Publications

Towards complete and error-free genome assemblies of all vertebrate species⟶

Arang Rhie,  Shane A. McCarthy,  Olivier Fedrigo,  Joana Damas,  Giulio Formenti,  Sergey Koren,  Marcela Uliano-Silva,  William Chow, Arkarachai Fungtammasan, Gregory L. Gedman, Lindsey J. Cantin,
Françoise Thibaud-Nissen,  Leanne Haggerty, Chul Lee, Byung June Ko, Juwan Kim,  Iliana Bista, Michelle Smith,  Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler,
Sadye Paez, Jason Howard, Sonja C. Vernes,  Tanya M. Lama,  Frank C. Grutzner,  Wesley C. Warren,  Christopher Balakrishnan,  Dave Burt,  Julia M. George, Matthew Biegler, David Iorns,  Andrew Digby, Daryl Eason,  Taylor Edwards,  Mark Wilkinson,
George F. Turner,  Axel Meyer,  Andreas F. Kautt,  Paolo Franchini,  H William Detrich III,  Hannes Svardal,  Maximilian Wagner, Gavin J.P. Naylor,  Martin Pippel,  Milan Malinsky, Mark Mooney, Maria Simbirsky,  Brett T. Hannigan,  Trevor Pesout, Marlys Houck, Ann Misuraca,  Sarah B Kingan, Richard Hall,  Zev Kronenberg, Jonas Korlach,  Ivan Sović,  Christopher Dunn,  Zemin Ning,
Alex Hastie,  Joyce Lee, Siddarth Selvaraj,  Richard E. Green, Nicholas H. Putnam, Jay Ghurye,  Erik Garrison,  Ying Sims,  Joanna Collins,  Sarah Pelan,  James Torrance,
Alan Tracey,  Jonathan Wood,  Dengfeng Guan,  Sarah E. London,  David F. Clayton,  Claudio V. Mello,  Samantha R. Friedrich,  Peter V. Lovell, Ekaterina Osipova,  Farooq O. Al-Ajli,  Simona Secomandi, Heebal Kim,  Constantina Theofanopoulou,  Yang Zhou, Robert S. Harris,  Kateryna D Makova,Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark,  Fergal Martin,  Kevin Howe,
Paul Flicek,  Brian P Walenz,  Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar,  Benedict Paten,  Robert H.S. Kraus,  Harris A. Lewin,  Andrew J. Crawford,  M. Thomas P. Gilbert,  Guojie Zhang, Byrappa Venkatesh,  Robert W. Murphy,  Klaus-Peter Koepfli,  Beth Shapiro,  Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet,  Emma C. Teeling,  Tandy Warnow,  Jennifer Marshall Graves, Oliver A. Ryder,  David Haussler, Stephen J. O'Brien,  Kerstin Howe, Eugene W. Myers,  Richard Durbin, Adam M. Phillippy,

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila⟶

Yi Liao, Xinwen Zhang, Mahul Chakraborty, and J.J. Emerson

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation⟶

Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphege P. Nora, Sana B. Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos & Jane A. Skok

An active chromatin interactome in relevant cell lines elucidates biological mechanisms at genetic risk loci for dermatological traits⟶

Chenfu Shi, Helen Ray-Jones, James Ding, Kate Duffus, Yao Fu, Vasanthi Priyadarshini Gaddi, Oliver Gough, Jenny Hankinson, Paul Martin, Amanda McGovern, Annie Yarwood, Patrick Gaffney,
Steve Eyre, Magnus Rattray, Richard B Warren, Gisela Orozco

Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution⟶

Prashant Shingate, Vydianathan Ravi, Aravind Prasad, Boon-Hui Tay, Kritika M. Garg, Balaji Chattopadhyay, Laura-Marie Yap, Frank E. Rheindt & Byrappa Venkatesh

Estrogen receptor α (ERα)-binding super enhancers drive key mediators that control uterine estrogen responses in mice⟶

Sylvia C. Hewitt, Sara A. Grimm, San-Pin Wu, Francesco J. DeMayo, and Kenneth S. Korach

Three-dimensional regulation of HOXA cluster genes by a cis-element in hematopoietic stem cell and leukemia.⟶

Xue Qing David Wang, Haley Gore, Pamela Himadewei, Fan Feng, Lu Yang, Wanding Zhou, Xinyu Wang, Chun-wei Chen, Jianzhong Su, Jie Liu, Gerd Pfeifer, Xiaotian Zhang

A WIZ/Cohesin/CTCF Complex Anchors DNA Loops to Define Gene Expression and Cell Identity⟶

Megan Justice, Zachary M. Carico, Holden C. Stefan, Jill M. Dowen

HiChIP-Peaks: A HiChIP peak calling algorithm⟶

Chenfu Shi, Magnus Rattray, Gisela Orozco

Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia⟶

Andreas Kloetgen, Palaniraja Thandapani, Panagiotis Ntziachristos, Yohana Ghebrechristos, Sofia Nomikou, Charalampos Lazaris, Xufeng Chen, Hai Hu, Sofia Bakogianni, Jingjing Wang, Yi Fu, Francesco Boccalatte, Hua Zhong, Elisabeth Paietta, Thomas Trimarchi, Yixing Zhu, Pieter Van Vlierberghe, Giorgio G. Inghirami, Timothee Lionnet, Iannis Aifantis & Aristotelis Tsirigos

Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer⟶

Tejaswi Iyyanki, Baozhen Zhang, Qiushi Jin, Hongbo Yang, Tingting Liu, Xiaotao Wang, Jie Xu, Fan Song, Yu Luan, Hironobu Yamashita, Lu Wang, Joshua Warrick, Jay Raman, Joshua J. Meeks, David Degraff, Feng Yue

Non-coding germline GATA3 variants alter chromatin topology and contribute to 2 pathogenesis of acute lymphoblastic leukemia⟶

Hongbo Yang, Hui Zhang, Yu Luan, Tingting Liu, Kathryn G Roberts, Mao-xiang Qian, Bo Zhang, Wenjian Yang, Virginia Perez-Andreu, Jie Xu, Sriranga Iyyanki, Da Kuang, Shalini C Reshmi, Julie Gastier-Foster, Colton Smith, Ching-Hon Pui, William E Evans, Stephen P Hunger, Leonidas C Platanias, Mary V Relling, Charles G Mullighan, Mignon L Loh, Feng Yue, Jun J Yang

A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons⟶

Sergio Espeso-Gil, Tobias Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan Auluck, Behnam Javidfar, Prashanth Rajarajan, Sandhya Chandrasekaran, Cyril J. Peter, Alanna Cote, Rebecca Birnbaum, Will Liao, Tyler Borrman, Jennifer Wiseman, Aaron Bell, Michael J. Bannon, Panagiotis Roussos, John F. Crary, Zhiping Weng, Stefano Marenco, Barbara Lipska, Nadejda M. Tsankova, Laura Huckins, Yan Jiang & Schahram Akbarian

Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation⟶

Coline Arnould, Vincent Rocher, Thomas Clouaire, Pierre Caron, Philippe E Mangeot, Emiliano P. Ricci, Raphael Mourad, Daan Noordermeer, Gaelle Legube

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations⟶

David Jebb, Zixia Huang, Martin Pippel, Graham M. Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S. Jermiin, Emilia C. Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A. Ray, Kevin A. M. Sullivan, Juliana G. Roscito, Bogdan M. Kirilenko, Liliana M. Dávalos, Angelique P. Corthals, Megan L. Power, Gareth Jones, Roger D. Ransome, Dina Dechmann, Andrea G. Locatelli, Sebastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Mark S. Springer, Michael Hiller, Sonja C. Vernes, Eugene W. Myers, Emma C. Teeling

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains⟶

Priscillia Lhoumaud, Sana Badri, Javier Rodriguez-Hernaez, Theodore Sakellaropoulos, Gunjan Sethia, Andreas Kloetgen, MacIntosh Cornwell, Sourya Bhattacharyya, Ferhat Ay, Richard Bonneau, Aristotelis Tsirigos & Jane A. Skok.

Efficient chromosome-scale haplotype-resolved assembly of human genomes⟶

Shilpa Garg,Arkarachai Fungtammasan,Andrew Carroll, Mike Chou, Anthony Schmitt, Xiang Zhou,Stephen Mac, Paul Peluso, Emily Hatas, Jay Ghurye, Jared Maguire,Medhat Mahmoud, Haoyu Cheng, David Heller, Justin M.Zook, Tobias Moemke, Tobias Marschall, Fritz J.Sedlazeck,John Aach,Chen-Shan Chin, George M. Church, Heng Li

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma⟶

Wen Fong Ooi, Amrita M Nargund, Kevin Junliang Lim, Shenli Zhang, Manjie Xing, Amit Mandoli, Jing Quan Lim, Shamaine Wei Ting Ho, Yu Guo, Xiaosai Yao, Suling Joyce Lin, Tannistha Nandi, Chang Xu, Xuewen Ong, Minghui Lee, Angie Lay-Keng Tan, Yue Ning Lam, Jing Xian Teo, Atsushi Kaneda, Kevin P White, Weng Khong Lim, Steven G Rozen, Bin Tean Teh, Shang Li, Anders J Skanderup, Patrick Tan

KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks⟶

Dafne Campigli Di Giammartino, Andreas Kloetgen, Alexander Polyzos, Yiyuan Liu, Daleum Kim, Dylan Murphy, Abderhman Abuhashem, Paola Cavaliere, Boaz Aronson, Veevek Shah, Noah Dephoure, Matthias Stadtfeld, Aristotelis Tsirigos and Effie Apostolou

RNA Interactions Are Essential for CTCF-Mediated Genome Organization⟶

Ricardo Saldaña-Meyer, Javier Rodriguez-Hernaez, Thelma Escobar, Mayilaadumveettil Nishana, Karina Jácome-López, Elphege P. Nora, Benoit G. Bruneau, Aristotelis Tsirigos, Mayra Furlan-Magaril, Jane Skok, Danny Reinberg

A compendium of promoter-centered long-range chromatin interactions in the human genome⟶

Inkyung Jung, Anthony Schmitt, Yarui Diao, Andrew J. Lee, Tristin Liu, Dongchan Yang, Catherine Tan, Junghyun Eom, Marilynn Chan, Sora Chee, Zachary Chiang, Changyoun Kim, Eliezer Masliah, Cathy L. Barr, Bin Li, Samantha Kuan, Dongsup Kim & Bing Ren

Integrating Hi-C links with assembly graphs for chromosome-scale assembly⟶

Jay Ghurye, Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy , Sergey Koren

Telomere-to-telomere assembly of a complete human X chromosome⟶

Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon, Valerie A Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G Bouffard, Alexander M Chang, Nancy F Hansen, Françoise Thibaud-Nissen, Anthony D Schmitt, Jon-Matthew Belton, Siddarth Selvaraj, Megan Y Dennis, Daniela C Soto, Ruta Sahasrabudhe, Gulhan Kaya, Josh Quick, Nicholas J Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, Rosa ana Risques, Tina A. Graves Lindsay, Robert Fulton, Ira Hall, Benedict Paten, Kerstin Howe, Winston Timp, Alice Young, James C Mullikin, Pavel A Pevzner, Beth A Sullivan, Evan A Eichler, Adam M. Phillippy

Dynamic changes in RNA-chromatin interactome promote endothelial dysfunction⟶

Riccardo Calandrelli, Lixia Xu, Yingjun Luo, Weixin Wu, Xiaochen Fan, Tri Nguyen, Chienju Chen, Kiran Sriram, Rama Natarajan, Zhen Bouman-Chen, Sheng Zhong

Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information⟶

Hui-Su Kim, Sungwon Jeon, Changjae Kim, Yeon Kyung Kim, Yun Sung Cho, Jungeun Kim, Asta Blazyte, Andrea Manica, Semin Lee, Jong Bhak

A distal super enhancer mediates estrogen-dependent mouse uterine–specific gene transcription of Insulin-like growth factor 1 (Igf1)⟶

Sylvia C Hewitt, Sydney L Lierz, Marleny Garcia, Katherine J. Hamilton, Artiom Gruzdev, Sara A. Grimm, John P Lydon, Francesco J. DeMayo and Kenneth S. Korach

Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression⟶

William W. Greenwald, He Li, Paola Benaglio, David Jakubosky, Hiroko Matsui, Anthony Schmitt, Siddarth Selvaraj, Matteo D’Antonio, Agnieszka D’Antonio-Chronowska, Erin N. Smith & Kelly A. Frazer

Click Below For Arima Genomics’ interviews with authors Kelly Frazer and Bill Greenwald

Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissues-of-origin⟶

Yaping Liu, Tzu-Yu Liu, David E Weinberg, Brandon W White, Chris J De La Torre, Catherine L Tan, Anthony D Schmitt, Siddarth Selvaraj, Vy Tran, Louise C Laurent, Luc Cabel, Francois-Clement Bidard, Girish Putcha, Imran S Haque

Disease and phenotype relevant genetic variants identified from histone acetylomes in human hearts⟶

Tan Wilson Lek Wen, George Anene, Eleanor Wong, Hui San Tan, Banfang Pan, Mick Lee, Matias Autio, Michael Morley, Kenneth Margulies, Thomas Cappola, Marie Loh, John Chambers, Shyam Prabhakar, Roger Foo

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk⟶

Prashanth Rajarajan, Tyler Borrman, Will Liao, Nadine Schrode, Erin Flaherty, Charlize Casiño, Samuel Powell, Chittampalli Yashaswini, Elizabeth A. LaMarca, Bibi Kassim, Behnam Javidfar, Sergio Espeso-Gil, Aiqun Li, Hyejung Won, Daniel H. Geschwind, Seok-Man Ho, Matthew MacDonald, Gabriel E. Hoffman, Panos Roussos, Bin Zhang, Chang-Gyu Hahn, Zhiping Weng, Kristen J. Brennand, Schahram Akbarian

Agnostic detection of genomic alterations by holistic DNA structural interrogation.⟶

Shultzaberger RK, Abrams RE, Sullivan CJ, Schmitt AD, Thompson TWJ, Dresios J

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function⟶

Verena M. Link, Sascha H. Duttke, Hyun B. Chun, Inge R. Holtman, Emma Westin, Marten A. Hoeksema, Yohei Abe, Dylan Skola, Casey E. Romanoski, Jenhan Tao, Gregory J. Fonseca, Ty D. Troutman, Nathanael J. Spann, Tobias Strid, Mashito Sakai, Miao Yu, Rong Hu, Rongxin Fang, Dirk Metzler, Bing Ren, Christopher K. Glass

Highly-accurate chromosome-length human genome assembly via hybrid analyses of Oxford Nanopore and Arima-HiC⟶

Arima-HiC when combined with contigs from Oxford Nanopore generates highly accurate and chromosome-length genome assemblies. To access open-source software developed by this team, see below:

Arima-HiC Mapping Pipeline

SALSA Scaffolder

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