Bioinformatics (Oxford, England)

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  Publication Venue For

  • Projected t-SNE for batch correction..  36:3522-3527. 2020
  • 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
  • Bayesian network-response regression..  33:1859-1866. 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
  • A hybrid bayesian approach for genome-wide association studies on related individuals..  31:3890-3896. 2015
  • The Bioinformatics Open Source Conference (BOSC) 2013..  31:299-300. 2015
  • Learning protein-DNA interaction landscapes by integrating experimental data through computational models..  30:2868-2874. 2014
  • An efficient parallel algorithm for accelerating computational protein design..  30:i255-i263. 2014
  • Learning phenotype densities conditional on many interacting predictors..  30:1562-1568. 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
  • Bayesian consensus clustering..  29:2610-2616. 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
  • Reconstructing spatiotemporal gene expression data from partial observations..  25:2581-2587. 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
  • Pathway analysis using random forests with bivariate node-split for survival outcomes.  26:250-258. 2009
  • The evolutionary forest algorithm..  23:1962-1968. 2007
  • SQUINT: a multiple alignment program and editor..  23:1553-1555. 2007
  • GATHER: a systems approach to interpreting genomic signatures..  22:2926-2933. 2006
  • Supporting the SBML layout extension.  22:2966-2967. 2006
  • Predicting methylation status of CpG islands in the human brain.  22:2204-2209. 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
  • Improved pruning algorithms and divide-and-conquer strategies for Dead-End Elimination, with application to protein design.  22:e174-e183. 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
  • Sample size for FDR-control in microarray data analysis..  21:3097-3104. 2005
  • DIG--a system for gene annotation and functional discovery..  21:2957-2959. 2005
  • Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.  21:1782-1788. 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
  • Erratum: High-throughput inference of protein-protein interfaces from unassigned NMR data (Bioinformatics (2005) (21) (i292-i301)).  21:3331-. 2005
  • High-throughput inference of protein-protein interfaces from unassigned NMR data.  21:i292-i301. 2005
  • Advances to Bayesian network inference for generating causal networks from observational biological data..  20:3594-3603. 2004
  • Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry..  20:2874-2877. 2004
  • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.  20:2878-2879. 2004
  • A Bayesian network approach to operon prediction..  19:1227-1235. 2003
  • Reconstructing the temporal ordering of biological samples using microarray data..  19:842-850. 2003
  • Identification of key concepts in biomedical literature using a modified Markov heuristic.  19:402-407. 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
  • Modelling regulatory pathways in E. coli from time series expression profiles. 2002