Rachel Karchin

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 29

Top Topics

Machine Learning

Squamous Cell Carcinoma

Induced Pluripotent Stem Cells

Top Venues

Nature medicine

Nature genetics

Science translational medicine

This page only lists publications with an associated author ORCID identifier.

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 I 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 Chi Hang Chu, Fengze Liu, Elliot K Fishman, Alan Yuille, Nicholas J Roberts, Elizabeth D Thompson, Robert B Scharpf, Toby C Cornish, Yucheng Jiao, Rachel Karchin, Ralph H Hruban, Pei Hsun Wu, Denis Wirtz, Laura D Wood
3D genomic mapping reveals multifocality of human pancreatic precancers. Nature 629 (8012) (2024)
Jiaying Lai, Yi Yang, Yunzhou Liu, Robert B Scharpf, Rachel Karchin
Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. Bioinformatics advances 4 (1) (2024)
Rachel Karchin, Predrag Radivojac, Anne H O'Donnell-Luria, Marc S Greenblatt, Michael Yevgeniy Tolstorukov, Dmitriy Sonkin
Improving transparency of computational tools for variant effect prediction. Nature genetics 56 (7) (2024)
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 I 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 Chi Hang Chu, Fengze Liu, Elliot K Fishman, Alan Yuille, Nicholas J Roberts, Elizabeth D Thompson, Robert B Scharpf, Toby C Cornish, Yucheng Jiao, Rachel Karchin, Ralph H Hruban, Pei Hsun Wu, Denis Wirtz, Laura D Wood
3D genomic mapping reveals multifocality of human pancreatic precancers. Nature 629 (8012) (2024)
Rachel Karchin, Predrag Radivojac, Anne H O'Donnell-Luria, Marc S Greenblatt, Michael Yevgeniy Tolstorukov, Dmitriy Sonkin
Improving transparency of computational tools for variant effect prediction. Nature genetics 56 (7) (2024)
Jiaying Lai, Yi Yang, Yunzhou Liu, Robert B Scharpf, Rachel Karchin
Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. Bioinformatics advances 4 (1) (2024)
Rachel Karchin, Predrag Radivojac, Anne H O'Donnell-Luria, Marc S Greenblatt, Michael Yevgeniy Tolstorukov, Dmitriy Sonkin
Improving transparency of computational tools for variant effect prediction. Nature genetics (2024)
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 I 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 Chi Hang Chu, Fengze Liu, Elliot K Fishman, Alan Yuille, Nicholas J Roberts, Elizabeth D Thompson, Robert B Scharpf, Toby C Cornish, Yucheng Jiao, Rachel Karchin, Ralph H Hruban, Pei Hsun Wu, Denis Wirtz, Laura D Wood
3D genomic mapping reveals multifocality of human pancreatic precancers. Nature 629 (8012) (2024)
Rachel Karchin, Predrag Radivojac, Anne H O'Donnell-Luria, Marc S Greenblatt, Michael Yevgeniy Tolstorukov, Dmitriy Sonkin
Improving transparency of computational tools for variant effect prediction. Nature genetics 56 (7) (2024)
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 I 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 Chi Hang Chu, Fengze Liu, Elliot K Fishman, Alan Yuille, Nicholas J Roberts, Elizabeth D Thompson, Robert B Scharpf, Toby C Cornish, Yucheng Jiao, Rachel Karchin, Ralph H Hruban, Pei Hsun Wu, Denis Wirtz, Laura D Wood
3D genomic mapping reveals multifocality of human pancreatic precancers. Nature (2024)
Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M Shao, Zineb Belcaid, Kristen A Marrone, Joseph C Murray, Kellie N Smit, Benjamin Levy, Josephine Feliciano, Christine L Hann, Vincent Lam, Drew M Pardoll, Rachel Karchin, Tanguy Y Seiwert, Julie R Brahmer, Patrick M Forde, Victor E Velculescu, Valsamo Anagnostou
Persistent mutation burden drives sustained anti-tumor immune responses. Nature medicine 29 (2) (2023)
Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M Shao, Zineb Belcaid, Kristen A Marrone, Joseph C Murray, Kellie N Smit, Benjamin Levy, Josephine Feliciano, Christine L Hann, Vincent Lam, Drew M Pardoll, Rachel Karchin, Tanguy Y Seiwert, Julie R Brahmer, Patrick M Forde, Victor E Velculescu, Valsamo Anagnostou
Persistent mutation burden drives sustained anti-tumor immune responses. Nature medicine (2023)
Benjamin Alexander Albert, Yunxiao Yang, Xiaoshan M Shao, Dipika Singh, Kellie N Smit, Valsamo Anagnostou, Rachel Karchin
Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity. Nature machine intelligence 5 (8) (2023)
Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M Shao, Zineb Belcaid, Kristen A Marrone, Joseph C Murray, Kellie N Smit, Benjamin Levy, Josephine Feliciano, Christine L Hann, Vincent Lam, Drew M Pardoll, Rachel Karchin, Tanguy Y Seiwert, Julie R Brahmer, Patrick M Forde, Victor E Velculescu, Valsamo Anagnostou
Persistent mutation burden drives sustained anti-tumor immune responses. Nature medicine (2023)
Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M Shao, Zineb Belcaid, Kristen A Marrone, Joseph C Murray, Kellie N Smit, Benjamin Levy, Josephine Feliciano, Christine L Hann, Vincent Lam, Drew M Pardoll, Rachel Karchin, Tanguy Y Seiwert, Julie R Brahmer, Patrick M Forde, Victor E Velculescu, Valsamo Anagnostou
Persistent mutation burden drives sustained anti-tumor immune responses. Nature medicine 29 (2) (2023)
Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M Shao, Zineb Belcaid, Kristen A Marrone, Joseph C Murray, Kellie N Smit, Benjamin Levy, Josephine Feliciano, Christine L Hann, Vincent Lam, Drew M Pardoll, Rachel Karchin, Tanguy Y Seiwert, Julie R Brahmer, Patrick M Forde, Victor E Velculescu, Valsamo Anagnostou
Persistent mutation burden drives sustained anti-tumor immune responses. Nature medicine 29 (2) (2023)
Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M Shao, Zineb Belcaid, Kristen A Marrone, Joseph C Murray, Kellie N Smit, Benjamin Levy, Josephine Feliciano, Christine L Hann, Vincent Lam, Drew M Pardoll, Rachel Karchin, Tanguy Y Seiwert, Julie R Brahmer, Patrick M Forde, Victor E Velculescu, Valsamo Anagnostou
Persistent mutation burden drives sustained anti-tumor immune responses. Nature medicine 29 (2) (2023)
Noushin Niknafs, Archana Balan, Christopher Cherry, Karlijn Hummelink, Kim Monkhorst, Xiaoshan M Shao, Zineb Belcaid, Kristen A Marrone, Joseph C Murray, Kellie N Smit, Benjamin Levy, Josephine Feliciano, Christine L Hann, Vincent Lam, Drew M Pardoll, Rachel Karchin, Tanguy Y Seiwert, Julie R Brahmer, Patrick M Forde, Victor E Velculescu, Valsamo Anagnostou
Persistent mutation burden drives sustained anti-tumor immune responses. Nature medicine 29 (2) (2023)
Xutong Gong, Rachel Karchin
Pan-Cancer HLA Gene-Mediated Tumor Immunogenicity and Immune Evasion. Molecular cancer research : MCR 20 (8) (2022)
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. Bioinformatics (Oxford, England) 38 (15) (2022)
Patrick M Forde, Valsamo Anagnostou, Zhuoxin Sun, Suzanne E Dahlberg, Hedy L Kindler, Noushin Niknafs, Thomas Purcell, Rafael Santana-Davila, Arkadiusz Z Dudek, Hossein Borghaei, Mara Lanis, Zineb Belcaid, Kellie N Smith, Archana Balan, James R White, Christopher Cherry, I K Ashok Sivakumar, Xiaoshan M Shao, Hok Yee Chan, Dipika Singh, Sampriti Thapa, Peter B Illei, Drew M Pardoll, Rachel Karchin, Victor E Velculescu, Julie R Brahmer, Suresh R Ramalingam
Durvalumab with platinum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial. Nature medicine 27 (11) (2021)
Valsamo Anagnostou, Noushin Niknafs, Kristen Marrone, Daniel C Bruhm, James R White, Jarushka Naidoo, Karlijn Hummelink, Kim Monkhorst, Ferry Lalezari, Mara Lanis, Samuel Rosner, Joshua E Reuss, Kellie N Smith, Vilmos Adleff, Kristen Rodgers, Zineb Belcaid, Lamia Rhymee, Benjamin Levy, Josephine Feliciano, Christine L Hann, David S Ettinger, Christos Georgiades, Franco Verde, Peter Illei, Qing Kay Li, Alexander S Baras, Edward Gabrielson, Malcolm V Brock, Rachel Karchin, Drew M Pardoll, Stephen B Baylin, Julie R Brahmer, Robert B Scharpf, Patrick M Forde, Victor E Velculescu
Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer. Nature cancer 1 (1) (2020)
Michaël Noë, Noushin Niknafs, Catherine G Fischer, Wenzel M Hackeng, Violeta Beleva Guthrie, Waki Hosoda, Marija Debeljak, Eniko Papp, Vilmos Adleff, James R White, Claudio Luchini, Antonio Pea, Aldo Scarpa, Giovanni Butturini, Giuseppe Zamboni, Paola Castelli, Seung-Mo Hong, Hirotsugu Shiroma, Nobuyoshi Hiraoka, Anthony J Gill, Jaswinder S Samra, G Johan A Offerhaus, Anne Hoorens, Joanne Verheij, Casper Jansen, N Volkan Adsay, Wei Jiang, Jordan Winter, Jorge Albores-Saavedra, Benoit Terris, Elizabeth D Thompson, Nicholas J Roberts, Ralph H Hruban, Rachel Karchin, Robert B Scharpf, Lodewijk A A Brosens, Victor E Velculescu, Laura D Wood
Genomic characterization of malignant progression in neoplastic pancreatic cysts. Nature communications 11 (1) (2020)
Simeon U Springer, David L Masica, Marco Dal Molin, Christopher B Douville, Christopher J Thoburn, Bahman Afsari, Lu Li, Joshua David Cohen, Elizabeth D Thompson, Peter J Allen, David S Klimstra, Mark A Schattner, C Max Schmidt, Michele T Yip-Schneider, Rachel E Simpson, Carlos Fernandez-Del Castillo, Mari A Mino-Kenudson, William Brugge, Randall E Brand, Aatur D Singhi, Aldo Scarpa, Rita Teresa Lawlor, Roberto Salvia, Giuseppe Zamboni, Seung-Mo Hong, Dae-Wook Hwang, Jin-Young Jang, Wooil Kwon, Niall Swan, Justin Geoghegan, Massimo Falconi, Stefano Crippa, Claudio Doglioni, Jorge Paulino, Richard D Schulick, Barish H Edil, Walter Park, Shinichi Yachida, Susumu Hijioka, Jeanin van Hooft, Jin He, Matthew J Weiss, Richard Burkhart, Martin Makary, Marcia I Canto, Michael G Goggins, Janine Ptak, Lisa Dobbyn, Joy Schaefer, Natalie Sillman, Maria Popoli, Alison P Klein, Cristian Tomasetti, Rachel Karchin, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Christopher L Wolfgang, Ralph H Hruban, Anne Marie Lennon
A multimodality test to guide the management of patients with a pancreatic cyst. Science translational medicine 11 (501) (2020)
Derrick E Wood, James R White, Andrew Georgiadis, Beth Van Emburgh, Sonya Parpart-Li, Jason Mitchell, Valsamo Anagnostou, Noushin Niknafs, Rachel Karchin, Eniko Papp, Christine McCord, Peter LoVerso, David Riley, Luis A Diaz, Siân Jones, Mark Sausen, Victor E Velculescu, Samuel V Angiuoli
A machine learning approach for somatic mutation discovery. Science translational medicine 10 (457) (2019)
Yuxuan Wang, Lu Li, Christopher B Douville, Joshua David Cohen, Ting-Tai Yen, Isaac Kinde, Karin Sundfelt, Susanne K Kjaer, Ralph H Hruban, Ie-Ming Shih, Tian-Li Wang, Robert J Kurman, Simeon Springer, Janine Ptak, Maria Popoli, Joy Schaefer, Natalie Sillman, Lisa Dobbyn, Edward J Tanner, Ana Angarita, Maria Lycke, Kirsten Marie Jochumsen, Bahman Afsari, Ludmila V Danilova, Douglas A Levine, Kris Jardon, Xing Zeng, Jocelyne Arseneau, Lili Fu, Luis A Diaz, Rachel Karchin, Cristian Tomasetti, Kenneth W Kinzler, Bert Vogelstein, Amanda N Fader, Lucy Gilbert, Nickolas Papadopoulos
Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers. Science translational medicine 10 (433) (2019)
Noushin Niknafs, Yi Zhong, John Alec Moral, Lance Zhang, Melody Xiaoshan Shao, April Lo, Alvin Makohon-Moore, Christine A Iacobuzio-Donahue, Rachel Karchin
Characterization of genetic subclonal evolution in pancreatic cancer mouse models. Nature communications 10 (1) (2019)
Laura Kasak, Constantina Bakolitsa, Zhiqiang Hu, Changhua Yu, Jasper Rine, Dago F Dimster-Denk, Gaurav Pandey, Greet De Baets, Yana Bromberg, Chen Cao, Emidio Capriotti, Rita Casadio, Joost Van Durme, Manuel Giollo, Rachel Karchin, Panagiostis Katsonis, Emanuela Leonardi, Olivier Lichtarge, Pier Luigi Martelli, David Masica, Sean D Mooney, Ayodeji Olatubosun, Predrag Radivojac, Frederic Rousseau, Lipika R Pal, Castrense Savojardo, Joost Schymkowitz, Janita Thusberg, Silvio C E Tosatto, Mauno Vihinen, Jouni Väliaho, Susanna Repo, John Moult, Steven E Brenner, Iddo Friedberg
Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Human mutation 40 (9) (2019)
Johannes G Reiter, Alvin P Makohon-Moore, Jeffrey M Gerold, Alexander Heyde, Marc A Attiyeh, Zachary A Kohutek, Collin J Tokheim, Alexia Brown, Rayne M DeBlasio, Juliana Niyazov, Amanda Zucker, Rachel Karchin, Kenneth W Kinzler, Christine A Iacobuzio-Donahue, Bert Vogelstein, Martin A Nowak
Minimal functional driver gene heterogeneity among untreated metastases. Science (New York, N.Y.) 361 (6406) (2018)