Kablammo: an interactive, web-based BLAST results visualizer

by Wintersinger, Jeff A, Wasmuth, James D
Published in Bioinformatics

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression

by Espiritu, Shadrielle Melijah G., Liu, Lydia Y., Rubanova, Yulia, Bhandari, Vinayak, Holgersen, Erle M., Szyca, Lesia M., Fox, Natalie S., Chua, Melvin L.K., Yamaguchi, Takafumi N., Heisler, Lawrence E., Livingstone, Julie, Wintersinger, Jeff, Yousif, Fouad, Lalonde, Emilie, Rouette, Alexandre, Salcedo, Adriana, Houlahan, Kathleen E., Li, Constance H., Huang, Vincent, Fraser, Michael, van der Kwast, Theodorus, Morris, Quaid D., Bristow, Robert G., Boutros, Paul C.
Published in Cell

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

by Sundermann, Linda K, Wintersinger, Jeff, Rätsch, Gunnar, Stoye, Jens, Morris, Quaid
Published in PLoS computational biology

Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm

by Kulman, Ethan, Wintersinger, Jeff, Morris, Quaid
Published in STAR protocols

Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree

by Wintersinger, Jeff A, Dobson, Stephanie M, Kulman, Ethan, Stein, Lincoln D, Dick, John E, Morris, Quaid
Published in Blood cancer discovery

A community effort to create standards for evaluating tumor subclonal reconstruction

by Salcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G, Deshwar, Amit G, David, Matei, Wilson, Nathan M, Dentro, Stefan, Wintersinger, Jeff A, Liu, Lydia Y, Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M, Buchanan, Alex, Lalansingh, Christopher M, P'ng, Christine, Anghel, Catalina V, Umar, Imaad, Lo, Bryan, Zou, William, Simpson, Jared T, Stuart, Joshua M, Anastassiou, Dimitris, Guan, Yuanfang, Ewing, Adam D, Ellrott, Kyle, Wedge, David C, Morris, Quaid, Van Loo, Peter, Boutros, Paul C
Published in Nature biotechnology

Multiomic Profiling of Central Nervous System Leukemia Identifies mRNA Translation as a Therapeutic Target

by Vanner, Robert J, Dobson, Stephanie M, Gan, Olga I, McLeod, Jessica, Schoof, Erwin M, Grandal, Ildiko, Wintersinger, Jeff A, Garcia-Prat, Laura, Hosseini, Mohsen, Xie, Stephanie Z, Jin, Liqing, Mbong, Nathan, Voisin, Veronique, Chan-Seng-Yue, Michelle, Kennedy, James A, Waanders, Esmé, Morris, Quaid, Porse, Bo, Chan, Steven M, Guidos, Cynthia J, Danska, Jayne S, Minden, Mark D, Mullighan, Charles G, Dick, John E
Published in Blood cancer discovery

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

by Dentro, Stefan C., Leshchiner, Ignaty, Haase, Kerstin, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Vázquez-García, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G., Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Anur, Pavana, Jolly, Clemency, Rosebrock, Daniel, Schumacher, Steven E., Fittall, Matthew, Drews, Ruben M., Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J., McGranahan, Nicholas, Swanton, Charles, Getz, Gad, Boutros, Paul C., Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T., Wang, Wenyi, Wedge, David C., Dentro, Stefan C., Leshchiner, Ignaty, Gerstung, Moritz, Jolly, Clemency, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D., Cao, Shaolong, Cmero, Marek, Cun, Yupeng, Dawson, Kevin J., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew, Getz, Gad, Ha, Gavin, Imielinski, Marcin, Ji, Yuan, Kleinheinz, Kortine, Lee, Juhee, Lee-Six, Henry, Livitz, Dimitri G., Malikic, Salem, Markowetz, Florian, Martincorena, Inigo, Mustonen, Ville, Oesper, Layla, Peifer, Martin, Peto, Myron, Raphael, Benjamin J., Rosebrock, Daniel, Salcedo, Adriana, Schumacher, Steven E., Sengupta, Subhajit, Shi, Ruian, Spiro, Oliver, Vázquez-García, Ignacio, Vembu, Shankar, Wheeler, David A., Yao, Xiaotong, Yuan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., Van Loo, Peter
Published in Cell

Abstract B2-59: PhyloSpan: Using multi-mutation reads to resolve subclonal architectures from heterogeneous tumor samples

by Deshwar, Amit G., Boyles, Levi, Wintersinger, Jeff, Boutros, Paul C., Teh, Yee Whye, Morris, Quaid, Morris, Quaid
Published in Cancer research (Chicago, Ill.)

Abstract 4865: PhyloSpan: using multi-mutation reads to resolve subclonal architectures from heterogeneous tumor samples

by Deshwar, Amit G., Boyles, Levi, Wintersinger, Jeff, Boutros, Paul C., Teh, Yee Whye, Morris, Quaid
Published in Cancer research (Chicago, Ill.)

Abstract 3000: Pervasive intra-tumour heterogeneity and subclonal selection across cancer types

by Dentro, Stefan, Leshchiner, Ignaty, Haase, Kerstin, Wintersinger, Jeff, Deshwar, Amit, Tarabichi, Maxime, Rubanova, Yulia, Yu, Kaixian, Vázquez García, Ignacio, Macintyre, Geoff, Kleinheinz, Kortine, Livitz, Dimitri, Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Ji, Yuan, Demeulemeester, Jonas, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steve, Fan, Yu, Fittall, Matthew, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David, Getz, Gad, Boutros, Paul, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, Cenk, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Wang, Wenyi, Spellman, Paul, Morris, Quaid, Wedge, David, Loo, Peter Van
Published in Cancer research (Chicago, Ill.)

Abstract 218: The evolutionary history of 2,658 cancers

by Jolly, Clemency, Gerstung, Moritz, Leshchiner, Ignaty, Dentro, Stefan C., Gonzalez, Santiago, Mitchell, Thomas J., Rubanova, Yulia, Anur, Pavana, Rosebrock, Daniel, Yu, Kaixian, Tarabichi, Maxime, Deshwar, Amit, Wintersinger, Jeff, Kleinheinz, Kortine, Vásquez-García, Ignacio, Haase, Kerstin, Sengupta, Subhajit, Macintyre, Geoff, Malikic, Salem, Donmez, Nilgun, Livitz, Dimitri G., Cmero, Mark, Demeulemeester, Jonas, Schumacher, Steve, Fan, Yu, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Boutros, Paul C., Bowtell, David D., Zhu, Hongtu, Getz, Gad, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S Cenk, Ji, Yuan, Peifer, Martin, Markowetz, Florian, Mustonen, Ville, Juan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., Loo, Peter Van