Rachel Karchin

Rachel Karchin

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Rachel Karchin

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Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations.

Gastroenterology 2019 10 5;157(4):1123-1137.e22. Epub 2019 Jun 5.

Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2019.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756950PMC
October 2019

CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers.

Cell Syst 2019 Jul 12;9(1):9-23.e8. Epub 2019 Jun 12.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD 21204, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6857794PMC
July 2019

Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations.

Mol Biol Evol 2018 06;35(6):1507-1519

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD.

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http://dx.doi.org/10.1093/molbev/msy036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967520PMC
June 2018

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit.

Cancer Res 2017 11;77(21):e35-e38

Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850945PMC
November 2017

Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society.

Hum Mutat 2017 04 14;38(4):460-463. Epub 2017 Feb 14.

Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/humu.23169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546288PMC
April 2017

Autologous reconstitution of human cancer and immune system in vivo.

Oncotarget 2017 Jan;8(2):2053-2068

Bloomberg-Kimmel Institute for Cancer Immunotherapy, SKCCC, Johns Hopkins Hospital, Baltimore, MD, USA.

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http://www.oncotarget.com/fulltext/14026
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http://dx.doi.org/10.18632/oncotarget.14026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356779PMC
January 2017

Evaluating the evaluation of cancer driver genes.

Proc Natl Acad Sci U S A 2016 12 22;113(50):14330-14335. Epub 2016 Nov 22.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218;

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http://dx.doi.org/10.1073/pnas.1616440113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167163PMC
December 2016

Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation.

PLoS Comput Biol 2016 08 18;12(8):e1005043. Epub 2016 Aug 18.

Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990343PMC
August 2016

Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

Cancer Res 2016 07 28;76(13):3719-31. Epub 2016 Apr 28.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-3190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930736PMC
July 2016

Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants.

PLoS Comput Biol 2016 05 12;12(5):e1004725. Epub 2016 May 12.

Department of Biomedical Engineering and The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865359PMC
May 2016

Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.

Cancer Prev Res (Phila) 2016 04 9;9(4):265-74. Epub 2016 Feb 9.

Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute, and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Surgery, Section of Otolaryngology-Head and Neck Surgery, The University of Chicago, Chicago, Illinois States.

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http://dx.doi.org/10.1158/1940-6207.CAPR-15-0316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818686PMC
April 2016

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).

Hum Mutat 2016 Jan 26;37(1):28-35. Epub 2015 Oct 26.

Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland.

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http://doi.wiley.com/10.1002/humu.22911
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http://dx.doi.org/10.1002/humu.22911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057310PMC
January 2016

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns.

Hum Mol Genet 2015 Nov 5;24(21):5995-6002. Epub 2015 Aug 5.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21210, USA and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,

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http://dx.doi.org/10.1093/hmg/ddv309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354780PMC
November 2015

A combination of molecular markers and clinical features improve the classification of pancreatic cysts.

Gastroenterology 2015 Nov 4;149(6):1501-10. Epub 2015 Aug 4.

The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University, Baltimore, Maryland; Department of Surgery, The Johns Hopkins University, Baltimore, Maryland; Department of Medicine, The Johns Hopkins University, Baltimore, Maryland. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2015.07.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782782PMC
November 2015

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.

PLoS Comput Biol 2015 Oct 5;11(10):e1004416. Epub 2015 Oct 5.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593588PMC
October 2015

Human genetics special issue on computational molecular medicine.

Hum Genet 2015 May;134(5):455-7

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, USA,

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http://dx.doi.org/10.1007/s00439-015-1545-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405483PMC
May 2015

Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity.

Hum Mol Genet 2015 Apr 8;24(7):1908-17. Epub 2014 Dec 8.

Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

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http://dx.doi.org/10.1093/hmg/ddu607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366609PMC
April 2015

Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features.

Cancer Prev Res (Phila) 2015 Apr 29;8(4):287-95. Epub 2015 Jan 29.

Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. Milton J. Dance Jr. Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland. Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.

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http://dx.doi.org/10.1158/1940-6207.CAPR-14-0366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383699PMC
April 2015

Germline & somatic mosaicism: the 2014 annual scientific meeting of the Human Genome Variation Society.

Hum Mutat 2015 Mar;36(3):390-3

Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota.

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http://dx.doi.org/10.1002/humu.22757DOI Listing
March 2015

A probabilistic model to predict clinical phenotypic traits from genome sequencing.

PLoS Comput Biol 2014 Sep 4;10(9):e1003825. Epub 2014 Sep 4.

Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154636PMC
September 2014

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

Hum Genet 2013 Nov 23;132(11):1235-43. Epub 2013 Jun 23.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, USA.

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http://dx.doi.org/10.1007/s00439-013-1325-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797853PMC
November 2013

Identifying Mendelian disease genes with the variant effect scoring tool.

BMC Genomics 2013 28;14 Suppl 3:S3. Epub 2013 May 28.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, 3400 N, Charles St, Baltimore, Maryland USA.

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http://dx.doi.org/10.1186/1471-2164-14-S3-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665549PMC
October 2013

Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene.

Nat Genet 2013 Oct 25;45(10):1160-7. Epub 2013 Aug 25.

1] Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA. [2] Perdana University Graduate School of Medicine, Serdang, Malaysia. [3] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/ng.2745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874936PMC
October 2013

A hybrid likelihood model for sequence-based disease association studies.

PLoS Genet 2013 24;9(1):e1003224. Epub 2013 Jan 24.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554549PMC
May 2013

CRAVAT: cancer-related analysis of variants toolkit.

Bioinformatics 2013 Mar 16;29(5):647-8. Epub 2013 Jan 16.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582272PMC
March 2013

Collections of simultaneously altered genes as biomarkers of cancer cell drug response.

Cancer Res 2013 Mar 21;73(6):1699-708. Epub 2013 Jan 21.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-12-3122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602343PMC
March 2013

Charting the landscape of tandem BRCT domain-mediated protein interactions.

Sci Signal 2012 Sep 18;5(242):rs6. Epub 2012 Sep 18.

Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.

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http://dx.doi.org/10.1126/scisignal.2002255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064718PMC
September 2012

Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis.

Hum Mutat 2012 Aug 22;33(8):1267-74. Epub 2012 May 22.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA.

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http://doi.wiley.com/10.1002/humu.22110
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http://dx.doi.org/10.1002/humu.22110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364283PMC
August 2012

Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers.

Genes Chromosomes Cancer 2012 May 3;51(5):480-9. Epub 2012 Feb 3.

Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.

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http://doi.wiley.com/10.1002/gcc.21935
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http://dx.doi.org/10.1002/gcc.21935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302210PMC
May 2012

Discriminative prediction of mammalian enhancers from DNA sequence.

Genome Res 2011 Dec 29;21(12):2167-80. Epub 2011 Aug 29.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.121905.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227105PMC
December 2011

Yeast two-hybrid junk sequences contain selected linear motifs.

Nucleic Acids Res 2011 Oct 23;39(19):e128. Epub 2011 Jul 23.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1093/nar/gkr600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201885PMC
October 2011

Integrating diverse genomic data using gene sets.

Genome Biol 2011 Oct 21;12(10):R105. Epub 2011 Oct 21.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2011-12-10-r105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333775PMC
October 2011

Evaluation of the disease liability of CFTR variants.

Methods Mol Biol 2011 ;742:355-72

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.1007/978-1-61779-120-8_21DOI Listing
September 2011

Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication.

Nucleic Acids Res 2011 Sep 26;39(16):7020-33. Epub 2011 May 26.

Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, 1156 High Street Santa Cruz, CA 95060, USA.

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http://dx.doi.org/10.1093/nar/gkr157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167613PMC
September 2011

Exonic DNA sequencing of ERBB4 in bipolar disorder.

PLoS One 2011 26;6(5):e20242. Epub 2011 May 26.

Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020242PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102700PMC
September 2011

Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories.

PLoS Comput Biol 2011 Sep 22;7(9):e1002184. Epub 2011 Sep 22.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1002184
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http://dx.doi.org/10.1371/journal.pcbi.1002184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178621PMC
September 2011

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

Bioinformatics 2011 Aug 17;27(15):2147-8. Epub 2011 Jun 17.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137226PMC
August 2011

Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival.

Cancer Res 2011 Jul 9;71(13):4550-61. Epub 2011 May 9.

Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland 21218, USA.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-11-0180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129415PMC
July 2011

Using bioinformatics to predict the functional impact of SNVs.

Bioinformatics 2011 Feb 15;27(4):441-8. Epub 2010 Dec 15.

Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2010/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btq695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105482PMC
February 2011

Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.

Protein Sci 2010 Nov;19(11):2110-21

Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, California, USA.

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http://doi.wiley.com/10.1002/pro.491
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http://dx.doi.org/10.1002/pro.491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005782PMC
November 2010

Accumulation of driver and passenger mutations during tumor progression.

Proc Natl Acad Sci U S A 2010 Oct 27;107(43):18545-50. Epub 2010 Sep 27.

Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1010978107
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http://dx.doi.org/10.1073/pnas.1010978107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972991PMC
October 2010

Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM).

Cancer Biol Ther 2010 Sep 1;10(6):582-7. Epub 2010 Oct 1.

Department of Biomedical Engineering and Institute for Computational Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Kimmel Cancer Center, Baltimore, MD, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040948PMC
http://dx.doi.org/10.4161/cbt.10.6.12537DOI Listing
September 2010

Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios.

Cancer Inform 2008 18;6:203-16. Epub 2008 Apr 18.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587343PMC
http://dx.doi.org/10.4137/cin.s618DOI Listing
May 2010

Detecting species-site dependencies in large multiple sequence alignments.

Nucleic Acids Res 2009 Oct 6;37(18):5959-68. Epub 2009 Aug 6.

Institute of Hygiene and Microbiology, Josef-Schneider-Strasse 2/E1, 97080, Germany.

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http://dx.doi.org/10.1093/nar/gkp634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764451PMC
October 2009

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

Cancer Res 2009 Aug 4;69(16):6660-7. Epub 2009 Aug 4.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21218, USA.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-09-1133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763410PMC
August 2009

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

Bioinformatics 2009 Jun 15;25(11):1431-2. Epub 2009 Apr 15.

Department of Bioinformatics, George Mason University, Fairfax, VA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276889PMC
June 2009

PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations.

Proteins 2009 May;75(2):499-508

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21218, USA.

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http://doi.wiley.com/10.1002/prot.22265
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http://dx.doi.org/10.1002/prot.22265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094910PMC
May 2009

MODBASE, a database of annotated comparative protein structure models and associated resources.

Nucleic Acids Res 2009 Jan 23;37(Database issue):D347-54. Epub 2008 Oct 23.

Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.

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http://salilab.org/pdf/Pieper_NucleicAcidsRes_2013a.pdf
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http://csmp.ucsf.edu/pdf/Pub28_PMID18948282.pdf
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn791
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http://dx.doi.org/10.1093/nar/gkn791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686492PMC
January 2009

Next generation tools for the annotation of human SNPs.

Authors:
Rachel Karchin

Brief Bioinform 2009 Jan;10(1):35-52

Biomedical Engineering Department and Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 212218, USA.

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http://dx.doi.org/10.1093/bib/bbn047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638621PMC
January 2009

PREDICT-2ND: a tool for generalized protein local structure prediction.

Bioinformatics 2008 Nov 30;24(21):2453-9. Epub 2008 Aug 30.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732275PMC
November 2008

Protein interactions and disease phenotypes in the ABC transporter superfamily.

Pac Symp Biocomput 2007 :51-63

Program in Biological and Medical Informatics, Department of Biopharmaceutical Sciences, University of California at San Francisco, CA 94158, USA.

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December 2007

Functional impact of missense variants in BRCA1 predicted by supervised learning.

PLoS Comput Biol 2007 Feb 28;3(2):e26. Epub 2006 Dec 28.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797820PMC
February 2007

MODBASE: a database of annotated comparative protein structure models and associated resources.

Nucleic Acids Res 2006 Jan;34(Database issue):D291-5

Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1093/nar/gkj059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347422PMC
January 2006

Calibrating E-values for hidden Markov models using reverse-sequence null models.

Bioinformatics 2005 Nov 25;21(22):4107-15. Epub 2005 Aug 25.

Department of Biomolecular Engineering, University of California, Santa Cruz, 95064, USA.

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https://users.soe.ucsc.edu/~karplus/papers/e-value-bioinform
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http://bioinformatics.oxfordjournals.org/content/21/22/4107.
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/bti629DOI Listing
November 2005

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

Bioinformatics 2005 Jun 12;21(12):2814-20. Epub 2005 Apr 12.

Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti442DOI Listing
June 2005

Evaluation of local structure alphabets based on residue burial.

Proteins 2004 May;55(3):508-18

Department of Biopharmaceutical Sciences, University of California, San Francisco 94143-2240, USA.

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https://pdfs.semanticscholar.org/6e0c/4fb3d8f7a6a3b97994955c
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http://doi.wiley.com/10.1002/prot.20008
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http://dx.doi.org/10.1002/prot.20008DOI Listing
May 2004