| 345 | -- | 348 | Marie-Dominique Devignes, Yves Moreau. th European Conference on Computational Biology |
| 349 | -- | 355 | Hannes Hauswedell, Jochen Singer, Knut Reinert. Lambda: the local aligner for massive biological data |
| 356 | -- | 363 | Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard. Fiona: a parallel and automatic strategy for read error correction |
| 364 | -- | 370 | Jocelyn Brayet, Farida Zehraoui, Laurence Jeanson-Leh, David Israeli, Fariza Tahi. Towards a piRNA prediction using multiple kernel fusion and support vector machine |
| 371 | -- | 378 | Sepideh Mazrouee, Wei Wang. FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs |
| 379 | -- | 385 | Volodymyr Kuleshov. Probabilistic single-individual haplotyping |
| 386 | -- | 392 | Céline Lévy-Leduc, Maud Delattre, Tristan Mary-Huard, Stéphane Robin. Two-dimensional segmentation for analyzing Hi-C data |
| 393 | -- | 400 | Raymond G. Cavalcante, Chee Lee, Ryan P. Welch, Snehal Patil, Terry E. Weymouth, Laura J. Scott, Maureen A. Sartor. Broad-Enrich: functional interpretation of large sets of broad genomic regions |
| 401 | -- | 407 | Theresa Schacht, Marcus Oswald, Roland Eils, Stefan B. Eichmüller, Rainer König. Estimating the activity of transcription factors by the effect on their target genes |
| 408 | -- | 414 | John A. Capra, Dennis Kostka. Modeling DNA methylation dynamics with approaches from phylogenetics |
| 415 | -- | 421 | Thorsten Will, Volkhard Helms. Identifying transcription factor complexes and their roles |
| 422 | -- | 429 | Taejin Ahn, Eunjin Lee, Nam Huh, Taesung Park. Personalized identification of altered pathways in cancer using accumulated normal tissue data |
| 430 | -- | 437 | Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane. Alignment-free protein interaction network comparison |
| 438 | -- | 444 | Somaye Hashemifar, Jinbo Xu. HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks |
| 445 | -- | 452 | Nir Atias, Michal Gershenzon, Katia Labazin, Roded Sharan. Experimental design schemes for learning Boolean network models |
| 453 | -- | 460 | YongSoo Kim, Jin-Hyeok Jang, Seungjin Choi, Daehee Hwang. TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information |
| 461 | -- | 467 | Tommi Suvitaival, Simon Rogers, Samuel Kaski. Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations |
| 468 | -- | 474 | Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee. Causal network inference using biochemical kinetics |
| 475 | -- | 481 | Peter Kreyssig, Christian Wozar, Stephan Peter, Tomas Veloz, Bashar Ibrahim, Peter Dittrich. Effects of small particle numbers on long-term behaviour in discrete biochemical systems |
| 482 | -- | 488 | Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson. PconsFold: improved contact predictions improve protein models |
| 489 | -- | 496 | Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Rolf Backofen. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci |
| 497 | -- | 504 | Suleiman A. Khan, Seppo Virtanen, Olli-P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski. Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis |
| 505 | -- | 511 | Gabriel Studer, Marco Biasini, Torsten Schwede. Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane) |
| 512 | -- | 518 | James H. Collier, Lloyd Allison, Arthur M. Lesk, Maria Garcia de la Banda, Arun Siddharth Konagurthu. A new statistical framework to assess structural alignment quality using information compression |
| 519 | -- | 526 | Manuel Lafond, Cedric Chauve, Riccardo Dondi, Nadia El-Mabrouk. Polytomy refinement for the correction of dubious duplications in gene trees |
| 527 | -- | 533 | Christina Kratsch, Alice Carolyn McHardy. RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees |
| 534 | -- | 540 | Philipp Benner, Miroslav Bacák, Pierre-Yves Bourguignon. Point estimates in phylogenetic reconstructions |
| 541 | -- | 548 | Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy Warnow. ASTRAL: genome-scale coalescent-based species tree estimation |
| 549 | -- | 555 | Michael P. Schroeder, Carlota Rubio-Perez, David Tamborero, Abel Gonzalez-Perez, Núria López-Bigas. OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action |
| 556 | -- | 563 | Mehmet Gönen, Adam A. Margolin. Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning |
| 564 | -- | 571 | Jingwen Yan, Lei Du, Sungeun Kim, Shannon L. Risacher, Heng Huang, Jason H. Moore, Andrew J. Saykin, Li Shen. Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm |
| 572 | -- | 578 | Rui Tian, Malay Kumar Basu, Emidio Capriotti. ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples |
| 579 | -- | 586 | Xueping Liu, Mónica Campillos. Unveiling new biological relationships using shared hits of chemical screening assay pairs |
| 587 | -- | 593 | Paolo Frasconi, Ludovico Silvestri, Paolo Soda, Roberto Cortini, Francesco Pavone, Giulio Iannello. Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images |
| 594 | -- | 600 | Vladimir Gligorijevic, Vuk Janjic, Natasa Przulj. Integration of molecular network data reconstructs Gene Ontology |
| 601 | -- | 608 | Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson, Robert Stevens. Extracting patterns of database and software usage from the bioinformatics literature |
| 609 | -- | 616 | Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac. The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective |
| 617 | -- | 623 | Andrea Gobbi, Francesco Iorio, Kevin J. Dawson, David C. Wedge, David Tamborero, Ludmil B. Alexandrov, Núria López-Bigas, Mathew Garnett, Giuseppe Jurman, Julio Saez-Rodriguez. Fast randomization of large genomic datasets while preserving alteration counts |
| 624 | -- | 630 | Nadav Rappoport, Amos Stern, Nathan Linial, Michal Linial. Entropy-driven partitioning of the hierarchical protein space |
| 631 | -- | 638 | Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer. Microarray R-based analysis of complex lysate experiments with MIRACLE |
| 639 | -- | 645 | Evangelos Bellos, Lachlan J. M. Coin. cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data |
| 2393 | -- | 2398 | Jihye Kim, Vihas T. Vasu, Rangnath Mishra, Katherine R. Singleton, Minjae Yoo, Sonia M. Leach, Eveline Farias-Hesson, Robert J. Mason, Jaewoo Kang, Preveen Ramamoorthy, Jeffrey A. Kern, Lynn E. Heasley, James H. Finigan, Aik Choon Tan. Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy |
| 2399 | -- | 2405 | Rotem Ben-Hamo, Moriah Gidoni, Sol Efroni. PhenoNet: identification of key networks associated with disease phenotype |
| 2406 | -- | 2413 | Nishanth Ulhas Nair, Sunil Kumar, Bernard M. E. Moret, Philipp Bucher. Probabilistic partitioning methods to find significant patterns in ChIP-Seq data |
| 2414 | -- | 2422 | Yongseok Park, Maria E. Figueroa, Laura S. Rozek, Maureen A. Sartor. MethylSig: a whole genome DNA methylation analysis pipeline |
| 2423 | -- | 2431 | Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander. k-mer-based estimation of bacterial community composition |
| 2432 | -- | 2439 | Walyd Khenoussi, Renaud Vanhoutrève, Olivier Poch, Julie D. Thompson. SIBIS: a Bayesian model for inconsistent protein sequence estimation |
| 2440 | -- | 2446 | Lizong Deng, Aiping Wu, Wentao Dai, Tingrui Song, Ya Cui, Taijiao Jiang. Exploring protein domain organization by recognition of secondary structure packing interfaces |
| 2447 | -- | 2455 | Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert. Efficient RNA isoform identification and quantification from RNA-Seq data with network flows |
| 2456 | -- | 2463 | Navodit Misra, Ewa Szczurek, Martin Vingron. Inferring the paths of somatic evolution in cancer |
| 2464 | -- | 2470 | Mehrab Ghanat Bari, Xuepo Ma, Jianqiu Zhang. PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM |
| 2471 | -- | 2479 | Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela. Exploration and retrieval of whole-metagenome sequencing samples |
| 2480 | -- | 2485 | Charny Park, Namhee Yu, Ikjung Choi, Wan Kyu Kim, Sanghyuk Lee. lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs |
| 2486 | -- | 2493 | Florian Gomez, Ralph Lukas Stoop, Ruedi Stoop. Universal dynamical properties preclude standard clustering in a large class of biochemical data |
| 2494 | -- | 2495 | Jan De Neve, Joris Meys, Jean-Pierre Ottoy, Lieven Clement, Olivier Thas. unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R |
| 2496 | -- | 2497 | Kamil Slowikowski, Xinli Hu, Soumya Raychaudhuri. SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci |
| 2498 | -- | 2500 | Weixin Wang, Panwen Wang, Feng Xu, Ruibang Luo, Maria P. Wong, Tak Wah Lam, Junwen Wang. FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data |
| 2501 | -- | 2502 | Alex Lancaster, Andrew Nutter-Upham, Susan Lindquist, Oliver D. King. PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition |
| 2503 | -- | 2505 | Gregory G. Faust, Ira M. Hall. SAMBLASTER: fast duplicate marking and structural variant read extraction |
| 2506 | -- | 2507 | Michael J. Sanderson. Ceiba: scalable visualization of phylogenies and 2D/3D image collections |
| 2508 | -- | 2510 | Guillermo Rodrigo, Alfonso Jaramillo. RiboMaker: computational design of conformation-based riboregulation |
| 2511 | -- | 2513 | George Rosenberger, Christina Ludwig, Hannes L. Röst, Ruedi Aebersold, Lars Malmström. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data |
| 2514 | -- | 2516 | Francesco Russo, Claudia Angelini. RNASeqGUI: a GUI for analysing RNA-Seq data |
| 2517 | -- | 2518 | Charlotte Soneson. compcodeR - an R package for benchmarking differential expression methods for RNA-seq data |
| 2519 | -- | 2520 | Thomas Nussbaumer, Karl G. Kugler, Kai Christian Bader, Sapna Sharma, Michael Seidel, Klaus F. X. Mayer. RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data |
| 2521 | -- | 2523 | Daniel Broudy, Trevor Killeen, Meena Choi, Nicholas Shulman, Deepak R. Mani, Susan E. Abbatiello, Deepak Mani, Rushdy Ahmad, Alexandria K. Sahu, Birgit Schilling, Kaipo Tamura, Yuval Boss, Vagisha Sharma, Bradford W. Gibson, Steven A. Carr, Olga Vitek, Michael J. MacCoss, Brendan MacLean. A framework for installable external tools in Skyline |
| 2524 | -- | 2526 | Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean, Olga Vitek. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments |
| 2527 | -- | 2528 | Ken-Chi Yang, Chia-Lang Hsu, Chen-Ching Lin, Hsueh-Fen Juan, Hsuan-Cheng Huang. Mirin: identifying microRNA regulatory modules in protein-protein interaction networks |
| 2529 | -- | 2531 | Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming. fastGapFill: efficient gap filling in metabolic networks |
| 2532 | -- | 2533 | Paul Müller, Petra Schwille, Thomas Weidemann. PyCorrFit - generic data evaluation for fluorescence correlation spectroscopy |
| 2534 | -- | 2536 | Jia-Hong Wang, Ling-Feng Zhao, Pei Lin, Xiao-Rong Su, Shi-Jun Chen, Li-Qiang Huang, Hua-Feng Wang, Hai Zhang, Zhen-Fu Hu, Kai-Tai Yao, Zhong-Xi Huang. GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms |
| 2537 | -- | 2539 | Jordan Plieskatt, Gabriel Rinaldi, Paul J. Brindley, Xinying Jia, Jeremy Potriquet, Jeffrey Bethony, Jason P. Mulvenna. Bioclojure: a functional library for the manipulation of biological sequences |
| 2540 | -- | 2542 | Daeun Ryu, SeongBeom Cho, Hun Kim, Sanghyuk Lee, Wan Kyu Kim. GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype |