Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data von Weiner, Adam C., Williams, Marc J., Shi, Hongyu, Vázquez-García, Ignacio, Salehi, Sohrab, Rusk, Nicole, Aparicio, Samuel, Shah, Sohrab P., McPherson, Andrew

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Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector von Ceglia, Nicholas, Sethna, Zachary, Freeman, Samuel S., Uhlitz, Florian, Bojilova, Viktoria, Rusk, Nicole, Burman, Bharat, Chow, Andrew, Salehi, Sohrab, Kabeer, Farhia, Aparicio, Samuel, Greenbaum, Benjamin D., Shah, Sohrab P., McPherson, Andrew

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Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers von Kabeer, Farhia, Tran, Hoa, Andronescu, Mirela, Singh, Gurdeep, Lee, Hakwoo, Salehi, Sohrab, Wang, Beixi, Biele, Justina, Brimhall, Jazmine, Gee, David, Cerda, Viviana, O'Flanagan, Ciara, Algara, Teresa, Kono, Takako, Beatty, Sean, Zaikova, Elena, Lai, Daniel, Lee, Eric, Moore, Richard, Mungall, Andrew J, Williams, Marc J, Roth, Andrew, Campbell, Kieran R, Shah, Sohrab P, Aparicio, Samuel

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Accurate determination of CRISPR-mediated gene fitness in transplantable tumours von Eirew, Peter, O’Flanagan, Ciara, Ting, Jerome, Salehi, Sohrab, Brimhall, Jazmine, Wang, Beixi, Biele, Justina, Algara, Teresa, Lee, So Ra, Hoang, Corey, Yap, Damian, McKinney, Steven, Bates, Cherie, Kong, Esther, Lai, Daniel, Beatty, Sean, Andronescu, Mirela, Zaikova, Elena, Funnell, Tyler, Ceglia, Nicholas, Chia, Stephen, Gelmon, Karen, Mar, Colin, Shah, Sohrab, Roth, Andrew, Bouchard-Côté, Alexandre, Aparicio, Samuel

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An Efficient Data Driven-Based Model for Prediction of the Total Sediment Load in Rivers von Noori, Roohollah, Ghiasi, Behzad, Salehi, Sohrab, Esmaeili Bidhendi, Mehdi, Raeisi, Amin, Partani, Sadegh, Meysami, Rojin, Mahdian, Mehran, Hosseinzadeh, Majid, Abolfathi, Soroush

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Detection of bacterial agents causing prostate infection by culture and molecular methods from biopsy specimens von Karami, Ali Akbar, Javadi, Amir, Salehi, Sohrab, Nasirian, Neda, Maali, Amirhosein, Bakhshalizadeh Shadkam, Maryam, Najari, Masoumeh, Rousta, Zahra, Alizadeh, Safar Ali

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Degradation of azo dye Acid Red 14 (AR14) from aqueous solution using H2O2/nZVI and S2O82–/nZVI processes in the presence of UV irradiation von Samarghandi, Mohammad Reza, Dargahi, Abdollah, Zolghadr Nasab, Hasan, Ghahramani, Esmail, Salehi, Sohrab

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ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data von Salehi, Sohrab, Steif, Adi, Roth, Andrew, Aparicio, Samuel, Bouchard-Côté, Alexandre, Shah, Sohrab P

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Clonal fitness inferred from time-series modelling of single-cell cancer genomes von Salehi, Sohrab, Kabeer, Farhia, Ceglia, Nicholas, Andronescu, Mirela, Williams, Marc J., Campbell, Kieran R., Masud, Tehmina, Wang, Beixi, Biele, Justina, Brimhall, Jazmine, Gee, David, Lee, Hakwoo, Ting, Jerome, Zhang, Allen W., Tran, Hoa, O’Flanagan, Ciara, Dorri, Fatemeh, Rusk, Nicole, de Algara, Teresa Ruiz, Lee, So Ra, Cheng, Brian Yu Chieh, Eirew, Peter, Kono, Takako, Pham, Jenifer, Grewal, Diljot, Lai, Daniel, Moore, Richard, Mungall, Andrew J., Marra, Marco A., McPherson, Andrew, Bouchard-Côté, Alexandre, Aparicio, Samuel, Shah, Sohrab P.

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Medium-Term Stone Recurrence after zero-fragment transperitoneal Laparoscopic Pyelolithotomy Compared with Percutaneous Nephrolithotomy for Large Single Renal Pelvis Stones von Pakmanesh, Hamid, MohammadSalehi, Sohrab, Mirzaei, Mahboubeh, Hashemian, Morteza, Eslami, Nazanin, Sharifian, Rayka

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Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes von Kim, Minsoo, Gorelick, Alexander N., Vàzquez-García, Ignacio, Williams, Marc J., Salehi, Sohrab, Shi, Hongyu, Weiner, Adam C., Ceglia, Nick, Funnell, Tyler, Park, Tricia, Boscenco, Sonia, O’Flanagan, Ciara H., Jiang, Hui, Grewal, Diljot, Tang, Cerise, Rusk, Nicole, Gammage, Payam A., McPherson, Andrew, Aparicio, Sam, Shah, Sohrab P., Reznik, Ed

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Single-cell genomic variation induced by mutational processes in cancer von Funnell, Tyler, O’Flanagan, Ciara H., Williams, Marc J., McPherson, Andrew, McKinney, Steven, Kabeer, Farhia, Lee, Hakwoo, Salehi, Sohrab, Vázquez-García, Ignacio, Shi, Hongyu, Leventhal, Emily, Masud, Tehmina, Eirew, Peter, Yap, Damian, Zhang, Allen W., Lim, Jamie L. P., Wang, Beixi, Brimhall, Jazmine, Biele, Justina, Ting, Jerome, Au, Vinci, Van Vliet, Michael, Liu, Yi Fei, Beatty, Sean, Lai, Daniel, Pham, Jenifer, Grewal, Diljot, Abrams, Douglas, Havasov, Eliyahu, Leung, Samantha, Bojilova, Viktoria, Moore, Richard A., Rusk, Nicole, Uhlitz, Florian, Ceglia, Nicholas, Weiner, Adam C., Zaikova, Elena, Douglas, J. Maxwell, Zamarin, Dmitriy, Weigelt, Britta, Kim, Sarah H., Da Cruz Paula, Arnaud, Reis-Filho, Jorge S., Martin, Spencer D., Li, Yangguang, Xu, Hong, de Algara, Teresa Ruiz, Lee, So Ra, Llanos, Viviana Cerda, Huntsman, David G., McAlpine, Jessica N., Shah, Sohrab P., Aparicio, Samuel

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TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma von Ennishi, Daisuke, Healy, Shannon, Bashashati, Ali, Saberi, Saeed, Hother, Christoffer, Mottok, Anja, Chan, Fong Chun, Chong, Lauren, Abraham, Libin, Kridel, Robert, Boyle, Merrill, Meissner, Barbara, Aoki, Tomohiro, Takata, Katsuyoshi, Woolcock, Bruce W., Viganò, Elena, Gold, Michael, Molday, Laurie L., Molday, Robert S., Telenius, Adele, Li, Michael Y., Wretham, Nicole, Dos Santos, Nancy, Wong, Mark, Viller, Natasja N., Uger, Robert A., Duns, Gerben, Baticados, Abigail, Madero, Angel, Bristow, Brianna N., Farinha, Pedro, Slack, Graham W., Ben-Neriah, Susana, Lai, Daniel, Zhang, Allen W., Salehi, Sohrab, Shulha, Hennady P., Chiu, Derek S., Mostafavi, Sara, Gerrie, Alina S., Huang, Da Wei, Rushton, Christopher, Villa, Diego, Sehn, Laurie H., Savage, Kerry J., Mungall, Andrew J., Weng, Andrew P., Bally, Marcel B., Morin, Ryan D., Cohen Freue, Gabriela V., Staudt, Louis M., Connors, Joseph M., Marra, Marco A., Shah, Sohrab P., Gascoyne, Randy D., Scott, David W., Steidl, Christian

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Screening of Chelidonium majus isoquinoline alkaloids reveals berberine and chelidonine as selective ligands for the nuclear receptors RORβ and HNF4α, respectively von Salehi, Sohrab, Schallmayer, Espen, Bandomir, Nils, Kärcher, Annette, Güth, Jan‐Frederik, Heitel, Pascal

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Degradation of azo dye Acid Red 14 (AR14) from aqueous solution using H 2 O 2 /nZVI and S 2 O 8 2- /nZVI processes in the presence of UV irradiation von Samarghandi, Mohammad Reza, Dargahi, Abdollah, Zolghadr Nasab, Hasan, Ghahramani, Esmail, Salehi, Sohrab

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Clonal fitness inferred from timeseries modeling of single cell cancer genomes von Salehi, Sohrab, Kabeer, Farhia, Ceglia, Nicholas, Andronescu, Mirela, Williams, Marc J., Campbell, Kieran R., Masud, Tehmina, Wang, Beixi, Biele, Justina, Brimhall, Jazmine, Gee, David, Lee, Hakwoo, Ting, Jerome, Zhang, Allen W., Tran, Hoa, O’Flanagan, Ciara, Dorri, Fatemeh, Rusk, Nicole, de Algara, Teresa Ruiz, Lee, So Ra, Cheng, Brian Yu Chieh, Eirew, Peter, Kono, Takako, Pham, Jenifer, Grewal, Diljot, Lai, Daniel, Moore, Richard, Mungall, Andrew J., Marra, Marco A., McPherson, Andrew, Bouchard-Côté, Alexandre, Aparicio, Samuel, Shah, Sohrab P.

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Cancer phylogenetic tree inference at scale from 1000s of single cell genomes von Salehi, Sohrab, Dorri, Fatemeh, Chern, Kevin, Kabeer, Farhia, Rusk, Nicole, Funnell, Tyler, Williams, Marc J., Lai, Daniel, Andronescu, Mirela, Campbell, Kieran R., McPherson, Andrew, Aparicio, Samuel, Roth, Andrew, Shah, Sohrab P., Bouchard-Côté, Alexandre

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Abstract 3480: TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma von Healy, Shannon, Ennishi, Daisuke, Bashashati, Ali, Saberi, Saeed, Hother, Christoffer, Mottok, Anja, Chan, Fong Chun, Chong, Lauren, Kridel, Robert, Boyle, Merrill, Meissner, Barbara, Aoki, Tomohiro, Takata, Katsuyoshi, Woolcock, Bruce W., Vigano, Elena, Abraham, Libin, Gold, Michael, Telenius, Adele, Farinha, Pedro, Slack, Graham, Ben-Neriah, Susana, Lai, Daniel, Zhang, Allen W., Salehi, Sohrab, Shulha, Hennady P., Chiu, Derek S., Mostafavi, Sara, Gerrie, Alina S., Villa, Diego, Sehn, Laurie H., Savage, Kerry J. J., Mungall, Andrew J. J., Weng, Andrew P., Bally, Marcel, Morin, Ryan D., Freue, Gabriela V. Cohen, Connors, Joseph M., Marra, Marco A., Shah, Sohrab P., Gascoyne1, Randy D., Scott, David W., Steidl, Christian, Steidl, Ulrich

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NOTCH1 Induces Differential Epigenomic Patterning and Genomic Organization in Fetal Liver- and Adult Bone Marrow-Derived Hematopoietic Progentiors von Giambra, Vincenzo, Lam, Sonya H, Belmonte, Miriam, Gusscott, Sam, Salehi, Sohrab, Chan, Fong Chun, Kridel, Robert, Lorzadeh, Alireza, Hoofd, Catherine, Steidl, Christian, Eaves, Connie J., Hirst, Martin, Weng, Andrew P.

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CDC7 inhibition impairs neuroendocrine transformation in lung and prostate tumors through MYC degradation von Quintanal-Villalonga, Alvaro, Kawasaki, Kenta, Redin, Esther, Uddin, Fathema, Rakhade, Swanand, Durani, Vidushi, Sabet, Amin, Shafer, Moniquetta, Karthaus, Wouter R., Zaidi, Samir, Zhan, Yingqian A., Manoj, Parvathy, Sridhar, Harsha, Kinyua, Dennis, Zhong, Hong, Mello, Barbara P., Ciampricotti, Metamia, Bhanot, Umesh K., Linkov, Irina, Qiu, Juan, Patel, Radhika A., Morrissey, Colm, Mehta, Sanjoy, Barnes, Jesse, Haffner, Michael C., Socci, Nicholas D., Koche, Richard P., de Stanchina, Elisa, Molina-Pinelo, Sonia, Salehi, Sohrab, Yu, Helena A., Chan, Joseph M., Rudin, Charles M.

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