NicE-seq: high resolution open chromatin profiling

Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell...

Genome Biology 2017 18:122

Published on: 28 June 2017

Statistical algorithms improve accuracy of gene fusion detection

SeqArray—a storage-efficient high-performance data format for WGS variant calls

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis

sis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data

SQC: secure quality control for meta-analysis of genome-wide association studies

ViPTree: the viral proteomic tree server

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2379–2380, https://doi.org/10.1093/bioinformatics/btx157

annotatr: genomic regions in context

modSaRa: a computationally efficient R package for CNV identification

Kart: a divide-and-conquer algorithm for NGS read alignment

BEESEM: estimation of binding energy models using HT-SELEX data

SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive

NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers

Cpipe: a comprehensive computational platform for sequence and structure-based analyses of Cysteine residues

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data

Identification of active miRNA promoters from nuclear run-on RNA sequencing

MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets

 Nucleic Acids Research, Volume 45, Issue 13, 27 July 2017, Pages e122,https://doi.org/10.1093/nar/gkx338

A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays

Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules

Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTran...

Genome Biology 2017 18:148

Published on: 4 August 2017

Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of singl...

JGenome Biology 2017 18:138

Published on: 24 July 2017

Enhanced methods to detect haplotypic effects on gene expression

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2307–2313, https://doi.org/10.1093/bioinformatics/btx142

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

Genome Res. August 2017 27: 1450-1459; Published in Advance May 18, 2017, doi:10.1101/gr.211656.116

Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions

A Zoom-Focus algorithm (ZFA) to locate the optimal testing region for rare variant association tests

Deep mining heterogeneous networks of biomedical linked data to predict novel drug–target associations

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2337–2344, https://doi.org/10.1093/bioinformatics/btx160

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets

SynergyFinder: a web application for analyzing drug combination dose–response matrix data

Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2416–2418, https://doi.org/10.1093/bioinformatics/btx185

CMDR based differential evolution identifies the epistatic interaction in genome-wide association studies

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2354–2362, https://doi.org/10.1093/bioinformatics/btx163

A transition-based joint model for disease named entity recognition and normalization

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2363–2371, https://doi.org/10.1093/bioinformatics/btx172

Mining heterogeneous causal effects for personalized cancer treatment

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2372–2378, https://doi.org/10.1093/bioinformatics/btx174

MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2419–2420, https://doi.org/10.1093/bioinformatics/btx159

IcyTree: rapid browser-based visualization for phylogenetic trees and networks

Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2392–2394, https://doi.org/10.1093/bioinformatics/btx155

ReMixT: clone-specific genomic structure estimation in cancer

Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequen...

Genome Biology 2017 18:140

Published on: 27 July 2017

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation ch...

Genome Biology 2017 18:141

Published on: 27 July 2017

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