| 1 | -- | 2 | Yves Moreau, Niko Beerenwinkel. ISMB/ECCB 2015 |
| 9 | -- | 16 | Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi. De novo meta-assembly of ultra-deep sequencing data |
| 17 | -- | 26 | David Amar, Daniel Yekutieli, Adi Maron-Katz, Talma Hendler, Ron Shamir. A hierarchical Bayesian model for flexible module discovery in three-way time-series data |
| 27 | -- | 34 | Ibrahim Numanagic, Salem Malikic, Victoria M. Pratt, Todd C. Skaar, David A. Flockhart, Süleyman Cenk Sahinalp. CYP2D6 using high-throughput sequencing data |
| 35 | -- | 43 | Cheng Yuan, Jikai Lei, James R. Cole, Yanni Sun. Reconstructing 16S rRNA genes in metagenomic data |
| 44 | -- | 52 | Siavash Mirarab, Tandy Warnow. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes |
| 53 | -- | 61 | Yana Safonova, Stefano Bonissone, Eugene Kurpilyansky, Ekaterina Starostina, Alla Lapidus, Jeremy Stinson, Laura DePalatis, Wendy Sandoval, Jennie Lill, Pavel A. Pevzner. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis |
| 62 | -- | 70 | Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field, Benjamin J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data |
| 71 | -- | 79 | Valentin Zulkower, Michel Page, Delphine Ropers, Johannes Geiselmann, Hidde de Jong. Robust reconstruction of gene expression profiles from reporter gene data using linear inversion |
| 80 | -- | 88 | Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher. Misassembly detection using paired-end sequence reads and optical mapping data |
| 89 | -- | 96 | Andrea Ocone, Laleh Haghverdi, Nikola S. Müller, Fabian J. Theis. Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data |
| 97 | -- | 105 | Christopher A. Penfold, Jonathan B. A. Millar, David L. Wild. Inferring orthologous gene regulatory networks using interspecies data fusion |
| 106 | -- | 115 | Franziska Zickmann, Bernhard Y. Renard. MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms |
| 116 | -- | 123 | Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng. Large-scale model quality assessment for improving protein tertiary structure prediction |
| 124 | -- | 132 | Laleh Soltan Ghoraie, Forbes J. Burkowski, Mu Zhu. Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins |
| 133 | -- | 141 | Xuefeng Cui, Hammad Naveed, Xin Gao. Finding optimal interaction interface alignments between biological complexes |
| 142 | -- | 150 | Y.-C. Harn, M. J. Powers, E. A. Shank, Vladimir Jojic. Deconvolving molecular signatures of interactions between microbial colonies |
| 151 | -- | 160 | Tomasz Oliwa, Yang Shen. cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions |
| 161 | -- | 170 | Yoshihiro Yamanishi, Yasuo Tabei, Masaaki Kotera. de novo pathway reconstruction using regioisomer-sensitive graph alignments |
| 171 | -- | 180 | Yuriy Hulovatyy, Huili Chen, Tijana Milenkovic. Exploring the structure and function of temporal networks with dynamic graphlets |
| 181 | -- | 189 | Danny S. Park, Brielin Brown, Celeste Eng, Scott Huntsman, Donglei Hu, Dara G. Torgerson, Esteban Gonzàlez Burchard, Noah Zaitlen. Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses |
| 190 | -- | 196 | James Y. Zou, Eran Halperin, Esteban Gonzàlez Burchard, Sriram Sankararaman. Inferring parental genomic ancestries using pooled semi-Markov processes |
| 197 | -- | 205 | Francesca Petralia, Pei Wang, Jialiang Yang, Zhidong Tu. Integrative random forest for gene regulatory network inference |
| 206 | -- | 213 | Farhad Hormozdiari, Gleb Kichaev, Wen-Yun Yang, Bogdan Pasaniuc, Eleazar Eskin. Identification of causal genes for complex traits |
| 214 | -- | 220 | Dorothee Childs, Sergio Grimbs, Joachim Selbig. Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns |
| 221 | -- | 229 | Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng, Shuigeng Zhou. Improving compound-protein interaction prediction by building up highly credible negative samples |
| 230 | -- | 239 | Marinka Zitnik, Blaz Zupan. Gene network inference by fusing data from diverse distributions |
| 240 | -- | 249 | Felipe Llinares-López, Dominik Grimm, Dean A. Bodenham, Udo Gieraths, Mahito Sugiyama, Beth Rowan, Karsten M. Borgwardt. Genome-wide detection of intervals of genetic heterogeneity associated with complex traits |
| 250 | -- | 257 | Zongliang Yue, Madhura M. Kshirsagar, Thanh Nguyen, Chayaporn Suphavilai, Michael T. Neylon, Liugen Zhu, Timothy Ratliff, Jake Yue Chen. PAGER: constructing PAGs and new PAG-PAG relationships for network biology |
| 258 | -- | 267 | Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz. Inferring models of multiscale copy number evolution for single-tumor phylogenetics |
| 268 | -- | 275 | Nora K. Speicher, Nico Pfeifer. Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery |
| 276 | -- | 283 | Yang Chen, Li Li, Guo-Qiang Zhang, Rong Xu. Phenome-driven disease genetics prediction toward drug discovery |
| 284 | -- | 292 | Yoo Ah Kim, Dong-Yeon Cho, Phuong Dao, Teresa M. Przytycka. MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types |
| 293 | -- | 302 | A. Grant Schissler, Vincent Gardeux, Qike Li, Ikbel Achour, Haiquan Li, Walter W. Piegorsch, Yves A. Lussier. Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival |
| 303 | -- | 310 | Damian Roqueiro, Menno J. Witteveen, Verneri Anttila, Gisela M. Terwindt, Arn M. J. M. van den Maagdenberg, Karsten M. Borgwardt. In silico phenotyping via co-training for improved phenotype prediction from genotype |
| 311 | -- | 319 | Amin Allahyar, Jeroen de Ridder. FERAL: network-based classifier with application to breast cancer outcome prediction |
| 320 | -- | 328 | Alice Schoenauer Sebag, Sandra Plancade, Céline Raulet-Tomkiewicz, Robert Barouki, Jean-Philippe Vert, Thomas Walter. A generic methodological framework for studying single cell motility in high-throughput time-lapse data |
| 329 | -- | 338 | Mingfu Shao, Bernard M. E. Moret. Comparing genomes with rearrangements and segmental duplications |
| 339 | -- | 347 | Ke Liu 0002, Shengwen Peng, Junqiu Wu, ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu. MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence |
| 348 | -- | 356 | Davy Weissenbacher, Tasnia Tahsin, Rachel Beard, Mari Figaro, Robert Rivera, Matthew Scotch, Graciela Gonzalez. Knowledge-driven geospatial location resolution for phylogeographic models of virus migration |
| 357 | -- | 364 | Sheng Wang, Hyunghoon Cho, ChengXiang Zhai, Bonnie Berger, Jian Peng 0001. Exploiting ontology graph for predicting sparsely annotated gene function |
| 365 | -- | 374 | Ramanuja Simha, Sebastian Briesemeister, Oliver Kohlbacher, Hagit Shatkay. Protein (multi-)location prediction: utilizing interdependencies via a generative model |
| 375 | -- | 384 | Andrew Palmer, Ekaterina Ovchinnikova, Mikael Thuné, Régis Lavigne, Blandine Guével, Andrey Dyatlov, Olga Vitek, Charles Pineau, Mats Borén, Theodore Alexandrov. Using collective expert judgements to evaluate quality measures of mass spectrometry images |
| 1881 | -- | 1888 | Marco Masseroli, Pietro Pinoli, Francesco Venco, Abdulrahman Kaitoua, Vahid Jalili, Fernando Palluzzi, Heiko Müller, Stefano Ceri. GenoMetric Query Language: a novel approach to large-scale genomic data management |
| 1889 | -- | 1896 | Li Chen, Chi Wang, Zhaohui S. Qin, Hao Wu. A novel statistical method for quantitative comparison of multiple ChIP-seq datasets |
| 1897 | -- | 1903 | Jacob Schreiber, Kevin Karplus. Analysis of nanopore data using hidden Markov models |
| 1904 | -- | 1912 | Manuel Holtgrewe, Léon Kuchenbecker, Knut Reinert. Methods for the detection and assembly of novel sequence in high-throughput sequencing data |
| 1913 | -- | 1919 | Eduard Zorita, Pol Cuscó, Guillaume J. Filion. Starcode: sequence clustering based on all-pairs search |
| 1920 | -- | 1928 | Carl Kingsford, Robert Patro. Reference-based compression of short-read sequences using path encoding |
| 1929 | -- | 1937 | Wenzhi Mao, Cihan Kaya, Anindita Dutta, Amnon Horovitz, Ivet Bahar. Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution |
| 1938 | -- | 1944 | Wei He, Zhi Liang, Maikun Teng, Liwen Niu. mFASD: a structure-based algorithm for discriminating different types of metal-binding sites |
| 1945 | -- | 1950 | Tobias Hamp, Burkhard Rost. Evolutionary profiles improve protein-protein interaction prediction from sequence |
| 1951 | -- | 1958 | Elihu C. Ihms, Mark P. Foster. MESMER: minimal ensemble solutions to multiple experimental restraints |
| 1959 | -- | 1965 | Norbert Jeszenoi, István Horváth, Mónika Bálint, David van der Spoel, Csaba Hetényi. Mobility-based prediction of hydration structures of protein surfaces |
| 1966 | -- | 1973 | Jed M. Zaretzki, Michael R. Browning, Tyler B. Hughes, S. Joshua Swamidass. Extending P450 site-of-metabolism models with region-resolution data |
| 1974 | -- | 1980 | Chen Xu, Zhengchang Su. Identification of cell types from single-cell transcriptomes using a novel clustering method |
| 1981 | -- | 1987 | Scott J. Hebbring, Majid Rastegar-Mojarad, Zhan Ye, John Mayer, Crystal Jacobson, Simon Lin. Application of clinical text data for phenome-wide association studies (PheWASs) |
| 1988 | -- | 1998 | Connor Clark, Jugal Kalita. A multiobjective memetic algorithm for PPI network alignment |
| 1999 | -- | 2006 | Joe Wandy, Rónán Daly, Rainer Breitling, Simon Rogers. Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets |
| 2007 | -- | 2016 | Peng Li, Chao Huang, Yingxue Fu, Jinan Wang, Ziyin Wu, Jinlong Ru, Chunli Zheng, Zihu Guo, Xuetong Chen, Wei Zhou, Wenjuan Zhang, Yan Li, Jianxin Chen, Aiping Lu, Yonghua Wang. Large-scale exploration and analysis of drug combinations |
| 2017 | -- | 2023 | Igor Nikolskiy, Gary Siuzdak, Gary J. Patti. Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry |
| 2024 | -- | 2031 | Aruna Jammalamadaka, Panuakdet Suwannatat, Steven K. Fisher, B. S. Manjunath, Tobias Höllerer, Gabriel Luna. Characterizing spatial distributions of astrocytes in the mammalian retina |
| 2032 | -- | 2034 | Artem Tarasov, Albert J. Vilella, Edwin Cuppen, Isaac J. Nijman, Pjotr Prins. Sambamba: fast processing of NGS alignment formats |
| 2035 | -- | 2037 | Jared O'Connell, Ole Schulz-Trieglaff, Emma Carlson, Matthew M. Hims, Niall A. Gormley, Anthony J. Cox. NxTrim: optimized trimming of Illumina mate pair reads |
| 2038 | -- | 2039 | Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Mario Caccamo. PolyMarker: A fast polyploid primer design pipeline |
| 2040 | -- | 2042 | Xuefeng Wang, Xiaoqing Yu, Wei Zhu, W. Richard McCombie, Eric Antoniou, R. Scott Powers, Nicholas O. Davidson, Ellen Li, Jennie Williams. A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing |
| 2043 | -- | 2045 | Felix Mueller-Planitz. Crossfinder-assisted mapping of protein crosslinks formed by site-specifically incorporated crosslinkers |
| 2046 | -- | 2048 | Anastasia V. Rudik, Alexander V. Dmitriev, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov. in silico prediction of sites of metabolism for drug-like compounds |
| 2049 | -- | 2051 | Xian Liu, Yuan Gao, Jianlong Peng, Yuan Xu, Yulan Wang, Nannan Zhou, Jing Xing, Xiaomin Luo, Hualiang Jiang, Mingyue Zheng. TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds |
| 2052 | -- | 2053 | Jonathan G. Lees, Jean-Karim Hériché, Ian Morilla, José M. Fernández, Priit Adler, Martin Krallinger, Jaak Vilo, Alfonso Valencia, Jan Ellenberg, Juan A. Ranea, Christine A. Orengo. FUN-L: gene prioritization for RNAi screens |
| 2054 | -- | 2055 | Görel Sundström, Neda Zamani, Manfred G. Grabherr, Evan Mauceli. Whiteboard: a framework for the programmatic visualization of complex biological analyses |
| 2056 | -- | 2058 | David Fenyö, Ronald C. Beavis. The GPMDB REST interface |
| 2059 | -- | 2060 | Christiana N. Fogg, Diane E. Kovats. Message from ISCB: Outstanding contributions to ISCB award |