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S

S. Cenk Şahinalp

national institutes of health

36H-index
143Paper Count
8.4KCitation Count
Published Papers 35
Publication Date
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Long-read sequencing of single cell-derived melanoma sublines reveals divergent and parallel genomic and epigenomic evolutionary trajectories
errNature Communications
IF15.7
err2026-07-16
err0
errOAAI
errYuelin Liu; Anton Goretsky; Ayse G. Keskus; Salem Malikic; Tanveer Ahmad; E. Michael Gertz; Farid Rashidi Mehrabadi; Michael Kelly; Maria O. Hernandez; Charlie Seibert; Juan Manuel Caravaca; Kayla Kline; Yongmei Zhao; Ying Wu; Biraj Shrestha; Bao Tran; Arindam Ghosh; Xiwen Cui; Antonella Sassano; Laksh Malik; Breeana Baker; Cornelis Blauwendraat; Kimberley J. Billingsley; Sandra Burkett; Eva Perez-Guijarro; Glenn Merlino; Erin K. Molloy; S. Cenk Sahinalp; Chi-Ping Day; Mikhail Kolmogorov
errShare
errSave
LCPan: efficient variation graph construction using locally consistent parsing
errGenome Biology
IF9.4
err2026-04-24
err0
errOAAI
errAkmuhammet Ashyralyyev; Zülal Bingöl; Begüm Filiz Öz; Kaiyuan Zhu; Salem Malikic; Uzi Vishkin; S. Cenk Sahinalp; Can Alkan
errShare
errSave
Chimeric antigen receptor T cells against the IGHV4-34 B cell receptor specifically eliminate neoplastic and autoimmune B cells
errScience Translational Medicine
IF14.6
err2026-02-04
err0
PREAI
errIvan J. Cohen; Audrey C. Bochi-Layec; Jean Lemoine; Scott Jenks; Pedram Bayat; Ki Hyun Kim; Huiwu Zhao; Ositadimma Ugwuanyi; Federico Stella; Guido Ghilardi; Giulia Gabrielli; Sarah McCuaig; Anastasia Iatrou; Elisavet Vlachonikola; Maria Karipidou; Eleni Bouziani; David Espie; Ranjani Ramasubramanian; Andreas Agathangelidis; Aditya Bhosale; Luca Paruzzo; Giovanni Medico; Bronte Kolar; Regina Bugrovsky; Puneeth Guruprasad; Li-Ping Wang; Jaryse Harris; Evgeny Arons; Yunlin Zhang; Raymone Pajarillo; Portia A. Kreiger; Chi-Ping Day; S. Cenk Sahinalp; Chih Hao Wu; Alessia Santi; Bria Fulmer; Marcos Cases; Matthew B. Palmer; Patrizia Porazzi; E. John Wherry; Robert J. Kreitman; Enrico Tiacci; Sokratis A. Apostolidis; Edward M. Behrens; Vijay Bhoj; Ignacio Sanz; Giorgio Inghirami; Stephen J. Schuster; Paolo Ghia; Kostas Stamatopoulos; Marco Ruella
errShare
errSave
Secure phasing of private genomes in a trusted execution environment with TX-Phase
errGENOME RESEARCH
IF5.5
err2025-12-01
err1
PREAI
errDokmai, Natnatee; Zhu, Kaiyuan; Sahinalp, S. Cenk; Cho, Hyunghoon
errShare
errSave
Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer
errBIOINFORMATICS
IF5.4
err2025-07-01
err0
errOAAI
errLi, Xuan Cindy; Liu, Yuelin; Schaffer, Alejandro A.; Mount, Stephen M.; Sahinalp, S. Cenk
errShare
errSave
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing
errNATURE BIOTECHNOLOGY
IF41.7
err2025-04-04
err1
PREAI
errKeskus, Ayse G.; Bryant, Asher; Ahmad, Tanveer; Yoo, Byunggil; Aganezov, Sergey; Goretsky, Anton; Donmez, Ataberk; Lansdon, Lisa A.; Rodriguez, Isabel; Park, Jimin; Liu, Yuelin; Cui, Xiwen; Gardner, Joshua; McNulty, Brandy; Sacco, Samuel; Shetty, Jyoti; Zhao, Yongmei; Tran, Bao; Narzisi, Giuseppe; Helland, Adrienne; Cook, Daniel E.; Chang, Pi-Chuan; Kolesnikov, Alexey; Carroll, Andrew; Molloy, Erin K.; Bi, Chengpeng; Walter, Adam; Gibson, Margaret; Pushel, Irina; Guest, Erin; Pastinen, Tomi; Shafin, Kishwar; Miga, Karen H.; Malikic, Salem; Day, Chi-Ping; Robine, Nicolas; Sahinalp, Cenk; Dean, Michael; Farooqi, Midhat S.; Paten, Benedict; Kolmogorov, Mikhail
errShare
errSave
Characterization of MAIT cells in glioblastoma reveals a potential immunosuppressive role through a MAIT-neutrophil axis
errNEURO-ONCOLOGY ADVANCES
IF4.1
err2025-01-01
err0
errOAAI
errKeretsu, Seketoulie; Hana, Taijun; Lee, Alexander; Kedei, Noemi; Malik, Nargis; Kim, Hye; Spurgeon, Jo; Khayrullina, Guzal; Ruf, Benjamin; Hara, Ayaka; Coombs, Morgan; Watowich, Matthew B.; Hari, Ananth; Ford, Michael K. B.; Sahinalp, S. Cenk; Watanabe, Masashi; Zaki, George; Gilbert, Mark R.; Cimino, Patrick J.; Prins, Robert; Terabe, Masaki
errShare
errSave
Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes
errSCIENCE ADVANCES
IF12.5
err2024-07-05
err2
errOAAI
errRobinson, Welles; Stone, Joshua K.; Schischlik, Fiorella; Gasmi, Billel; Kelly, Michael C.; Seibert, Charlie; Dadkhah, Kimia; Gertz, E. Michael; Lee, Joo Sang; Zhu, Kaiyuan; Ma, Lichun; Wang, Xin Wei; Sahinalp, S. Cenk; Patro, Rob; Leiserson, Mark D. M.; Harris, Curtis C.; Schaffer, Alejandro A.; Ruppin, Eytan
errShare
errSave
Melanoma clonal subline analysis reveals genetic factors driving intra-tumor heterogeneity
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errKeskus, Ayse; Goretsky, Anton; Liu, Yuelin; Cui, Xiwen; Ahmad, Tanveer; Guijarro, Eva Perez; Bryant, Asher; Malloy, Erin; Malikic, Salem; Merlino, Glenn; Day, Chi-Ping; Sahinalp, Cenk; Kolmogorov, Mikhail
errShare
errSave
Computational pharmacogenotype extraction from clinical next-generation sequencing
errFRONTIERS IN ONCOLOGY
IF3.3
err2023-07-04
err7
errOAAI
errShugg, Tyler; Ly, Reynold C.; Osei, Wilberforce; Rowe, Elizabeth J.; Granfield, Caitlin A.; Lynnes, Ty C.; Medeiros, Elizabeth B.; Hodge, Jennelle C.; Breman, Amy M.; Schneider, Bryan P.; Sahinalp, S. Cenk; Numanagic, Ibrahim; Salisbury, Benjamin A.; Bray, Steven M.; Ratcliff, Ryan; Skaar, Todd C.
errShare
errSave
An efficient genotyper and star-allele caller for pharmacogenomics
errGENOME RESEARCH
IF5.5
err2023-01-19
err16
errOAAI
errHari, Ananth; Zhou, Qinghui; Gonzaludo, Nina; Harting, John; Scott, Stuart A.; Qin, Xiang; Scherer, Steve; Sahinalp, S. Cenk; Numanagic, Ibrahim
errShare
errSave
Pathway and network analysis of more than 2500 whole cancer genomes (vol 11, 729, 2020)
errNATURE COMMUNICATIONS
IF15.7
err2022-12-08
err0
errOAAI
errReyna, Matthew A.; Haan, David; Paczkowska, Marta; Verbeke, Lieven P. C.; Vazquez, Miguel; Kahraman, Abdullah; Pulido-Tamayo, Sergio; Barenboim, Jonathan; Wadi, Lina; Dhingra, Priyanka; Shrestha, Raunak; Getz, Gad; Lawrence, Michael S.; Pedersen, Jakob Skou; Rubin, Mark A.; Wheeler, David A.; Brunak, Sren; Izarzugaza, Jose M. G.; Khurana, Ekta; Marchal, Kathleen; von Mering, Christian; Sahinalp, S. Cenk; Valencia, Alfonso; Reimand, Jueri; Stuart, Joshua M.; Raphael, Benjamin J.
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errSave
Strain level microbial detection and quantification with applications to single cell metagenomics
errNATURE COMMUNICATIONS
IF15.7
err2022-10-28
err4
errOAAI
errZhu, Kaiyuan; Schaeffer, Alejandro A.; Robinson, Welles; Xu, Junyan; Ruppin, Eytan; Ergun, A. Funda; Ye, Yuzhen; Sahinalp, S. Cenk
errShare
errSave
Big data in basic and translational cancer research
errNATURE REVIEWS CANCER
IF66.8
err2022-09-05
err101
errOAAI
errJiang, Peng; Sinha, Sanju; Aldape, Kenneth; Hannenhalli, Sridhar; Sahinalp, Cenk; Ruppin, Eytan
errShare
errSave
Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing
errJOURNAL OF MOLECULAR DIAGNOSTICS
IF3.4
err2022-06-01
err12
errOAAI
errLy, Reynold C.; Shugg, Tyler; Ratcliff, Ryan; Osei, Wilberforce; Lynnes, Ty C.; Pratt, Victoria M.; Schneider, Bryan P.; Radovich, Milan; Bray, Steven M.; Salisbury, Benjamin A.; Parikh, Baiju; Sahinalp, S. Cenk; Numanagic, Ibrahim; Skaar, Todd C.
errShare
errSave
CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype AnalysisA GeT-RM Collaborative Project
errJOURNAL OF MOLECULAR DIAGNOSTICS
IF3.4
err2022-04-01
err27
errOAAI
errGaedigk, Andrea; Boone, Erin C.; Scherer, Steven E.; Lee, Seung-been; Numanagic, Ibrahim; Sahinalp, Cenk; Smith, Joshua D.; McGee, Sean; Radhakrishnan, Aparna; Qin, Xiang; Wang, Wendy Y.; Farrow, Emily G.; Gonzaludo, Nina; Halpern, Aaron L.; Nickerson, Deborah A.; Miller, Neil A.; Pratt, Victoria M.; Kalman, Lisa, V
errShare
errSave
Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma
errMOLECULAR & CELLULAR PROTEOMICS
IF5.5
err2021-01-01
err21
errOAAI
errQi, Yue A.; Maity, Tapan K.; Cultraro, Constance M.; Misra, Vikram; Zhang, Xu; Ade, Catherine; Gao, Shaojian; Milewski, David; Nguyen, Khoa D.; Ebrahimabadi, Mohammad H.; Hanada, Ken-ichi; Khan, Javed; Sahinalp, Cenk; Yang, James C.; Guha, Udayan
errShare
errSave
Clonal Evolution and Heterogeneity of Osimertinib Acquired Resistance Mechanisms in EGFR Mutant Lung Cancer
errCELL REPORTS MEDICINE
IF10.6
err2020-04-01
err109
errOAAI
errRoper, Nitin; Brown, Anna-Leigh; Wei, Jun S.; Pack, Svetlana; Trindade, Christopher; Kim, Chul; Restifo, Olivia; Gao, Shaojian; Sindiri, Sivasish; Mehrabadi, Farid; El Meskini, Rajaa; Ohler, Zoe Weaver; Maity, Tapan K.; Venugopalan, Abhilash; Cultraro, Constance M.; Akoth, Elizabeth; Padiernos, Emerson; Chen, Haobin; Kesarwala, Aparna; Smart, DeeDee K.; Nilubol, Naris; Rajan, Arun; Piotrowska, Zofia; Xi, Liqiang; Raffeld, Mark; Panchenko, Anna R.; Sahinalp, Cenk; Hewitt, Stephen; Hoang, Chuong D.; Khan, Javed; Guha, Udayan
errShare
errSave
Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data
errNATURE COMMUNICATIONS
IF15.7
err2019-06-21
err87
errOAAI
errMalikic, Salem; Jahn, Katharina; Kuipers, Jack; Sahinalp, S. Cenk; Beerenwinkel, Niko
errShare
errSave
The evolutionary history of 2,658 cancers
errCANCER RESEARCH
IF16.6
err2018-07-01
err0
PREAI
errJolly, 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; Vasquez-Garcia, 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.; Van Loo, Peter
errShare
errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
G
Gad Getz
H-index: 248 · Papers: 1.8K
E
Evan E. Eichler
H-index: 191 · Papers: 864
M
Marco A. Marra
H-index: 190 · Papers: 1.3K
R
Richard A. Gibbs
H-index: 190 · Papers: 1.3K
S
Steven J.M. Jones
H-index: 189 · Papers: 1.3K
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