James M McFarland (James McFarland)

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 22

Top Topics

Multiple Myeloma

Childhood Cancer

Top Venues

Nature communications

Cancer discovery

Nature genetics

The Journal of neuroscience : the official journal of the Society for Neuroscience

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

Publications

Sean A Misek, Aaron Fultineer, Jérémie Kalfon, Javad Noorbakhsh, Isabella Boyle, Priyanka Roy, Joshua M 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
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries. Nature communications 15 (1) (2024)
Sean A Misek, Aaron Fultineer, Jérémie Kalfon, Javad Noorbakhsh, Isabella Boyle, Priyanka Roy, Joshua M 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
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries. Nature communications 15 (1) (2024)
Sean A Misek, Aaron Fultineer, Jérémie Kalfon, Javad Noorbakhsh, Isabella Boyle, Priyanka Roy, Joshua M 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
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries. Nature communications 15 (1) (2024)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas. Cancer discovery 13 (3) (2023)
Ricardo de Matos Simoes, Ryosuke Shirasaki, Sondra L Downey-Kopyscinski, Geoffrey M Matthews, Benjamin G Barwick, Vilas A Gupta, Daphné Dupéré-Richer, Shizuka Yamano, Yiguo Hu, Michal Sheffer, Eugen Dhimolea, Olga Dashevsky, Sara Gandolfi, Kazuya Ishiguro, Robin M Meyers, Jordan G Bryan, Neekesh V Dharia, Paul J Hengeveld, Johanna B Brüggenthies, Huihui Tang, Andrew J Aguirre, Quinlan L Sievers, Benjamin L Ebert, Brian J Glassner, Christopher J Ott, James E Bradner, Nicholas P Kwiatkowski, Daniel Auclair, Joan Levy, Jonathan J Keats, Richard W J Groen, Nathanael S Gray, Aedin C Culhane, James M McFarland, Joshua M Dempster, Jonathan D Licht, Lawrence H Boise, William C Hahn, Francisca Vazquez, Aviad Tsherniak, Constantine S Mitsiades
Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias. Nature cancer 4 (5) (2023)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas. Cancer discovery 13 (3) (2023)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas. Cancer discovery 13 (3) (2023)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A ubiquitination cascade regulating the integrated stress response and survival in carcinomas. Cancer discovery (2022)
Lucia Trastulla, Javad Noorbakhsh, Francisca Vazquez, James M McFarland, Francesco Iorio
Computational estimation of quality and clinical relevance of cancer cell lines. Molecular systems biology 18 (7) (2022)
Jessica W Tsai, Paloma Cejas, Dayle K Wang, Smruti K Patel, David W Wu, Phonepasong Arounleut, Xin Wei, Ningxuan Zhou, Sudeepa Syamala, Frank P B Dubios, Alexander Crane, Kristine Pelton, Jayne Vogelzang, Cecilia Sousa, Audrey Baguette, Xiaolong Chen, Alexandra-Larisa Condurat, Sarah E Dixon-Clarke, Kevin Ning Zhou, Sophie D Lu, Elizabeth M Gonzalez, Madison S Chacon, Jeromy J Digiacomo, Rushil Kumbhani, Dana R Novikov, J'Ya Hunter, Maria Tsoli, David S Ziegler, Uta Dirksen, Natalie Jager, Gnana Prakash Balasubramanian, Christof Maria Kramm, Michaela Nathrath, Stefan S Bielack, Suzanne J Baker, Jinghui Zhang, James M McFarland, Gad A Getz, François Aguet, Nada Jabado, Olaf Witt, Stefan M Pfister, Keith L Ligon, Volker Hovestadt, Claudia L Kleinman, Henry W Long, David T W Jones, Pratiti Bandopadhayay, Timothy N Phoenix
FOXR2 Is an Epigenetically Regulated Pan-Cancer Oncogene That Activates ETS Transcriptional Circuits. Cancer research 82 (17) (2022)
Daniel P Bondeson, Brenton R Paolella, Adhana Asfaw, Michael V Rothberg, Thomas A Skipper, Carly Langan, Gabriel Mesa, Alfredo Gonzalez, Lauren E Surface, Kentaro Ito, Mariya Kazachkova, William N Colgan, Allison Warren, Joshua M Dempster, John Michael Krill-Burger, Maria Ericsson, Andrew A Tang, Iris Fung, Emily S Chambers, Mai Abdusamad, Nancy Dumont, John G Doench, Federica Piccioni, David E Root, Jesse S Boehm, William C Hahn, Michael Mannstadt, James M McFarland, Francisca Vazquez, Todd R Golub
Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer. Nature cancer 3 (6) (2022)
Riaz Gillani, Bo Kyung Alex Seong, Jett Crowdis, Jake R Conway, Neekesh V Dharia, Saif Alimohamed, Brian J Haas, Kyuho Han, Jihye Park, Felix Dietlein, Meng Xiao He, Alma Imamovic, Clement Ma, Michael C Bassik, Jesse S Boehm, Francisca Vazquez, Alexander Gusev, David R Liu, Katherine A Janeway, James M McFarland, Kimberly Stegmaier, Eliezer M Van Allen
Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. Cancer research 81 (15) (2021)
Yael Cohen-Sharir, James M McFarland, Mai Abdusamad, Carolyn Marquis, Sara V Bernhard, Mariya Kazachkova, Helen Tang, Marica R Ippolito, Kathrin Laue, Johanna Zerbib, Heidi L H Malaby, Andrew Jones, Lisa-Marie Stautmeister, Irena Bockaj, René Wardenaar, Nicholas Lyons, Ankur K Nagaraja, Adam J Bass, Diana Carolina Johanna Spierings, Floris Foijer, Rameen Beroukhim, Stefano Santaguida, Todd R Golub, Jason Stumpff, Zuzana Storchová, Uri Ben-David
Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature 590 (7846) (2021)
Allison Warren, Yejia Chen, Andrew Jones, Tsukasa Shibue, William C Hahn, Jesse S Boehm, Francisca Vazquez, Aviad Tsherniak, James M McFarland
Global computational alignment of tumor and cell line transcriptional profiles. Nature communications 12 (1) (2021)
Javad Noorbakhsh, Francisca Vazquez, James M McFarland
Bridging the gap between cancer cell line models and tumours using gene expression data. British journal of cancer 125 (3) (2021)
Zhong Wu, Jin Zhou, Xiaoyang Zhang, Zhouwei Zhang, Yingtian Xie, Jie Bin Liu, Zandra V Ho, Arpit Panda, Xintao Qiu, Paloma Cejas, Israel Cañadas, Fahire Goknur Akarca, James M McFarland, Ankur K Nagaraja, Louisa B Goss, Nikolas Kesten, Longlong Si, Klothilda Lim, Yanli Liu, Yanxi Zhang, Ji Yeon Baek, Yang Liu, Deepa T Patil, Jonathan P Katz, Josephine Hai, Chunyang Bao, Matthew Stachler, Jun Qi, Jeffrey J Ishizuka, Hiroshi Nakagawa, Anil K Rustgi, Kwok-Kin Wong, Matthew Meyerson, David A Barbie, Myles Brown, Henry W Long, Adam J Bass
Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence. Nature genetics 53 (6) (2021)
Clare Pacini, Joshua M Dempster, Isabella Boyle, Emanuel Gonçalves, Hanna Najgebauer, Emre Karakoc, Dieudonne van der Meer, Andrew Barthorpe, Howard Lightfoot, Patricia Jaaks, James M McFarland, Mathew J Garnett, Aviad Tsherniak, Francesco Iorio
Integrated cross-study datasets of genetic dependencies in cancer. Nature communications 12 (1) (2021)
Neekesh V Dharia, Guillaume Kugener, Lillian M Guenther, Clare F Malone, Adam D Durbin, Andrew L Hong, Thomas P Howard, Pratiti Bandopadhayay, Caroline S Wechsler, Iris Fung, Allison C Warren, Joshua M Dempster, John Michael Krill-Burger, Brenton R Paolella, Phoebe Moh, Nishant Jha, Andrew Tang, Phillip G Montgomery, Jesse S Boehm, William C Hahn, Charles W M Roberts, James M McFarland, Aviad Tsherniak, Todd R Golub, Francisca Vazquez, Kimberly Stegmaier
A first-generation pediatric cancer dependency map. Nature genetics 53 (4) (2021)
Gabriela S Kinker, Alissa C Greenwald, Rotem Tal, Zhanna Orlova, Michael S Cuoco, James M McFarland, Allison Warren, Christopher Rodman, Jennifer A Roth, Samantha A Bender, Bhavna Kumar, James W Rocco, Pedro A C M Fernandes, Christopher C Mader, Hadas Keren-Shaul, Alexander Plotnikov, Haim Barr, Aviad Tsherniak, Orit Rozenblatt-Rosen, Valery Krizhanovsky, Sidharth V Puram, Aviv Regev, Michael Mints
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity. Nature genetics 52 (11) (2020)
James M McFarland, Brenton R Paolella, Allison Warren, Kathryn R 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
Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action. Nature communications 11 (1) (2020)
James M McFarland, Bruce G Cumming, Daniel A Butts
Variability and Correlations in Primary Visual Cortical Neurons Driven by Fixational Eye Movements. The Journal of neuroscience : the official journal of the Society for Neuroscience 36 (23) (2017)
Yuwei Cui, Liu D Liu, James M McFarland, Christopher C Pack, Daniel A Butts
Inferring Cortical Variability from Local Field Potentials. The Journal of neuroscience : the official journal of the Society for Neuroscience 36 (14) (2016)
James M McFarland, Adrian G Bondy, Richard C Saunders, Bruce G Cumming, Daniel A Butts
Saccadic modulation of stimulus processing in primary visual cortex. Nature communications 6 (2015)