Journal: Bioinformatics

Volume 27, Issue 13

7 -- 14Denis C. Bauer, Kai Willadsen, Fabian A. Buske, Kim-Anh Lê Cao, Timothy L. Bailey, Graham Dellaire, Mikael Bodén. Sorting the nuclear proteome
15 -- 23Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane. Environment specific substitution tables improve membrane protein alignment
24 -- 33Marcin J. Mizianty, Lukasz A. Kurgan. Sequence-based prediction of protein crystallization, purification and production propensity
34 -- 42Charles 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 -- 51Arun Siddharth Konagurthu, Lloyd Allison, Peter J. Stuckey, Arthur M. Lesk. Piecewise linear approximation of protein structures using the principle of minimum message length
52 -- 60Andrej J. Savol, Virginia M. Burger, Pratul K. Agarwal, Arvind Ramanathan, Chakra Chennubhotla. QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
61 -- 68S. Shivashankar, S. Srivathsan, B. Ravindran, Ashish V. Tendulkar. Multi-view methods for protein structure comparison using latent dirichlet allocation
69 -- 76Min Xu, Martin Beck, Frank Alber. Template-free detection of macromolecular complexes in cryo electron tomograms
77 -- 84André Altmann, Peter Weber, Carina Quast, Monika Rex-Haffner, Elisabeth B. Binder, Bertram Müller-Myhsok. vipR: variant identification in pooled DNA using R
85 -- 93Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
94 -- 101Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin. Meta-IDBA: a ::::de Novo:::: assembler for metagenomic data
102 -- 110Zhiyong Wang, Jinbo Xu. A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling
111 -- 119Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun-ichi Tsujii, Sophia Ananiadou. Discovering and visualizing indirect associations between biomedical concepts
120 -- 128Sanmitra Bhattacharya, Viet Ha-Thuc, Padmini Srinivasan. MeSH: a window into full text for document summarization
129 -- 136Christian Höner zu Siederdissen, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker. A folding algorithm for extended RNA secondary structures
137 -- 141Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner. Error correction of high-throughput sequencing datasets with non-uniform coverage
142 -- 148Regev Schweiger, Michal Linial, Nathan Linial. Generative probabilistic models for protein-protein interaction networks - the biclique perspective
149 -- 158Günhan Gülsoy, Tamer Kahveci. RINQ: Reference-based Indexing for Network Queries
159 -- 166Zhipeng Xie, Chee Keong Kwoh, Xiaoli Li, Min Wu. Construction of co-complex score matrix for protein complex prediction from AP-MS data
167 -- 176Yong Chen, Tao Jiang, Rui Jiang. Uncover disease genes by maximizing information flow in the phenome-interactome network
177 -- 185Noa Novershtern, Aviv Regev, Nir Friedman. Physical Module Networks: an integrative approach for reconstructing transcription regulation
186 -- 195Sara Berthoumieux, Matteo Brilli, Hidde de Jong, Daniel Kahn, Eugenio Cinquemani. Identification of metabolic network models from incomplete high-throughput datasets
196 -- 204Ankur P. Parikh, Wei Wu, Ross E. Curtis, Eric P. Xing. TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages
205 -- 213Phuong Dao, Kendric Wang, Colin Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp. Optimally discriminative subnetwork markers predict response to chemotherapy
214 -- 221Tony Kam-Thong, Benno Pütz, Nazanin Karbalai, Bertram Müller-Myhsok, Karsten M. Borgwardt. Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs
222 -- 229Jing Li, Benjamin Horstman, Yixuan Chen. Detecting epistatic effects in association studies at a genomic level based on an ensemble approach
230 -- 238Theodore Alexandrov, Jan Hendrik Kobarg. Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering
239 -- 247Hanchuan Peng, Fuhui Long, Gene Myers. Automatic 3D neuron tracing using all-path pruning
248 -- 256Celine Scornavacca, Franziska Zickmann, Daniel H. Huson. Tanglegrams for rooted phylogenetic trees and networks
257 -- 265Haris Gavranovic, Cedric Chauve, Jérôme Salse, Eric Tannier. Mapping ancestral genomes with massive gene loss: A matrix sandwich problem
266 -- 274Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette. Predicting site-specific human selective pressure using evolutionary signatures
275 -- 282Michael F. Lin, Irwin Jungreis, Manolis Kellis. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
283 -- 287Nicola 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 -- 294Nicholas A. Furlotte, Hyun Min Kang, Chun Ye, Eleazar Eskin. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity
295 -- 303Michael 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 -- 309Susanne Balzer, Ketil Malde, Inge Jonassen. Systematic exploration of error sources in pyrosequencing flowgram data
310 -- 316Guangxu 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 -- 323David Golan, Saharon Rosset. Accurate estimation of heritability in genome wide studies using random effects models
324 -- 332Suyash Shringarpure, Daegun Won, Eric P. Xing. StructHDP: automatic inference of number of clusters and population structure from admixed genotype data
333 -- 341Sofia 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 -- 348Limin Li, Barbara Rakitsch, Karsten M. Borgwardt. ccSVM: correcting Support Vector Machines for confounding factors in biological data classification
349 -- 356Filipe Santana, Daniel Schober, Zulma Medeiros, Fred Freitas, Stefan Schulz. Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases
357 -- 365Henning Redestig, Ivan G. Costa. Detection and interpretation of metabolite-transcript coresponses using combined profiling data
366 -- 373Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder, Ralf Zimmer. From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems
374 -- 382Edoardo M. Airoldi, Katherine A. Heller, Ricardo Silva. Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
383 -- 391Pawel 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 -- 400Julia Sivriver, Naomi Habib, Nir Friedman. An integrative clustering and modeling algorithm for dynamical gene expression data
401 -- 409Shihua 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 -- 1748Guy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman. Genome Analysis
1749 -- 1753Yong 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 -- 1757Roberto Chignola, Vladislav Vyshemirsky, Marcello Farina, Alessio Del Fabbro, Edoardo Milotti. Modular model of TNFα cytotoxicity
1758 -- 1764Zhiming Dai, Xianhua Dai, Qian Xiang. Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast
1765 -- 1771Josue Samayoa, Fitnat H. Yildiz, Kevin Karplus. Identification of prokaryotic small proteins using a comparative genomic approach
1772 -- 1779Qiwei Li, Xiaodan Fan, Tong Liang, Shuo-Yen Robert Li. An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences
1780 -- 1787Tzong-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 -- 1797Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai. A detailed investigation of accessibilities around target sites of siRNAs and miRNAs
1798 -- 1805Sungroh Yoon, Jinkyu Kim, Justine Hum, Hanjoo Kim, Seunghyun Park, Wipapat Kladwang, Rhiju Das. HiTRACE: high-throughput robust analysis for capillary electrophoresis
1806 -- 1813Ferenc 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 -- 1821Tingjun Hou, Youyong Li, Wei Wang. Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy
1822 -- 1831Lori A. Dalton, Edward R. Dougherty. Application of the Bayesian MMSE estimator for classification error to gene expression microarray data
1832 -- 1838Sushmita Roy, Margaret Werner-Washburne, Terran Lane. A multiple network learning approach to capture system-wide condition-specific responses
1839 -- 1845Hendrik Rohn, Christian Klukas, Falk Schreiber. Creating views on integrated multidomain data
1846 -- 1853Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Eunji Shin, Sanghyun Park. Integrative gene network construction for predicting a set of complementary prostate cancer genes
1854 -- 1859Charles Jackson, Estelle Glory-Afshar, Robert F. Murphy, Jelena Kovacevic. Model building and intelligent acquisition with application to protein subcellular location classification
1860 -- 1866Jesse Gillis, Paul Pavlidis. The role of indirect connections in gene networks in predicting function
1867 -- 1868Clifford A. Meyer, Housheng H. He, Myles Brown, X. Shirley Liu. BINOCh: binding inference from nucleosome occupancy changes
1869 -- 1870Brian Walenz, Liliana Florea. Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing
1871 -- 1872Fernando 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 -- 1875Hariklia 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 -- 1877Gabriele Sales, Chiara Romualdi. ::::parmigene:::: - a parallel R package for mutual information estimation and gene network reconstruction
1878 -- 1879Matti Kankainen, Peddinti V. Gopalacharyulu, Liisa Holm, Matej Oresic. MPEA - metabolite pathway enrichment analysis
1880 -- 1881Ross 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 -- 1883Sebastian Bauer, Peter N. Robinson, Julien Gagneur. Model-based gene set analysis for Bioconductor