7 | -- | 14 | Denis C. Bauer, Kai Willadsen, Fabian A. Buske, Kim-Anh Lê Cao, Timothy L. Bailey, Graham Dellaire, Mikael Bodén. Sorting the nuclear proteome |
15 | -- | 23 | Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane. Environment specific substitution tables improve membrane protein alignment |
24 | -- | 33 | Marcin J. Mizianty, Lukasz A. Kurgan. Sequence-based prediction of protein crystallization, purification and production propensity |
34 | -- | 42 | Charles W. O Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger. A method for probing the mutational landscape of amyloid structure |
43 | -- | 51 | Arun Siddharth Konagurthu, Lloyd Allison, Peter J. Stuckey, Arthur M. Lesk. Piecewise linear approximation of protein structures using the principle of minimum message length |
52 | -- | 60 | Andrej J. Savol, Virginia M. Burger, Pratul K. Agarwal, Arvind Ramanathan, Chakra Chennubhotla. QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin |
61 | -- | 68 | S. Shivashankar, S. Srivathsan, B. Ravindran, Ashish V. Tendulkar. Multi-view methods for protein structure comparison using latent dirichlet allocation |
69 | -- | 76 | Min Xu, Martin Beck, Frank Alber. Template-free detection of macromolecular complexes in cryo electron tomograms |
77 | -- | 84 | André Altmann, Peter Weber, Carina Quast, Monika Rex-Haffner, Elisabeth B. Binder, Bertram Müller-Myhsok. vipR: variant identification in pooled DNA using R |
85 | -- | 93 | Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming |
94 | -- | 101 | Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin. Meta-IDBA: a ::::de Novo:::: assembler for metagenomic data |
102 | -- | 110 | Zhiyong Wang, Jinbo Xu. A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling |
111 | -- | 119 | Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun-ichi Tsujii, Sophia Ananiadou. Discovering and visualizing indirect associations between biomedical concepts |
120 | -- | 128 | Sanmitra Bhattacharya, Viet Ha-Thuc, Padmini Srinivasan. MeSH: a window into full text for document summarization |
129 | -- | 136 | Christian Höner zu Siederdissen, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker. A folding algorithm for extended RNA secondary structures |
137 | -- | 141 | Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner. Error correction of high-throughput sequencing datasets with non-uniform coverage |
142 | -- | 148 | Regev Schweiger, Michal Linial, Nathan Linial. Generative probabilistic models for protein-protein interaction networks - the biclique perspective |
149 | -- | 158 | Günhan Gülsoy, Tamer Kahveci. RINQ: Reference-based Indexing for Network Queries |
159 | -- | 166 | Zhipeng Xie, Chee Keong Kwoh, Xiaoli Li, Min Wu. Construction of co-complex score matrix for protein complex prediction from AP-MS data |
167 | -- | 176 | Yong Chen, Tao Jiang, Rui Jiang. Uncover disease genes by maximizing information flow in the phenome-interactome network |
177 | -- | 185 | Noa Novershtern, Aviv Regev, Nir Friedman. Physical Module Networks: an integrative approach for reconstructing transcription regulation |
186 | -- | 195 | Sara Berthoumieux, Matteo Brilli, Hidde de Jong, Daniel Kahn, Eugenio Cinquemani. Identification of metabolic network models from incomplete high-throughput datasets |
196 | -- | 204 | Ankur P. Parikh, Wei Wu, Ross E. Curtis, Eric P. Xing. TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages |
205 | -- | 213 | Phuong Dao, Kendric Wang, Colin Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp. Optimally discriminative subnetwork markers predict response to chemotherapy |
214 | -- | 221 | Tony Kam-Thong, Benno Pütz, Nazanin Karbalai, Bertram Müller-Myhsok, Karsten M. Borgwardt. Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs |
222 | -- | 229 | Jing Li, Benjamin Horstman, Yixuan Chen. Detecting epistatic effects in association studies at a genomic level based on an ensemble approach |
230 | -- | 238 | Theodore Alexandrov, Jan Hendrik Kobarg. Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering |
239 | -- | 247 | Hanchuan Peng, Fuhui Long, Gene Myers. Automatic 3D neuron tracing using all-path pruning |
248 | -- | 256 | Celine Scornavacca, Franziska Zickmann, Daniel H. Huson. Tanglegrams for rooted phylogenetic trees and networks |
257 | -- | 265 | Haris Gavranovic, Cedric Chauve, Jérôme Salse, Eric Tannier. Mapping ancestral genomes with massive gene loss: A matrix sandwich problem |
266 | -- | 274 | Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette. Predicting site-specific human selective pressure using evolutionary signatures |
275 | -- | 282 | Michael F. Lin, Irwin Jungreis, Manolis Kellis. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions |
283 | -- | 287 | Nicola Bonzanni, Nianshu Zhang, Stephen G. Oliver, Jasmin Fisher. The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in ::::Saccharomyces cerevisiae:::: |
288 | -- | 294 | Nicholas A. Furlotte, Hyun Min Kang, Chun Ye, Eleazar Eskin. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity |
295 | -- | 303 | Michael B. Mayhew, Joshua W. Robinson, Boyoun Jung, Steven B. Haase, Alexander J. Hartemink. A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments |
304 | -- | 309 | Susanne Balzer, Ketil Malde, Inge Jonassen. Systematic exploration of error sources in pyrosequencing flowgram data |
310 | -- | 316 | Guangxu Jin, Hong Zhao, Xiaobo Zhou, Stephen T. C. Wong. An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data |
317 | -- | 323 | David Golan, Saharon Rosset. Accurate estimation of heritability in genome wide studies using random effects models |
324 | -- | 332 | Suyash Shringarpure, Daegun Won, Eric P. Xing. StructHDP: automatic inference of number of clusters and population structure from admixed genotype data |
333 | -- | 341 | Sofia Kyriazopoulou-Panagiotopoulou, Dorna Kashef Haghighi, Sarah J. Aerni, Andreas Sundquist, Sivan Bercovici, Serafim Batzoglou. Reconstruction of genealogical relationships with applications to Phase III of HapMap |
342 | -- | 348 | Limin Li, Barbara Rakitsch, Karsten M. Borgwardt. ccSVM: correcting Support Vector Machines for confounding factors in biological data classification |
349 | -- | 356 | Filipe Santana, Daniel Schober, Zulma Medeiros, Fred Freitas, Stefan Schulz. Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases |
357 | -- | 365 | Henning Redestig, Ivan G. Costa. Detection and interpretation of metabolite-transcript coresponses using combined profiling data |
366 | -- | 373 | Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder, Ralf Zimmer. From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems |
374 | -- | 382 | Edoardo M. Airoldi, Katherine A. Heller, Ricardo Silva. Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning |
383 | -- | 391 | Pawel P. Labaj, Germán G. Leparc, Bryan E. Linggi, Lye Meng Markillie, H. Steven Wiley, David P. Kreil. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling |
392 | -- | 400 | Julia Sivriver, Naomi Habib, Nir Friedman. An integrative clustering and modeling algorithm for dynamical gene expression data |
401 | -- | 409 | Shihua Zhang, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou. A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules |
1741 | -- | 1748 | Guy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman. Genome Analysis |
1749 | -- | 1753 | Yong E. Zhang, Maria D. Vibranovski, Benjamin H. Krinsky, Manyuan Long. A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes |
1754 | -- | 1757 | Roberto Chignola, Vladislav Vyshemirsky, Marcello Farina, Alessio Del Fabbro, Edoardo Milotti. Modular model of TNFα cytotoxicity |
1758 | -- | 1764 | Zhiming Dai, Xianhua Dai, Qian Xiang. Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast |
1765 | -- | 1771 | Josue Samayoa, Fitnat H. Yildiz, Kevin Karplus. Identification of prokaryotic small proteins using a comparative genomic approach |
1772 | -- | 1779 | Qiwei Li, Xiaodan Fan, Tong Liang, Shuo-Yen Robert Li. An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences |
1780 | -- | 1787 | Tzong-Yi Lee, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, Cheng-Tsung Lu. Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences |
1788 | -- | 1797 | Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai. A detailed investigation of accessibilities around target sites of siRNAs and miRNAs |
1798 | -- | 1805 | Sungroh Yoon, Jinkyu Kim, Justine Hum, Hanjoo Kim, Seunghyun Park, Wipapat Kladwang, Rhiju Das. HiTRACE: high-throughput robust analysis for capillary electrophoresis |
1806 | -- | 1813 | Ferenc Zsila, Zsolt Bikadi, David Malik, Peter Hari, Imre Pechan, Attila Bérces, Eszter Hazai. Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking |
1814 | -- | 1821 | Tingjun Hou, Youyong Li, Wei Wang. Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy |
1822 | -- | 1831 | Lori A. Dalton, Edward R. Dougherty. Application of the Bayesian MMSE estimator for classification error to gene expression microarray data |
1832 | -- | 1838 | Sushmita Roy, Margaret Werner-Washburne, Terran Lane. A multiple network learning approach to capture system-wide condition-specific responses |
1839 | -- | 1845 | Hendrik Rohn, Christian Klukas, Falk Schreiber. Creating views on integrated multidomain data |
1846 | -- | 1853 | Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Eunji Shin, Sanghyun Park. Integrative gene network construction for predicting a set of complementary prostate cancer genes |
1854 | -- | 1859 | Charles Jackson, Estelle Glory-Afshar, Robert F. Murphy, Jelena Kovacevic. Model building and intelligent acquisition with application to protein subcellular location classification |
1860 | -- | 1866 | Jesse Gillis, Paul Pavlidis. The role of indirect connections in gene networks in predicting function |
1867 | -- | 1868 | Clifford A. Meyer, Housheng H. He, Myles Brown, X. Shirley Liu. BINOCh: binding inference from nucleosome occupancy changes |
1869 | -- | 1870 | Brian Walenz, Liliana Florea. Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing |
1871 | -- | 1872 | Fernando Muñiz-Fernandez, Angel Carreño-Torres, Carlos Morcillo-Suarez, Arcadi Navarro. Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management |
1873 | -- | 1875 | Hariklia Eleftherohorinou, Johanna C. Andersson-Assarsson, Robin G. Walters, Julia S. El-Sayed Moustafa, Lachlan J. M. Coin, Peter Jacobson, Lena M. S. Carlsson, Alexandra I. F. Blakemore, Philippe Froguel, Andrew J. Walley, Mario Falchi. famCNV: copy number variant association for quantitative traits in families |
1876 | -- | 1877 | Gabriele Sales, Chiara Romualdi. ::::parmigene:::: - a parallel R package for mutual information estimation and gene network reconstruction |
1878 | -- | 1879 | Matti Kankainen, Peddinti V. Gopalacharyulu, Liisa Holm, Matej Oresic. MPEA - metabolite pathway enrichment analysis |
1880 | -- | 1881 | Ross E. Curtis, Amos Yuen, Le Song, Anuj Goyal, Eric P. Xing. TVNViewer: An interactive visualization tool for exploring networks that change over time or space |
1882 | -- | 1883 | Sebastian Bauer, Peter N. Robinson, Julien Gagneur. Model-based gene set analysis for Bioconductor |