Chapter 6: Structural variation and medical genomics. by Benjamin J Raphael

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Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data by Simone Zaccaria, Benjamin J. Raphael

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A zero-agnostic model for copy number evolution in cancer. by Henri Schmidt, Palash Sashittal, Benjamin J Raphael

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Using controls to limit false discovery in the era of big data by Matthew M. Parks, Benjamin J. Raphael, Charles E. Lawrence

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Accurate computation of survival statistics in genome-wide studies. by Fabio Vandin, Alexandra Papoutsaki, Benjamin J Raphael, Eli Upfal

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Simultaneous identification of multiple driver pathways in cancer. by Mark D M Leiserson, Dima Blokh, Roded Sharan, Benjamin J Raphael

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ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model by Palash Sashittal, Haochen Zhang, Christine A. Iacobuzio-Donahue, Benjamin J. Raphael

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Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. by Ali Bashir, Stanislav Volik, Colin Collins, Vineet Bafna, Benjamin J Raphael

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SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types by Tae Yoon Park, Mark D.M. Leiserson, Gunnar W. Klau, Benjamin J. Raphael

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Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells. by Lulu Cao, Yiyuan Ding, Norris Hung, Kebing Yu, Anna Ritz, Benjamin J Raphael, Arthur R Salomon

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Complexity and algorithms for copy-number evolution problems by Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira

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Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease. by Alexander S Brodsky, Andrew Fischer, Daniel H Miller, Souriya Vang, Shannon MacLaughlan, Hsin-Ta Wu, Jovian Yu, Margaret Steinhoff, Colin Collins, Peter J S Smith, Benjamin J Raphael, Laurent Brard

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Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor by Sasi Arunachalam, Karol Szlachta, Samuel W. Brady, Xiaotu Ma, Bensheng Ju, Bridget Shaner, Heather L. Mulder, John Easton, Benjamin J. Raphael, Matthew Myers, Christopher Tinkle, Sariah J. Allen, Brent A. Orr, Cynthia J. Wetmore, Suzanne J. Baker, Jinghui Zhang

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Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes by Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium

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

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Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment by Hua Sun, Song Cao, R. Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael C. Wendl, Sherri R. Davies, Matthew H. Bailey, Tina M. Primeau, Jeremy Hoog, Jacqueline L. Mudd, Dennis A. Dean, Rajesh Patidar, Li Chen, Matthew A. Wyczalkowski, Reyka G. Jayasinghe, Fernanda Martins Rodrigues, Nadezhda V. Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian A. Van Tine, Cynthia X. Ma, Rebecca Aft, Katherine C. Fuh, Julie K. Schwarz, Jose P. Zevallos, Sidharth V. Puram, John F. Dipersio, The NCI PDXNet Consortium, Brandi Davis-Dusenbery, Matthew J. Ellis, Michael T. Lewis, Michael A. Davies, Meenhard Herlyn, Bingliang Fang, Jack A. Roth, Alana L. Welm, Bryan E. Welm, Funda Meric-Bernstam, Feng Chen, Ryan C. Fields, Shunqiang Li, Ramaswamy Govindan, James H. Doroshow, Jeffrey A. Moscow, Yvonne A. Evrard, Jeffrey H. Chuang, Benjamin J. Raphael, Li Ding

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Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment by Hua Sun, Song Cao, R. Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael C. Wendl, Sherri R. Davies, Matthew H. Bailey, Tina M. Primeau, Jeremy Hoog, Jacqueline L. Mudd, Dennis A. Dean, Rajesh Patidar, Li Chen, Matthew A. Wyczalkowski, Reyka G. Jayasinghe, Fernanda Martins Rodrigues, Nadezhda V. Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian A. Van Tine, Cynthia X. Ma, Rebecca Aft, Katherine C. Fuh, Julie K. Schwarz, Jose P. Zevallos, Sidharth V. Puram, John F. Dipersio, The NCI PDXNet Consortium, Brandi Davis-Dusenbery, Matthew J. Ellis, Michael T. Lewis, Michael A. Davies, Meenhard Herlyn, Bingliang Fang, Jack A. Roth, Alana L. Welm, Bryan E. Welm, Funda Meric-Bernstam, Feng Chen, Ryan C. Fields, Shunqiang Li, Ramaswamy Govindan, James H. Doroshow, Jeffrey A. Moscow, Yvonne A. Evrard, Jeffrey H. Chuang, Benjamin J. Raphael, Li Ding

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