Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

by James M. McFarland, Brenton R. Paolella, Allison Warren, Kathryn Geiger-Schuller, Tsukasa Shibue, Michael Rothberg, Olena Kuksenko, William N. Colgan, Andrew Jones, Emily Chambers, Danielle Dionne, Samantha Bender, Brian M. Wolpin, Mahmoud Ghandi, Itay Tirosh, Orit Rozenblatt-Rosen, Jennifer A. Roth, Todd R. Golub, Aviv Regev, Andrew J. Aguirre, Francisca Vazquez, Aviad Tsherniak
Published 2020-08-01

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

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

by John P. Ray, Carl G. de Boer, Charles P. Fulco, Caleb A. Lareau, Masahiro Kanai, Jacob C. Ulirsch, Ryan Tewhey, Leif S. Ludwig, Steven K. Reilly, Drew T. Bergman, Jesse M. Engreitz, Robbyn Issner, Hilary K. Finucane, Eric S. Lander, Aviv Regev, Nir Hacohen
Published 2020-03-01

Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase

by Colin W. Garvie, Xiaoyun Wu, Malvina Papanastasiou, Sooncheol Lee, James Fuller, Gavin R. Schnitzler, Steven W. Horner, Andrew Baker, Terry Zhang, James P. Mullahoo, Lindsay Westlake, Stephanie H. Hoyt, Marcus Toetzl, Matthew J. Ranaghan, Luc de Waal, Joseph McGaunn, Bethany Kaplan, Federica Piccioni, Xiaoping Yang, Martin Lange, Adrian Tersteegen, Donald Raymond, Timothy A. Lewis, Steven A. Carr, Andrew D. Cherniack, Christopher T. Lemke, Matthew Meyerson, Heidi Greulich
Published 2021-07-01

Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation

by Ayshwarya Subramanian, Eriene-Heidi Sidhom, Maheswarareddy Emani, Katherine Vernon, Nareh Sahakian, Yiming Zhou, Maria Kost-Alimova, Michal Slyper, Julia Waldman, Danielle Dionne, Lan T. Nguyen, Astrid Weins, Jamie L. Marshall, Orit Rosenblatt-Rosen, Aviv Regev, Anna Greka
Published 2019-11-01

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

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

Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds

by Deborah O. Dele-Oni, Karen E. Christianson, Shawn B. Egri, Alvaro Sebastian Vaca Jacome, Katherine C. DeRuff, James Mullahoo, Vagisha Sharma, Desiree Davison, Tak Ko, Michael Bula, Joel Blanchard, Jennie Z. Young, Lev Litichevskiy, Xiaodong Lu, Daniel Lam, Jacob K. Asiedu, Caidin Toder, Adam Officer, Ryan Peckner, Michael J. MacCoss, Li-Huei Tsai, Steven A. Carr, Malvina Papanastasiou, Jacob D. Jaffe
Published 2021-08-01

Rapid and deep-scale ubiquitylation profiling for biology and translational research

by Namrata D. Udeshi, Deepak C. Mani, Shankha Satpathy, Shaunt Fereshetian, Jessica A. Gasser, Tanya Svinkina, Meagan E. Olive, Benjamin L. Ebert, Philipp Mertins, Steven A. Carr
Published 2020-01-01

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

by Himel Mallick, Eric A. Franzosa, Lauren J. Mclver, Soumya Banerjee, Alexandra Sirota-Madi, Aleksandar D. Kostic, Clary B. Clish, Hera Vlamakis, Ramnik J. Xavier, Curtis Huttenhower
Published 2019-07-01

Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants

by Lisa Brenan, Aleksandr Andreev, Ofir Cohen, Sasha Pantel, Atanas Kamburov, Davide Cacchiarelli, Nicole S. Persky, Cong Zhu, Mukta Bagul, Eva M. Goetz, Alex B. Burgin, Levi A. Garraway, Gad Getz, Tarjei S. Mikkelsen, Federica Piccioni, David E. Root, Cory M. Johannessen
Published 2016-10-01

Author Correction: Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

by Jellert T. Gaublomme, Bo Li, Cristin McCabe, Abigail Knecht, Yiming Yang, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Dionne, Lan Nguyen, Philip L. De Jager, Bertrand Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt-Rosen, Aviv Regev
Published 2020-11-01

Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data

by Greta Pintacuda, Frederik H. Lassen, Yu-Han H. Hsu, April Kim, Jacqueline M. Martín, Edyta Malolepsza, Justin K. Lim, Nadine Fornelos, Kevin C. Eggan, Kasper Lage
Published 2021-05-01

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

by Jellert T. Gaublomme, Bo Li, Cristin McCabe, Abigail Knecht, Yiming Yang, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Dionne, Lan Nguyen, Philip L. De Jager, Bertrand Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt-Rosen, Aviv Regev
Published 2019-07-01

Regulation of purine metabolism connects KCTD13 to a metabolic disorder with autistic features

by Jon M. Madison, Karen Duong, Ellen F. Vieux, Namrata D. Udeshi, Sumaiya Iqbal, Elise Requadt, Shaunt Fereshetian, Michael C. Lewis, Antonio S. Gomes, Kerry A. Pierce, Randall J. Platt, Feng Zhang, Arthur J. Campbell, Dennis Lal, Florence F. Wagner, Clary B. Clish, Steven A. Carr, Morgan Sheng, Edward M. Scolnick, Jeffrey R. Cottrell
Published 2021-01-01

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

ClusterMap for multi-scale clustering analysis of spatial gene expression

by Yichun He, Xin Tang, Jiahao Huang, Jingyi Ren, Haowen Zhou, Kevin Chen, Albert Liu, Hailing Shi, Zuwan Lin, Qiang Li, Abhishek Aditham, Johain Ounadjela, Emanuelle I. Grody, Jian Shu, Jia Liu, Xiao Wang
Published 2021-10-01

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

Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma

by Pratiti Bandopadhayay, Federica Piccioni, Ryan O’Rourke, Patricia Ho, Elizabeth M. Gonzalez, Graham Buchan, Kenin Qian, Gabrielle Gionet, Emily Girard, Margo Coxon, Matthew G. Rees, Lisa Brenan, Frank Dubois, Ofer Shapira, Noah F. Greenwald, Melanie Pages, Amanda Balboni Iniguez, Brenton R. Paolella, Alice Meng, Claire Sinai, Giovanni Roti, Neekesh V. Dharia, Amanda Creech, Benjamin Tanenbaum, Prasidda Khadka, Adam Tracy, Hong L. Tiv, Andrew L. Hong, Shannon Coy, Rumana Rashid, Jia-Ren Lin, Glenn S. Cowley, Fred C. Lam, Amy Goodale, Yenarae Lee, Kathleen Schoolcraft, Francisca Vazquez, William C. Hahn, Aviad Tsherniak, James E. Bradner, Michael B. Yaffe, Till Milde, Stefan M. Pfister, Jun Qi, Monica Schenone, Steven A. Carr, Keith L. Ligon, Mark W. Kieran, Sandro Santagata, James M. Olson, Prafulla C. Gokhale, Jacob D. Jaffe, David E. Root, Kimberly Stegmaier, Cory M. Johannessen, Rameen Beroukhim
Published 2019-06-01

High-throughput automated microfluidic sample preparation for accurate microbial genomics

by Soohong Kim, Joachim De Jonghe, Anthony B. Kulesa, David Feldman, Tommi Vatanen, Roby P. Bhattacharyya, Brittany Berdy, James Gomez, Jill Nolan, Slava Epstein, Paul C. Blainey
Published 2017-01-01