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Research

Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources

  • Xiaoyu Zhuo
  • Chad Tomlinson
  • Edward A. Belter
  • Prashant Kumar Kuntala
  • Wesley N. Saintilnord
  • Juan Jiang Tina Lindsay Juan F. Macias-Velasco Robert S. Fulton Ting Wang Derek Albracht Ivan A. Alexandrov Jamie Allen Alawi A. Alsheikh-Ali Nicolas Altemose Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Floris P. Barthel Edward A. Belter Halle D. Bender Andrew P. Blair Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Silvia Buonaiuto Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Mark J.P. Chaisson Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Hiram Clawson Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Danilo Dubocanin 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 E. Garza Margarita Geleta Mohammadmersad Ghorbani Tina A. Graves-Lindsay Richard E. Green Cristian Groza Bida Gu Andrea Guarracino Melissa Gymrek Maximilian Haeussler Leanne Haggerty Ira M. Hall Nancy F. Hansen Yue Hao Mohammad Amiruddin Hashmi David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Alexander G. Ioannidis Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Maryam Jehangir Juan Jiang Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Charles H. Langley Ben Langmead Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Jonathan LoTempio Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Walfred Ma Juan F. Macias-Velasco Kateryna D. Makova Maximillian G. Marin Christopher Markovic Tobias Marschall Franco L. Marsico 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 Pilar N. Ossorio Chie Owa Sadye Paez Benedict Paten Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan T. Rhyker Ranallo-Benavidez Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Fedor Ryabov Samuel Sacco Farnaz Salehi 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 Ahmad Abou Tayoun Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Ivo Violich 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
  • ... [+208 authors] ...,
  • Wenjin Zhang
  • Ying Zhou
  • Xiaoyu Zhuo
  • Giulia Zunino
  • First Published May 14, 2026
Research

Epigenetic characterization of pseudogenes across human tissues

  • Yunzhe Jiang
  • Beatrice Borsari
  • Mark Gerstein
  • First Published April 15, 2026
Resource

The PanOryza pangene catalog of Asian cultivated rice

  • Bruno Contreras-Moreira
  • Eshan Sharma
  • Shradha Saraf
  • Guy Naamati
  • Parul Gupta
  • Justin Elser Dmytro Chebotarov Kapeel Chougule Zhenyuan Lu Sharon Wei Andrew Olson Ian Tsang Disha Lodha Yong Zhou Zhichao Yu Wen Zhao Jianwei Zhang Sandeep Amberkar Kawinnat Sue-Ob Zhi Sun Maria Martin Kenneth L. McNally Doreen Ware Eric W. Deutsch Dario Copetti
  • ... [+20 authors] ...,
  • Rod A. Wing
  • Pankaj Jaiswal
  • Sarah Dyer
  • Andrew R. Jones
  • First Published December 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
Research

Oryza" > Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza

  • Chenbo Gong
  • Yicheng Huang
  • Mengmeng Liu
  • Yong Zhou
  • Yinwei Xu
  • Nahed Mohammed Xintong Qiao Andrea Zuccolo Weibo Xie
  • ... [+4 authors] ...,
  • Rod A. Wing
  • Jianwei Zhang
  • Fei Zhou
  • Yongjun Lin
  • First Published April 25, 2025
Resource

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

  • Michelle Kudron
  • Louis Gevirtzman
  • Alec Victorsen
  • Bridget C. Lear
  • Jiahao Gao
  • Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
  • ... [+16 authors] ...,
  • LaDeana Hillier
  • Susan E. Celniker
  • Valerie Reinke
  • Robert H. Waterston
  • First Published October 22, 2024
Method

Accurate sequencing of DNA motifs able to form alternative (non-B) structures

  • Matthias H. Weissensteiner
  • Marzia A. Cremona
  • Wilfried M. Guiblet
  • Nicholas Stoler
  • Robert S. Harris
  • Monika Cechova
  • ... [+1 authors] ...,
  • Kristin A. Eckert
  • Francesca Chiaromonte
  • Yi-Fei Huang
  • Kateryna D. Makova
  • First Published July 11, 2023
In memoriam

C. Thomas Caskey (1938–2022)

  • Richard A. Gibbs
  • Aravinda Chakravarti
  • Evan E. Eichler
  • Eric D. Green
  • Richard M. Myers
  • Anne C. Ferguson-Smith
  • Kateryna D. Makova
  • Hillary E. Sussman
  • First Published February 17, 2022
Research

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome

  • Wilfried M. Guiblet
  • Michael DeGiorgio
  • Xiaoheng Cheng
  • Francesca Chiaromonte
  • Kristin A. Eckert
  • Yi-Fei Huang
  • Kateryna D. Makova
  • First Published June 29, 2021
Resource

Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9

  • Yonghua Sun
  • Bo Zhang
  • Lingfei Luo
  • De-Li Shi
  • Han Wang
  • Zongbin Cui Honghui Huang Ying Cao Xiaodong Shu Wenqing Zhang Jianfeng Zhou Yun Li Jiulin Du Qingshun Zhao Jun Chen Hanbing Zhong Tao P. Zhong Li Li Jing-Wei Xiong Jinrong Peng Wuhan Xiao Jian Zhang Jihua Yao Zhan Yin Xianming Mo Gang Peng Jun Zhu Yan Chen Yong Zhou Dong Liu Weijun Pan Yiyue Zhang Hua Ruan Feng Liu Zuoyan Zhu Anming Meng The ZAKOC Consortium Yonghua Sun Luyuan Pan Houpeng Wang Weixun Xie Mudan He Ding Ye Kuoyu Li Feng Xiong Liyue Liu Linglu Li Yun Zhang Bo Zhang Da Liu Zhenchao Cheng Yingying Hu Qian Wu Zhou Luo Yutian Zhang Yingdan Wu Wenyuan Li Lingfei Luo Jianlong Ma Dashuang Mo Pengcheng Cai Jinzi Chen Junhui Sun Yang Zhou Chuan Wu Rui Ni De-Li Shi Ming Shao Yan-Jun Zhang Li-Jun Feng Xiao-Ning Cheng Ji-Tong Li Yan-Yi Xing Yan Zhang Ya-Ping Meng Bei-Bei Yu Han Wang Jian Huang Shuqing Zhang Cheng Ji Yicheng Tan Jingjing Wang Fanmiao Zhang Mingyong Wang Guodong Huang Zhaomin Zhong Wei Zhang Zongbin Cui Yong Long Guili Song Xiaohui Li Xixi Li Kai Chen Jing Ren Junjun Yan Qing Li Honghui Huang Hua Ruan Shicheng Zhu Xuejiao Chen Jingjing Pan Faming Jiang Jiehui Chen Chao Huang Guoping Dong Xiaogui Yi Ying Cao Ruikun Hu Weilai Huang Jiangfang Liu Hong WangXiao Dong Shu Jianhong Xia Shaoyang Zhao Pengtao Wang Xiuhua Wu Wenqing Zhang Yiyue Zhang Mengchang Xu Wei Liu Zhibing Huang Qing Lin Mei Wu Jianfeng Zhou Aibo Sheng Peipei Tang Xiaoxia Gong Wei Mou Congcong Zu Yun Li Ling Lu Yunzhang Liu Xiaozhi Rong Jianyang Chen Jiulin Du Jiwen Bu Xufei Du Tingting Liu Shanye Gu Qingshun Zhao Zhangji Dong Xiaohua Dong Shasha Cao Yunyun Yue Chun Gu Meijing Liu Jun Chen Hongjian Gong Hanbing Zhong Xuanjun Yang Jiahao Chen Qiushi Xu Tao P. Zhong Daqin Jin Peilu She Jianjian Sun Kaa Seng Lai Li Li Yu Zhang Yanyan Shi Fangying Zhao Jing-Wei Xiong Meijun Pang Lu Gao Lei Lei Jinrong Peng Jane Lo Wuhan Xiao Xiaolian Cai Gang Ouyang Jian Zhang Weirui Ma Liyun Miao Jihua Yao Yu Hu Zhan Yin Xianming Mo Xue Li Gang Peng Cuizhen Zhang Fenghua Wang Jun Zhu Ruimeng Yang Hao Yuan Yan Chen Yi Pan Yong Zhou Dong Liu Feng Zhao Weijun Pan Feng Liu Yanyan Ding Yuanyuan Xue Lu Wang Yifan Zhang Dongyuan Ma Xinyan Lu Shuai Gao Jun Xia Zuoyan Zhu Anming Meng Xingfeng Liu Juhui Qiu Bo Gong Luxi Chen Cong Xiong Likun Yao
  • ... [+202 authors] ...,
  • Cencan Xing
  • Yixia Wang
  • Weimin Shen
  • Jiawei Sun
  • First Published December 12, 2019
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