Rachel Karchin

According to our database, Rachel Karchin authored at least 26 papers between 1998 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

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., August, 2023

2022

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

2017

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, James R. Eshleman, Syed Z. Ali, Elliot K. Fishman, Ihab R. Kamel, Siva P. Raman, Atif K. Zaheer, Nita Ahuja, Martin A. Makary, Matthew J. Weiss, Kenzo Hirose, John L. Cameron, Neda Rezaee, Jin He, Young Joon Ahn, Wenchuan Wu, Yuxuan Wang, Simeon Springer, Luis L. Diaz Jr., Nickolas Papadopoulos, Ralph H. Hruban, Kenneth W. Kinzler, Bert Vogelstein, Rachel Karchin, Anne Marie Lennon

J. Am. Medical Informatics Assoc., 2017

2016

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

David L. Masica, Rachel Karchin

PLoS Comput. Biol., 2016

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

Rachel Karchin, Ruth Nussinov

PLoS Comput. Biol., 2016

2015

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

2014

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

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

Session Introduction.

Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

2012

Session Introduction.

Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

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

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

Using bioinformatics to predict the functional impact of SNVs.

Melissa S. Cline, Rachel Karchin

Bioinform., 2011

Workshop Introduction.

Michael F. Ochs, Rachel Karchin, Habtom W. Ressom, Robert Gentleman

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2009

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

Ursula Pieper, 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

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

Michael C. Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin

Bioinform., 2009

Next generation tools for the annotation of human SNPs.

Rachel Karchin

Briefings Bioinform., 2009

2008

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

Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, Kevin Karplus

Bioinform., 2008

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

Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily.

Libusha Kelly, Rachel Karchin, Andrej Sali

Proceedings of the Biocomputing 2007, 2007

2006

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

Ursula Pieper, Narayanan Eswar, Fred P. Davis, Hannes Braberg, Mallur S. Madhusudhan, Andrea Rossi, Marc A. Martí-Renom, Rachel Karchin, Ben M. Webb, David Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, Andrej Sali

Nucleic Acids Res., 2006

2005

Calibrating <i>E</i>-values for hidden Markov models using reverse-sequence null models.

Kevin Karplus, Rachel Karchin, George Shackelford, Richard Hughey

Bioinform., 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, Narayanan Eswar, David Haussler, Andrej Sali

Bioinform., 2005

Improving Functional Annotation of Non-Synonomous SNPs with Information Theory.

Rachel Karchin, Libusha Kelly, Andrej Sali

Proceedings of the Biocomputing 2005, 2005

2002

Classifying G-protein coupled receptors with support vector machines.

Rachel Karchin, Kevin Karplus, David Haussler

Bioinform., 2002

1998

Weighting hidden Markov models for maximum discrimination.

Rachel Karchin, Richard Hughey

Bioinform., 1998