Jean-Pierre Kocher

Jean-Pierre Kocher

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Jean-Pierre Kocher

Jean-Pierre Kocher

Publications by authors named "Jean-Pierre Kocher"

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Coverage profile correction of shallow-depth circulating cell-free DNA sequencing via multidistance learning.

Pac Symp Biocomput 2020 ;25:599-610

Department of Health Sciences Research, Mayo Clinic College of Medicine and Sciences, 200 1st Street SW, Rochester, MN 55901, USA,

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January 2020

CpGtools: A Python Package for DNA Methylation Analysis.

Bioinformatics 2019 Dec 6. Epub 2019 Dec 6.

Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz916DOI Listing
December 2019

Ccne1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice.

Gastroenterology 2019 07 13;157(1):210-226.e12. Epub 2019 Mar 13.

Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00165085193355
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http://dx.doi.org/10.1053/j.gastro.2019.03.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800187PMC
July 2019

Prognostic subclass of intrahepatic cholangiocarcinoma by integrative molecular-clinical analysis and potential targeted approach.

Hepatol Int 2019 Jul 18;13(4):490-500. Epub 2019 Jun 18.

Department of Surgery, Dongsan Medical Center, School of Medicine, Keimyung University, 56 Dalseong-ro, Jung-gu, Daegu, 700-712, Republic of Korea.

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http://dx.doi.org/10.1007/s12072-019-09954-3DOI Listing
July 2019

Novel Neural Network Approach to Predict Drug-Target Interactions Based on Drug Side Effects and Genome-Wide Association Studies.

Hum Hered 2018 22;83(2):79-91. Epub 2018 Oct 22.

Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona,

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https://www.karger.com/Article/FullText/492574
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http://dx.doi.org/10.1159/000492574DOI Listing
March 2019

Predict drug sensitivity of cancer cells with pathway activity inference.

BMC Med Genomics 2019 01 31;12(Suppl 1):15. Epub 2019 Jan 31.

Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0449-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357358PMC
January 2019

Detection and visualization of complex structural variants from long reads.

BMC Bioinformatics 2018 Dec 21;19(Suppl 20):508. Epub 2018 Dec 21.

Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1186/s12859-018-2539-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302372PMC
December 2018

A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas.

BMC Genomics 2018 Nov 27;19(1):841. Epub 2018 Nov 27.

Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA.

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http://dx.doi.org/10.1186/s12864-018-5177-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258141PMC
November 2018

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

J Comput Biol 2018 09 22;25(9):1040-1049. Epub 2018 Jun 22.

1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota.

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https://www.liebertpub.com/doi/10.1089/cmb.2018.0056
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http://dx.doi.org/10.1089/cmb.2018.0056DOI Listing
September 2018

Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine.

BMC Med Genomics 2018 Sep 14;11(Suppl 3):67. Epub 2018 Sep 14.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1186/s12920-018-0391-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157028PMC
September 2018

Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance.

Clin Cancer Res 2018 07 4;24(14):3299-3308. Epub 2018 Apr 4.

Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic, Rochester, Minnesota.

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http://dx.doi.org/10.1158/1078-0432.CCR-17-3008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050078PMC
July 2018

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

BMC Bioinformatics 2018 07 17;19(1):271. Epub 2018 Jul 17.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1186/s12859-018-2260-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050683PMC
July 2018

Correction to: the impact of pharmacokinetic gene profiles across human cancers.

BMC Cancer 2018 07 18;18(1):743. Epub 2018 Jul 18.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1186/s12885-018-4593-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050650PMC
July 2018

The impact of pharmacokinetic gene profiles across human cancers.

BMC Cancer 2018 May 21;18(1):577. Epub 2018 May 21.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1186/s12885-018-4345-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963084PMC
May 2018

Author Correction: UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.

Sci Rep 2018 Mar 20;8(1):5124. Epub 2018 Mar 20.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1038/s41598-018-23183-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861083PMC
March 2018

Early genetic aberrations in patients with sporadic colorectal cancer.

Mol Carcinog 2018 Jan 18;57(1):114-124. Epub 2017 Oct 18.

Division of Internal Medicine, Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.

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http://dx.doi.org/10.1002/mc.22738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716916PMC
January 2018

Linnorm: improved statistical analysis for single cell RNA-seq expression data.

Nucleic Acids Res 2017 Dec;45(22):e179

Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA.

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http://dx.doi.org/10.1093/nar/gkx828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727406PMC
December 2017

Corrigendum: Linnorm: improved statistical analysis for single cell RNA-seq expression data.

Nucleic Acids Res 2017 12;45(22):13097

Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA.

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http://dx.doi.org/10.1093/nar/gkx1189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728397PMC
December 2017

Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation.

Epigenomics 2017 11 2;9(11):1423-1435. Epub 2017 Oct 2.

Divisions of Nephrology & Hypertension, Mayo Clinic, Arizona, AZ, USA.

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http://dx.doi.org/10.2217/epi-2017-0050DOI Listing
November 2017

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.

Sci Rep 2017 10 27;7(1):14196. Epub 2017 Oct 27.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1038/s41598-017-14595-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660178PMC
October 2017

Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma.

JCO Precis Oncol 2017 1;2017. Epub 2017 Aug 1.

David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala'Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor, Aaron S. Mansfield, Amulya A. Nageswara Rao, Grzegorz S. Nowakowski, Animesh Pardanani, Sameer A. Parikh, John C. Cheville, Andrew L. Feldman, Ramesh K. Ramanathan, Steven I. Robinson, Heidi D. Finnes, Jennifer B. McCormick, Robert R. McWilliams, Aminah Jatoi, Mrinal M. Patnaik, Eric D. Wieben, Tammy M. McAllister, Kandelaria M. Rumilla, Sarah E. Kerr, Konstantinos N. Lazaridis, Gianrico Farrugia, Karl J. Clark, Eric W. Klee, and Martin E. Fernandez-Zapico, Mayo Clinic, Rochester; Ernesto Resnik, Bio-Techne, Minneapolis, MN; Sikander Ailawadhi, Asher A. Chanan-Khan, and Richard W. Joseph, Mayo Clinic, Jacksonville, FL; Jan B. Egan, Alan H. Bryce, Estrella M. Carballido, KellyK. Curtis, Chelsea D. Gawryletz, Thai H. Ho,Nathalie Meurice, Ramesh K. Ramanathan, Raoul Tibes, Alvin C. Silva, A. Keith Stewart, and Mitesh J. Borad, Mayo Clinic, Phoenix, AZ; and Eileen J. Kennedy, University of Georgia, Athens, GA.

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http://dx.doi.org/10.1200/PO.17.00018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369924PMC
August 2017

Exploring genetic associations with ceRNA regulation in the human genome.

Nucleic Acids Res 2017 Jun;45(10):5653-5665

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkx331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449616PMC
June 2017

CircularLogo: A lightweight web application to visualize intra-motif dependencies.

BMC Bioinformatics 2017 May 22;18(1):269. Epub 2017 May 22.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1186/s12859-017-1680-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440937PMC
May 2017

Predicting regulatory variants with composite statistic.

Bioinformatics 2016 09 6;32(18):2729-36. Epub 2016 Jun 6.

Centre for Genomic Sciences, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280872PMC
September 2016

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

BMC Bioinformatics 2016 Apr 13;17:162. Epub 2016 Apr 13.

Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First St SW, Harvick 3rd, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1186/s12859-016-0974-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831187PMC
April 2016

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

Bioinformatics 2016 Feb 7;32(3):469-71. Epub 2015 Oct 7.

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115.

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http://dx.doi.org/10.1093/bioinformatics/btv577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757944PMC
February 2016

Measure transcript integrity using RNA-seq data.

BMC Bioinformatics 2016 Feb 3;17:58. Epub 2016 Feb 3.

Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1186/s12859-016-0922-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739097PMC
February 2016

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies.

Nucleic Acids Res 2016 Jan 28;44(D1):D869-76. Epub 2015 Nov 28.

Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China

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http://dx.doi.org/10.1093/nar/gkv1317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702921PMC
January 2016

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

Bioinformatics 2015 Dec 26;31(24):3991-3. Epub 2015 Aug 26.

Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905,USA.

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http://dx.doi.org/10.1093/bioinformatics/btv497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692967PMC
December 2015

IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries.

PLoS One 2014 15;9(12):e114804. Epub 2014 Dec 15.

Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114804PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266640PMC
November 2015

Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling.

Epigenomics 2015 Oct 18;7(7):1099-110. Epub 2015 May 18.

Department of Health Sciences Research, Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN 55905, USA.

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https://www.futuremedicine.com/doi/10.2217/epi.15.43
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http://dx.doi.org/10.2217/epi.15.43DOI Listing
October 2015

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis.

Epigenomics 2015 Aug 14;7(5):813-28. Epub 2015 Sep 14.

Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.2217/epi.15.21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790440PMC
August 2015

Cardiomyopathy and Worsened Ischemic Heart Failure in SM22-α Cre-Mediated Neuropilin-1 Null Mice: Dysregulation of PGC1α and Mitochondrial Homeostasis.

Arterioscler Thromb Vasc Biol 2015 Jun 16;35(6):1401-12. Epub 2015 Apr 16.

From the Department of Biochemistry and Molecular Biology (Y.W., Y.C., S.B., A.K.S., E.W., L.H.H., S.K.D., E.B.L., D.M.), Center for Regenerative Medicine, Marriott Heart Disease Research Program, Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Medical Genetics (S.Y., A.T.), Department of Anesthesiology (V.N., J.C.-P., E.N.C.), Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Health Science Program (K.S., J.-P.A.K.), Department of Gastroenterology (V.S.), and Thoracic Diseases Research Unit, Department of Biochemistry and Molecular Biology (E.B.L.), Mayo Clinic, Rochester, MN; Molecular Cardiology and Angiogenesis Laboratory, Department of Surgery (M.T., M.J., M.T.R., J.A.S., N.M.) and Department of Cell Biology, Center for Vascular Biology (K.P.C.), University of Connecticut Health Center, Farmington; Department of Surgery, Saint Mary's Hospital, Waterbury, CT (M.J., M.T.R., J.A.S.); and Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT (M.S.).

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http://dx.doi.org/10.1161/ATVBAHA.115.305566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441604PMC
June 2015

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data.

PeerJ 2015 19;3:e970. Epub 2015 May 19.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.7717/peerj.970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451017PMC
June 2015

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

BMC Bioinformatics 2015 Jun 6;16:185. Epub 2015 Jun 6.

Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First St SW, Harvick 3rd, Rochester, MN, 55905, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/s12859-015-0609-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457984PMC
June 2015

Genome-wide analysis of loss of heterozygosity in breast infiltrating ductal carcinoma distant normal tissue highlights arm specific enrichment and expansion across tumor stages.

PLoS One 2014 18;9(4):e95783. Epub 2014 Apr 18.

Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095783PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991715PMC
May 2015

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

Bioinformatics 2015 May 7;31(10):1668-70. Epub 2015 Jan 7.

Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807355PMC
May 2015

Epidaurus: aggregation and integration analysis of prostate cancer epigenome.

Nucleic Acids Res 2015 Jan 5;43(2):e7. Epub 2014 Nov 5.

Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA

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http://dx.doi.org/10.1093/nar/gku1079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333365PMC
January 2015

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

Bioinformatics 2014 Dec 27;30(23):3414-6. Epub 2014 Aug 27.

Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, Department of Laboratory Medicine and Pathology, Division of Hematology, Department of Internal Medicine, Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296157PMC
December 2014

From days to hours: reporting clinically actionable variants from whole genome sequencing.

PLoS One 2014 5;9(2):e86803. Epub 2014 Feb 5.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086803PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914798PMC
November 2014

MACE: model based analysis of ChIP-exo.

Nucleic Acids Res 2014 Nov 23;42(20):e156. Epub 2014 Sep 23.

Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA

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http://dx.doi.org/10.1093/nar/gku846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227761PMC
November 2014

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

PLoS One 2013 16;8(12):e83356. Epub 2013 Dec 16.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083356PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3865185PMC
October 2014

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

Bioinformatics 2014 Sep 29;30(18):2678-80. Epub 2014 May 29.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Division of Epidemiology, Department of Health Sciences Research, Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155258PMC
September 2014

Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E.

Epigenetics 2014 Aug 7;9(8):1184-93. Epub 2014 Jul 7.

Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester, MN USA; Department of Neurology; Mayo Clinic; Rochester, MN USA; Department of Medical Genetics; Mayo Clinic; Rochester, MN USA.

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http://dx.doi.org/10.4161/epi.29676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164503PMC
August 2014

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.

BMC Bioinformatics 2014 Aug 15;15:280. Epub 2014 Aug 15.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2105-15-280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152589PMC
August 2014

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

Bioinformatics 2014 Jul 10;30(13):1920-2. Epub 2014 Mar 10.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071205PMC
July 2014

Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

Physiol Genomics 2014 Jul 6;46(13):482-95. Epub 2014 May 6.

Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota; Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota; Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota; Transplant Center, Mayo Clinic, Rochester, Minnesota; and Division of General Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota

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http://dx.doi.org/10.1152/physiolgenomics.00015.2014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080280PMC
July 2014

Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics.

Bioconjug Chem 2014 Jun 22;25(6):1078-90. Epub 2014 May 22.

Department of Biochemistry and Molecular Biology, ‡Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, ⊥Molecular Medicine Program, and #Proteomics Research Center, Mayo Clinic , Rochester, Minnesota 55905, United States.

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http://dx.doi.org/10.1021/bc500084fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128259PMC
June 2014

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data.

BMC Genomics 2014 Jun 3;15:423. Epub 2014 Jun 3.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2164-15-423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070549PMC
June 2014

Clinical proteome informatics workbench detects pathogenic mutations in hereditary amyloidoses.

J Proteome Res 2014 May 3;13(5):2352-8. Epub 2014 Apr 3.

Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Mayo Proteomics Core, and ∥Department of Molecular Genetics, Mayo Clinic , Rochester 55905, Minnesota, United States.

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http://dx.doi.org/10.1021/pr4011475DOI Listing
May 2014

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

Bioinformatics 2014 Apr 18;30(7):1006-7. Epub 2013 Dec 18.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA, Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967108PMC
April 2014

Murine leukemia virus uses NXF1 for nuclear export of spliced and unspliced viral transcripts.

J Virol 2014 Apr 29;88(8):4069-82. Epub 2014 Jan 29.

Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA.

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http://dx.doi.org/10.1128/JVI.03584-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993726PMC
April 2014

Calculating sample size estimates for RNA sequencing data.

J Comput Biol 2013 Dec 20;20(12):970-8. Epub 2013 Aug 20.

1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota.

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http://dx.doi.org/10.1089/cmb.2012.0283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884PMC
December 2013

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

Bioinformatics 2013 Nov 19;29(22):2877-83. Epub 2013 Aug 19.

Department of Biostatistics, Biostatistics Shared Resource Core, VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23284, USA, Division of Biomedical Statistics and Informatics and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810845PMC
November 2013

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.

Nucleic Acids Res 2013 Apr 17;41(6):e74. Epub 2013 Jan 17.

Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/nar/gkt006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616698PMC
April 2013

Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples.

BMC Res Notes 2013 Jan 30;6:33. Epub 2013 Jan 30.

Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1756-0500-6-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626608PMC
January 2013

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

Bioinformatics 2012 Aug 10;28(16):2180-1. Epub 2012 Jun 10.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413387PMC
August 2012

Mass homozygotes accumulation in the NCI-60 cancer cell lines as compared to HapMap Trios, and relation to fragile site location.

PLoS One 2012 9;7(2):e31628. Epub 2012 Feb 9.

Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031628PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276511PMC
July 2012

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

J Am Med Inform Assoc 2011 Dec 21;18 Suppl 1:i144-9. Epub 2011 Sep 21.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.

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https://academic.oup.com/jamia/article-lookup/doi/10.1136/am
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http://dx.doi.org/10.1136/amiajnl-2011-000351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241172PMC
December 2011

Batch effect correction for genome-wide methylation data with Illumina Infinium platform.

BMC Med Genomics 2011 Dec 16;4:84. Epub 2011 Dec 16.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street, Rochester, MN 55905, USA.

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http://bmcmedgenomics.biomedcentral.com/articles/10.1186/175
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http://dx.doi.org/10.1186/1755-8794-4-84DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265417PMC
December 2011

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.

Nucleic Acids Res 2011 Aug 27;39(15):e100. Epub 2011 May 27.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.

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http://dx.doi.org/10.1093/nar/gkr362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159479PMC
August 2011

SNPPicker: high quality tag SNP selection across multiple populations.

BMC Bioinformatics 2011 May 2;12:129. Epub 2011 May 2.

Department of Biomedical Statistics and Informatics, Mayo Clinic, 200 1st street SW, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2105-12-129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096984PMC
May 2011

Classification of medication status change in clinical narratives.

AMIA Annu Symp Proc 2010 Nov 13;2010:762-6. Epub 2010 Nov 13.

Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041444PMC
November 2010

Copy number variation and cytidine analogue cytotoxicity: a genome-wide association approach.

BMC Genomics 2010 Jun 4;11:357. Epub 2010 Jun 4.

Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2164-11-357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894803PMC
June 2010

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays.

BMC Bioinformatics 2010 Jun 29;11:356. Epub 2010 Jun 29.

Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2105-11-356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910027PMC
June 2010

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

BMC Genomics 2009 Nov 16;10:531. Epub 2009 Nov 16.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2164-10-531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781828PMC
November 2009

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

BMC Bioinformatics 2009 Apr 3;10:102. Epub 2009 Apr 3.

Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, NY, USA.

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http://dx.doi.org/10.1186/1471-2105-10-102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678095PMC
April 2009

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

Bioinformatics 2008 Sep 24;24(18):2023-9. Epub 2008 Jul 24.

Department of Computer Science and Engineering, University of Minnesota, Twin Cities, Bioinformatics Core, Mayo Clinic College of Medicine, Rochester, MN, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn383DOI Listing
September 2008