Rachel Karchin

Publication Activity (10 Years)

Years Active: 1998-2024
Publications (10 Years): 6

Top Topics

Maximum Parsimony

Genome Sequencing

Major Histocompatibility Complex

Top Venues

PLoS Comput. Biol.

Nat. Mac. Intell.

J. Am. Medical Informatics Assoc.

Publications

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, Rebecca Reichel, Sarah Graham, Alexander Damanakis, Catherine G. Fischer, Stephanie Mou, Cameron Metz, Julie Granger, Xiao-Ding Liu, Niklas Bachmann, Yutong Zhu, Yunzhou Liu, Cristina Almagro-Pérez, Ann Chenyu Jiang, Jeonghyun Yoo, Bridgette Kim, Scott Du, Eli Foster, Jocelyn Y. Hsu, Paula Andreu Rivera, Linda C. Chu, Fengze Liu, Elliot K. Fishman, Alan L. Yuille, Nicholas J. Roberts, Elizabeth D. Thompson, Robert B. Scharpf, Toby C. Cornish, Yuchen Jiao, Rachel Karchin, Ralph H. Hruban, Pei-Hsun Wu, Denis Wirtz, Laura D. Wood
3D genomic mapping reveals multifocality of human pancreatic precancers. Nat. 629 (8012) (2024)
Benjamin Alexander Albert, Yunxiao Yang, Xiaoshan M. Shao, Dipika Singh, Kellie N. Smith, Valsamo Anagnostou, Rachel Karchin
Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity. Nat. Mac. Intell. 5 (8) (2023)
Lily Zheng, Noushin Niknafs, Laura D. Wood, Rachel Karchin, Robert B. Scharpf
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. Bioinform. 38 (15) (2022)
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
A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts. J. Am. Medical Informatics Assoc. 24 (1) (2017)
David L. Masica, Rachel Karchin
Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants. PLoS Comput. Biol. 12 (5) (2016)
Rachel Karchin, Ruth Nussinov
Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation. PLoS Comput. Biol. 12 (8) (2016)
Noushin Niknafs, Violeta Beleva Guthrie, Daniel Q. Naiman, Rachel Karchin
SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. PLoS Comput. Biol. 11 (10) (2015)
Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace Yeo, Violeta Beleva Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean D. Mooney, Rachel Karchin
A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. PLoS Comput. Biol. 10 (9) (2014)
Christopher Douville, Hannah Carter, Rick Kim, Noushin Niknafs, Mark Diekhans, Peter D. Stenson, David N. Cooper, Michael C. Ryan, Rachel Karchin
CRAVAT: cancer-related analysis of variants toolkit. Bioinform. 29 (5) (2013)
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
Session Introduction. Pacific Symposium on Biocomputing (2013)
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader
Session Introduction. Pacific Symposium on Biocomputing (2012)
Violeta Beleva Guthrie, Jennifer Allen, Manel Camps, Rachel Karchin
Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories. PLoS Comput. Biol. 7 (9) (2011)
Michael F. Ochs, Rachel Karchin, Habtom W. Ressom, Robert Gentleman
Workshop Introduction. Pacific Symposium on Biocomputing (2011)
Melissa S. Cline, Rachel Karchin
Using bioinformatics to predict the functional impact of SNVs. Bioinform. 27 (4) (2011)
Wing Chung Wong, Dewey Kim, Hannah Carter, Mark Diekhans, Michael C. Ryan, Rachel Karchin
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinform. 27 (15) (2011)
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
MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 37 (Database-Issue) (2009)
Michael C. Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinform. 25 (11) (2009)
Rachel Karchin
Next generation tools for the annotation of human SNPs. Briefings Bioinform. 10 (1) (2009)
Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, Kevin Karplus
PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinform. 24 (21) (2008)
Rachel Karchin, Alvaro N. A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. PLoS Comput. Biol. 3 (2) (2007)
Libusha Kelly, Rachel Karchin, Andrej Sali
Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. Pacific Symposium on Biocomputing (2007)
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
MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34 (Database-Issue) (2006)
Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinform. 21 (12) (2005)
Rachel Karchin, Libusha Kelly, Andrej Sali
Improving Functional Annotation of Non-Synonomous SNPs with Information Theory. Pacific Symposium on Biocomputing (2005)
Kevin Karplus, Rachel Karchin, George Shackelford, Richard Hughey
-values for hidden Markov models using reverse-sequence null models. Bioinform. 21 (22) (2005)
Rachel Karchin, Kevin Karplus, David Haussler
Classifying G-protein coupled receptors with support vector machines. Bioinform. 18 (1) (2002)
Rachel Karchin, Richard Hughey
Weighting hidden Markov models for maximum discrimination. Bioinform. 14 (9) (1998)