Journal: Bioinformatics

Volume 31, Issue 10

1521 -- 1525Tobias Hamp, Burkhard Rost. More challenges for machine-learning protein interactions
1526 -- 1535Keegan D. Korthauer, Christina Kendziorski. MADGiC: a model-based approach for identifying driver genes in cancer
1536 -- 1543Hashem A. Shihab, Mark F. Rogers, Julian Gough, Matthew E. Mort, David N. Cooper, Ian N. M. Day, Tom R. Gaunt, Colin Campbell. An integrative approach to predicting the functional effects of non-coding and coding sequence variation
1544 -- 1552Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm. PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment
1553 -- 1560Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu. Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping
1561 -- 1568Hisaki Ikebata, Ryo Yoshida. Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets
1569 -- 1576Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz. k-mer counting
1577 -- 1583Kouichi Kimura, Asako Koike. Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data
1584 -- 1591Maria D. Chikina, Elena Zaslavsky, Stuart C. Sealfon. CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations
1592 -- 1598Thomas Bleazard, Janine A. Lamb, Sam Griffiths-Jones. Bias in microRNA functional enrichment analysis
1599 -- 1606Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew E. Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels
1607 -- 1613Qunyuan Zhang, Haley Abel, Alan Wells, Petra Lenzini, Felicia Gomez, Michael A. Province, Alan A. Templeton, George M. Weinstock, Nita H. Salzman, Ingrid B. Borecki. Selection of models for the analysis of risk-factor trees: leveraging biological knowledge to mine large sets of risk factors with application to microbiome data
1614 -- 1622Vân Anh Huynh-Thu, Guido Sanguinetti. Combining tree-based and dynamical systems for the inference of gene regulatory networks
1623 -- 1631Kieran O'Neill, Nima Aghaeepour, Jeremy Parker, Donna Hogge, Aly Karsan, Bakul Dalal, Ryan R. Brinkman. Deep profiling of multitube flow cytometry data
1632 -- 1639Darren Davis, Ömer Nebil Yaveroglu, Noël Malod-Dognin, Aleksandar Stojmirovic, Natasa Przulj. Topology-function conservation in protein-protein interaction networks
1640 -- 1647Renaud Richardet, Jean-Cédric Chappelier, Martin Telefont, Sean Hill. Large-scale extraction of brain connectivity from the neuroscientific literature
1648 -- 1654Deepak Nag Ayyala, Shili Lin. GrammR: graphical representation and modeling of count data with application in metagenomics
1655 -- 1662Heidi Dowst, Benjamin Pew, Chris Watkins, Apollo Mcowiti, Jonathan Barney, Shijing Qu, Lauren B. Becnel. Acquire: an open-source comprehensive cancer biobanking system
1663 -- 1664Wolfgang Kaisers, Heiner Schaal, Holger Schwender. rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples
1665 -- 1667Burkhard Steuernagel, Florian Jupe, Kamil Witek, Jonathan D. G. Jones, Brande B. H. Wulff. NLR-parser: rapid annotation of plant NLR complements
1668 -- 1670Liguo Wang, Jinfu J. Nie, Jean-Pierre Kocher. PVAAS: identify variants associated with aberrant splicing from RNA-seq
1671 -- 1673Guoli Ji, Lei Li, Qingshun Quinn Li, Xiangdong Wu, Jingyi Fu, Gong Chen, Xiaohui Wu. PASPA: a web server for mRNA poly(A) site predictions in plants and algae
1674 -- 1676Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak Wah Lam. de Bruijn graph
1677 -- 1679Tom Druet, Michel Georges. LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors
1680 -- 1682Paul R. Staab, Sha Zhu, Dirk Metzler, Gerton Lunter. scrm: efficiently simulating long sequences using the approximated coalescent with recombination
1683 -- 1685Israel Steinfeld, Roy Navon, Michael L. Creech, Zohar Yakhini, Anya Tsalenko. ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types
1686 -- 1688Sara Aibar, Celia Fontanillo, Conrad Droste, Javier De Las Rivas. Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering
1689 -- 1691Jing Peng, Xinyi Shi, Yiming Sun, Dongye Li, Baohui Liu, Fanjiang Kong, Xiaohui Yuan. QTLMiner: QTL database curation by mining tables in literature
1692 -- 1694Pan Tong, Kevin R. Coombes, Faye M. Johnson, Lauren A. Byers, Lixia Diao, Diane D. Liu, J. Jack Lee, John V. Heymach, Jing Wang 0006. drexplorer: A tool to explore dose-response relationships and drug-drug interactions
1695 -- 1697Mark Davies, Nathan Dedman, Anne Hersey, George Papadatos, Matthew D. Hall, Lourdes Cucurull-Sanchez, Phil Jeffrey, Samiul Hasan, Peter J. Eddershaw, John P. Overington. ADME SARfari: comparative genomics of drug metabolizing systems
1698 -- 1700Jacinte Beerten, Joost J. J. van Durme, Rodrigo Gallardo, Emidio Capriotti, Louise Serpell, Frederic Rousseau, Joost Schymkowitz. WALTZ-DB: a benchmark database of amyloidogenic hexapeptides