Weighting hidden Markov models for maximum discrimination. - Rachel Karchin; Richard Hughey (Bioinform., 1998)

Classifying G-protein coupled receptors with support vector machines. - Rachel Karchin; Kevin Karplus; David Haussler (Bioinform., 2002)

Improving Functional Annotation of Non-Synonomous SNPs with Information Theory. - Rachel Karchin; Libusha Kelly; Andrej Sali (Pacific Symposium on Biocomputing, 2005)

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. - Rachel Karchin; Mark Diekhans; Libusha Kelly; Daryl J. Thomas; Ursula Pieper 001; Narayanan Eswar; David Haussler; Andrej Sali (Bioinform., 2005)

Calibrating E-values for hidden Markov models using reverse-sequence null models. - Kevin Karplus; Rachel Karchin; George Shackelford; Richard Hughey (Bioinform., 2005)

MODBASE: a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Narayanan Eswar; Fred P. Davis; Hannes Braberg; Mallur S. Madhusudhan; Andrea Rossi 005; Marc A. Martí-Renom; Rachel Karchin; Ben M. Webb; David Eramian; Min-Yi Shen; Libusha Kelly; et al. (Nucleic Acids Res., 2006)

Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. - Libusha Kelly; Rachel Karchin; Andrej Sali (Pacific Symposium on Biocomputing, 2007)

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. - Rachel Karchin; Alvaro N. A. Monteiro; Sean V. Tavtigian; Marcelo A. Carvalho; Andrej Sali (PLoS Comput. Biol., 2007)

PREDICT-2ND: a tool for generalized protein local structure prediction. - Sol Katzman; Christian Barrett; Grant Thiltgen; Rachel Karchin; Kevin Karplus (Bioinform., 2008)

Next generation tools for the annotation of human SNPs. - Rachel Karchin (Briefings Bioinform., 2009)

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. - Michael C. Ryan; Mark Diekhans; Stephanie Lien; Yun Liu 013; Rachel Karchin (Bioinform., 2009)

MODBASE, a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Narayanan Eswar; Ben M. Webb; David Eramian; Libusha Kelly; David T. Barkan; Hannah Carter; Parminder Mankoo; Rachel Karchin; Marc A. Martí-Renom; Fred P. Davis; Andrej Sali (Nucleic Acids Res., 2009)

Workshop Introduction. - Michael F. Ochs; Rachel Karchin; Habtom W. Ressom; Robert Gentleman (Pacific Symposium on Biocomputing, 2011)

Using bioinformatics to predict the functional impact of SNVs. - Melissa S. Cline; Rachel Karchin (Bioinform., 2011)

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. - Wing Chung Wong; Dewey Kim; Hannah Carter; Mark Diekhans; Michael C. Ryan; Rachel Karchin (Bioinform., 2011)

Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories. - Violeta Beleva Guthrie; Jennifer Allen; Manel Camps; Rachel Karchin (PLoS Comput. Biol., 2011)

Session Introduction. - Rachel Karchin; Michael F. Ochs; Joshua M. Stuart; Joel S. Bader (Pacific Symposium on Biocomputing, 2012)

Session Introduction. - Rachel Karchin; Michael F. Ochs; Joshua M. Stuart; Trey Ideker; Joel S. Bader (Pacific Symposium on Biocomputing, 2013)

CRAVAT: cancer-related analysis of variants toolkit. - Christopher Douville; Hannah Carter; Rick Kim; Noushin Niknafs; Mark Diekhans; Peter D. Stenson; David N. Cooper; Michael C. Ryan; Rachel Karchin (Bioinform., 2013)

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. - Yun-Ching Chen; Christopher Douville; Cheng Wang; Noushin Niknafs; Grace H. T. Yeo; Violeta Beleva Guthrie; Hannah Carter; Peter D. Stenson; David N. Cooper; Biao Li; Sean D. Mooney; Rachel Karchin (PLoS Comput. Biol., 2014)

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. - Noushin Niknafs; Violeta Beleva Guthrie; Daniel Q. Naiman; Rachel Karchin (PLoS Comput. Biol., 2015)

Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation. - Rachel Karchin; Ruth Nussinov (PLoS Comput. Biol., 2016)

Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants. - David L. Masica; Rachel Karchin (PLoS Comput. Biol., 2016)

A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts. - David L. Masica; Marco Dal Molin; Christopher L. Wolfgang; Tyler M. Tomita; Mohammad R. Ostovaneh; Amanda Blackford; Robert A. Moran; Joanna K. Law; Thomas Barkley; Michael Goggins; Marcia Irene Canto; Meredith E. Pittman; et al. (J. Am. Medical Informatics Assoc., 2017)

Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. - Lily Zheng; Noushin Niknafs; Laura D. Wood; Rachel Karchin; Robert B. Scharpf (Bioinform., 2022)

Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity. - Benjamin Alexander Albert; Yunxiao Yang; Xiaoshan M. Shao; Dipika Singh; Kellie N. Smith; Valsamo Anagnostou; Rachel Karchin (Nat. Mac. Intell., 2023)

3D genomic mapping reveals multifocality of human pancreatic precancers. - Alicia M. Braxton; Ashley L. Kiemen; Mia P. Grahn; André Forjaz; Jeeun Parksong; Jaanvi Mahesh Babu; Jiaying Lai; Lily Zheng; Noushin Niknafs; Liping Jiang; Haixia Cheng; Qianqian Song; et al. (Nat., 2024)