Genotyping and Copy Number Analysis of Immunoglobulin Heavy Chain Variable Genes Using Long Reads by Michael Ford, Ehsan Haghshenas, Corey T. Watson, S. Cenk Sahinalp

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Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads by Michael Ford, Ehsan Haghshenas, Corey T. Watson, S. Cenk Sahinalp

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A multi-labeled tree dissimilarity measure for comparing “clonal trees” of tumor progression by Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, S. Cenk Sahinalp

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Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data by Salem Malikic, Katharina Jahn, Jack Kuipers, S. Cenk Sahinalp, Niko Beerenwinkel

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smyRNA: a novel Ab initio ncRNA gene finder. by Raheleh Salari, Cagri Aksay, Emre Karakoc, Peter J Unrau, Iman Hajirasouliha, S Cenk Sahinalp

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Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. by Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S Cenk Sahinalp, Evan E Eichler

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Publisher Correction: Optimal compressed representation of high throughput sequence data via light assembly by Antonio A. Ginart, Joseph Hui, Kaiyuan Zhu, Ibrahim Numanagić, Thomas A. Courtade, S. Cenk Sahinalp, David N. Tse

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Learning-augmented sketching offers improved performance for privacy preserving and secure GWAS by Junyan Xu, Kaiyuan Zhu, Jieling Cai, Can Kockan, Natnatee Dokmai, Hyunghoon Cho, David P. Woodruff, S. Cenk Sahinalp

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Strain level microbial detection and quantification with applications to single cell metagenomics by Kaiyuan Zhu, Alejandro A. Schäffer, Welles Robinson, Junyan Xu, Eytan Ruppin, A. Funda Ergun, Yuzhen Ye, S. Cenk Sahinalp

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Geny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes by Qinghui Zhou, Mazyar Ghezelji, Ananth Hari, Ananth Hari, Michael K. B. Ford, Connor Holley, S. Cenk Sahinalp, Ibrahim Numanagić

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PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension by Feng Chen, Chenghong Wang, Wenrui Dai, Xiaoqian Jiang, Noman Mohammed, Md Momin Al Aziz, Md Nazmus Sadat, Cenk Sahinalp, Kristin Lauter, Shuang Wang

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Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes by Ibrahim Numanagić, Salem Malikić, Michael Ford, Xiang Qin, Lorraine Toji, Milan Radovich, Todd C. Skaar, Victoria M. Pratt, Bonnie Berger, Steve Scherer, S. Cenk Sahinalp

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Robustness of Massively Parallel Sequencing Platforms. by Pınar Kavak, Bayram Yüksel, Soner Aksu, M Oguzhan Kulekci, Tunga Güngör, Faraz Hach, S Cenk Şahinalp, Turkish Human Genome Project, Can Alkan, Mahmut Şamil Sağıroğlu

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Correction to: ReMixT: clone-specific genomic structure estimation in cancer by Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah

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ReMixT: clone-specific genomic structure estimation in cancer by Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah

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deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. by Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G F Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A Marra, Martin Hirst, Torsten O Nielsen, S Cenk Sahinalp, David Huntsman, Sohrab P Shah

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Computational pharmacogenotype extraction from clinical next-generation sequencing by Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagić, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar

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Clonal Evolution and Heterogeneity of Osimertinib Acquired Resistance Mechanisms in EGFR Mutant Lung Cancer by Nitin Roper, Anna-Leigh Brown, Jun S. Wei, Svetlana Pack, Christopher Trindade, Chul Kim, Olivia Restifo, Shaojian Gao, Sivasish Sindiri, Farid Mehrabadi, Rajaa El Meskini, Zoe Weaver Ohler, Tapan K. Maity, Abhilash Venugopalan, Constance M. Cultraro, Elizabeth Akoth, Emerson Padiernos, Haobin Chen, Aparna Kesarwala, DeeDee K. Smart, Naris Nilubol, Arun Rajan, Zofia Piotrowska, Liqiang Xi, Mark Raffeld, Anna R. Panchenko, Cenk Sahinalp, Stephen Hewitt, Chuong D. Hoang, Javed Khan, Udayan Guha

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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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BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma by Raunak Shrestha, Noushin Nabavi, Yen-Yi Lin, Fan Mo, Shawn Anderson, Stanislav Volik, Hans H. Adomat, Dong Lin, Hui Xue, Xin Dong, Robert Shukin, Robert H. Bell, Brian McConeghy, Anne Haegert, Sonal Brahmbhatt, Estelle Li, Htoo Zarni Oo, Antonio Hurtado-Coll, Ladan Fazli, Joshua Zhou, Yarrow McConnell, Andrea McCart, Andrew Lowy, Gregg B. Morin, Tianhui Chen, Mads Daugaard, S. Cenk Sahinalp, Faraz Hach, Stephane Le Bihan, Martin E. Gleave, Yuzhuo Wang, Andrew Churg, Colin C. Collins

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