PyClone: statistical inference of clonal population structure in cancer
Roth, Andrew, Khattra, Jaswinder, Yap, Damian, Wan, Adrian, Laks, Emma, Biele, Justina, Ha, Gavin, Aparicio, Samuel, Bouchard-Côté, Alexandre, Shah, Sohrab P
Published in Nature methods (01.04.2014)
Published in Nature methods (01.04.2014)
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clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
Campbell, Kieran R, Steif, Adi, Laks, Emma, Zahn, Hans, Lai, Daniel, McPherson, Andrew, Farahani, Hossein, Kabeer, Farhia, O'Flanagan, Ciara, Biele, Justina, Brimhall, Jazmine, Wang, Beixi, Walters, Pascale, Bouchard-Côté, Alexandre, Aparicio, Samuel, Shah, Sohrab P
Published in Genome Biology (12.03.2019)
Published in Genome Biology (12.03.2019)
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Clonal genotype and population structure inference from single-cell tumor sequencing
Roth, Andrew, McPherson, Andrew, Laks, Emma, Biele, Justina, Yap, Damian, Wan, Adrian, Smith, Maia A, Nielsen, Cydney B, McAlpine, Jessica N, Aparicio, Samuel, Bouchard-Côté, Alexandre, Shah, Sohrab P
Published in Nature methods (01.07.2016)
Published in Nature methods (01.07.2016)
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High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations
Hui, Tony, Cao, Qi, Wegrzyn-Woltosz, Joanna, O'Neill, Kieran, Hammond, Colin A., Knapp, David J.H.F., Laks, Emma, Moksa, Michelle, Aparicio, Samuel, Eaves, Connie J., Karsan, Aly, Hirst, Martin
Published in Stem cell reports (14.08.2018)
Published in Stem cell reports (14.08.2018)
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Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data
P. E. de Souza, Camila, Andronescu, Mirela, Masud, Tehmina, Kabeer, Farhia, Biele, Justina, Laks, Emma, Lai, Daniel, Ye, Patricia, Brimhall, Jazmine, Wang, Beixi, Su, Edmund, Hui, Tony, Cao, Qi, Wong, Marcus, Moksa, Michelle, Moore, Richard A, Hirst, Martin, Aparicio, Samuel, Shah, Sohrab P
Published in PLoS computational biology (01.09.2020)
Published in PLoS computational biology (01.09.2020)
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Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
Leung, Kaston, Klaus, Anders, Lin, Bill K., Laks, Emma, Biele, Justina, Lai, Daniel, Bashashati, Ali, Huang, Yi-Fei, Aniba, Radhouane, Moksa, Michelle, Steif, Adi, Mes-Masson, Anne-Marie, Hirst, Martin, Shah, Sohrab P., Aparicio, Samuel, Hansen, Carl L.
Published in Proceedings of the National Academy of Sciences - PNAS (26.07.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (26.07.2016)
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Scalable whole-genome single-cell library preparation without preamplification
Zahn, Hans, Steif, Adi, Laks, Emma, Eirew, Peter, VanInsberghe, Michael, Shah, Sohrab P, Aparicio, Samuel, Hansen, Carl L
Published in Nature methods (01.02.2017)
Published in Nature methods (01.02.2017)
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TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
Ha, Gavin, Roth, Andrew, Khattra, Jaswinder, Ho, Julie, Yap, Damian, Prentice, Leah M, Melnyk, Nataliya, McPherson, Andrew, Bashashati, Ali, Laks, Emma, Biele, Justina, Ding, Jiarui, Le, Alan, Rosner, Jamie, Shumansky, Karey, Marra, Marco A, Gilks, C Blake, Huntsman, David G, McAlpine, Jessica N, Aparicio, Samuel, Shah, Sohrab P
Published in Genome research (01.11.2014)
Published in Genome research (01.11.2014)
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Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
McPherson, Andrew, Roth, Andrew, Laks, Emma, Masud, Tehmina, Bashashati, Ali, Zhang, Allen W, Ha, Gavin, Biele, Justina, Yap, Damian, Wan, Adrian, Prentice, Leah M, Khattra, Jaswinder, Smith, Maia A, Nielsen, Cydney B, Mullaly, Sarah C, Kalloger, Steve, Karnezis, Anthony, Shumansky, Karey, Siu, Celia, Rosner, Jamie, Chan, Hector Li, Ho, Julie, Melnyk, Nataliya, Senz, Janine, Yang, Winnie, Moore, Richard, Mungall, Andrew J, Marra, Marco A, Bouchard-Côté, Alexandre, Gilks, C Blake, Huntsman, David G, McAlpine, Jessica N, Aparicio, Samuel, Shah, Sohrab P
Published in Nature genetics (01.07.2016)
Published in Nature genetics (01.07.2016)
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Journal Article
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
Ha, Gavin, Roth, Andrew, Khattra, Jaswinder, Ho, Julie, Yap, Damian, Prentice, Leah M, Melnyk, Nataliya, McPherson, Andrew, Bashashati, Ali, Laks, Emma
Published in Genome research (01.11.2014)
Published in Genome research (01.11.2014)
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Journal Article
Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data
Camila P E De Souza, Andronescu, Mirela, Masud, Tehmina, Kabeer, Farhia, Biele, Justina, Laks, Emma, Lai, Daniel, Ye, Patricia, Brimhall, Jazmine, Wang, Beixi, Su, Edmund, Hui, Tony, Cao, Qi, Wong, Marcus, Moksa, Michelle, Moore, Richard A, Hirst, Martin, Aparicio, Samuel, Shah, Sohrab P
Published in bioRxiv (21.02.2020)
Published in bioRxiv (21.02.2020)
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clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers
Campbell, Kieran R, Steif, Adi, Laks, Emma, Zahn, Hans, Lai, Daniel, Mcpherson, Andrew, Farahani, Hossein, Kabeer, Farhia, O'flanagan, Ciara, Biele, Justina, Brimhall, Jazmine, Wang, Beixi, Walters, Pascale, Consortium, Imaxt, Alexandre Bouchard-C t, Aparicio, Samuel, Shah, Sohrab P
Published in bioRxiv (11.06.2018)
Published in bioRxiv (11.06.2018)
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Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires
Laks, Emma, Zahn, Hans, Lai, Daniel, Mcpherson, Andrew, Steif, Adi, Brimhall, Jazmine, Biele, Justina, Wang, Beixi, Masud, Tehmina, Grewal, Diljot, Nielsen, Cydney, Leung, Samantha, Bojilova, Viktoria, Smith, Maia, Golovko, Oleg, Poon, Steven, Eirew, Peter, Kabeer, Farhia, Ruiz De Algara, Teresa, So Ra Lee, M Jafar Taghiyar, Huebner, Curtis, Ngo, Jessica, Chan, Tim, Vatrt-Watts, Spencer, Walters, Pascale, Abrar, Nafis, Chan, Sophia, Wiens, Matt, Martin, Lauren, R Wilder Scott, Underhill, Michael T, Chavez, Elizabeth, Steidl, Christian, Da Costa, Daniel, Ma, Yusanne, Coope, Robin J N, Corbett, Richard, Pleasance, Stephen, Moore, Richard, Mungall, Andy J, Consortium, Cruk Imaxt, Marra, Marco A, Hansen, Carl, Shah, Sohrab, Aparicio, Samuel
Published in bioRxiv (13.09.2018)
Published in bioRxiv (13.09.2018)
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