| 1 | -- | 2 | Nir Ben-Tal. Editorial |
| 9 | -- | 17 | Saket Navlakha, Joseph Suhan, Alison L. Barth, Ziv Bar-Joseph. A high-throughput framework to detect synapses in electron microscopy images |
| 18 | -- | 26 | Sarah J. Aerni, Xiao Liu, Chuong B. Do, Samuel S. Gross, Andy Nguyen, Stephen D. Guo, Fuhui Long, Hanchuan Peng, Stuart S. Kim, Serafim Batzoglou. Caenorhabditis elegans |
| 27 | -- | 35 | Iulian Pruteanu-Malinici, William H. Majoros, Uwe Ohler. Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields |
| 36 | -- | 43 | Noa Liscovitch, Uri Shalit, Gal Chechik. FuncISH: learning a functional representation of neural ISH images |
| 44 | -- | 52 | Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou. A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text |
| 53 | -- | 61 | Wyatt T. Clark, Predrag Radivojac. Information-theoretic evaluation of predicted ontological annotations |
| 62 | -- | 70 | Andrew J. Sedgewick, Stephen C. Benz, Shahrooz Rabizadeh, Patrick Soon-Shiong, Charles J. Vaske. Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM |
| 71 | -- | 79 | Yaron Orenstein, Ron Shamir. k-mers with applications to protein-binding microarrays and synthetic enhancers |
| 80 | -- | 88 | Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens. Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model |
| 89 | -- | 97 | Hai-son Le, Ziv Bar-Joseph. Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation |
| 98 | -- | 107 | Hiroyuki Kuwahara, Ming Fan, Suojin Wang, Xin Gao. A framework for scalable parameter estimation of gene circuit models using structural information |
| 108 | -- | 116 | Dina Hafez, Ting Ni, Sayan Mukherjee, Jun Zhu, Uwe Ohler. Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation |
| 117 | -- | 125 | Fantine Mordelet, John Horton, Alexander J. Hartemink, Barbara E. Engelhardt, Raluca Gordân. Stability selection for regression-based models of transcription factor-DNA binding specificity |
| 126 | -- | 134 | Yuhao Wang, Jianyang Zeng. Predicting drug-target interactions using restricted Boltzmann machines |
| 135 | -- | 144 | Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Toshiaki Tokimatsu, Susumu Goto. de novo reconstruction of metabolic pathways from metabolome-scale compound sets |
| 145 | -- | 153 | Gamze Abaka, Türker Bíyíkoglu, Cesim Erten. CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways |
| 154 | -- | 161 | Rodrigo Liberal, John W. Pinney. Simple topological properties predict functional misannotations in a metabolic network |
| 162 | -- | 170 | Dan He. IBD-Groupon: an efficient method for detecting group-wise identity-by-descent regions simultaneously in multiple individuals based on pairwise IBD relationships |
| 171 | -- | 179 | Chloé-Agathe Azencott, Dominik Grimm, Mahito Sugiyama, Yoshinobu Kawahara, Karsten M. Borgwardt. Efficient network-guided multi-locus association mapping with graph cuts |
| 180 | -- | 188 | Pier Francesco Palamara, Itsik Pe'er. Inference of historical migration rates via haplotype sharing |
| 189 | -- | 198 | Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz. in situ hybridization data from tumor cell populations |
| 199 | -- | 209 | Carlo Vittorio Cannistraci, Gregorio Alanis-Lobato, Timothy Ravasi. Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding |
| 210 | -- | 216 | Alexander Lan, Michal Ziv-Ukelson, Esti Yeger Lotem. A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks |
| 217 | -- | 226 | Meghana Kshirsagar, Jaime G. Carbonell, Judith Klein-Seetharaman. Multitask learning for host-pathogen protein interactions |
| 227 | -- | 236 | Anthony Gitter, Ziv Bar-Joseph. Identifying proteins controlling key disease signaling pathways |
| 237 | -- | 246 | Robert Patro, Carl Kingsford. Predicting protein interactions via parsimonious network history inference |
| 247 | -- | 256 | Zhidong Xue, Dong Xu, Yan Wang, Yang Zhang. ThreaDom: extracting protein domain boundary information from multiple threading alignments |
| 257 | -- | 265 | Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu. Protein threading using context-specific alignment potential |
| 266 | -- | 273 | Zhiyong Wang, Jinbo Xu. Predicting protein contact map using evolutionary and physical constraints by integer programming |
| 274 | -- | 282 | Min Xu, Frank Alber. Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms |
| 283 | -- | 290 | Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger. Compressive genomics for protein databases |
| 291 | -- | 299 | Zhaojun Zhang, Shunping Huang, Jack Wang, Xiang Zhang, Fernando Pardo-Manuel de Villena, Leonard McMillan, Wei Wang 0010. GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment |
| 300 | -- | 307 | Elmirasadat Forouzmand, Hamidreza Chitsaz. The RNA Newton polytope and learnability of energy parameters |
| 308 | -- | 315 | Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution |
| 316 | -- | 325 | Bo Xie, Boris R. Jankovic, Vladimir B. Bajic, Le Song, Xin Gao. Poly(A) motif prediction using spectral latent features from human DNA sequences |
| 326 | -- | 334 | Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Ming-Ju Lv, Xin-Guang Zhu, Francis Y. L. Chin. IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels |
| 335 | -- | 343 | Kousik Kundu, Fabrizio Costa, Rolf Backofen. A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains |
| 344 | -- | 351 | David Golan, Paul Medvedev. Using state machines to model the Ion Torrent sequencing process and to improve read error rates |
| 352 | -- | 360 | Derek Aguiar, Sorin Istrail. Haplotype assembly in polyploid genomes and identical by descent shared tracts |
| 361 | -- | 370 | Lin Huang, Victoria Popic, Serafim Batzoglou. Short read alignment with populations of genomes |
| 1589 | -- | 1592 | Mireia Olivella, Angel Gonzalez, Leonardo Pardo, Xavier Deupi. Relation between sequence and structure in membrane proteins |
| 1593 | -- | 1599 | Yoonsoo Hahn. Evidence for the dissemination of cryptic non-coding RNAs transcribed from intronic and intergenic segments by retroposition |
| 1600 | -- | 1606 | Matthias Barann, Daniela Esser, Ulrich C. Klostermeier, Tuuli Lappalainen, Anne Luzius, Jan W. P. Kuiper, Ole Ammerpohl, Inga Vater, Reiner Siebert, Vyacheslav Amstislavskiy, Ralf Sudbrak, Hans Lehrach, Stefan Schreiber, Philip Rosenstiel. Janus - a comprehensive tool investigating the two faces of transcription |
| 1607 | -- | 1613 | Thomas Schnattinger, Uwe Schöning, Hans A. Kestler. Structural RNA alignment by multi-objective optimization |
| 1614 | -- | 1622 | Xiang Chen, Jian-Ding Qiu, Shao-Ping Shi, Sheng-Bao Suo, Shu-Yun Huang, Ru-Ping Liang. Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites |
| 1623 | -- | 1630 | Jan Kirrbach, Miriam Krugliak, Christian L. Ried, Philipp Pagel, Isaiah T. Arkin, Dieter Langosch. Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins |
| 1631 | -- | 1637 | Adam Roberts, Lorian Schaeffer, Lior Pachter. Updating RNA-Seq analyses after re-annotation |
| 1638 | -- | 1646 | Martin A. Rijlaarsdam, David J. Rijlaarsdam, Ad J. M. Gillis, Lambert C. J. Dorssers, Leendert H. J. Looijenga. miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data |
| 1647 | -- | 1653 | Katja Hebestreit, Martin Dugas, Hans-Ulrich Klein. Detection of significantly differentially methylated regions in targeted bisulfite sequencing data |
| 1654 | -- | 1662 | Behnam Neyshabur, Ahmadreza Khadem, Somaye Hashemifar, Seyed Shahriar Arab. NETAL: a new graph-based method for global alignment of protein-protein interaction networks |
| 1663 | -- | 1670 | María Jesús García-Godoy, Esteban López-Camacho, Ismael Navas Delgado, José Francisco Aldana Montes. Sharing and executing linked data queries in a collaborative environment |
| 1671 | -- | 1678 | Midori A. Harris, Antonia Lock, Jürg Bähler, Stephen G. Oliver, Valerie Wood. FYPO: the fission yeast phenotype ontology |
| 1679 | -- | 1681 | Christoph Bartenhagen, Martin Dugas. RSVSim: an R/Bioconductor package for the simulation of structural variations |
| 1682 | -- | 1684 | Hákon Jónsson, Aurelien Ginolhac, Mikkel Schubert, Philip L. F. Johnson, Ludovic Orlando. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters |
| 1685 | -- | 1686 | Clare Sloggett, Nuwan Goonasekera, Enis Afgan. BioBlend: automating pipeline analyses within Galaxy and CloudMan |
| 1687 | -- | 1689 | Miriam Rubio-Camarillo, Gonzalo Gómez-López, José M. Fernández, Alfonso Valencia, David G. Pisano. RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses |
| 1690 | -- | 1692 | Joseph C. Pearson, Stephen T. Crews. cis-regulatory modules |
| 1693 | -- | 1695 | Brett Trost, Ryan Arsenault, Philip Griebel, Scott Napper, Anthony J. Kusalik. DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites |
| 1696 | -- | 1697 | Paul Brown, Laura Baxter, Richard Hickman, Jim Beynon, Jonathan D. Moore, Sascha Ott. MEME-LaB: motif analysis in clusters |
| 1698 | -- | 1699 | Brian Jiménez-García, Carles Pons, Juan Fernández-Recio. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring |
| 1700 | -- | 1701 | Saskia D. Hiltemann, Elizabeth A. McClellan, Jos van Nijnatten, Sebastiaan Horsman, Ivo Palli, Ines Teles Alves, Thomas Hartjes, Jan Trapman, Peter van der Spek, Guido Jenster, Andrew Stubbs. iFUSE: integrated fusion gene explorer |
| 1702 | -- | 1703 | Daniel Stöckel, Oliver Müller, Tim Kehl, Andreas Gerasch, Christina Backes, Alexander Rurainski, Andreas Keller, Michael Kaufmann, Hans-Peter Lenhof. NetworkTrail - a web service for identifying and visualizing deregulated subnetworks |
| 1704 | -- | 1705 | Louis-Philippe Lemieux Perreault, Sylvie Provost, Marc-André Legault, Amina Barhdadi, Marie-Pierre Dube. pyGenClean: efficient tool for genetic data clean up before association testing |
| 1706 | -- | 1707 | Chuan-Yih Yu, Anoop M. Mayampurath, Yunli Hu, Shiyue Zhou, Yehia Mechref, Haixu Tang. Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry |
| 1708 | -- | 1709 | Antti Häkkinen, Anantha Barathi Muthukrishnan, Andre Mora, José Manuel Fonseca, Andre S. Ribeiro. Escherichia coli |
| 1710 | -- | 1712 | Catherine Voegele, Baptiste Bouchereau, Nivonirina Robinot, James McKay, Philippe Damiecki, Lucile Alteyrac. A universal open-source Electronic Laboratory Notebook |