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
Published 2020-03-01

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
Published 2020-09-01

Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.

by Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, S Cenk Sahinalp
Published 2007-07-01

A multi-labeled tree dissimilarity measure for comparing “clonal trees” of tumor progression

by Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, S. Cenk Sahinalp
Published 2019-07-01

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
Published 2019-06-01

Tumor Phylogeny Topology Inference via Deep Learning

by Erfan Sadeqi Azer, Mohammad Haghir Ebrahimabadi, Salem Malikić, Roni Khardon, S. Cenk Sahinalp
Published 2020-11-01

smyRNA: a novel Ab initio ncRNA gene finder.

by Raheleh Salari, Cagri Aksay, Emre Karakoc, Peter J Unrau, Iman Hajirasouliha, S Cenk Sahinalp
Published 2009-01-01

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
Published 2007-09-01

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
Published 2018-02-01

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
Published 2018-04-01

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
Published 2017-07-01

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
Published 2018-02-01

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
Published 2015-01-01

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
Published 2017-10-01

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
Published 2017-07-01

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
Published 2011-05-01

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
Published 2020-04-01

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
Published 2020-02-01

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
Published 2019-02-01