Rachel Karchin

27 papers Misc 5Journal 22

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	3D genomic mapping reveals multifocality of human pancreatic precancers. Nat. 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
2023	J	`jnl`	Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity. Nat. Mac. Intell. Benjamin Alexander Albert, Yunxiao Yang, Xiaoshan M. Shao, Dipika Singh, Kellie N. Smith, Valsamo Anagnostou, Rachel Karchin
2022	J	`jnl`	Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. Bioinform. Lily Zheng, Noushin Niknafs, Laura D. Wood, Rachel Karchin, Robert B. Scharpf
2017	J	`jnl`	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. 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
2016	J	`jnl`	Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation. PLoS Comput. Biol. Rachel Karchin, Ruth Nussinov
2016	J	`jnl`	Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants. PLoS Comput. Biol. David L. Masica, Rachel Karchin
2015	J	`jnl`	SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. PLoS Comput. Biol. Noushin Niknafs, Violeta Beleva Guthrie, Daniel Q. Naiman, Rachel Karchin
2014	J	`jnl`	A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. PLoS Comput. Biol. 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
2013	J	`jnl`	CRAVAT: cancer-related analysis of variants toolkit. Bioinform. Christopher Douville, Hannah Carter, Rick Kim, Noushin Niknafs, Mark Diekhans, Peter D. Stenson, David N. Cooper, Michael C. Ryan, Rachel Karchin
2013	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
2012	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader
2011	J	`jnl`	CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinform. Wing Chung Wong, Dewey Kim, Hannah Carter, Mark Diekhans, Michael C. Ryan, Rachel Karchin
2011	J	`jnl`	Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories. PLoS Comput. Biol. Violeta Beleva Guthrie, Jennifer Allen, Manel Camps, Rachel Karchin
2011	J	`jnl`	Using bioinformatics to predict the functional impact of SNVs. Bioinform. Melissa S. Cline, Rachel Karchin
2011	Misc	`conf`	Workshop Introduction. Pacific Symposium on Biocomputing Michael F. Ochs, Rachel Karchin, Habtom W. Ressom, Robert Gentleman
2009	J	`jnl`	LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinform. Michael C. Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin
2009	J	`jnl`	MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 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
2009	J	`jnl`	Next generation tools for the annotation of human SNPs. Briefings Bioinform. Rachel Karchin
2008	J	`jnl`	PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinform. Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, Kevin Karplus
2007	J	`jnl`	Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. PLoS Comput. Biol. Rachel Karchin, Alvaro N. A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali
2007	Misc	`conf`	Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily. Pacific Symposium on Biocomputing Libusha Kelly, Rachel Karchin, Andrej Sali
2006	J	`jnl`	MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 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
2005	J	`jnl`	Calibrating Bioinform. Kevin Karplus, Rachel Karchin, George Shackelford, Richard Hughey
2005	Misc	`conf`	Improving Functional Annotation of Non-Synonomous SNPs with Information Theory. Pacific Symposium on Biocomputing Rachel Karchin, Libusha Kelly, Andrej Sali
2005	J	`jnl`	LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinform. Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali
2002	J	`jnl`	Classifying G-protein coupled receptors with support vector machines. Bioinform. Rachel Karchin, Kevin Karplus, David Haussler
1998	J	`jnl`	Weighting hidden Markov models for maximum discrimination. Bioinform. Rachel Karchin, Richard Hughey