| 7 | -- | 12 | Luís Pedro Coelho, Tao Peng, Robert F. Murphy. Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing |
| 13 | -- | 20 | Steffen Jaensch, Markus Decker, Anthony A. Hyman, Eugene W. Myers. Automated tracking and analysis of centrosomes in early ::::Caenorhabditis elegans:::: embryos |
| 21 | -- | 28 | Sinan Kockara, Mutlu Mete, Vincent Yip, Brendan Lee, Kemal Aydin. A soft kinetic data structure for lesion border detection |
| 29 | -- | 37 | Yu-Shi Lin, Chung-Chih Lin, Yuh-Show Tsai, Tien-Chuan Ku, Yi-Hung Huang, Chun-Nan Hsu. A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images |
| 38 | -- | 46 | Hanchuan Peng, Zongcai Ruan, Deniz Atasoy, Scott Sternson. Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model |
| 47 | -- | 56 | Kriti Puniyani, Christos Faloutsos, Eric P. Xing. SPEX:::2:::: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images |
| 57 | -- | 63 | Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomancak. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets |
| 64 | -- | 70 | Ranga Srinivasan, Qing Li, Xiaobo Zhou, Ju Lu, Jeff Lichtman, Stephen T. C. Wong. Reconstruction of the neuromuscular junction connectome |
| 71 | -- | 78 | Matthew Holford, Ekta Khurana, Kei-Hoi Cheung, Mark Gerstein. Using semantic web rules to reason on an ontology of pseudogenes |
| 79 | -- | 87 | Adam J. Richards, Brian Muller, Matthew Shotwell, L. Ashley Cowart, Bärbel Rohrer, Xinghua Lu. Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph |
| 88 | -- | 96 | Thomas Wächter, Michael Schroeder. Semi-automated ontology generation within OBO-Edit |
| 97 | -- | 105 | Kai Zhang, Joe W. Gray, Bahram Parvin. Sparse multitask regression for identifying common mechanism of response to therapeutic targets |
| 106 | -- | 114 | David Tolliver, Charalampos E. Tsourakakis, Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz. Robust unmixing of tumor states in array comparative genomic hybridization data |
| 115 | -- | 123 | Vincent Ranwez, Alexis Criscuolo, Emmanuel J. P. Douzery. SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics |
| 124 | -- | 131 | Leo van Iersel, Steven Kelk, Regula Rupp, Daniel H. Huson. Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters |
| 132 | -- | 139 | Alexandros Stamatakis, Nikolaos Alachiotis. Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data |
| 140 | -- | 148 | Yufeng Wu. Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees |
| 149 | -- | 157 | Jeroen de Ridder, Alice Gerrits, Jan Bot, Gerald de Haan, Marcel J. T. Reinders, Lodewyk F. A. Wessels. Inferring combinatorial association logic networks in multimodal genome-wide screens |
| 158 | -- | 167 | Richard S. Savage, Zoubin Ghahramani, Jim E. Griffin, Bernard J. de la Cruz, David L. Wild. Discovering transcriptional modules by Bayesian data integration |
| 168 | -- | 174 | Rendong Yang, Zhen Su. Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation |
| 175 | -- | 182 | Sivan Bercovici, Christopher Meek, Ydo Wexler, Dan Geiger. Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping |
| 183 | -- | 190 | Dan He, Arthur Choi, Knot Pipatsrisawat, Adnan Darwiche, Eleazar Eskin. Optimal algorithms for haplotype assembly from whole-genome sequence data |
| 191 | -- | 198 | Xin Li, Xiaolin Yin, Jing Li. Efficient identification of identical-by-descent status in pedigrees with many untyped individuals |
| 199 | -- | 207 | Eric Yi Liu, Qi Zhang, Leonard McMillan, Fernando Pardo-Manuel de Villena, Wei Wang 0010. Efficient genome ancestry inference in complex pedigrees with inbreeding |
| 208 | -- | 216 | Kriti Puniyani, Seyoung Kim, Eric P. Xing. Multi-population GWA mapping via multi-task regularized regression |
| 217 | -- | 227 | Xiang Zhang, Shunping Huang, Fei Zou, Wei Wang 0010. TEAM: efficient two-locus epistasis tests in human genome-wide association study |
| 228 | -- | 236 | Ariel Jaimovich, Ruty Rinott, Maya Schuldiner, Hanah Margalit, Nir Friedman. Modularity and directionality in genetic interaction maps |
| 237 | -- | 245 | Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M. Stuart. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM |
| 246 | -- | 254 | Yoshihiro Yamanishi, Masaaki Kotera, Minoru Kanehisa, Susumu Goto. Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework |
| 255 | -- | 260 | Keren Yizhak, Tomer Benyamini, Wolfram Liebermeister, Eytan Ruppin, Tomer Shlomi. Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model |
| 261 | -- | 268 | Shihua Zhang, Daven Vasishtan, Min Xu, Maya Topf, Frank Alber. A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps |
| 269 | -- | 277 | Tsung-Han Chiang, David Hsu, Jean-Claude Latombe. Markov dynamic models for long-timescale protein motion |
| 278 | -- | 286 | Feng Lou, Peter Clote. Thermodynamics of RNA structures by Wang-Landau sampling |
| 287 | -- | 293 | Anoop Kumar, Lenore Cowen. Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution |
| 294 | -- | 300 | Jian Peng, Jinbo Xu. Low-homology protein threading |
| 301 | -- | 309 | Mitul Saha, Michael Levitt, Wah Chiu. MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures |
| 310 | -- | 317 | Feng Zhao, Jian Peng, Jinbo Xu. Fragment-free approach to protein folding using conditional neural fields |
| 318 | -- | 324 | Vikas Bansal. A statistical method for the detection of variants from next-generation resequencing of DNA pools |
| 325 | -- | 333 | Yoseph Barash, Benjamin J. Blencowe, Brendan J. Frey. Model-based detection of alternative splicing signals |
| 334 | -- | 342 | Xiaoyu Chen, Michael M. Hoffman, Jeff A. Bilmes, Jay R. Hesselberth, William Stafford Noble. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data |
| 343 | -- | 349 | Adrian V. Dalca, Stephen M. Rumble, Samuel Levy, Michael Brudno. VARiD: A variation detection framework for color-space and letter-space platforms |
| 350 | -- | 357 | Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery |
| 358 | -- | 366 | Marco Pellegrini, M. Elena Renda, Alessio Vecchio. TRStalker: an efficient heuristic for finding fuzzy tandem repeats |
| 367 | -- | 373 | Jared T. Simpson, Richard Durbin. Efficient construction of an assembly string graph using the FM-index |
| 374 | -- | 381 | Brian Kemper, Takuya Matsuzaki, Yukiko Matsuoka, Yoshimasa Tsuruoka, Hiroaki Kitano, Sophia Ananiadou, Jun-ichi Tsujii. PathText: a text mining integrator for biological pathway visualizations |
| 382 | -- | 390 | Jari Björne, Filip Ginter, Sampo Pyysalo, Jun-ichi Tsujii, Tapio Salakoski. Complex event extraction at PubMed scale |
| 391 | -- | 398 | Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Oresic, Samuel Kaski. Multivariate multi-way analysis of multi-source data |
| 399 | -- | 406 | Ding Ye, Yan Fu, Ruixiang Sun, Haipeng Wang, Zuofei Yuan, Hao Chi, Simin He. Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate |
| 1473 | -- | 1476 | Daria V. Dibrova, Michael Y. Galperin, Armen Y. Mulkidjanian. Characterization of the N-ATPase, a distinct, laterally transferred Na:::+:::-translocating form of the bacterial F-type membrane ATPase |
| 1477 | -- | 1480 | Robson Francisco de Souza, L. Aravind. UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes |
| 1481 | -- | 1487 | David M. Kristensen, Lavanya Kannan, Michael K. Coleman, Yuri I. Wolf, Alexander Sorokin, Eugene V. Koonin, Arcady R. Mushegian. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches |
| 1488 | -- | 1492 | Joshua Orvis, Jonathan Crabtree, Kevin Galens, Aaron Gussman, Jason M. Inman, Eduardo Lee, Sreenath Nampally, David Riley, Jaideep P. Sundaram, Victor Felix, Brett Whitty, Anup Mahurkar, Jennifer R. Wortman, Owen White, Samuel V. Angiuoli. Ergatis: a web interface and scalable software system for bioinformatics workflows |
| 1493 | -- | 1499 | Kota Kasahara, Kengo Kinoshita, Toshihisa Takagi. Ligand-binding site prediction of proteins based on known fragment-fragment interactions |
| 1500 | -- | 1505 | Douglas W. Bryant Jr., Rongkun Shen, Henry D. Priest, Weng-Keen Wong, Todd C. Mockler. Supersplat - spliced RNA-seq alignment |
| 1506 | -- | 1512 | Inho Park, Kwang H. Lee, Doheon Lee. Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets |
| 1513 | -- | 1519 | Natthakan Iam-on, Tossapon Boongoen, Simon Garrett. LCE: a link-based cluster ensemble method for improved gene expression data analysis |
| 1520 | -- | 1527 | Sepp Hochreiter, Ulrich Bodenhofer, Martin Heusel, Andreas Mayr, Andreas Mitterecker, Adetayo Kasim, Tatsiana Khamiakova, Suzy Van Sanden, Dan Lin, Willem Talloen, Luc Bijnens, Hinrich W. H. Göhlmann, Ziv Shkedy, Djork-Arné Clevert. FABIA: factor analysis for bicluster acquisition |
| 1528 | -- | 1534 | Wolfram Liebermeister, Jannis Uhlendorf, Edda Klipp. Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation |
| 1535 | -- | 1541 | Xinghua Lou, Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Sebastian Boppel, Christian Graf, Chung-Tien Lee, Judith A. J. Steen, Hanno Steen, Matthias P. Mayer, Fred A. Hamprecht. Deuteration distribution estimation with improved sequence coverage for HX/MS experiments |
| 1542 | -- | 1547 | Sabine Pérès, Liza Felicori, Stéphanie Rialle, Elodie Jobard, Franck Molina. Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions |
| 1548 | -- | 1555 | Allison P. Heath, George N. Bennett, Lydia E. Kavraki. Finding metabolic pathways using atom tracking |
| 1556 | -- | 1563 | Noushin Ghaffari, Ivan Ivanov, Xiaoning Qian, Edward R. Dougherty. A CoD-based reduction algorithm for designing stationary control policies on Boolean networks |
| 1564 | -- | 1565 | Bong-Hyun Kim, Qian Cong, Nick V. Grishin. HangOut: generating clean PSI-BLAST profiles for domains with long insertions |
| 1566 | -- | 1568 | Eric Bonnet, Ying He, Kenny Billiau, Yves Van de Peer. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics |
| 1569 | -- | 1571 | Jeet Sukumaran, Mark T. Holder. DendroPy: a Python library for phylogenetic computing |
| 1572 | -- | 1573 | Matthew D. Wilkerson, D. Neil Hayes. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking |
| 1576 | -- | 1577 | Aloke Phatak, Harri T. Kiiveri, Line Harder Clemmensen, William J. Wilson. NetRaVE: constructing dependency networks using sparse linear regression |