The Cancer Dependency Map enables drug mechanism‐of‐action investigations

by Francisca Vazquez, Jesse S Boehm
Published 2020-07-01

Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects

by Joshua M. Dempster, Isabella Boyle, Francisca Vazquez, David E. Root, Jesse S. Boehm, William C. Hahn, Aviad Tsherniak, James M. McFarland
Published 2021-12-01

Global computational alignment of tumor and cell line transcriptional profiles

by Allison Warren, Yejia Chen, Andrew Jones, Tsukasa Shibue, William C. Hahn, Jesse S. Boehm, Francisca Vazquez, Aviad Tsherniak, James M. McFarland
Published 2021-01-01

Systematic morphological profiling of human gene and allele function via Cell Painting

by Mohammad Hossein Rohban, Shantanu Singh, Xiaoyun Wu, Julia B Berthet, Mark-Anthony Bray, Yashaswi Shrestha, Xaralabos Varelas, Jesse S Boehm, Anne E Carpenter
Published 2017-03-01

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects.

by Shantanu Singh, Xiaoyun Wu, Vebjorn Ljosa, Mark-Anthony Bray, Federica Piccioni, David E Root, John G Doench, Jesse S Boehm, Anne E Carpenter
Published 2015-01-01

Weekly SARS-CoV-2 screening of asymptomatic kindergarten to grade 12 students and staff helps inform strategies for safer in-person learning

by Shira Doron, Robin R. Ingalls, Anne Beauchamp, Jesse S. Boehm, Helen W. Boucher, Linda H. Chow, Linda Corridan, Katey Goehringer, Doug Golenbock, Liz Larsen, David Lussier, Marcia Testa, Andrea Ciaranello
Published 2021-11-01

Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal

by J. Michael Krill-Burger, Joshua M. Dempster, Ashir A. Borah, Brenton R. Paolella, David E. Root, Todd R. Golub, Jesse S. Boehm, William C. Hahn, James M. McFarland, Francisca Vazquez, Aviad Tsherniak
Published 2023-08-01

CK1epsilon is required for breast cancers dependent on beta-catenin activity.

by So Young Kim, Ian F Dunn, Ron Firestein, Piyush Gupta, Leslie Wardwell, Kara Repich, Anna C Schinzel, Ben Wittner, Serena J Silver, David E Root, Jesse S Boehm, Sridhar Ramaswamy, Eric S Lander, William C Hahn
Published 2010-02-01

Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries

by Sean A. Misek, Aaron Fultineer, Jeremie Kalfon, Javad Noorbakhsh, Isabella Boyle, Priyanka Roy, Joshua Dempster, Lia Petronio, Katherine Huang, Alham Saadat, Thomas Green, Adam Brown, John G. Doench, David E. Root, James M. McFarland, Rameen Beroukhim, Jesse S. Boehm
Published 2024-06-01

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

by James M. McFarland, Zandra V. Ho, Guillaume Kugener, Joshua M. Dempster, Phillip G. Montgomery, Jordan G. Bryan, John M. Krill-Burger, Thomas M. Green, Francisca Vazquez, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Aviad Tsherniak
Published 2018-11-01

PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment

by Yashaswi Shrestha, Michael Quigley, Travis Hughes, Robert T Manguso, Natalie B Collins, Rose Al Abosy, Brian C Miller, Kevin Bi, Qihong Zhao, Jeffrey J Ishizuka, Kathleen B Yates, Hans W Pope, Marc Wadsworth, Alex K Shalek, Jesse S Boehm, William C Hahn, John G Doench, W Nicholas Haining
Published 2022-03-01

Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development.

by Krinio Giannikou, Izabela A Malinowska, Trevor J Pugh, Rachel Yan, Yuen-Yi Tseng, Coyin Oh, Jaegil Kim, Magdalena E Tyburczy, Yvonne Chekaluk, Yang Liu, Nicola Alesi, Geraldine A Finlay, Chin-Lee Wu, Sabina Signoretti, Matthew Meyerson, Gad Getz, Jesse S Boehm, Elizabeth P Henske, David J Kwiatkowski
Published 2016-08-01

A GPX4-dependent cancer cell state underlies the clear-cell morphology and confers sensitivity to ferroptosis

by Yilong Zou, Michael J. Palte, Amy A. Deik, Haoxin Li, John K. Eaton, Wenyu Wang, Yuen-Yi Tseng, Rebecca Deasy, Maria Kost-Alimova, Vlado Dančík, Elizaveta S. Leshchiner, Vasanthi S. Viswanathan, Sabina Signoretti, Toni K. Choueiri, Jesse S. Boehm, Bridget K. Wagner, John G. Doench, Clary B. Clish, Paul A. Clemons, Stuart L. Schreiber
Published 2019-04-01

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

by Joshua M. Dempster, Clare Pacini, Sasha Pantel, Fiona M. Behan, Thomas Green, John Krill-Burger, Charlotte M. Beaver, Scott T. Younger, Victor Zhivich, Hanna Najgebauer, Felicity Allen, Emanuel Gonçalves, Rebecca Shepherd, John G. Doench, Kosuke Yusa, Francisca Vazquez, Leopold Parts, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Mathew J. Garnett, Aviad Tsherniak, Francesco Iorio
Published 2019-12-01

Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q

by Jasper E. Neggers, Brenton R. Paolella, Adhana Asfaw, Michael V. Rothberg, Thomas A. Skipper, Annan Yang, Radha L. Kalekar, John M. Krill-Burger, Neekesh V. Dharia, Guillaume Kugener, Jérémie Kalfon, Chen Yuan, Nancy Dumont, Alfredo Gonzalez, Mai Abdusamad, Yvonne Y. Li, Liam F. Spurr, Westley W. Wu, Adam D. Durbin, Brian M. Wolpin, Federica Piccioni, David E. Root, Jesse S. Boehm, Andrew D. Cherniack, Aviad Tsherniak, Andrew L. Hong, William C. Hahn, Kimberly Stegmaier, Todd R. Golub, Francisca Vazquez, Andrew J. Aguirre
Published 2020-12-01

Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q

by Jasper E. Neggers, Brenton R. Paolella, Adhana Asfaw, Michael V. Rothberg, Thomas A. Skipper, Annan Yang, Radha L. Kalekar, John M. Krill-Burger, Neekesh V. Dharia, Guillaume Kugener, Jérémie Kalfon, Chen Yuan, Nancy Dumont, Alfredo Gonzalez, Mai Abdusamad, Yvonne Y. Li, Liam F. Spurr, Westley W. Wu, Adam D. Durbin, Brian M. Wolpin, Federica Piccioni, David E. Root, Jesse S. Boehm, Andrew D. Cherniack, Aviad Tsherniak, Andrew L. Hong, William C. Hahn, Kimberly Stegmaier, Todd R. Golub, Francisca Vazquez, Andrew J. Aguirre
Published 2021-07-01

Integrated genetic and pharmacologic interrogation of rare cancers

by Andrew L. Hong, Yuen-Yi Tseng, Glenn S. Cowley, Oliver Jonas, Jaime H. Cheah, Bryan D. Kynnap, Mihir B. Doshi, Coyin Oh, Stephanie C. Meyer, Alanna J. Church, Shubhroz Gill, Craig M. Bielski, Paula Keskula, Alma Imamovic, Sara Howell, Gregory V. Kryukov, Paul A. Clemons, Aviad Tsherniak, Francisca Vazquez, Brian D. Crompton, Alykhan F. Shamji, Carlos Rodriguez-Galindo, Katherine A. Janeway, Charles W. M. Roberts, Kimberly Stegmaier, Paul van Hummelen, Michael J. Cima, Robert S. Langer, Levi A. Garraway, Stuart L. Schreiber, David E. Root, William C. Hahn, Jesse S. Boehm
Published 2016-06-01

Targeting TRIP13 in favorable histology Wilms tumor with nuclear export inhibitors synergizes with doxorubicin

by Karuna Mittal, Garrett W. Cooper, Benjamin P. Lee, Yongdong Su, Katie T. Skinner, Jenny Shim, Hunter C. Jonus, Won Jun Kim, Mihir Doshi, Diego Almanza, Bryan D. Kynnap, Amanda L. Christie, Xiaoping Yang, Glenn S. Cowley, Brittaney A. Leeper, Christopher L. Morton, Bhakti Dwivedi, Taylor Lawrence, Manali Rupji, Paula Keskula, Stephanie Meyer, Catherine M. Clinton, Manoj Bhasin, Brian D. Crompton, Yuen-Yi Tseng, Jesse S. Boehm, Keith L. Ligon, David E. Root, Andrew J. Murphy, David M. Weinstock, Prafulla C. Gokhale, Jennifer M. Spangle, Miguel N. Rivera, Elizabeth A. Mullen, Kimberly Stegmaier, Kelly C. Goldsmith, William C. Hahn, Andrew L. Hong
Published 2024-04-01

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition

by Andrew L Hong, Yuen-Yi Tseng, Jeremiah A Wala, Won-Jun Kim, Bryan D Kynnap, Mihir B Doshi, Guillaume Kugener, Gabriel J Sandoval, Thomas P Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine M Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine M Clinton, Alanna J Church, Brian D Crompton, Katherine A Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A Clemons, Stuart L Schreiber, David E Root, Prafulla C Gokhale, Susan N Chi, Elizabeth A Mullen, Charles WM Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L Ligon, Jesse S Boehm, William C Hahn
Published 2019-03-01

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

by Viktor A. Adalsteinsson, Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Gregory Gydush, Sarah C. Reed, Denisse Rotem, Justin Rhoades, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignaty Leshchiner, Jaegil Kim, Chip Stewart, Mara Rosenberg, Joshua M. Francis, Cheng-Zhong Zhang, Ofir Cohen, Coyin Oh, Huiming Ding, Paz Polak, Max Lloyd, Sairah Mahmud, Karla Helvie, Margaret S. Merrill, Rebecca A. Santiago, Edward P. O’Connor, Seong H. Jeong, Rachel Leeson, Rachel M. Barry, Joseph F. Kramkowski, Zhenwei Zhang, Laura Polacek, Jens G. Lohr, Molly Schleicher, Emily Lipscomb, Andrea Saltzman, Nelly M. Oliver, Lori Marini, Adrienne G. Waks, Lauren C. Harshman, Sara M. Tolaney, Eliezer M. Van Allen, Eric P. Winer, Nancy U. Lin, Mari Nakabayashi, Mary-Ellen Taplin, Cory M. Johannessen, Levi A. Garraway, Todd R. Golub, Jesse S. Boehm, Nikhil Wagle, Gad Getz, J. Christopher Love, Matthew Meyerson
Published 2017-11-01