S. Cenk Şahinalp - Publications, H-index & Citations

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S. Cenk Şahinalp

Indiana University Bloomington

41H-index

131Paper Count

1.9WCitation Count

Published Papers 23

Publication Date

Learning-augmented sketching offers improved performance for privacy preserving and secure GWAS

ISCIENCE

IF4.1

2025-02-01

OAAI

Xu, Junyan; Zhu, Kaiyuan; Cai, Jieling; Kockan, Can; Dokmai, Natnatee; Cho, Hyunghoon; Woodruff, David P.; Sahinalp, S. Cenk

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Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones

CELL SYSTEMS

IF7.7

2025-01-01

OAAI

Hirsch, M. G.; Pal, Soumitra; Mehrabadi, Farid Rashidi; Malikic, Salem; Gruen, Charli; Sassano, Antonella; Perez-Guijarro, Eva; Merlino, Glenn; Sahinalp, S. Cenk; Molloy, Erin K.; Day, Chi-Ping; Przytycka, Teresa M.

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Geny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes

FRONTIERS IN IMMUNOLOGY

IF5.9

2024-12-23

OAAI

Zhou, Qinghui; Ghezelji, Mazyar; Hari, Ananth; Ford, Michael K. B.; Holley, Connor; Sahinalp, S. Cenk; Numanagic, Ibrahim

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Structural variant dynamics in melanoma: Unraveling tumor heterogeneity and evolution

CANCER RESEARCH

IF16.6

2024-03-22

PREAI

Cui, Xiwen; Keskus, Ayse G.; Mehrabadi, Farid R.; Malikic, Salem; Kolmogorov, Mikhail; Day, Chi-Ping; Merlino, Glenn; Sahinalp, S. Cenk

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Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models

CANCER RESEARCH

IF16.6

2023-04-04

PREAI

Li, Xuan C.; Liu, Yuelin; Mehrabadi, Farid Rashidi; Schaffer, Alejandro A.; Pratt, Drew; Crawford, David R.; Malikic, Salem; Molloy, Erin K.; Gopalan, Vishaka; Mount, Stephen M.; Ruppin, Eytan; Aldape, Kenneth; Sahinalp, S. Cenk

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Analytical validation of a computational method for pharmacogenetic genotyping from clinical exome sequencing

GENETICS IN MEDICINE

IF6.2

2022-03-01

OAAI

Ly, Reynold; Shugg, Tyler; Ratcliff, Ryan; Osei, Wilberforce; Pratt, Victoria; Schneider, Bryan; Radovich, Milan; Bray, Steven; Salisbury, Benjamin; Parikh, Baiju; Sahinalp, S. Cenk; Numanagic, Ibrahim; Skaar, Todd

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Privacy-preserving genotype imputation in a trusted execution environment

CELL SYSTEMS

IF7.7

2021-10-01

OAAI

Dokmai, Natnatee; Kockan, Can; Zhu, Kaiyuan; Wang, XiaoFeng; Sahinalp, S. Cenk; Cho, Hyunghoon

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Pathway and network analysis of more than 2500 whole cancer genomes

NATURE COMMUNICATIONS

IF15.7

2020-02-05

OAAI

Reyna, 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, Soren; Izarzugaza, Jose M. G.; Khurana, Ekta; Marchal, Kathleen; von Mering, Christian; Sahinalp, S. Cenk; Valencia, Alfonso; Reimand, Juri; Stuart, Joshua M.; Raphael, Benjamin J.

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PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data

GENOME RESEARCH

IF5.5

2019-10-18

OAAI

Malikic, Salem; Mehrabadi, Farid Rashidi; Ciccolella, Simone; Rahman, Md. Khaledur; Ricketts, Camir; Haghshenas, Ehsan; Seidman, Daniel; Hach, Faraz; Hajirasouliha, Iman; Sahinalp, S. Cenk

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Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks

GIGASCIENCE

IF3.9

2019-04-11

OAAI

Hodzic, Ermin; Shrestha, Raunak; Zhu, Kaiyuan; Cheng, Kuoyuan; Collins, Colin C.; Sahinalp, S. Cenk

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Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA

NUCLEIC ACIDS RESEARCH

IF13.1

2019-02-13

OAAI

Gawronskii, Alexander R.; Lin, Yen-Yi; McConeghy, Brian; LeBihan, Stephane; Asghari, Hossein; Kockan, Can; Orabi, Baraa; Adra, Nabil; Pili, Roberto; Collins, Colin C.; Sahinalp, S. Cenk; Hach, Faraz

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Stromal Gene Expression is Predictive for Metastatic Primary Prostate Cancer

EUROPEAN UROLOGY

IF25.2

2018-04-01

OAAI

Mo, Fan; Lin, Dong; Takhar, Mandeep; Ramnarine, Varune Rohan; Dong, Xin; Bell, Robert H.; Volik, Stanislav V.; Wang, Kendric; Xue, Hui; Wang, Yuwei; Haegert, Anne; Anderson, Shawn; Brahmbhatt, Sonal; Erho, Nicholas; Wang, Xinya; Gout, Peter W.; Morris, James; Karnes, R. Jeffrey; Den, Robert B.; Klein, Eric A.; Schaeffer, Edward M.; Ross, Ashley; Ren, Shancheng; Sahinalp, S. Cenk; Li, Yingrui; Xu, Xun; Wang, Jun; Wang, Jian; Gleave, Martin E.; Davicioni, Elai; Sun, Yinghao; Wang, Yuzhuo; Collin, Colin C.

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Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

NATURE COMMUNICATIONS

IF15.7

2018-02-26

OAAI

Numanagic, Ibrahim; Malikic, Salem; Ford, Michael; Qin, Xiang; Toji, Lorraine; Radovich, Milan; Skaar, Todd C.; Pratt, Victoria M.; Berger, Bonnie; Scherer, Steve; Sahinalp, S. Cenk

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ReMixT: clone-specific genomic structure estimation in cancer (vol 18, 140, 2017)

GENOME BIOLOGY

IF9.4

2017-10-06

OAAI

McPherson, Andrew W.; Roth, Andrew; Ha, Gavin; Chauve, Cedric; Steif, Adi; de Souza, Camila P. E.; Eirew, Peter; Bouchard-Cote, Alexandre; Aparicio, Sam; Sahinalp, S. Cenk; Shah, Sohrab P.

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ReMixT: clone-specific genomic structure estimation in cancer

GENOME BIOLOGY

IF9.4

2017-07-27

OAAI

McPherson, Andrew W.; Roth, Andrew; Ha, Gavin; Chauve, Cedric; Steif, Adi; de Souza, Camila P. E.; Eirew, Peter; Bouchard-Cote, Alexandre; Aparicio, Sam; Sahinalp, S. Cenk; Shah, Sohrab P.

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HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology

GENOME RESEARCH

IF5.5

2017-07-18

OAAI

Shrestha, Raunak; Hodzic, Ermin; Sauerwald, Thomas; Dao, Phuong; Wang, Kendric; Yeung, Jake; Anderson, Shawn; Vandin, Fabio; Haffari, Gholamreza; Collins, Colin C.; Sahinalp, S. Cenk

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From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer

JOURNAL OF PATHOLOGY

IF5.2

2012-06-06

171

OAAI

Lapuk, Anna V.; Wu, Chunxiao; Wyatt, Alexander W.; McPherson, Andrew; McConeghy, Brian J.; Brahmbhatt, Sonal; Mo, Fan; Zoubeidi, Amina; Anderson, Shawn; Bell, Robert H.; Haegert, Anne; Shukin, Robert; Wang, Yuzhuo; Fazli, Ladan; Hurtado-Coll, Antonio; Jones, Edward C.; Hach, Faraz; Hormozdiari, Fereydoun; Hajirasouliha, Iman; Boutros, Paul C.; Bristow, Robert G.; Zhao, Yongjun; Marra, Marco A.; Fanjul, Andrea; Maher, Christopher A.; Chinnaiyan, Arul M.; Rubin, Mark A.; Beltran, Himisha; Sahinalp, S. Cenk; Gleave, Martin E.; Volik, Stanislav V.; Collins, Colin C.

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Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer

JOURNAL OF PATHOLOGY

IF5.2

2012-03-21

OAAI

Wu, Chunxiao; Wyatt, Alexander W.; Lapuk, Anna V.; McPherson, Andrew; McConeghy, Brian J.; Bell, Robert H.; Anderson, Shawn; Haegert, Anne; Brahmbhatt, Sonal; Shukin, Robert; Mo, Fan; Li, Estelle; Fazli, Ladan; Hurtado-Coll, Antonio; Jones, Edward C.; Butterfield, Yaron S.; Hach, Faraz; Hormozdiari, Fereydoun; Hajirasouliha, Iman; Boutros, Paul C.; Bristow, Robert G.; Jones, Steven J. M.; Hirst, Martin; Marra, Marco A.; Maher, Christopher A.; Chinnaiyan, Arul M.; Sahinalp, S. Cenk; Gleave, Martin E.; Volik, Stanislav V.; Collins, Colin C.

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Alu repeat discovery and characterization within human genomes

GENOME RESEARCH

IF5.5

2010-12-03

OAAI

Hormozdiari, Fereydoun; Alkan, Can; Ventura, Mario; Hajirasouliha, Iman; Malig, Maika; Hach, Faraz; Yorukoglu, Deniz; Phuong Dao; Bakhshi, Marzieh; Sahinalp, S. Cenk; Eichler, Evan E.

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Conifers have a unique small RNA silencing signature

RNA

IF5

2008-06-19

OAAI

Dolgosheina, Elena V.; Morin, Ryan D.; Aksay, Gozde; Sahinalp, S. Cenk; Magrini, Vincent; Mardis, Elaine R.; Mattsson, Jim; Unrau, Peter J.

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Research Directions