| 1 | -- | 9 | Vinita Periwal, Vinod Scaria. Insights into structural variations and genome rearrangements in prokaryotic genomes |
| 10 | -- | 16 | Pablo Cingolani, Rob Sladek, Mathieu Blanchette. BigDataScript: a scripting language for data pipelines |
| 17 | -- | 24 | Ka Chun Wong, Yue Li, Chengbin Peng, Zhaolei Zhang. SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles |
| 25 | -- | 32 | LiPing Li, Enguo Chen, Chun Yang, Jun Zhu, Pushkala Jayaraman, Jeff de Pons, Catherine C. Kaczorowski, Howard J. Jacob, Andrew S. Greene, Matthew R. Hodges, Allen W. Cowley Jr., Mingyu Liang, Haiming Xu, Peng-Yuan Liu, Yan Lu. Improved rat genome gene prediction by integration of ESTs with RNA-Seq information |
| 33 | -- | 39 | P. R. Shidhi, Prashanth Suravajhala, Aysha Nayeema, Achuthsankar S. Nair, Shailja Singh, Pawan K. Dhar. Making novel proteins from pseudogenes |
| 40 | -- | 47 | Mufleh Al-Shatnawi, M. Omair Ahmad, M. N. Shanmukha Swamy. Prediction of Indel flanking regions in protein sequences using a variable-order Markov model |
| 48 | -- | 55 | Mahmoud M. Ibrahim, Scott A. Lacadie, Uwe Ohler. JAMM: a peak finder for joint analysis of NGS replicates |
| 56 | -- | 61 | Darren T. Houniet, Thahira J. Rahman, Saeed Al Turki, Matthew E. Hurles, Yaobo Xu, Judith A. Goodship, Bernard Keavney, Mauro F. Santibanez-Koref. Using population data for assessing next-generation sequencing performance |
| 62 | -- | 68 | Hongwei Wang, Qiang Sun, Wenyuan Zhao, Lishuang Qi, Yunyan Gu, Pengfei Li, Mengmeng Zhang, Yang Li, Shu-Lin Liu, Zheng Guo. Individual-level analysis of differential expression of genes and pathways for personalized medicine |
| 69 | -- | 75 | Antti Häkkinen, Andre S. Ribeiro. Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data |
| 76 | -- | 83 | Sheng Qin, Fei Ma, Liming Chen. Gene regulatory networks by transcription factors and microRNAs in breast cancer |
| 84 | -- | 93 | Yaomin Xu, Xingyi Guo, Jiayang Sun, Zhongming Zhao. Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation |
| 94 | -- | 101 | Bie M. P. Verbist, Kim Thys, Joke Reumers, Yves Wetzels, Koen Van der Borght, Willem Talloen, Jeroen Aerssens, Lieven Clement, Olivier Thas. VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering |
| 102 | -- | 108 | Yotsawat Pomyen, Marcelo Segura, Timothy M. D. Ebbels, Hector C. Keun. Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets |
| 109 | -- | 111 | Julien Lajugie, Nicolas Fourel, Eric E. Bouhassira. GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface |
| 112 | -- | 113 | Pierre Lindenbaum, Richard Redon. mod_bio: Apache modules for Next-Generation sequencing data |
| 114 | -- | 115 | Mick Watson, Marian Thomson, Judith E. Risse, Richard Talbot, Javier Santoyo Lopez, Karim Gharbi, Mark L. Blaxter. poRe: an R package for the visualization and analysis of nanopore sequencing data |
| 116 | -- | 118 | Kenichi Chiba, Yuichi Shiraishi, Yasunobu Nagata, Kenichi Yoshida, Seiya Imoto, Seishi Ogawa, Satoru Miyano. Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data |
| 119 | -- | 120 | Wei Chen, Xitong Zhang, Jordan Brooker, Hao Lin, Liqing Zhang, Kuo-Chen Chou. PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions |
| 121 | -- | 122 | Anna Katharina Hildebrandt, Daniel Stöckel, Nina M. Fischer, Luis de la Garza, Jens Krüger 0002, Stefan Nickels, Marc Röttig, Charlotta Schärfe, Marcel Schumann, Philipp Thiel, Hans-Peter Lenhof, Oliver Kohlbacher, Andreas Hildebrandt. ballaxy: web services for structural bioinformatics |
| 123 | -- | 125 | Iain H. Moal, Brian Jiménez-García, Juan Fernández-Recio. CCharPPI web server: computational characterization of protein-protein interactions from structure |
| 126 | -- | 127 | Gregory B. Quinn, Chunxiao Bi, Cole H. Christie, Kyle Pang, Andreas Prlic, Takanori Nakane, Christine Zardecki, Maria Voigt, Helen M. Berman, Philip E. Bourne, Peter W. Rose. Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank |
| 128 | -- | 130 | Steffen Sass, Florian Buettner, Nikola S. Müller, Fabian J. Theis. RAMONA: a Web application for gene set analysis on multilevel omics data |
| 131 | -- | 133 | Murat Can Cobanoglu, Zoltán N. Oltvai, D. Lansing Taylor, Ivet Bahar. BalestraWeb: efficient online evaluation of drug-target interactions |
| 134 | -- | 136 | John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin. cddApp: a Cytoscape app for accessing the NCBI conserved domain database |
| 137 | -- | 139 | Niya Wang, Ting Gong, Robert Clarke, Lulu Chen, Ie-Ming Shih, Zhen Zhang, Douglas A. Levine, Jianhua Xuan, Yue Wang. UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples |
| 140 | -- | 142 | Manuel Corpas, Rafael C. Jimenez, Erik Bongcam-Rudloff, Aidan Budd, Michelle D. Brazas, Pedro L. Fernandes, Bruno A. Gaëta, Celia W. G. van Gelder, Eija Korpelainen, Fran Lewitter, Annette McGrath, Daniel MacLean, Patricia M. Palagi, Kristian Rother, Jan Taylor, Allegra Via, Mick Watson, Maria Victoria Schneider, Teresa K. Attwood. The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers |
| 143 | -- | 145 | Andrew Yates, Kathryn Beal, Stephen Keenan, William M. McLaren, Miguel Pignatelli, Graham R. S. Ritchie, Magali Ruffier, Kieron Taylor, Alessandro Vullo, Paul Flicek. The Ensembl REST API: Ensembl Data for Any Language |
| 146 | -- | 150 | Ilan Samish, Philip E. Bourne, Rafael J. Najmanovich. Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics |