| 1 | -- | 7 | Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan. Binary Interval Search: a scalable algorithm for counting interval intersections |
| 8 | -- | 14 | Massimo Andreatta, Ole Lund, Morten Nielsen. Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach |
| 15 | -- | 21 | Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras. STAR: ultrafast universal RNA-seq aligner |
| 22 | -- | 28 | Russell Bonneville, Victor X. Jin. A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes |
| 29 | -- | 38 | Wenhui Wang, Xiaolin Yin, Yoon Soo Pyon, Matthew Hayes, Jing Li. Rare variant discovery and calling by sequencing pooled samples with overlaps |
| 39 | -- | 46 | Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén. DLocalMotif: a discriminative approach for discovering local motifs in protein sequences |
| 47 | -- | 53 | Alex W. Slater, Javier I. Castellanos, Manfred J. Sippl, Francisco Melo. Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments |
| 54 | -- | 61 | Jamie R. Hill, Charlotte M. Deane. MP-T: improving membrane protein alignment for structure prediction |
| 62 | -- | 68 | Benjamin Merget, David Zilian, Tobias Müller, Christoph A. Sotriffer. Mycobacterium tuberculosis permeability prediction tool for small molecules |
| 69 | -- | 76 | Thomas L. Vincent, Peter J. Green, Derek N. Woolfson. LOGICOIL - multi-state prediction of coiled-coil oligomeric state |
| 77 | -- | 83 | Florian Erhard, Lars Dölken, Ralf Zimmer. RIP-chip enrichment analysis |
| 84 | -- | 91 | Androniki Menelaou, Jonathan Marchini. Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold |
| 92 | -- | 98 | Chia-Hsin Liu, Ker-Chau Li, Shinsheng Yuan. Human protein-protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence |
| 99 | -- | 105 | Xi Chen, Hemant Ishwaran. Pathway hunting by random survival forests |
| 106 | -- | 113 | Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference |
| 114 | -- | 116 | Shiyuyun Tang, Ivan Antonov, Mark Borodovsky. MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences |
| 117 | -- | 118 | Arturo Magana-Mora, Haitham Ashoor, Boris R. Jankovic, Allan Kamau, Karim Awara, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic. Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants |
| 119 | -- | 121 | Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada. PBSIM: PacBio reads simulator - toward accurate genome assembly |
| 122 | -- | 123 | Zhengwei Zhu, Beifang Niu, Jing Chen, Sitao Wu, Shulei Sun, Weizhong Li. MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data |
| 124 | -- | 125 | Lu Zhang, Jing Zhang, Jing Yang, Dingge Ying, Yu-Lung Lau, Wanling Yang. PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data |
| 126 | -- | 128 | Dimitrios Vlachakis, Dimosthenis Tsagkrasoulis, Vasileios Megalooikonomou, Sophia Kossida. Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit |
| 129 | -- | 131 | Mario Fasold, Hans Binder. AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data |
| 132 | -- | 134 | Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez. DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data |
| 135 | -- | 136 | Hailiang Huang, Sandeep Tata, Robert J. Prill. BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters |
| 137 | -- | 139 | Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li 0007, Satoru Miyano. XiP: a computational environment to create, extend and share workflows |
| 140 | -- | 142 | Patrick W. Sheppard, Muruhan Rathinam, Mustafa Khammash. SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks |
| 143 | -- | 145 | Michael Weitzel, Katharina Nöh, Tolga Dalman, Sebastian Niedenführ, Birgit Stute, Wolfgang Wiechert. 13C-metabolic flux analysis |
| 146 | -- | 147 | Mark Woodbridge, Christopher D. Tomlinson, Sarah A. Butcher. ADAM: automated data management for research datasets |