Publications

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

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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

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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

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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

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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

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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

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Dynamic 3D chromosomal landscapes in acute 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

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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

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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

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HiChIP-Peaks: A HiChIP peak calling algorithm

Chenfu Shi, Magnus Rattray and Gisela Orozco

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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

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NSD2 overexpression drives clustered chromatin and transcriptional changes in insulated domains

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

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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

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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

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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

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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 (2018)

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Agnostic detection of genomic alterations by holistic DNA structural interrogation.

Shultzaberger RK, Abrams RE, Sullivan CJ, Schmitt AD, Thompson TWJ, Dresios J (2018)

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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 (2018)

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

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

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: