Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

by Ding, Jiarui, Condon, Anne, Shah, Sohrab P
Published in Nature communications

Eleven grand challenges in single-cell data science

by Lähnemann, David, Köster, Johannes, Szczurek, Ewa, McCarthy, Davis J, Hicks, Stephanie C, Robinson, Mark D, Vallejos, Catalina A, Campbell, Kieran R, Beerenwinkel, Niko, Mahfouz, Ahmed, Pinello, Luca, Skums, Pavel, Stamatakis, Alexandros, Attolini, Camille Stephan-Otto, Aparicio, Samuel, Baaijens, Jasmijn, Balvert, Marleen, Barbanson, Buys de, Cappuccio, Antonio, Corleone, Giacomo, Dutilh, Bas E, Florescu, Maria, Guryev, Victor, Holmer, Rens, Jahn, Katharina, Lobo, Thamar Jessurun, Keizer, Emma M, Khatri, Indu, Kielbasa, Szymon M, Korbel, Jan O, Kozlov, Alexey M, Kuo, Tzu-Hao, Lelieveldt, Boudewijn P F, Mandoiu, Ion I, Marioni, John C, Marschall, Tobias, Mölder, Felix, Niknejad, Amir, Rączkowska, Alicja, Reinders, Marcel, Ridder, Jeroen de, Saliba, Antoine-Emmanuel, Somarakis, Antonios, Stegle, Oliver, Theis, Fabian J, Yang, Huan, Zelikovsky, Alex, McHardy, Alice C, Raphael, Benjamin J, Shah, Sohrab P, Schönhuth, Alexander
Published in Genome Biology

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

by Nguyen, Bastien, Fong, Christopher, Luthra, Anisha, Smith, Shaleigh A., DiNatale, Renzo G., Nandakumar, Subhiksha, Walch, Henry, Chatila, Walid K., Madupuri, Ramyasree, Kundra, Ritika, Bielski, Craig M., Mastrogiacomo, Brooke, Donoghue, Mark T.A., Boire, Adrienne, Chandarlapaty, Sarat, Ganesh, Karuna, Harding, James J., Iacobuzio-Donahue, Christine A., Razavi, Pedram, Reznik, Ed, Rudin, Charles M., Zamarin, Dmitriy, Abida, Wassim, Abou-Alfa, Ghassan K., Aghajanian, Carol, Cercek, Andrea, Chi, Ping, Feldman, Darren, Ho, Alan L., Iyer, Gopakumar, Janjigian, Yelena Y., Morris, Michael, Motzer, Robert J., O’Reilly, Eileen M., Postow, Michael A., Raj, Nitya P., Riely, Gregory J., Robson, Mark E., Rosenberg, Jonathan E., Safonov, Anton, Shoushtari, Alexander N., Tap, William, Teo, Min Yuen, Varghese, Anna M., Voss, Martin, Yaeger, Rona, Zauderer, Marjorie G., Abu-Rustum, Nadeem, Garcia-Aguilar, Julio, Bochner, Bernard, Hakimi, Abraham, Jarnagin, William R., Jones, David R., Molena, Daniela, Morris, Luc, Rios-Doria, Eric, Russo, Paul, Singer, Samuel, Strong, Vivian E., Chakravarty, Debyani, Ellenson, Lora H., Gopalan, Anuradha, Reis-Filho, Jorge S., Weigelt, Britta, Ladanyi, Marc, Gonen, Mithat, Shah, Sohrab P., Massague, Joan, Gao, Jianjiong, Zehir, Ahmet, Berger, Michael F., Solit, David B., Bakhoum, Samuel F., Sanchez-Vega, Francisco, Schultz, Nikolaus
Published in Cell

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study

by Kridel, Robert, Chan, Fong Chun, Mottok, Anja, Boyle, Merrill, Farinha, Pedro, Tan, King, Meissner, Barbara, Bashashati, Ali, McPherson, Andrew, Roth, Andrew, Shumansky, Karey, Yap, Damian, Ben-Neriah, Susana, Rosner, Jamie, Smith, Maia A, Nielsen, Cydney, Giné, Eva, Telenius, Adele, Ennishi, Daisuke, Mungall, Andrew, Moore, Richard, Morin, Ryan D, Johnson, Nathalie A, Sehn, Laurie H, Tousseyn, Thomas, Dogan, Ahmet, Connors, Joseph M, Scott, David W, Steidl, Christian, Marra, Marco A, Gascoyne, Randy D, Shah, Sohrab P
Published in PLoS medicine

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

by Eirew, Peter, Steif, Adi, Khattra, Jaswinder, Ha, Gavin, Yap, Damian, Farahani, Hossein, Gelmon, Karen, Chia, Stephen, Mar, Colin, Wan, Adrian, Laks, Emma, Biele, Justina, Shumansky, Karey, Rosner, Jamie, McPherson, Andrew, Nielsen, Cydney, Roth, Andrew J L, Lefebvre, Calvin, Bashashati, Ali, de Souza, Camila, Siu, Celia, Aniba, Radhouane, Brimhall, Jazmine, Oloumi, Arusha, Osako, Tomo, Bruna, Alejandra, Sandoval, Jose L, Algara, Teresa, Greenwood, Wendy, Leung, Kaston, Cheng, Hongwei, Xue, Hui, Wang, Yuzhuo, Lin, Dong, Mungall, Andrew J, Moore, Richard, Zhao, Yongjun, Lorette, Julie, Nguyen, Long, Huntsman, David, Eaves, Connie J, Hansen, Carl, Marra, Marco A, Caldas, Carlos, Shah, Sohrab P, Aparicio, Samuel
Published in Nature (London)

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

by O'Flanagan, Ciara H, Campbell, Kieran R, Zhang, Allen W, Kabeer, Farhia, Lim, Jamie L P, Biele, Justina, Eirew, Peter, Lai, Daniel, McPherson, Andrew, Kong, Esther, Bates, Cherie, Borkowski, Kelly, Wiens, Matt, Hewitson, Brittany, Hopkins, James, Pham, Jenifer, Ceglia, Nicholas, Moore, Richard, Mungall, Andrew J, McAlpine, Jessica N, Shah, Sohrab P, Aparicio, Samuel
Published in Genome Biology

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

by Zhang, Allen W., McPherson, Andrew, Milne, Katy, Kroeger, David R., Hamilton, Phineas T., Miranda, Alex, Funnell, Tyler, Little, Nicole, de Souza, Camila P.E., Laan, Sonya, LeDoux, Stacey, Cochrane, Dawn R., Lim, Jamie L.P., Yang, Winnie, Roth, Andrew, Smith, Maia A., Ho, Julie, Tse, Kane, Zeng, Thomas, Shlafman, Inna, Mayo, Michael R., Moore, Richard, Failmezger, Henrik, Heindl, Andreas, Wang, Yi Kan, Bashashati, Ali, Grewal, Diljot S., Brown, Scott D., Lai, Daniel, Wan, Adrian N.C., Nielsen, Cydney B., Huebner, Curtis, Tessier-Cloutier, Basile, Anglesio, Michael S., Bouchard-Côté, Alexandre, Yuan, Yinyin, Wasserman, Wyeth W., Gilks, C. Blake, Karnezis, Anthony N., Aparicio, Samuel, McAlpine, Jessica N., Huntsman, David G., Holt, Robert A., Nelson, Brad H., Shah, Sohrab P.
Published in Cell

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours

by Xu, Hong, Di Antonio, Marco, McKinney, Steven, Mathew, Veena, Ho, Brandon, O'Neil, Nigel J, Santos, Nancy Dos, Silvester, Jennifer, Wei, Vivien, Garcia, Jessica, Kabeer, Farhia, Lai, Daniel, Soriano, Priscilla, Banáth, Judit, Chiu, Derek S, Yap, Damian, Le, Daniel D, Ye, Frank B, Zhang, Anni, Thu, Kelsie, Soong, John, Lin, Shu-Chuan, Tsai, Angela Hsin Chin, Osako, Tomo, Algara, Teresa, Saunders, Darren N, Wong, Jason, Xian, Jian, Bally, Marcel B, Brenton, James D, Brown, Grant W, Shah, Sohrab P, Cescon, David, Mak, Tak W, Caldas, Carlos, Stirling, Peter C, Hieter, Phil, Balasubramanian, Shankar, Aparicio, Samuel
Published in Nature communications

Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition

by Ennishi, Daisuke, Takata, Katsuyoshi, Béguelin, Wendy, Duns, Gerben, Mottok, Anja, Farinha, Pedro, Bashashati, Ali, Saberi, Saeed, Boyle, Merrill, Meissner, Barbara, Ben-Neriah, Susana, Woolcock, Bruce W, Telenius, Adèle, Lai, Daniel, Teater, Matt, Kridel, Robert, Savage, Kerry J, Sehn, Laurie H, Morin, Ryan D, Marra, Marco A, Shah, Sohrab P, Connors, Joseph M, Gascoyne, Randy D, Scott, David W, Melnick, Ari M, Steidl, Christian
Published in Cancer discovery

Type-specific cell line models for type-specific ovarian cancer research

by Anglesio, Michael S, Wiegand, Kimberly C, Melnyk, Nataliya, Chow, Christine, Salamanca, Clara, Prentice, Leah M, Senz, Janine, Yang, Winnie, Spillman, Monique A, Cochrane, Dawn R, Shumansky, Karey, Shah, Sohrab P, Kalloger, Steve E, Huntsman, David G
Published in PloS one

The clonal and mutational evolution spectrum of primary triple―negative breast cancers

by SHAH, Sohrab P, ROTH, Andrew, BASHASHATI, Ali, PRENTICE, Leah M, KHATTRA, Jaswinder, BURLEIGH, Angela, YAP, Damian, BERNARD, Virginie, MCPHERSON, Andrew, SHUMANSKY, Karey, CRISAN, Anamaria, GIULIANY, Ryan, GOYA, Rodrigo, HERAVI-MOUSSAVI, Alireza, ROSNER, Jamie, LAI, Daniel, BIROL, Inane, VARHOL, Richard, TAM, Angela, DHALLA, Noreen, ZENG, Thomas, MA, Kevin, CHAN, Simon K, OLOUMI, Arusha, GRIFFITH, Malachi, MORADIAN, Annie, GRACE CHENG, S.-W, MORIN, Gregg B, WATSON, Peter, GELMON, Karen, CHIA, Stephen, CHIN, Suet-Feung, CURTIS, Christina, RUEDA, Oscar M, HA, Gavin, PHAROAH, Paul D, DAMARAJU, Sambasivarao, MACKEY, John, HOON, Kelly, HARKINS, Timothy, TADIGOTLA, Vasisht, SIGAROUDINIA, Mahvash, GASCARD, Philippe, TLSTY, Thea, COSTELLO, Joseph F, YONGJUN ZHAO, MEYER, Irmtraud M, EAVES, Connie J, WASSERMAN, Wyeth W, JONES, Steven, HUNTSMAN, David, HIRST, Martin, CALDAS, Carlos, MARRA, Marco A, APARICIO, Samuel, TURASHVILI, Gulisa, JIARUI DING, TSE, Kane, HAFFARI, Gholamreza
Published in Nature (London)

Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells

by Shi, Hongyu, Williams, Marc J, Satas, Gryte, Weiner, Adam C, McPherson, Andrew, Shah, Sohrab P
Published in Nature communications

Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma

by Twa, David D.W., Chan, Fong Chun, Ben-Neriah, Susana, Woolcock, Bruce W., Mottok, Anja, Tan, King L., Slack, Graham W., Gunawardana, Jay, Lim, Raymond S., McPherson, Andrew W., Kridel, Robert, Telenius, Adele, Scott, David W., Savage, Kerry J., Shah, Sohrab P., Gascoyne, Randy D., Steidl, Christian
Published in Blood

Epigenetic dysregulation from chromosomal transit in micronuclei

by Agustinus, Albert S, Al-Rawi, Duaa, Dameracharla, Bhargavi, Raviram, Ramya, Jones, Bailey S C L, Stransky, Stephanie, Scipioni, Lorenzo, Luebeck, Jens, Di Bona, Melody, Norkunaite, Danguole, Myers, Robert M, Duran, Mercedes, Choi, Seongmin, Weigelt, Britta, Yomtoubian, Shira, McPherson, Andrew, Toufektchan, Eléonore, Keuper, Kristina, Mischel, Paul S, Mittal, Vivek, Shah, Sohrab P, Maciejowski, John, Storchova, Zuzana, Gratton, Enrico, Ly, Peter, Landau, Dan, Bakhoum, Mathieu F, Koche, Richard P, Sidoli, Simone, Bafna, Vineet, David, Yael, Bakhoum, Samuel F
Published in Nature (London)

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models

by Funnell, Tyler, Zhang, Allen W, Grewal, Diljot, McKinney, Steven, Bashashati, Ali, Wang, Yi Kan, Shah, Sohrab P
Published in PLoS computational biology

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

by Ha, Gavin, Roth, Andrew, Lai, Daniel, Bashashati, Ali, Ding, Jiarui, Goya, Rodrigo, Giuliany, Ryan, Rosner, Jamie, Oloumi, Arusha, Shumansky, Karey, Chin, Suet-Feung, Turashvili, Gulisa, Hirst, Martin, Caldas, Carlos, Marra, Marco A, Aparicio, Samuel, Shah, Sohrab P
Published in Genome research

Ovarian cancer mutational processes drive site-specific immune evasion

by Vázquez-García, Ignacio, Uhlitz, Florian, Ceglia, Nicholas, Lim, Jamie L P, Wu, Michelle, Mohibullah, Neeman, Niyazov, Juliana, Ruiz, Arvin Eric B, Boehm, Kevin M, Bojilova, Viktoria, Fong, Christopher J, Funnell, Tyler, Grewal, Diljot, Havasov, Eliyahu, Leung, Samantha, Pasha, Arfath, Patel, Druv M, Pourmaleki, Maryam, Rusk, Nicole, Shi, Hongyu, Vanguri, Rami, Williams, Marc J, Zhang, Allen W, Broach, Vance, Chi, Dennis S, Da Cruz Paula, Arnaud, Gardner, Ginger J, Kim, Sarah H, Lennon, Matthew, Long Roche, Kara, Sonoda, Yukio, Zivanovic, Oliver, Kundra, Ritika, Viale, Agnes, Derakhshan, Fatemeh N, Geneslaw, Luke, Issa Bhaloo, Shirin, Maroldi, Ana, Nunez, Rahelly, Pareja, Fresia, Stylianou, Anthe, Vahdatinia, Mahsa, Bykov, Yonina, Grisham, Rachel N, Liu, Ying L, Lakhman, Yulia, Nikolovski, Ines, Kelly, Daniel, Gao, Jianjiong, Schietinger, Andrea, Hollmann, Travis J, Bakhoum, Samuel F, Soslow, Robert A, Ellenson, Lora H, Abu-Rustum, Nadeem R, Aghajanian, Carol, Friedman, Claire F, McPherson, Andrew, Weigelt, Britta, Zamarin, Dmitriy, Shah, Sohrab P
Published in Nature (London)

Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin–specific clinical impact

by Ennishi, Daisuke, Mottok, Anja, Ben-Neriah, Susana, Shulha, Hennady P., Farinha, Pedro, Chan, Fong Chun, Meissner, Barbara, Boyle, Merrill, Hother, Christoffer, Kridel, Robert, Lai, Daniel, Saberi, Saeed, Bashashati, Ali, Shah, Sohrab P., Morin, Ryan D., Marra, Marco A., Savage, Kerry J., Sehn, Laurie H., Steidl, Christian, Connors, Joseph M., Gascoyne, Randy D., Scott, David W.
Published in Blood

CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion

by Tien, Jerry F, Mazloomian, Alborz, Cheng, S-W Grace, Hughes, Christopher S, Chow, Christalle C T, Canapi, Leanna T, Oloumi, Arusha, Trigo-Gonzalez, Genny, Bashashati, Ali, Xu, James, Chang, Vicky C-D, Shah, Sohrab P, Aparicio, Samuel, Morin, Gregg B
Published in Nucleic acids research

Ovarian and endometrial endometrioid carcinomas have distinct CTNNB1 and PTEN mutation profiles

by McConechy, Melissa K, Ding, Jiarui, Senz, Janine, Yang, Winnie, Melnyk, Nataliya, Tone, Alicia A, Prentice, Leah M, Wiegand, Kimberly C, McAlpine, Jessica N, Shah, Sohrab P, Lee, Cheng-Han, Goodfellow, Paul J, Gilks, C Blake, Huntsman, David G
Published in Modern pathology