| 389 | -- | 392 | Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder. ECCB 2016: The 15th European Conference on Computational Biology |
| 396 | -- | 404 | Michael Lenz, Nadia J. T. Roumans, Roel G. Vink, Marleen A. van Baak, Edwin C. M. Mariman, Ilja C. W. Arts, Theo M. de Kok, Gökhan Ertaylan. Estimating real cell size distribution from cross-section microscopy imaging |
| 405 | -- | 412 | Chantriolnt-Andreas Kapourani, Guido Sanguinetti. Higher order methylation features for clustering and prediction in epigenomic studies |
| 413 | -- | 420 | Nanne Aben, Daniel J. Vis, Magali Michaut, Lodewyk F. A. Wessels. TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types |
| 421 | -- | 429 | Charles J. Labuzzetta, Margaret L. Antonio, Patricia M. Watson, Robert C. Wilson, Lauren A. Laboissonniere, Jeffrey M. Trimarchi, Baris Genc, P. Hande Ozdinler, Dennis K. Watson, Paul E. Anderson. Complementary feature selection from alternative splicing events and gene expression for phenotype prediction |
| 430 | -- | 436 | William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg. P-values with an empirical adaptation of Brown's method |
| 437 | -- | 444 | Sunjoo Bang, Jae-Hoon Kim, Hyunjung Shin. Causality modeling for directed disease network |
| 445 | -- | 454 | Thanh Le Van, Matthijs van Leeuwen, Ana Carolina Fierro, Dries De Maeyer, Jimmy Van den Eynden, Lieven P. C. Verbeke, Luc De Raedt, Kathleen Marchal, Siegfried Nijssen. Simultaneous discovery of cancer subtypes and subtype features by molecular data integration |
| 455 | -- | 463 | Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli-P. Kallioniemi, Tero Aittokallio, Samuel Kaski. Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization |
| 464 | -- | 472 | Dalia Cohn-Alperovich, Alona Rabner, Ilona Kifer, Yael Mandel-Gutfreund, Zohar Yakhini. Mutual enrichment in aggregated ranked lists with applications to gene expression regulation |
| 473 | -- | 478 | Georg Summer, Thomas Kelder, Marijana Radonjic, Marc van Bilsen, Suzan Wopereis, Stephane Heymans. The Network Library: a framework to rapidly integrate network biology resources |
| 479 | -- | 486 | Kedar Tatwawadi, Mikel Hernaez, Idoia Ochoa, Tsachy Weissman. GTRAC: fast retrieval from compressed collections of genomic variants |
| 487 | -- | 493 | Siavash Sheikhizadeh, M. Eric Schranz, Mehmet Akdel, Dick de Ridder, Sandra Smit. PanTools: representation, storage and exploration of pan-genomic data |
| 494 | -- | 502 | Ilan Shomorony, Samuel H. Kim, Thomas A. Courtade, David N. C. Tse. Information-optimal genome assembly via sparse read-overlap graphs |
| 503 | -- | 510 | Andreas D. M. Gunawan, Bingxin Lu, Louxin Zhang. A program for verification of phylogenetic network models |
| 511 | -- | 519 | Tarmo Äijö, Xiaojing Yue, Anjana Rao, Harri Lähdesmäki. LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs |
| 520 | -- | 528 | Jikai Lei, Yanni Sun. Assemble CRISPRs from metagenomic sequencing data |
| 529 | -- | 537 | Nan Du, Yanni Sun. Improve homology search sensitivity of PacBio data by correcting frameshifts |
| 538 | -- | 544 | Ariya Shajii, Deniz Yörükoglu, Yun William Yu, Bonnie Berger. k-mer matching |
| 545 | -- | 551 | Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve. CoLoRMap: Correcting Long Reads by Mapping short reads |
| 552 | -- | 558 | Olga V. Matveeva, Yury D. Nechipurenko, Evgeniy Riabenko, Chikako Ragan, Nafisa N. Nazipova, Aleksey Y. Ogurtsov, Svetlana A. Shabalina. Optimization of signal-to-noise ratio for efficient microarray probe design |
| 559 | -- | 566 | Shay Ben-Elazar, Benny Chor, Zohar Yakhini. Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data |
| 567 | -- | 575 | Samuele Girotto, Cinzia Pizzi, Matteo Comin. MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures |
| 576 | -- | 585 | Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa, Rolf Backofen. Characterizing leader sequences of CRISPR loci |
| 586 | -- | 594 | Sungyoung Lee, Sungkyoung Choi, Young-Jin Kim, Bong-Jo Kim, Heungsun Hwang, Taesung Park. Pathway-based approach using hierarchical components of collapsed rare variants |
| 595 | -- | 604 | Kathrin Trappe, Tobias Marschall, Bernhard Y. Renard. Detecting horizontal gene transfer by mapping sequencing reads across species boundaries |
| 605 | -- | 610 | Wenbao Yu, Seungyeoun Lee, Taesung Park. A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions |
| 611 | -- | 619 | Jaehoon Lee, Young-Jin Kim, Juyoung Lee, Bong-Jo Kim, Seungyeoun Lee, Taesung Park. Gene-set association tests for next-generation sequencing data |
| 620 | -- | 628 | Djordje Djordjevic, Kenro Kusumi, Joshua W. K. Ho. XGSA: A statistical method for cross-species gene set analysis |
| 629 | -- | 638 | Tuomo Hartonen, Biswajyoti Sahu, Kashyap Dave, Teemu Kivioja, Jussi Taipale. PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments |
| 639 | -- | 648 | Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi. DeepChrome: deep-learning for predicting gene expression from histone modifications |
| 649 | -- | 657 | I. Gregor, Alexander Schönhuth, Alice Carolyn McHardy. Snowball: strain aware gene assembly of metagenomes |
| 658 | -- | 664 | Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu. ModuleAlign: module-based global alignment of protein-protein interaction networks |
| 665 | -- | 671 | Konstantinos D. Tsirigos, Arne Elofsson, Pantelis G. Bagos. PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins |
| 672 | -- | 679 | Sheng Wang, Jianzhu Ma, Jinbo Xu. AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields |
| 680 | -- | 684 | Robert Vaser, Dario Pavlovic, Mile Sikic. SWORD - a highly efficient protein database search |
| 685 | -- | 692 | Olga S. Voitenko, Andi Dhroso, Anna Feldmann, Dmitry Korkin, Olga V. Kalinina. Patterns of amino acid conservation in human and animal immunodeficiency viruses |
| 693 | -- | 701 | Émilie Neveu, David W. Ritchie, Petr Popov, Sergei Grudinin. PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation |
| 702 | -- | 709 | Thang V. Pham, Connie R. Jimenez. Simulated linear test applied to quantitative proteomics |
| 710 | -- | 717 | Thach Nguyen, Michael Habeck. A probabilistic model for detecting rigid domains in protein structures |
| 718 | -- | 726 | Bernhard Steiert, Jens Timmer, Clemens Kreutz. 1 regularization facilitates detection of cell type-specific parameters in dynamical systems |
| 727 | -- | 735 | Hesam Montazeri, Jack Kuipers, Roger D. Kouyos, Jürg Böni, Sabine Yerly, Thomas Klimkait, Vincent Aubert, Huldrych F. Günthard, Niko Beerenwinkel, The Swiss Hiv Cohort Study. Large-scale inference of conjunctive Bayesian networks |
| 736 | -- | 745 | Mark D. M. Leiserson, Matthew A. Reyna, Benjamin J. Raphael. A weighted exact test for mutually exclusive mutations in cancer |
| 746 | -- | 754 | Matthew Ruffalo, Ziv Bar-Joseph. Genome wide predictions of miRNA regulation by transcription factors |
| 755 | -- | 762 | Max Sajitz-Hermstein, Nadine Töpfer, Sabrina Kleessen, Alisdair R. Fernie, Zoran Nikoloski. iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models |
| 763 | -- | 771 | Hung-Cuong Trinh, Yung-Keun Kwon. Edge-based sensitivity analysis of signaling networks by using Boolean dynamics |
| 772 | -- | 780 | Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry. Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation |
| 781 | -- | 789 | Konstantinos Koutroumpas, Paolo Ballarini, Irene Votsi, Paul-Henry Cournède. Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach |
| 790 | -- | 797 | Daniel Sánchez-Taltavull, Matthew MacLeod, Theodore J. Perkins. On cross-conditional and fluctuation correlations in competitive RNA networks |
| 2567 | -- | 2576 | Jiarui Ding, Sohrab P. Shah, Anne Condon. densityCut: an efficient and versatile topological approach for automatic clustering of biological data |
| 2577 | -- | 2581 | Elias Dohmen, Lukas P. M. Kremer, Erich Bornberg-Bauer, Carsten Kemena. DOGMA: domain-based transcriptome and proteome quality assessment |
| 2582 | -- | 2589 | Ivan Sovic, Kresimir Krizanovic, Karolj Skala, Mile Sikic. de novo assembly of nanopore reads |
| 2590 | -- | 2597 | Liam Harold Childs, Soulafa Mamlouk, Jörgen Brandt, Christine Sers, Ulf Leser. SoFIA: a data integration framework for annotating high-throughput datasets |
| 2598 | -- | 2603 | T. Bernard Bigdeli, Donghyung Lee, Bradley Todd Webb, Brien P. Riley, Vladimir I. Vladimirov, Ayman H. Fanous, Kenneth S. Kendler, Silviu-Alin Bacanu. A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans |
| 2604 | -- | 2610 | Raivo Kolde, Kaspar Märtens, Kaie Lokk, Sven Laur, Jaak Vilo. seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data |
| 2611 | -- | 2617 | Eric Z. Chen, Hongzhe Li. A two-part mixed-effects model for analyzing longitudinal microbiome compositional data |
| 2618 | -- | 2625 | Zheng-Zheng Tang, Guanhua Chen, Alexander V. Alekseyenko. PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances |
| 2626 | -- | 2635 | Sudhakar Sahoo, Michal P. Switnicki, Jakob Skou Pedersen. ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction |
| 2636 | -- | 2641 | Ganapathi Varma Saripella, Erik L. L. Sonnhammer, Kristoffer Forslund. Benchmarking the next generation of homology inference tools |
| 2642 | -- | 2649 | Gelio Alves, Yi-Kuo Yu. Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution |
| 2650 | -- | 2658 | David W. Ritchie. Calculating and scoring high quality multiple flexible protein structure alignments |
| 2659 | -- | 2663 | Liang Niu, Zongli Xu, Jack A. Taylor. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip |
| 2664 | -- | 2671 | HuiMin Luo, Jianxin Wang, Min Li, Junwei Luo, Xiaoqing Peng, Fang-Xiang Wu, Yi Pan. Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm |
| 2672 | -- | 2680 | Francesco Pappalardo, Epifanio Fichera, Nicoletta Paparone, Alessandro Lombardo, Marzio Pennisi, Giulia Russo, Marco Leotta, Francesco Pappalardo, Alessandro Pedretti, Francesco De Fiore, Santo Motta. A computational model to predict the immune system activation by citrus-derived vaccine adjuvants |
| 2681 | -- | 2685 | Daniel Lobo, Junji Morokuma, Michael Levin. hnf4 as a regulatory gene in planarian regeneration |
| 2686 | -- | 2691 | Jonathan D. Wren. Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades |
| 2692 | -- | 2695 | Zheng Xu, Guosheng Zhang, Cong Wu, Yun Li, Ming Hu. FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data |
| 2696 | -- | 2698 | Elena Yavorska Harris, Rachid Ounit, Stefano Lonardi. BRAT-nova: fast and accurate mapping of bisulfite-treated reads |
| 2699 | -- | 2701 | Paul P. S. Wang, Wendy T. Parker, Susan Branford, Andreas W. Schreiber. BAM-matcher: a tool for rapid NGS sample matching |
| 2702 | -- | 2703 | Ben J. Woodcroft, Joel A. Boyd, Gene W. Tyson. OrfM: a fast open reading frame predictor for metagenomic data |
| 2704 | -- | 2706 | Bianca K. Stöcker, Johannes Köster, Sven Rahmann. SimLoRD: Simulation of Long Read Data |
| 2707 | -- | 2709 | B. D. Pickett, S. M. Karlinsey, C. E. Penrod, M. J. Cormier, Mark T. W. Ebbert, Dennis K. Shiozawa, C. J. Whipple, Perry G. Ridge. SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences |
| 2710 | -- | 2712 | Marianna Sakka, Grigorios Tzortzis, Michalis D. Mantzaris, Nick Bekas, Tahsin F. Kellici, Aristidis Likas, Dimitrios Galaris, Ioannis P. Gerothanassis, Andreas G. Tzakos. PRESS: PRotEin S-Sulfenylation server |
| 2713 | -- | 2715 | Ivan H. Goenawan, Kenneth Bryan, David J. Lynn. DyNet: visualization and analysis of dynamic molecular interaction networks |
| 2716 | -- | 2718 | Devin K. Schweppe, Chunxiang Zheng, Juan D. Chavez, Arti T. Navare, Xia Wu, Jimmy K. Eng, James E. Bruce. XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data |
| 2719 | -- | 2721 | Maciej J. Swat, Pierre Grenon, Sarala M. Wimalaratne. ProbOnto: ontology and knowledge base of probability distributions |
| 2722 | -- | 2724 | Anna Lukasik, Maciej Wójcikowski, Piotr Zielenkiewicz. Tools4miRs - one place to gather all the tools for miRNA analysis |
| 2725 | -- | 2726 | Julia Varga, László Dobson, Gábor E. Tusnády. TOPDOM: database of conservatively located domains and motifs in proteins |
| 2727 | -- | 0 | Li Teng, Bing He, Jiahui Wang, Kai Tan. 4DGenome: a comprehensive database of chromatin interactions |