Inferring nonlinear neuronal computation based on physiologically plausible inputs
McFarland, James M, Cui, Yuwei, Butts, Daniel A
Published in PLoS computational biology (01.07.2013)
Published in PLoS computational biology (01.07.2013)
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Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects
Dempster, Joshua M, Boyle, Isabella, Vazquez, Francisca, Root, David E, Boehm, Jesse S, Hahn, William C, Tsherniak, Aviad, McFarland, James M
Published in Genome Biology (20.12.2021)
Published in Genome Biology (20.12.2021)
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Bridging the gap between cancer cell line models and tumours using gene expression data
Noorbakhsh, Javad, Vazquez, Francisca, McFarland, James M.
Published in British journal of cancer (03.08.2021)
Published in British journal of cancer (03.08.2021)
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Patient-derived xenografts undergo mouse-specific tumor evolution
Ben-David, Uri, Ha, Gavin, Tseng, Yuen-Yi, Greenwald, Noah F, Oh, Coyin, Shih, Juliann, McFarland, James M, Wong, Bang, Boehm, Jesse S, Beroukhim, Rameen, Golub, Todd R
Published in Nature genetics (01.11.2017)
Published in Nature genetics (01.11.2017)
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Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells
Meyers, Robin M, Bryan, Jordan G, McFarland, James M, Weir, Barbara A, Sizemore, Ann E, Xu, Han, Dharia, Neekesh V, Montgomery, Phillip G, Cowley, Glenn S, Pantel, Sasha, Goodale, Amy, Lee, Yenarae, Ali, Levi D, Jiang, Guozhi, Lubonja, Rakela, Harrington, William F, Strickland, Matthew, Wu, Ting, Hawes, Derek C, Zhivich, Victor A, Wyatt, Meghan R, Kalani, Zohra, Chang, Jaime J, Okamoto, Michael, Stegmaier, Kimberly, Golub, Todd R, Boehm, Jesse S, Vazquez, Francisca, Root, David E, Hahn, William C, Tsherniak, Aviad
Published in Nature genetics (01.12.2017)
Published in Nature genetics (01.12.2017)
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Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration
McFarland, James M., Ho, Zandra V., Kugener, Guillaume, Dempster, Joshua M., Montgomery, Phillip G., Bryan, Jordan G., Krill-Burger, John M., Green, Thomas M., Vazquez, Francisca, Boehm, Jesse S., Golub, Todd R., Hahn, William C., Root, David E., Tsherniak, Aviad
Published in Nature communications (02.11.2018)
Published in Nature communications (02.11.2018)
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Integrated cross-study datasets of genetic dependencies in cancer
Pacini, Clare, Dempster, Joshua M., Boyle, Isabella, Gonçalves, Emanuel, Najgebauer, Hanna, Karakoc, Emre, van der Meer, Dieudonne, Barthorpe, Andrew, Lightfoot, Howard, Jaaks, Patricia, McFarland, James M., Garnett, Mathew J., Tsherniak, Aviad, Iorio, Francesco
Published in Nature communications (12.03.2021)
Published in Nature communications (12.03.2021)
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Global computational alignment of tumor and cell line transcriptional profiles
Warren, Allison, Chen, Yejia, Jones, Andrew, Shibue, Tsukasa, Hahn, William C., Boehm, Jesse S., Vazquez, Francisca, Tsherniak, Aviad, McFarland, James M.
Published in Nature communications (04.01.2021)
Published in Nature communications (04.01.2021)
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Mutational processes shape the landscape of TP53 mutations in human cancer
Giacomelli, Andrew O., Yang, Xiaoping, Lintner, Robert E., McFarland, James M., Duby, Marc, Kim, Jaegil, Howard, Thomas P., Takeda, David Y., Ly, Seav Huong, Kim, Eejung, Gannon, Hugh S., Hurhula, Brian, Sharpe, Ted, Goodale, Amy, Fritchman, Briana, Steelman, Scott, Vazquez, Francisca, Tsherniak, Aviad, Aguirre, Andrew J., Doench, John G., Piccioni, Federica, Roberts, Charles W. M., Meyerson, Matthew, Getz, Gad, Johannessen, Cory M., Root, David E., Hahn, William C.
Published in Nature genetics (01.10.2018)
Published in Nature genetics (01.10.2018)
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Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity
Kinker, Gabriela S., Greenwald, Alissa C., Tal, Rotem, Orlova, Zhanna, Cuoco, Michael S., McFarland, James M., Warren, Allison, Rodman, Christopher, Roth, Jennifer A., Bender, Samantha A., Kumar, Bhavna, Rocco, James W., Fernandes, Pedro A. C. M., Mader, Christopher C., Keren-Shaul, Hadas, Plotnikov, Alexander, Barr, Haim, Tsherniak, Aviad, Rozenblatt-Rosen, Orit, Krizhanovsky, Valery, Puram, Sidharth V., Regev, Aviv, Tirosh, Itay
Published in Nature genetics (01.11.2020)
Published in Nature genetics (01.11.2020)
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Aneuploidy increases resistance to chemotherapeutics by antagonizing cell division
Replogle, John Michael, Zhou, Wen, Amaro, Adrianna E., McFarland, James M., Villalobos-Ortiz, Mariana, Ryan, Jeremy, Letai, Anthony, Yilmaz, Omer, Sheltzer, Jason, Lippard, Stephen J., Ben-David, Uri, Amon, Angelika
Published in Proceedings of the National Academy of Sciences - PNAS (01.12.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (01.12.2020)
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Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition
Cohen-Sharir, Yael, McFarland, James M., Abdusamad, Mai, Marquis, Carolyn, Bernhard, Sara V., Kazachkova, Mariya, Tang, Helen, Ippolito, Marica R., Laue, Kathrin, Zerbib, Johanna, Malaby, Heidi L. H., Jones, Andrew, Stautmeister, Lisa-Marie, Bockaj, Irena, Wardenaar, René, Lyons, Nicholas, Nagaraja, Ankur, Bass, Adam J., Spierings, Diana C. J., Foijer, Floris, Beroukhim, Rameen, Santaguida, Stefano, Golub, Todd R., Stumpff, Jason, Storchová, Zuzana, Ben-David, Uri
Published in Nature (London) (18.02.2021)
Published in Nature (London) (18.02.2021)
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Speed controls the amplitude and timing of the hippocampal gamma rhythm
Chen, Zhiping, Resnik, Evgeny, McFarland, James M, Sakmann, Bert, Mehta, Mayank R
Published in PloS one (24.06.2011)
Published in PloS one (24.06.2011)
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Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
Raghavan, Srivatsan, Winter, Peter S., Navia, Andrew W., Williams, Hannah L., DenAdel, Alan, Lowder, Kristen E., Galvez-Reyes, Jennyfer, Kalekar, Radha L., Mulugeta, Nolawit, Kapner, Kevin S., Raghavan, Manisha S., Borah, Ashir A., Liu, Nuo, Väyrynen, Sara A., Costa, Andressa Dias, Ng, Raymond W.S., Wang, Junning, Hill, Emma K., Ragon, Dorisanne Y., Brais, Lauren K., Jaeger, Alex M., Spurr, Liam F., Li, Yvonne Y., Cherniack, Andrew D., Booker, Matthew A., Cohen, Elizabeth F., Tolstorukov, Michael Y., Wakiro, Isaac, Rotem, Asaf, Johnson, Bruce E., McFarland, James M., Sicinska, Ewa T., Jacks, Tyler E., Sullivan, Ryan J., Shapiro, Geoffrey I., Clancy, Thomas E., Perez, Kimberly, Rubinson, Douglas A., Ng, Kimmie, Cleary, James M., Crawford, Lorin, Manalis, Scott R., Nowak, Jonathan A., Wolpin, Brian M., Hahn, William C., Aguirre, Andrew J., Shalek, Alex K.
Published in Cell (09.12.2021)
Published in Cell (09.12.2021)
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Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action
McFarland, James M., Paolella, Brenton R., Warren, Allison, Geiger-Schuller, Kathryn, Shibue, Tsukasa, Rothberg, Michael, Kuksenko, Olena, Colgan, William N., Jones, Andrew, Chambers, Emily, Dionne, Danielle, Bender, Samantha, Wolpin, Brian M., Ghandi, Mahmoud, Tirosh, Itay, Rozenblatt-Rosen, Orit, Roth, Jennifer A., Golub, Todd R., Regev, Aviv, Aguirre, Andrew J., Vazquez, Francisca, Tsherniak, Aviad
Published in Nature communications (27.08.2020)
Published in Nature communications (27.08.2020)
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Journal Article
Developing Resistance Training Skill Literacy in Youth
Faigenbaum, Avery D., McFarland, James E.
Published in Journal of physical education, recreation & dance (12.02.2023)
Published in Journal of physical education, recreation & dance (12.02.2023)
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Computational estimation of quality and clinical relevance of cancer cell lines
Trastulla, Lucia, Noorbakhsh, Javad, Vazquez, Francisca, McFarland, James, Iorio, Francesco
Published in Molecular systems biology (01.07.2022)
Published in Molecular systems biology (01.07.2022)
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Cancer research needs a better map
Boehm, Jesse S., Garnett, Mathew J., Adams, David J., Francies, Hayley E., Golub, Todd R., Hahn, William C. , Iorio, Francesco, McFarland, James M., Parts, Leopold, Vazquez, Francisca
Published in Nature (London) (28.01.2021)
Published in Nature (London) (28.01.2021)
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