Bioinformatics

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  Publication Venue For

  • maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines. 2021
  • A Bayesian Hierarchical Model to Estimate DNA Methylation Conservation in Colorectal Tumors. 2021
  • dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit. 2020
  • CPS analysis: self-contained validation of biomedical data clustering..  36:3516-3521. 2020
  • Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping..  36:3254-3256. 2020
  • Bayesian estimation of genetic regulatory effects in high-throughput reporter assays..  36:331-338. 2020
  • Predicting gene structure changes resulting from genetic variants via exon definition features..  34:3616-3623. 2018
  • 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
  • Applying family analyses to electronic health records to facilitate genetic research..  34:635-642. 2018
  • Domain prediction with probabilistic directional context..  33:2471-2478. 2017
  • High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE..  33:1437-1446. 2017
  • Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates..  32:50-57. 2016
  • SNiPA: an interactive, genetic variant-centered annotation browser..  31:1334-1336. 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
  • ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers..  30:1771-1773. 2014
  • WebGLORE: a web service for Grid LOgistic REgression..  29:3238-3240. 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
  • SVA: software for annotating and visualizing sequenced human genomes..  27:1998-2000. 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
  • Gradient lasso for Cox proportional hazards model..  25:1775-1781. 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
  • 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
  • Matching isotopic distributions from metabolically labeled samples..  24:i339-i347. 2008
  • lumi: a pipeline for processing Illumina microarray..  24:1547-1548. 2008
  • Extending assembly of short DNA sequences to handle error..  23:2942-2944. 2007
  • Genomic sweeping for hypermethylated genes..  23:281-288. 2007
  • 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
  • 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
  • Quantification of transcription factor expression from Arabidopsis images..  22:e323-e331. 2006
  • AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. 2007
  • Using dynamic programming to create isotopic distribution maps from mass spectra. 2007