Bioinformatics (Oxford, England)

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  Publication Venue For

  • bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens..  34:3581-3583. 2018
  • Extrema-weighted feature extraction for functional data..  34:2457-2464. 2018
  • rqt: an R package for gene-level meta-analysis..  33:3129-3130. 2017
  • Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations..  33:2337-2344. 2017
  • Domain prediction with probabilistic directional context..  33:2471-2478. 2017
  • Bayesian network-response regression..  33:1859-1866. 2017
  • High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE..  33:1437-1446. 2017
  • T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life..  33:1160-1168. 2017
  • Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates..  32:50-57. 2016
  • A hybrid bayesian approach for genome-wide association studies on related individuals..  31:3890-3896. 2015
  • SNiPA: an interactive, genetic variant-centered annotation browser..  31:1334-1336. 2015
  • The Bioinformatics Open Source Conference (BOSC) 2013..  31:299-300. 2015
  • Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data..  30:3287-3288. 2014
  • Learning protein-DNA interaction landscapes by integrating experimental data through computational models..  30:2868-2874. 2014
  • Improved transcript isoform discovery using ORF graphs..  30:1958-1964. 2014
  • Learning phenotype densities conditional on many interacting predictors..  30:1562-1568. 2014
  • ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers..  30:1771-1773. 2014
  • Bayesian joint analysis of heterogeneous genomics data..  30:1370-1376. 2014
  • Effects of serelaxin in subgroups of patients with acute heart failure: Results fromRELAX-AHF.  29:3128-3136. 2013
  • Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data..  29:3174-3180. 2013
  • WebGLORE: a web service for Grid LOgistic REgression..  29:3238-3240. 2013
  • Bayesian consensus clustering..  29:2610-2616. 2013
  • Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields..  29:i27-i35. 2013
  • Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation..  29:i108-i116. 2013
  • Stability selection for regression-based models of transcription factor-DNA binding specificity..  29:i117-i125. 2013
  • Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping..  28:i375-i381. 2012
  • A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments..  27:i295-i303. 2011
  • FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.  27:1922-1928. 2011
  • Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning..  27:i374-i382. 2011
  • An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes..  26:2109-2115. 2010
  • Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images..  26:761-769. 2010
  • GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis..  26:560-564. 2010
  • Pathway analysis using random forests with bivariate node-split for survival outcomes..  26:250-258. 2010
  • Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images.  26:761-769. 2009
  • Reconstructing spatiotemporal gene expression data from partial observations..  25:2581-2587. 2009
  • Gradient lasso for Cox proportional hazards model..  25:1775-1781. 2009
  • Domain-oriented edge-based alignment of protein interaction networks..  25:i240-i246. 2009
  • FDR made easy in differential feature discovery and correlation analyses..  25:1461-1462. 2009
  • From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations..  25:i63-i68. 2009
  • DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages..  25:692-694. 2009
  • Serial dilution curve: a new method for analysis of reverse phase protein array data..  25:650-654. 2009
  • Complexity reduction in context-dependent DNA substitution models..  25:175-182. 2009
  • Pathway analysis using random forests with bivariate node-split for survival outcomes.  26:250-258. 2009
  • F-Seq: a feature density estimator for high-throughput sequence tags..  24:2537-2538. 2008
  • Algorithm for backrub motions in protein design..  24:i196-i204. 2008
  • lumi: a pipeline for processing Illumina microarray..  24:1547-1548. 2008
  • The evolutionary forest algorithm..  23:1962-1968. 2007
  • Dead-end elimination with backbone flexibility..  23:i185-i194. 2007
  • SQUINT: a multiple alignment program and editor..  23:1553-1555. 2007
  • Genomic sweeping for hypermethylated genes..  23:281-288. 2007
  • GATHER: a systems approach to interpreting genomic signatures..  22:2926-2933. 2006
  • Predicting methylation status of CpG islands in the human brain.  22:2204-2209. 2006
  • Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching..  22:2059-2065. 2006
  • Pathway analysis using random forests classification and regression..  22:2028-2036. 2006
  • Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles..  22:e108-e116. 2006
  • How accurately can we control the FDR in analyzing microarray data?.  22:1730-1736. 2006
  • Informative priors based on transcription factor structural class improve de novo motif discovery..  22:e384-e392. 2006
  • COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations..  22:779-788. 2006
  • SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations..  22:438-444. 2006
  • Sequence features of DNA binding sites reveal structural class of associated transcription factor..  22:157-163. 2006
  • SNPselector: a web tool for selecting SNPs for genetic association studies..  21:4181-4186. 2005
  • SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization..  21:3697-3699. 2005
  • Statistical analysis of antigen receptor spectratype data..  21:3394-3400. 2005
  • DIG--a system for gene annotation and functional discovery..  21:2957-2959. 2005
  • Sample size for FDR-control in microarray data analysis..  21:3097-3104. 2005
  • High-throughput inference of protein-protein interfaces from unassigned NMR data..  21 Suppl 1:i292-i301. 2005
  • Erratum: Bayesian analysis of signaling networks embryonic stem cell fate decisions (Bioinformatics (2005) vol. 21 (741-753)).  21:1750. 2005
  • Theoretical and practical advances in genome halving..  21:869-879. 2005
  • Bayesian analysis of signaling networks governing embryonic stem cell fate decisions..  21:741-753. 2005
  • Advances to Bayesian network inference for generating causal networks from observational biological data..  20:3594-3603. 2004
  • Reconstructing the temporal ordering of biological samples using microarray data..  19:842-850. 2003
  • Modeling biological systems using Dynetica--a simulator of dynamic networks..  19:435-436. 2003
  • Rank order metrics for quantifying the association of sequence features with gene regulation..  19:212-218. 2003
  • Evaluating functional network inference using simulations of complex biological systems..  18 Suppl 1:S216-S224. 2002
  • Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition..  17 Suppl 1:S199-S206. 2001
  • Molecular classification of multiple tumor types..  17 Suppl 1:S316-S322. 2001
  • Interpolated markov chains for eukaryotic promoter recognition..  15:362-369. 1999
  • The LabBase system for data management in large scale biology research laboratories..  14:562-574. 1998
  • CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions. 2017
  • AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. 2007