Bioinformatics

DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.  38:i359-i368. 2022

PASSION: An ensemble neural network approach for identifying the binding sites of RBPs on circRNAs.  36:4276-4282. 2020

DeepCleave: A deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.  36:1057-1065. 2020

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.  36:704-712. 2020

MRLR: Unraveling high-resolution meiotic recombination by linked reads.  36:10-16. 2020

MULTiPly: A novel multi-layer predictor for discovering general and specific types of promoters.  35:2957-2965. 2019

Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization..  35:2885. 2019

Bastion3: A two-layer ensemble predictor of type III secreted effectors.  35:2017-2028. 2019

Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization.  35:1395-1403. 2019

Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.  34:4223-4231. 2018

SnapperDB: a database solution for routine sequencing analysis of bacterial isolates.  34:3028-3029. 2018

Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors.  34:2546-2555. 2018

IFeature: A Python package and web server for features extraction and selection from protein and peptide sequences.  34:2499-2502. 2018

anexVis: Visual analytics framework for analysis of RNA expression.  34:2510-2512. 2018

R2DGC: Threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R.  34:1789-1791. 2018

PROSPERous: High-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.  34:684-687. 2018

POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.  33:2756-2758. 2017

Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy..  33:2182-2190. 2017

ARNApipe: A balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments.  33:1727-1729. 2017

PAGER: Constructing PAGs and new PAG-PAG relationships for network biology.  31:i250-i257. 2015

A self-updating road map of the Cancer Genome Atlas.  29:1333-1340. 2013

Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads.  29:2427-2434. 2013

Rainbow: An integrated tool for efficient clustering and assembling RAD-seq reads.  28:2732-2737. 2012

Genotype calling from next-generation sequencing data using haplotype information of reads.  28:938-946. 2012

High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans.  27:1384-1389. 2011

Length bias correction for RNA-seq data in gene set analyses.  27:662-669. 2011

Inverse perturbation for optimal intervention in gene regulatory networks.  27:103-110. 2011

Fluctuation anaLysis calculator: A web tool for the determination of mutation rate using Luria-Delbück fluctuation analysis.  25:1564-1565. 2009

Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns.  23:2399-2406. 2007

HaploBuild: An algorithm to construct non-contiguous associated haplotypes in family based genetic studies.  23:2190-2192. 2007

OBO-Edit - An ontology editor for biologists.  23:2198-2200. 2007

R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses.  23:641-643. 2007

Computational prediction of novel components of lung transcriptional networks.  23:21-29. 2007

SScore: An R package for detecting differential gene expression without gene expression summaries.  22:1272-1274. 2006

Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays.  21:4255-4262. 2005

A statistical model for HIV-1 sequence classification using the subtype analyser (STAR).  21:3535-3540. 2005

An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments.  20:235-241. 2004

Poxvirus Orthologous Clusters (POCs).  18:1544-1545. 2002

Analysis of genomic sequences by Chaos Game Representation.  17:429-437. 2001

Pathway analysis in metabolic databases via differential metabolic display (DMD).  16:825-836. 2000