Group Normalization for Genomic Data

по Ghandi, Mahmoud, Beer, Michael A.
Опубликовано 2012

Robust k-mer frequency estimation using gapped k-mers

по Ghandi, Mahmoud, Mohammad-Noori, Morteza, Beer, Michael A.
Опубликовано 2013

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

по Ghandi, Mahmoud, Lee, Dongwon, Mohammad-Noori, Morteza, Beer, Michael A.
Опубликовано 2014

ERK Mutations Confer Resistance to Mitogen-Activated Protein Kinase Pathway Inhibitors

по Goetz, Eva M., Ghandi, Mahmoud, Treacy, Daniel J., Wagle, Nikhil, Garraway, Levi A.
Опубликовано в: Cancer Res (2014)

The Molecular Signatures Database (MSigDB) hallmark gene set collection

по Liberzon, Arthur, Birger, Chet, Thorvaldsdóttir, Helga, Ghandi, Mahmoud, Mesirov, Jill P., Tamayo, Pablo
Опубликовано в: Cell Syst (2015)

gkmSVM: an R package for gapped-kmer SVM

по Ghandi, Mahmoud, Mohammad-Noori, Morteza, Ghareghani, Narges, Lee, Dongwon, Garraway, Levi, Beer, Michael A.
Опубликовано в: Bioinformatics (2016)

Allele-specific DNA methylation and its interplay with repressive histone marks at promoter-mutant TERT genes

по Stern, Josh Lewis, Paucek, Richard D., Huang, Franklin W., Ghandi, Mahmoud, Nwumeh, Ronald, Costello, James C., Cech, Thomas R.
Опубликовано в: Cell Rep (2017)

Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes

по Stern, Josh Lewis, Paucek, Richard D., Huang, Franklin W., Ghandi, Mahmoud, Nwumeh, Ronald, Costello, James C., Cech, Thomas R.
Опубликовано в: Cell Rep (2020)

Systematic functional characterization of resistance to PI3K inhibition in breast cancer

по Le, Xiuning, Antony, Rajee, Razavi, Pedram, Treacy, Daniel J., Luo, Flora, Ghandi, Mahmoud, Castel, Pau, Scaltriti, Maurizio, Baselga, Jose, Garraway, Levi A.
Опубликовано в: Cancer Discov (2016)

Suppression of 19S proteasome subunits marks emergence of an altered cell state in diverse cancers

по Tsvetkov, Peter, Sokol, Ethan, Jin, Dexter, Brune, Zarina, Thiru, Prathapan, Ghandi, Mahmoud, Garraway, Levi A., Gupta, Piyush B., Santagata, Sandro, Whitesell, Luke, Lindquist, Susan
Опубликовано в: Proc Natl Acad Sci U S A (2017)

ARID1B is a specific vulnerability in ARID1A-mutant cancers

по Helming, Katherine C., Wang, Xiaofeng, Wilson, Boris G., Vazquez, Francisca, Haswell, Jeffrey R., Manchester, Haley E., Kim, Youngha, Kryukov, Gregory V., Ghandi, Mahmoud, Aguirre, Andrew J., Jagani, Zainab, Wang, Zhong, Garraway, Levi A., Hahn, William C., Roberts, Charles W. M.
Опубликовано 2014

DNA methyltransferase inhibition overcomes diphthamide pathway deficiencies underlying CD123-targeted treatment resistance

по Togami, Katsuhiro, Pastika, Timothy, Stephansky, Jason, Ghandi, Mahmoud, Christie, Amanda L., Jones, Kristen L., Johnson, Carl A., Lindsay, Ross W., Brooks, Christopher L., Letai, Anthony, Craig, Jeffrey W., Pozdnyakova, Olga, Weinstock, David M., Montero, Joan, Aster, Jon C., Johannessen, Cory M., Lane, Andrew A.
Опубликовано в: J Clin Invest (2019)

Pediatric-type nodal follicular lymphoma: a biologically distinct lymphoma with frequent MAPK pathway mutations

по Louissaint, Abner, Schafernak, Kristian T., Geyer, Julia T., Kovach, Alexandra E., Ghandi, Mahmoud, Gratzinger, Dita, Roth, Christine G., Paxton, Christian N., Kim, Sunhee, Namgyal, Chungdak, Morin, Ryan, Morgan, Elizabeth A., Neuberg, Donna S., South, Sarah T., Harris, Marian H., Hasserjian, Robert P., Hochberg, Ephraim P., Garraway, Levi A., Harris, Nancy Lee, Weinstock, David M.
Опубликовано в: Blood (2016)

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

по Nusinow, David P., Szpyt, John, Ghandi, Mahmoud, Rose, Christopher M., McDonald, E. Robert, Kalocsay, Marian, Jané-Valbuena, Judit, Gelfand, Ellen, Schweppe, Devin K., Jedrychowski, Mark, Golji, Javad, Porter, Dale A., Rejtar, Tomas, Wang, Y. Karen, Kryukov, Gregory V., Stegmeier, Frank, Erickson, Brian K., Garraway, Levi A., Sellers, William R., Gygi, Steven P.
Опубликовано в: Cell (2020)

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

по 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
Опубликовано в: Nat Commun (2020)

Locally disordered methylation forms the basis of intra-tumor methylome variation in chronic lymphocytic leukemia

по Landau, Dan A., Clement, Kendell, Ziller, Michael J., Boyle, Patrick, Fan, Jean, Gu, Hongcang, Stevenson, Kristen, Sougnez, Carrie, Wang, Lili, Li, Shuqiang, Kotliar, Dylan, Zhang, Wandi, Ghandi, Mahmoud, Garraway, Levi, Fernandes, Stacey M., Livak, Kenneth J., Gabriel, Stacey, Gnirke, Andreas, Lander, Eric S., Brown, Jennifer R., Neuberg, Donna, Kharchenko, Peter V., Hacohen, Nir, Getz, Gad, Meissner, Alexander, Wu, Catherine J.
Опубликовано в: Cancer Cell (2014)

Defining a Cancer Dependency Map

по Tsherniak, Aviad, Vazquez, Francisca, Montgomery, Phil G., Weir, Barbara A., Kryukov, Gregory, Cowley, Glenn S., Gill, Stanley, Harrington, William F., Pantel, Sasha, Krill-Burger, John M., Meyers, Robin M., Ali, Levi, Goodale, Amy, Lee, Yenarae, Jiang, Guozhi, Hsiao, Jessica, Gerath, William F.J., Howell, Sara, Merkel, Erin, Ghandi, Mahmoud, Garraway, Levi A., Root, David E., Golub, Todd R., Boehm, Jesse S., Hahn, William C.
Опубликовано в: Cell (2017)

The Landscape of Cancer Cell Line Metabolism

по Li, Haoxin, Ning, Shaoyang, Ghandi, Mahmoud, Kryukov, Gregory V., Gopal, Shuba, Deik, Amy, Souza, Amanda, Pierce, Kerry, Keskula, Paula, Hernandez, Desiree, Ann, Julie, Shkoza, Dojna, Apfel, Verena, Zou, Yilong, Vazquez, Francisca, Barretina, Jordi, Pagliarini, Raymond A., Galli, Giorgio G., Root, David E., Hahn, William C., Tsherniak, Aviad, Giannakis, Marios, Schreiber, Stuart L., Clish, Clary B., Garraway, Levi A., Sellers, William R.
Опубликовано в: Nat Med (2019)

Consistency of drug profiles and predictors in large-scale cancer cell line data

по Stransky, Nicolas, Ghandi, Mahmoud, Kryukov, Gregory V., Garraway, Levi A., Amzallag, Arnaud, Pruteanu-Malinici, Iulian, Haber, Daniel A., Ramaswamy, Sridhar, Benes, Cyril H., Lehár, Joseph, Liu, Manway, Sonkin, Dmitriy, Kauffmann, Audrey, Venkatesan, Kavitha, Edelman, Elena J., Riester, Markus, Barretina, Jordi, Caponigro, Giordano, Schlegel, Robert, Sellers, William, Stegmeier, Frank, Morrissey, Michael, Menden, Michael P., Iorio, Francesco, Stratton, Michael R., McDermott, Ultan, Saez-Rodriguez, Julio, Garnett, Mathew J.
Опубликовано в: Nature (2015)

Genetic and transcriptional evolution alters cancer cell line drug response

по Ben-David, Uri, Siranosian, Benjamin, Ha, Gavin, Tang, Helen, Oren, Yaara, Hinohara, Kunihiko, Strathdee, Craig A., Dempster, Joshua, Lyons, Nicholas J., Burns, Robert, Nag, Anwesha, Kugener, Guillaume, Cimini, Beth, Tsvetkov, Peter, Maruvka, Yosef E., O’Rourke, Ryan, Garrity, Anthony, Tubelli, Andrew A., Bandopadhayay, Pratiti, Tsherniak, Aviad, Vazquez, Francisca, Wong, Bang, Birger, Chet, Ghandi, Mahmoud, Thorner, Aaron R., Bittker, Joshua A., Meyerson, Matthew, Getz, Gad, Beroukhim, Rameen, Golub, Todd R.
Опубликовано в: Nature (2018)