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Method

Secure phasing of private genomes in a trusted execution environment with TX-Phase

  • Natnatee Dokmai
  • Kaiyuan Zhu
  • S. Cenk Sahinalp
  • Hyunghoon Cho
  • First Published November 12, 2025
Method

Genotyping of selected germline adaptive immune system loci using short-read sequencing data

  • Michael K.B. Ford
  • Ananth Hari
  • Meredith Yeager
  • Lisa Mirabello
  • Stephen Chanock
  • Ibrahim Numanagić
  • S. Cenk Sahinalp
  • First Published August 5, 2025
Method

r-index-based pangenome indexing" > Accurate short-read alignment through r-index-based pangenome indexing

  • Rahul Varki
  • Massimiliano Rossi
  • Eddie Ferro
  • Marco Oliva
  • Erik Garrison
  • Ben Langmead
  • Christina Boucher
  • First Published June 12, 2025
Method

Highly accurate assembly polishing with DeepPolisher

  • Mira Mastoras
  • Mobin Asri
  • Lucas Brambrink
  • Prajna Hebbar
  • Alexey Kolesnikov
  • Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Richard Durbin Jana Ebler Evan E Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa' A. Garrison John Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
  • ... [+196 authors] ...,
  • Wenjin Zhang
  • Ying Zhou
  • Ivo Violich
  • Giulia Zunino
  • First Published May 19, 2025
Method

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

  • Sergey Koren
  • Zhigui Bao
  • Andrea Guarracino
  • Shujun Ou
  • Sara Goodwin
  • Katharine M. Jenike Julian Lucas Brandy McNulty Jimin Park Mikko Rautiainen Arang Rhie Dick Roelofs Harrie Schneiders Ilse Vrijenhoek Koen Nijbroek Olle Nordesjo Sergey Nurk Mike Vella Katherine R. Lawrence Doreen Ware Michael C. Schatz Erik Garrison Sanwen Huang
  • ... [+18 authors] ...,
  • William Richard McCombie
  • Karen H. Miga
  • Alexander H.J. Wittenberg
  • Adam M. Phillippy
  • First Published November 6, 2024
Method

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

  • Yuelin Liu
  • Xuan Cindy Li
  • Farid Rashidi Mehrabadi
  • Alejandro A. Schäffer
  • Drew Pratt
  • David R. Crawford Salem Malikić Erin K. Molloy Vishaka Gopalan
  • ... [+4 authors] ...,
  • Stephen M. Mount
  • Eytan Ruppin
  • Kenneth D. Aldape
  • S. Cenk Sahinalp
  • First Published June 14, 2023
Method

An efficient genotyper and star-allele caller for pharmacogenomics

  • Ananth Hari
  • Qinghui Zhou
  • Nina Gonzaludo
  • John Harting
  • Stuart A. Scott
  • Xiang Qin
  • Steve Scherer
  • S. Cenk Sahinalp
  • Ibrahim Numanagić
  • First Published January 19, 2023
Method

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

  • Salem Malikic
  • Farid Rashidi Mehrabadi
  • Simone Ciccolella
  • Md. Khaledur Rahman
  • Camir Ricketts
  • Ehsan Haghshenas
  • ... [+1 authors] ...,
  • Daniel Seidman
  • Faraz Hach
  • Iman Hajirasouliha
  • S. Cenk Sahinalp
  • First Published October 18, 2019
Method

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

  • Raunak Shrestha
  • Ermin Hodzic
  • Thomas Sauerwald
  • Phuong Dao
  • Kendric Wang
  • Jake Yeung Shawn Anderson
  • ... [+2 authors] ...,
  • Fabio Vandin
  • Gholamreza Haffari
  • Colin C. Collins
  • S. Cenk Sahinalp
  • First Published July 18, 2017
Method

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

  • Andrew McPherson
  • Chunxiao Wu
  • Alexander W. Wyatt
  • Sohrab Shah
  • Colin Collins
  • S. Cenk Sahinalp
  • First Published June 28, 2012
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