mice using a mouse model. A18 - Matt Gannon, Rachel Stevens, Molly Griffith, Mark Bardgett:
The effects of early-life risperidone administration on forebrain neurotrophin expression during adulthood. A19 - Dana Marshall, Jianan Dong, Leon Dent, Siddharth Pratap:
The antibiotic resistance proteome of Acinetobacter baumanii MDR isolate MMC#4. A20 - Farid Yaghouby, Ting Zhang, Martin Striz, James Crawford, Kevin D. Donohue, Bruce F. O'Hara, Sridhar Sunderam:
Experimental and computational analysis of mouse sleep-wake dynamics. A21 - Uta Ziegler, Yuanan Diao, Claus Ernst, Anthony Montemayor:
Computational investigation of DNA packing in confinement. A22 - Marc Beck, Roman V. Yampolskiy:
DNA as a medium for hiding data. A23 - Jonathan Babbage, Naga Nagisetty, Steven P. Larmore, Jacqueline Fiore:
Delivering informatics for clinical research in developing countries. A24
Volume 13, Number S-13, August 2012
- Jiexin Zhang, Kevin R. Coombes:
Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups. S1 - Jorge R. Herskovic, Devika Subramanian, Trevor Cohen, Pamela A. Bozzo-Silva, Charles F. Bearden, Elmer V. Bernstam:
Graph-based signal integration for high-throughput phenotyping. S2 - Bong-Hyun Kim, Bhadrachalam Chitturi, Nick V. Grishin:
Self consistency grouping: a stringent clustering method. S3 - Priyakshi Mahanta, Hasin Afzal Ahmed, Dhruba K. Bhattacharyya, Jugal K. Kalita:
An effective method for network module extraction from microarray data. S4 - Guoshuai Cai, Hua Li, Yue Lu, Xuelin Huang, Juhee Lee, Peter Müller, Yuan Ji, Shoudan Liang:
Accuracy of RNA-Seq and its dependence on sequencing depth. S5 - Yuan Ji, Riten Mitra, Fernando Quintana, Alejandro Jara, Peter Müller, Ping Liu, Yue Lu, Shoudan Liang:
BM-BC: a Bayesian method of base calling for Solexa sequence data. S6 - Peng Qiu, Li Zhang:
Identification of markers associated with global changes in DNA methylation regulation in cancers. S7 - Kenneth Sundberg, Mark J. Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith A. Crandall:
Phylogenetic search through partial tree mixing. S8 - Catherine H. Schein, David M. Bowen, Jessica A. Lewis, Kyung Choi, Aniko Paul, Gerbrand J. van der Heden van Noort, Wenzhe Lu, Dmitri V. Filippov:
Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals. S9 - Bradley M. Broom, Kim-Anh Do, Devika Subramanian:
Model averaging strategies for structure learning in Bayesian networks with limited data. S10 - Kevin Riehle, Cristian Coarfa, Andrew R. Jackson, Jun Ma, Arpit Tandon, Sameer Paithankar, Sriram Raghuraman, Toni-Ann Mistretta, Delphine Saulnier, Sabeen Raza, Maria Diaz, Robert Shulman, Kjersti Aagaard, James Versalovic, Aleksandar Milosavljevic:
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. S11
Volume 13, Number S-14, September 2012
- Riccardo Bellazzi, Marco Masseroli, Shawn N. Murphy, Amnon Shabo, Paolo Romano:
Clinical Bioinformatics: challenges and opportunities. S1 - Francesco Sambo, Emanuele Trifoglio, Barbara Di Camillo, Gianna Maria Toffolo, Claudio Cobelli:
Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data. S2 - Matteo Re, Giorgio Valentini:
Cancer module genes ranking using kernelized score functions. S3 - Xian Yang, Rui Han, Yike Guo, Jeremy T. Bradley, Benita Cox, Robert Dickinson, Richard Kitney:
Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA. S4 - Ivan Merelli, Federica Viti, Luciano Milanesi:
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. S5 - Alberto Malovini, Nicola Barbarini, Riccardo Bellazzi, Francesca De Michelis:
Hierarchical Naive Bayes for genetic association studies. S6 - Vladan Mijatovic, Ilaria Iacobucci, Marco Sazzini, Luciano Xumerle, Antonio Mori, Pier Franco Pignatti, Giovanni Martinelli, Giovanni Malerba:
Imputation reliability on DNA biallelic markers for drug metabolism studies. S7 - Francesca Nadalin, Francesco Vezzi, Alberto Policriti:
GapFiller: a de novo assembly approach to fill the gap within paired reads. S8 - Sophie Coutant, Chloé Cabot, Arnaud Lefebvre, Martine Léonard, Élise Prieur-Gaston, Dominique Campion, Thierry Lecroq, Hélène Dauchel:
EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics. S9 - Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio:
The human "magnesome": detecting magnesium binding sites on human proteins. S10 - Lina Fatima Soualmia, Élise Prieur-Gaston, Zied Moalla, Thierry Lecroq, Stéfan Jacques Darmoni:
Matching health information seekers' queries to medical terms. S11 - Pietro Liò, Nicola Paoletti, Mohammad Ali Moni, Kathryn Atwell, Emanuela Merelli, Marco Viceconti:
Modelling osteomyelitis. S12 - Irene Sánchez-Linares, Horacio Emilio Pérez Sánchez, José M. Cecilia, José M. García:
High-Throughput parallel blind Virtual Screening using BINDSURF. S13 - Paola Lecca, Daniele Morpurgo:
Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth. S14
Volume 13, Number S-15, September 2012
- Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Susan Bridges, Doris M. Kupfer:
Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference. S1 - Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan, Jake Y. Chen:
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. S2 - Gang Fu, Xiaofei Nan, Haining Liu, Ronak Y. Patel, Pankaj R. Daga, Yixin Chen, Dawn Wilkins, Robert J. Doerksen:
Implementation of multiple-instance learning in drug activity prediction. S3 - Joseph S. Reddy, Ranjit Kumar, James M. Watt, Mark L. Lawrence, Shane C. Burgess, Bindu Nanduri:
Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213. S4 - Andrey A. Ptitsyn, Leonid L. Moroz:
Computational workflow for analysis of gain and loss of genes in distantly related genomes. S5 - Halil Bisgin, Zhichao Liu, Reagan Kelly, Hong Fang, Xiaowei Xu, Weida Tong:
Investigating drug repositioning opportunities in FDA drug labels through topic modeling. S6 - Fan Zhang, Renee Drabier:
IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis. S7 - Yixiang Zhang, Sanmin Liu, Susie Y. Dai, Joshua S. Yuan:
Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses. S8 - Ruchi Verma, Ulrich Melcher:
A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins. S9 - Dongxia Yao, Qiang Wei, Wenying Xu, Ryan D. Syrenne, Joshua S. Yuan, Zhen Su:
Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis. S10 - Lifeng Zhang, Daniel Berleant, Yi Wang, Ling Li, Diane J. Cook, Eve Syrkin Wurtele:
BirdsEyeView (BEV): graphical overviews of experimental data. S11 - Gaihua Zhang, Zhen Su:
Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization. S12 - Tibor Pechan, Steven R. Gwaltney:
Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide. S13 - Zhifa Liu, Brandon M. Malone, Changhe Yuan:
Empirical evaluation of scoring functions for Bayesian network model selection. S14
Volume 13, Number S-16, November 2012
- Kelvin Ma, Olga Vitek, Alexey I. Nesvizhskii:
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. S1 - Kyowon Jeong, Sangtae Kim, Nuno Bandeira:
False discovery rates in spectral identification. S2 - Viktor Granholm, William Stafford Noble, Lukas Käll:
A cross-validation scheme for machine learning algorithms in shotgun proteomics. S3 - Yong Fuga Li, Predrag Radivojac:
Computational approaches to protein inference in shotgun proteomics. S4 - Yuliya V. Karpievitch, Alan R. Dabney, Richard D. Smith:
Normalization and missing value imputation for label-free LC-MS analysis. S5 - Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek:
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. S6 - Ann L. Oberg, Douglas W. Mahoney:
Statistical methods for quantitative mass spectrometry proteomic experiments with labeling. S7 - Sven Nahnsen, Oliver Kohlbacher:
In silico design of targeted SRM-based experiments. S8 - Deepak R. Mani, Susan E. Abbatiello, Steven A. Carr:
Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. S9 - Melissa Key:
A tutorial in displaying mass spectrometry-based proteomic data using heat maps. S10 - Theodore Alexandrov:
MALDI imaging mass spectrometry: statistical data analysis and current computational challenges. S11 - Jürgen Cox, Matthias Mann:
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. S12 - Marina Bessarabova, Alexander Ishkin, Lellean JeBailey, Tatiana Nikolskaya, Yuri Nikolsky:
Knowledge-based analysis of proteomics data. S13
Volume 13, Number S-17, December 2012
- Christian Schönbach, Sissades Tongsima, Jonathan H. Chan, Vladimir Brusic, Tin Wee Tan, Shoba Ranganathan:
InCoB2012 Conference: from biological data to knowledge to technological breakthroughs. S1 - Rithvik Vinekar, Chandra Verma, Indira Ghosh:
Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases. S2 - Hui-Ling Huang, Phasit Charoenkwan, Te-Fen Kao, Hua-Chin Lee, Fang-Lin Chang, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Wen-Liang Chen, Shinn-Ying Ho:
Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition. S3 - Chian Teo, Steven R. Shave, Adam Leow Thean Chor, Abu Salleh, Mohd Basyaruddin Abdul Rahman, Malcolm D. Walkinshaw, Bimo Ario Tejo:
Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening. S4 - Mahmoud ElHefnawi, Mohammad ElGamacy, Mohamed Fares:
Multiple virtual screening approaches for finding new Hepatitis c virus RNA-dependent RNA polymerase inhibitors: Structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors. S5 - Minho Lee, Dongsup Kim:
Large-scale reverse docking profiles and their applications. S6 - Bhyravabhotla Jayaram, Tanya Singh, Goutam Mukherjee, Abhinav Mathur, Shashank Shekhar, Vandana Shekhar:
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. S7 - Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara:
An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. S8 - Atima Tharatipyakul, Somrak Numnark, Duangdao Wichadakul, Supawadee Ingsriswang:
ChemEx: information extraction system for chemical data curation. S9 - Mostafa M. Abbas, Mohamed Abouelhoda, Hazem M. Bahig:
A hybrid method for the exact planted (l, d) motif finding problem and its parallelization. S10 - Felix A. Krüger, Raghd Rostom, John P. Overington:
Mapping small molecule binding data to structural domains. S11 - Je-Gun Joung, Soo-Jin Kim, Soo-Yong Shin, Byoung-Tak Zhang:
A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset. S12 - Emily Chia-Yu Su, Jia-Ming Chang, Cheng-Wei Cheng, Ting-Yi Sung, Wen-Lian Hsu:
Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing. S13 - Rambabu Chinta, Joo Huang Tan, Martin Wasser:
The study of muscle remodeling in Drosophila metamorphosis using in vivo microscopy and bioimage informatics. S14 - Chuan Hock Koh, Sucheendra K. Palaniappan, P. S. Thiagarajan, Limsoon Wong:
Improved statistical model checking methods for pathway analysis. S15 - Sriganesh Srihari, Hon Wai Leong:
Temporal dynamics of protein complexes in PPI Networks: a case study using yeast cell cycle dynamics. S16 - Kevin Lim, Limsoon Wong:
CMPF: Class-switching minimized pathfinding in metabolic networks. S17 - Saowaluck Kaewkamnerd, Chairat Uthaipibull, Apichart Intarapanich, Montri Pannarut, Sastra Chaotheing, Sissades Tongsima:
An automatic device for detection and classification of malaria parasite species in thick blood film. S18 - En-Yu Lai, Wei-Bung Wang, Tao Jiang, Kun-Pin Wu:
A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree. S19 - Liang Zhao, Limsoon Wong, Lanyuan Lu, Steven C. H. Hoi, Jinyan Li:
B-cell epitope prediction through a graph model. S20 - Carlo Bianca, Ferdinando Chiacchio, Francesco Pappalardo, Marzio Pennisi:
Mathematical modeling of the immune system recognition to mammary carcinoma antigen. S21 - Mohamed El-Kalioby, Mohamed Abouelhoda, Jan Krüger, Robert Giegerich, Alexander Sczyrba, Dennis P. Wall, Peter J. Tonellato:
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. S22 - Sungin Park, Soo-Yong Shin, Kyu-Baek Hwang:
CFMDS: CUDA-based fast multidimensional scaling for genome-scale data. S23 - Ranjeeta Menon, Gagan Garg, Robin B. Gasser, Shoba Ranganathan:
TranSeqAnnotator: large-scale analysis of transcriptomic data. S24 - Mogeeb A. A. Mosleh, Hayat Manssor, Sorayya Malek, Pozi Milow, Aishah Salleh:
A preliminary study on automated freshwater algae recognition and classification system. S25 - Devendra Kumar Biswal, Manish Debnath, Shakti Kumar, Pramod Tandon:
Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding. S26
Volume 13, Number S-18, December 2012
- Alexander Goncearenco, Priscila Grynberg, Olga B. Botvinnik, Geoff MacIntyre, Thomas Abeel:
Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012. A1 - Jing Gong, Yin Tong, Hong-Mei Zhang, An-Yuan Guo:
miRNASNP: a database of miRNA related SNPs and their effects on miRNA function. A2 - Shruthi Viswanath, Chengyong Yang:
Color call improvement in next generation sequencing using multi-class support vector machines. A3 - Huy Q. Dinh:
Epi-letters - how to describe epigenetic signatures. A4 - Kyungtaek Lim, Yoshikazu Furuta, Ichizo Kobayashi:
Unexpected variations in translation initiation machinery. A5 - Yingying Wei, Xia Li, Qianfei Wang, Hongkai Ji:
iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding. A6 - Ernesto Iacucci, Léon-Charles Tranchevent, Dusan Popovic, Georgios A. Pavlopoulos, Bart De Moor, Reinhard Schneider, Yves Moreau:
A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs. A7 - Kyle D. Bemis, Livia Eberlin, Christina Ferreira, R. Cooks, Olga Vitek:
Spatial segmentation and feature selection for desi imaging mass spectrometry data with spatially-aware sparse clustering. A8 - Tulip Nandu, Meeta Pradhan, Mathew J. Palakal:
Elucidating gene signatures that control the circadian rhythm in cyanobacteria using bioinformatics methods. A9 - Oliver Voggenreiter, Stefan Bleuler, Wilhelm Gruissem:
Exact biclustering algorithm for the analysis of large gene expression data sets. A10 - Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky:
TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads. A11 - Heewook Lee, Ellen Popodi, Patricia L. Foster, Haixu Tang:
Detecting structural variants involving repetitive elements: capturing transposition events of IS elements in the genome of Escherichia coli. A12 - Ignacio S. Caballero, Gracia Bonilla, Judy Y. Yen, John H. Connor:
Diagnosing Lassa virus infection by tracking the antiviral response. A13
Volume 13, Number S-19, December 2012
- Sergey Aganezov Jr., Max A. Alekseyev:
On pairwise distances and median score of three genomes under DCJ. S1 - Mathieu Blanchette:
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. S2 - Daniel Doerr, Annelyse Thévenin, Jens Stoye:
Gene family assignment-free comparative genomics. S3 - Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk:
A flexible ancestral genome reconstruction method based on gapped adjacencies. S4 - Maryam Haghighi, David Sankoff:
Medians seek the corners, and other conjectures. S5 - Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler:
From event-labeled gene trees to species trees. S6 - Katharina Jahn, Henner Sudek, Jens Stoye:
Multiple genome comparison based on overlap regions of pairwise local alignments. S7 - Katharina Jahn, Chunfang Zheng, Jakub Kovác, David Sankoff:
A consolidation algorithm for genomes fractionated after higher order polyploidization. S8 - Ahmad Mahmoody, Crystal L. Kahn, Benjamin J. Raphael:
Reconstructing genome mixtures from partial adjacencies. S9 - Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo:
Compareads: comparing huge metagenomic experiments. S10 - Ján Manuch, Murray Patterson, Roland Wittler, Cédric Chauve, Eric Tannier:
Linearization of ancestral multichromosomal genomes. S11 - Hyun Jung Park, Luay Nakhleh:
Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria. S12 - Mingfu Shao, Yu Lin:
Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion. S13 - Poly H. da Silva, Raphael Machado, Simone Dantas, Marília D. V. Braga:
Restricted DCJ-indel model: sorting linear genomes with DCJ and indels. S14 - Krister M. Swenson, Nadia El-Mabrouk:
Gene trees and species trees: irreconcilable differences. S15 - Olivier Tremblay Savard, Krister M. Swenson:
A graph-theoretic approach for inparalog detection. S16 - Filippo Utro, Omar Cornejo, Donald Livingstone, Juan Motamayor, Laxmi Parida:
ARG-based genome-wide analysis of cacao cultivars. S17 - Xiaolong Wu, Yun Heo, Izzat El Hajj, Wen-mei W. Hwu, Deming Chen, Jian Ma:
TIGER: tiled iterative genome assembler. S18
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