| 1 | -- | 2 | Serafim Batzoglou, Russell Schwartz. Editorial |
| 9 | -- | 18 | Cristina G. Ghiurcuta, Bernard M. E. Moret. Evaluating synteny for improved comparative studies |
| 19 | -- | 25 | Ya'ara Arkin, Elior Rahmani, Marcus E. Kleber, Reijo Laaksonen, Winfried März, Eran Halperin. EPIQ - efficient detection of SNP-SNP epistatic interactions for quantitative traits |
| 26 | -- | 33 | Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert. A statistical approach for inferring the 3D structure of the genome |
| 34 | -- | 42 | Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker. Inferring gene ontologies from pairwise similarity data |
| 43 | -- | 51 | Terumasa Tokunaga, Osamu Hirose, Shotaro Kawaguchi, Yu Toyoshima, Takayuki Teramoto, Hisaki Ikebata, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida. Automated detection and tracking of many cells by using 4D live-cell imaging data |
| 52 | -- | 59 | Anika Oellrich, Julius Jacobsen, Irene Papatheodorou, Damian Smedley. Using association rule mining to determine promising secondary phenotyping hypotheses |
| 60 | -- | 68 | Nagarajan Natarajan, Inderjit S. Dhillon. Inductive matrix completion for predicting gene-disease associations |
| 69 | -- | 77 | Kourosh Zarringhalam, Ahmed Enayetallah, Padmalatha Reddy, Daniel Ziemek. Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks |
| 78 | -- | 86 | Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data |
| 87 | -- | 95 | Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation |
| 96 | -- | 104 | Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci. Large scale analysis of signal reachability |
| 105 | -- | 112 | Christoph Bernau, Markus Riester, Anne-Laure Boulesteix, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron, Lorenzo Trippa. Cross-study validation for the assessment of prediction algorithms |
| 113 | -- | 120 | Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki. Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation |
| 121 | -- | 129 | Michael K. K. Leung, Hui Yuan Xiong, Leo J. Lee, Brendan J. Frey. Deep learning of the tissue-regulated splicing code |
| 130 | -- | 138 | Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer. Functional association networks as priors for gene regulatory network inference |
| 139 | -- | 148 | Wei Cheng, Xiang Zhang, Zhishan Guo, Yu Shi, Wei Wang. Graph-regularized dual Lasso for robust eQTL mapping |
| 149 | -- | 156 | Anke Penzlin, Martin S. Lindner, Joerg Doellinger, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard. Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics |
| 157 | -- | 164 | Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu. Metabolite identification through multiple kernel learning on fragmentation trees |
| 165 | -- | 174 | Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Ai Muto, Yuki Moriya, Toshiaki Tokimatsu, Susumu Goto. Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach |
| 175 | -- | 184 | A. Ercument Cicek, Kathryn Roeder, Gultekin Özsoyoglu. MIRA: mutual information-based reporter algorithm for metabolic networks |
| 185 | -- | 194 | Richard Leslie, Christopher J. O'Donnell, Andrew D. Johnson. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database |
| 195 | -- | 203 | Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael. Detecting independent and recurrent copy number aberrations using interval graphs |
| 204 | -- | 211 | Farhad Hormozdiari, Jong Wha J. Joo, Akshay Wadia, Feng Guan, Rafail Ostrovsky, Amit Sahai, Eleazar Eskin. Privacy preserving protocol for detecting genetic relatives using rare variants |
| 212 | -- | 218 | Ladislav Rampásek, Aryan Arbabi, Michael Brudno. Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing |
| 219 | -- | 227 | Mengfei Cao, Christopher M. Pietras, Xian Feng, Kathryn J. Doroschak, Thomas Schaffner, Jisoo Park, Hao Zhang, Lenore J. Cowen, Benjamin J. Hescott. New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence |
| 228 | -- | 236 | Lei Huang, Fuhai Li, Jianting Sheng, Xiaofeng Xia, Jinwen Ma, Ming Zhan, Stephen T. C. Wong. DrugComboRanker: drug combination discovery based on target network analysis |
| 237 | -- | 245 | Marc Hulsman, Christos Dimitrakopoulos, Jeroen de Ridder. Scale-space measures for graph topology link protein network architecture to function |
| 246 | -- | 254 | Marinka Zitnik, Blaz Zupan. Gene network inference by probabilistic scoring of relationships from a factorized model of interactions |
| 255 | -- | 263 | Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng. An efficient parallel algorithm for accelerating computational protein design |
| 264 | -- | 273 | Jing Ren, Qian Liu, John Ellis, Jinyan Li. Tertiary structure-based prediction of conformational B-cell epitopes through B factors |
| 274 | -- | 282 | Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen. BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles |
| 283 | -- | 292 | Zhaojun Zhang, Wei Wang. RNA-Skim: a rapid method for RNA-Seq quantification at transcript level |
| 293 | -- | 301 | Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey A. Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son K. Pham, Anton Korobeynikov, Alla Lapidus, Pavel A. Pevzner. ExSPAnder: a universal repeat resolver for DNA fragment assembly |
| 302 | -- | 309 | Mikhail Kolmogorov, Brian J. Raney, Benedict Paten, Son K. Pham. Ragout - a reference-assisted assembly tool for bacterial genomes |
| 310 | -- | 318 | Alastair M. Kilpatrick, Bruce Ward, Stuart Aitken. Stochastic EM-based TFBS motif discovery with MITSU |
| 319 | -- | 328 | Ergude Bao, Tao Jiang, Thomas Girke. de novo genome assembly guided by closely related references |
| 329 | -- | 337 | Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin. Accurate viral population assembly from ultra-deep sequencing data |
| 1643 | -- | 1650 | Guofeng Meng, Martin Vingron. Condition-specific target prediction from motifs and expression |
| 1651 | -- | 1659 | Seyed Yahya Anvar, Kristiaan J. van der Gaag, Jaap W. F. van der Heijden, Marcel H. A. M. Veltrop, Rolf H. A. M. Vossen, Rick H. de Leeuw, Cor Breukel, Henk P. J. Buermans, J. Sjef Verbeek, Peter de Knijff, Johan T. den Dunnen, Jeroen F. J. Laros. TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes |
| 1660 | -- | 1666 | Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li, Xin Zhou, Tak Wah Lam, Yingrui Li, Xun Xu, Gane Ka-Shu Wong, Jun Wang. de novo transcriptome assembly with short RNA-Seq reads |
| 1667 | -- | 1673 | Daniel Quang, Xiaohui Xie. EXTREME: an online EM algorithm for motif discovery |
| 1674 | -- | 1680 | Yang Cao, Lei Li. Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model |
| 1681 | -- | 1689 | Ken Nagata, Arlo Randall, Pierre Baldi. Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures |
| 1690 | -- | 1697 | Kevin H. Eng, Bret M. Hanlon. Discrete mixture modeling to address genetic heterogeneity in time-to-event regression |
| 1698 | -- | 1706 | H. Robert Frost, Jason H. Moore. Optimization of gene set annotations via entropy minimization over variable clusters (EMVC) |
| 1707 | -- | 1713 | Anthony Youzhi Cheng, Yik-Ying Teo, Rick Twee-Hee Ong. Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals |
| 1714 | -- | 1720 | Jin Zhou, Erwin Tantoso, Lai-Ping Wong, Rick Twee-Hee Ong, Jin-Xin Bei, Yi Li, Jianjun Liu, Chiea-Chuen Khor, Yik-Ying Teo. iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array |
| 1721 | -- | 1729 | Fazle E. Faisal, Tijana Milenkovic. Dynamic networks reveal key players in aging |
| 1730 | -- | 1738 | Nikhil Prakash Damle, Debasisa Mohanty. Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network |
| 1739 | -- | 1746 | Hsiu-Sen Chiang, Dong-Her Shih, Binshan Lin, Ming-Hung Shih. An APN model for Arrhythmic beat classification |
| 1747 | -- | 1754 | Eduard Hermann, Stephanie Bleicken, Yamunadevi Subburaj, Ana J. García-Sáez. Automated analysis of giant unilamellar vesicles using circular Hough transformation |
| 1755 | -- | 1756 | Yeonok Lee, Debashis Ghosh, Ross C. Hardison, Yu Zhang. MRHMMs: Multivariate Regression Hidden Markov Models and the variantS |
| 1757 | -- | 1758 | Jordi Deu-Pons, Michael P. Schroeder, Nuria Lopez-Bigas. jHeatmap: an interactive heatmap viewer for the web |
| 1759 | -- | 1761 | Ramon Diaz-Uriarte. ADaCGH2: parallelized analysis of (big) CNA data |
| 1762 | -- | 1764 | Adrian Lärkeryd, Kerstin Myrtennäs, Edvin Karlsson, Chinmay Kumar Dwibedi, Mats Forsman, Pär Larsson, Anders Johansson, Andreas Sjödin. CanSNPer: a hierarchical genotype classifier of clonal pathogens |
| 1765 | -- | 1766 | Maxim I. Pyatkov, Anton N. Pankratov. SBARS: fast creation of dotplots for DNA sequences on different scales using GA-, GC-content |
| 1767 | -- | 1768 | Francisco J. López-Domingo, Javier P. Florido, Antonio Rueda, Joaquín Dopazo, Javier Santoyo Lopez. ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing |
| 1769 | -- | 1770 | Tim Seifert, Andreas Lund, Benny Kneissl, Sabine C. Mueller, Christofer S. Tautermann, Andreas Hildebrandt. SKINK: a web server for string kernel based kink prediction in α-helices |
| 1771 | -- | 1773 | Brian G. Pierce, Kevin Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, Zhiping Weng. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers |
| 1774 | -- | 1776 | Ling-Hong Hung, Ram Samudrala. fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data |
| 1777 | -- | 1779 | Xi Wang, Murray J. Cairns. SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing |
| 1780 | -- | 1781 | Mario Huerta, Marc Munyi, David Expósito, Enric Querol, Juan Cedano. MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes |
| 1782 | -- | 1784 | Matias D. Butti, Hernan Chanfreau, Diego Martinez, Diego García, Ezequiel Lacunza, Martin C. Abba. BioPlat: a software for human cancer biomarker discovery |
| 1785 | -- | 1786 | Rodrigo Santamaría, Roberto Therón, Luis Quintales. BicOverlapper 2.0: visual analysis for gene expression |
| 1787 | -- | 1788 | Diego Carrella, Francesco Napolitano, Rossella Rispoli, Mario Miglietta, Annamaria Carissimo, Luisa Cutillo, Francesco Sirci, Francesco Gregoretti, Diego di Bernardo. Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis |
| 1789 | -- | 1790 | Emre Guney, Javier Garcia-Garcia, Baldo Oliva. GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms |
| 1791 | -- | 1792 | Kim M. Rutherford, Midori A. Harris, Antonia Lock, Stephen G. Oliver, Valerie Wood. Canto: an online tool for community literature curation |