Jean-Pierre A. Kocher

Orcid: 0000-0002-0260-6773

Affiliations:
  • Mayo Clinic College of Medicine, Rochester, USA


According to our database1, Jean-Pierre A. Kocher authored at least 41 papers between 2008 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2024
Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation.
BMC Bioinform., December, 2024

2022
Telogator: a method for reporting chromosome-specific telomere lengths from long reads.
Bioinform., 2022

2021
CpGtools: a python package for DNA methylation analysis.
Bioinform., 2021

2020
Coverage Profile Correction of Shallow-Depth Circulating Cell-Free DNA Sequencing via Multi-Distance Learning.
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2018
Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models.
J. Comput. Biol., 2018

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

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

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

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

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

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

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

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

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

Predicting regulatory variants with composite statistic.
Bioinform., 2016

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

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

2015
Time course transcriptome data analysis for in vitro modeling of dilated cardiomyopathy using patient-derived induced pluripotent stem cells.
BMC Bioinform., December, 2015

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

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

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

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

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

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

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

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

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

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

2013
Calculating Sample Size Estimates for RNA Sequencing Data.
J. Comput. Biol., 2013

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

Biomedical Informatics and the Future of Medicine.
Proceedings of the Advances in Biomedical Infrastructure 2013, 2013

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

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

2011
Multilevel Parallelization of AutoDock 4.2.
J. Cheminformatics, 2011

Drug side effect extraction from clinical narratives of psychiatry and psychology patients.
J. Am. Medical Informatics Assoc., 2011

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

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

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

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


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