Jean-Pierre A. Kocher

According to our database1, Jean-Pierre A. Kocher authored at least 35 papers between 2008 and 2018.

Collaborative distances:



In proceedings 
PhD thesis 




Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models.
Journal of Computational Biology, 2018

Detection and visualization of complex structural variants from long reads.
BMC Bioinformatics, 2018

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.
BMC Bioinformatics, 2018

mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers.
Nucleic Acids Research, 2017

CircularLogo: A lightweight web application to visualize intra-motif dependencies.
BMC Bioinformatics, 2017

Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.
Briefings in Bioinformatics, 2017

Unraveling complex local genomic rearrangements from long-read data.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies.
Nucleic Acids Research, 2016

Measure transcript integrity using RNA-seq data.
BMC Bioinformatics, 2016

Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.
BMC Bioinformatics, 2016

Predicting regulatory variants with composite statistic.
Bioinformatics, 2016

CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies.
Bioinformatics, 2016

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.
Briefings in Bioinformatics, 2016

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.
BMC Bioinformatics, 2015

PVAAS: identify variants associated with aberrant splicing from RNA-seq.
Bioinformatics, 2015

glmgraph: an R package for variable selection and predictive modeling of structured genomic data.
Bioinformatics, 2015

Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing.
Proceedings of the BIOINFORMATICS 2015, 2015

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.
BMC Bioinformatics, 2014

Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome.
BMC Bioinformatics, 2014

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
BMC Bioinformatics, 2014

CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Bioinformatics, 2014

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.
Bioinformatics, 2014

RVboost: RNA-seq variants prioritization using a boosting method.
Bioinformatics, 2014

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.
Bioinformatics, 2014

Calculating Sample Size Estimates for RNA Sequencing Data.
Journal of Computational Biology, 2013

A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis.
Bioinformatics, 2013

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
Bioinformatics, 2012

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
Bioinformatics, 2012

Multilevel Parallelization of AutoDock 4.2.
J. Cheminformatics, 2011

Drug side effect extraction from clinical narratives of psychiatry and psychology patients.
JAMIA, 2011

SNPPicker: High quality tag SNP selection across multiple populations.
BMC Bioinformatics, 2011

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays.
BMC Bioinformatics, 2010

GLOSSI: a method to assess the association of genetic loci-sets with complex diseases.
BMC Bioinformatics, 2009

Robust and efficient identification of biomarkers by classifying features on graphs.
Bioinformatics, 2008

Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction.
Proceedings of the 8th IEEE International Conference on Data Mining (ICDM 2008), 2008