Rachel Karchin

发表

Improving Functional Annotation of Non-Synonomous SNPs with Information Theory

Andrej Sali, Libusha Kelly, Rachel Karchin, 2005, Pacific Symposium on Biocomputing.

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

Marc A. Martí-Renom, Francisco Melo, Narayanan Eswar, 2005, Nucleic Acids Res..

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

Richard Hughey, Kevin Karplus, Rachel Karchin, 2005, Bioinform..

Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily

Andrej Sali, Libusha Kelly, Rachel Karchin, 2007, Pacific Symposium on Biocomputing.

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning

Andrej Sali, Rachel Karchin, Sean V. Tavtigian, 2006, PLoS Comput. Biol..

A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts

Young Joon Ahn, Elliot K. Fishman, Yuxuan Wang, 2017, J. Am. Medical Informatics Assoc..

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

Cheng Wang, Biao Li, Sean D. Mooney, 2014, PLoS Comput. Biol..

Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

Steven E. Brenner, Xi Luo, Lea M. Starita, 2019, Genome Medicine.

Prediction of peptide binding to MHC Class I proteins in the age of deep learning

Rachel Karchin, Rohit Bhattacharya, Ashok Sivakumar, 2017 .

Classifying G-protein coupled receptors with support vector machines

David Haussler, Kevin Karplus, Rachel Karchin, 2002, Bioinform..

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit

Collin Tokheim, Michael C. Ryan, Rachel Karchin, 2017 .

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

Hannah Carter, Mark Diekhans, Michael C. Ryan, 2011, Bioinform..

Next generation tools for the annotation of human SNPs

Rachel Karchin, R. Karchin, 2009, Briefings Bioinform..

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Elizabeth Brunk, Binghuang Cai, Yang Zhang, 2017, Genome Medicine.

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

David Haussler, Narayanan Eswar, Ursula Pieper, 2005, Bioinform..

Weighting hidden Markov models for maximum discrimination

Richard Hughey, Rachel Karchin, R. Hughey, 1998, Bioinform..

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

Ruth Nussinov, Rachel Karchin, 2016, PLoS Comput. Biol..

CRAVAT: cancer-related analysis of variants toolkit

Hannah Carter, Mark Diekhans, Peter D. Stenson, 2013, Bioinform..

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

Yun Liu, Mark Diekhans, Michael C. Ryan, 2009, Bioinform..

Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories

Rachel Karchin, Violeta Beleva Guthrie, Jennifer Allen, 2011, PLoS Comput. Biol..

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

Rachel Karchin, David L. Masica, R. Karchin, 2016, PLoS Comput. Biol..

Joint Xena-Trinity-Cistrome-Cravat/MuPIT Collaboration

Rachel Karchin, Aviv Regev, Xiaole Shirley Liu, 2014 .

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

Marc A. Martí-Renom, Narayanan Eswar, Ursula Pieper, 2008, Nucleic acids research.

Evaluating the Evaluation of Cancer Driver Genes

Collin Tokheim, Rachel Karchin, Kenneth W. Kinzler, 2016 .

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

Daniel Q. Naiman, Rachel Karchin, Noushin Niknafs, 2015, bioRxiv.

Using bioinformatics to predict the functional impact of SNVs

Melissa S. Cline, Rachel Karchin, M. Cline, 2011, Bioinform..

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

Kevin Karplus, Rachel Karchin, Christian Barrett, 2008, Bioinform..

Comparative Protein Structure Modeling 831 831

Narayanan Eswar, Ursula Pieper, Andrej Sali, 2005 .

Evaluation of local structure alphabets based on residue burial

Kevin Karplus, Rachel Karchin, Melissa Cline, 2004, Proteins.

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

Yunfan Fan, Rachel Karchin, David L. Masica, 2018, Molecular biology and evolution.

Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis.

Andrej Sali, Rachel Karchin, Rebecca Sutphen, 2007, Cancer research.

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

Rachel Karchin, David L Masica, R. Karchin, 2015, Human molecular genetics.

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

Rachel Karchin, David L Masica, R. Karchin, 2012, Human mutation.

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

Stephen C. J. Parker, Valer Gotea, Hannah Carter, 2013, Proceedings of the National Academy of Sciences.

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

Jin-Young Jang, Amanda Blackford, Mari Mino-Kenudson, 2015, Gastroenterology.

Systematic Functional Annotation of Somatic Mutations in Cancer.

Ken Chen, Li Ding, Jun Li, 2018, Cancer cell.

Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.

Chunling Hu, Rachel Karchin, Fergus J Couch, 2018, American journal of human genetics.

Evaluation of machine learning methods to predict peptide binding to MHC Class I proteins

Collin Tokheim, Rachel Karchin, Victor E. Velculescu, 2017, bioRxiv.

Assessing computational predictions of the phenotypic effect of cystathionine‐beta‐synthase variants

Silvio C. E. Tosatto, Predrag Radivojac, Mauno Vihinen, 2019, Human mutation.

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

Mark Diekhans, Peter D. Stenson, Rachel Karchin, 2013, Human Genetics.

Human bile contains MicroRNA‐laden extracellular vesicles that can be used for cholangiocarcinoma diagnosis

Susan Hutfless, Clifford R Weiss, Rachel Karchin, 2014, Hepatology.

A machine learning approach for somatic mutation discovery

Rachel Karchin, Valsamo Anagnostou, David Riley, 2018, Science Translational Medicine.

Comprehensive Characterization of Cancer Driver Genes and Mutations (vol 173, 371.e1, 2018)

Li Ding, Peter J. Park, Niranjan Nagarajan, 2018 .

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit

Collin Tokheim, Michael C. Ryan, Rachel Karchin, 2017, bioRxiv.

Single‐cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions

Rachel Karchin, Jin He, L. Wood, 2019, The Journal of pathology.

Predicting the functional consequences of somatic missense mutations found in tumors.

Hannah Carter, Rachel Karchin, H. Carter, 2014, Methods in molecular biology.

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

George P Patrinos, Rachel Karchin, David L. Masica, 2013, Nature Genetics.

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

Rachel Karchin, Saraswati Sukumar, P. Mankoo, 2009, Proteins.

Integrating diverse genomic data using gene sets

Giovanni Parmigiani, Luigi Marchionni, Rachel Karchin, 2011, Genome Biology.

Assessing aneuploidy with repetitive element sequencing

Tian-Li Wang, Rachel Karchin, Robert E. Schoen, 2019, Proceedings of the National Academy of Sciences.