Hi-C & HiChIP NGS Applications

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Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species⟶

Larissa Ramsay, Chu Shin Koh, Sateesh Kagale, Dongying Gao, Sukhjiwan Kaur, Teketel Haile, Tadesse S. Gela, Li-An Chen, Zhe Cao, David J. Konkin, Helena Toegelová, Jaroslav Doležel, Benjamin D. Rosen, Robert Stonehouse, Jodi L. Humann, Dorrie Main, Clarice J. Coyne, Rebecca J. McGee, Douglas R. Cook, R. Varma Penmetsa, Albert Vandenberg, Crystal Chan, Sabine Banniza, David Edwards, Philipp E. Bayer, Jacqueline Batley, Sripada M. Udupa, Kirstin E. Bett

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing⟶

Hollis A Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony D Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa M Komoroske, Tanya Lama, Andrew J Crawford, Robert W Murphy, Samara Brown, Alan F Scott, Phillip A Morin, Erich D Jarvis, Olivier Fedrigo

The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research⟶

Anna K. Childers , Scott M. Geib, Sheina B. Sim, Monica F. Poelchau, Brad S. Coates, Tyler J. Simmonds, Erin D. Scully, Timothy P. L. Smith, Christopher P. Childers, Renee L. Corpuz, Kevin Hackett and Brian Scheffler

Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation⟶

Sudarshan Pinglay, Milica Bulajić , Dylan P. Rahe , Emily Huang , Ran Brosh , Sergei German , John A. Cadley , Lila Rieber , Nicole Easo , Shaun Mahony , Matthew T. Maurano, Liam J. Holt, Esteban O. Mazzoni, Jef D. Boeke

Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis⟶

Ying Li, Ziwei Liao, Huacheng Luo, Aissa Benyoucef, Yuanyuan Kang, Qian Lai, Sinisa Dovat, Barbara Miller, Iouri Chepelev, Yangqiu Li, Keji Zhao, Marjorie Brand, Suming Huang

Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens⟶

Rui Lopes, Kathleen Sprouffske, Caibin Sheng, Esther C. H. Uijttewaal, Adriana Emma Wesdorp, Jan Dahinden, Simon Wengert, Juan Diaz-Miyar, Umut Yildiz, Melusine Bleu, Verena Apfel, Fanny Mermet-Meillon, Rok Krese, Mathias Eder, André Vidas Olsen, Philipp Hoppe, Judith Knehr, Walter Carbone, Rachel Cuttat, Annick Waldt, Marc Altorfer, Ulrike Naumann, Joachim Weischenfeldt, Antoine deWeck, Audrey Kauffmann, Guglielmo Roma, Dirk Schübeler and Giorgio G. Galli

The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758⟶

Dan Mead, Ilik Saccheri, Carl J. Yung, Konrad Lohse, Carla Lohse, Philip Ashmole, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Michael A. Quail, Jale Dolucan, Shane A. McCarthy, Kerstin Howe, Jonathan Wood, James Torrance, Alan Tracey, Sam Whiteford, Richard Challis, Richard Durbin, Mark Blaxter

Epigenetic therapy suppresses endocrine-resistant breast tumour growth by re-wiring ER-mediated 3D chromatin interactions⟶

Joanna Achinger-Kawecka, Clare Stirzaker, Kee-Ming Chia, Neil Portman, Elyssa Campbell, Qian Du, Geraldine Laven-Law, Shalima S. Nair, Aliza Yong, Ashleigh Wilkinson, Samuel Clifton, Heloisa H. Milioli, Anthony Schmitt, Emily S. Wong, Theresa E. Hickey, Elgene Lim, Susan J. Clark

The conserved sex regulator DMRT1 recruits SOX9 in sexual cell fate reprogramming⟶

Robin E Lindeman, Mark W Murphy, Kellie S Agrimson, Rachel L Gewiss, Vivian J Bardwell, Micah D Gearhart, David Zarkower

Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells⟶

Riccardo Calandrelli, Xingzhao Wen, Tri C. Nguyen, Chien-Ju Chen, Zhijie Qi, Weizhong Chen, Zhangming Yan, Weixin Wu, Kathia Zaleta-Rivera, Rong Hu, Miao Yu, Yuchuan Wang, View ORCID ProfileJian Ma, Bing Ren, Sheng Zhong

Enhancer hijacking drives oncogenic BCL11B expression in lineage ambiguous stem cell leukemia⟶

Lindsey E Montefiori, Sonja Bendig, Zhaohui Gu, Xiaolong Chen, Petri Polonen, Xiaotu Ma, Alex Murison, Andy Zeng, Laura Garcia-Prat, Kirsten Dickerson, Ilaria Iacobucci, Sherif Abdelhamed, Ryan Hiltenbrand, Paul E Mead, Cyrus M Mehr, Beisi Xu, Zhongshan Cheng, Ti-Cheng Chang, Tamara Westover, Jing Ma, Anna Stengel, Shunsuke Kimura, Chunxu Qu, Marcus B Valentine, Marissa Rashkovan, Selina Luger, Mark R Litzow, Jacob M Rowe, Monique L. den Boer, Victoria Wang, Jun Yin, Steven M Kornblau, Stephen P Hunger, Mignon L Loh, Ching-Hon Pui, Wenjian Yang, Kristine R Crews, Kathryn G Roberts, Jun J. Yang, Mary V Relling, William E Evans, Wendy Stock, Elisabeth M Paietta, Adolfo A Ferrando, Jinghui Zhang, Wolfgang Kern, Torsten Haferlach, Gang Wu, John E Dick, Jeffery M Klco, Claudia Haferlach and Charles G Mullighan

RNA surveillance controls 3D genome structure via stable cohesin-chromosome interaction⟶

Yujin Chun, Sungwook Han, Taemook Kim, Yoonjung Choi, Daeyoup Lee

Single nuclei transcriptome of the Lesser Duckweed Lemna minuta reveals cell trajectories for an entire plant⟶

Bradley W. Abramson, Mark Novotny, Nolan T. Hartwick, Kelly Colt, Brian D. Aevermann, Richard H. Scheuermann, Todd P. Michael

Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution⟶

Claire R. Peart, Christina Williams, Saurabh D. Pophaly, Benjamin A. Neely, Frances M. D. Gulland, David J. Adams, Bee Ling Ng, William Cheng, Michael E. Goebel, Olivier Fedrigo, Bettina Haase, Jacquelyn Mountcastle, Arkarachai Fungtammasan, Giulio Formenti, Joanna Collins, Jonathan Wood, Ying Sims, James Torrance, Alan Tracey, Kerstin Howe, Arang Rhie, Joseph I. Hoffman, Jeremy Johnson, Erich D. Jarvis, Matthew Breen, Jochen B. W. Wolf

Epigenomic landscape and 3D genome structure in pediatric high-grade glioma⟶

Juan Wang, Tina Yi-Ting Huang, Ye Hou, Elizabeth Bartom, Xinyan Lu, Ali Shilatifard, Feng Yue, Amanda Saratsis

CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer⟶

Musaddeque Ahmed, Fraser Soares, Ji-Han Xia, Yue Yang, Jing Li, Haiyang Guo, Peiran Su, Yijun Tian, Hyung Joo Lee, Miranda Wang, Nayeema Akhtar, Kathleen E. Houlahan, Almudena Bosch, Stanley Zhou, Parisa Mazrooei, Junjie T. Hua, Sujun Chen, Jessica Petricca, Yong Zeng, Alastair Davies, Michael Fraser, David A. Quigley, Felix Y. Feng, Paul C. Boutros, Mathieu Lupien, Amina Zoubeidi, Liang Wang, Martin J. Walsh, Ting Wang, Shancheng Ren, Gong-Hong Wei & Housheng Hansen He

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes⟶

Xiaotao Wang, Jie Xu, Baozhen Zhang, Ye Hou, Fan Song, Huijue Lyu & Feng Yue

A chromosome-level genome assembly of the parasitoid wasp, Cotesia glomerata⟶

Brendan J Pinto, Jerome J Weis, Tony Gamble, Paul J Ode, Ryan Paul, Jennifer M Zaspel

The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769⟶

Kerstin Howe, Melinda Dwinell, Mary Shimoyama, Craig Corton, Emma Betteridge, Alexander Dove, Michael A. Quail, Michelle Smith, Laura Saba, Robert W. Williams, Hao Chen, Anne E. Kwitek, Shane A. McCarthy, Marcela Uliano-Silva, William Chow, Alan Tracey, James Torrance, Ying Sims1, Richard Challis, Jonathan Threlfall, Mark Blaxter

The genome sequence of the common pipistrelle, Pipistrellus pipistrellus Schreber 1774⟶

Christopher Vine, Emma C. Teeling, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Michael A. Quail, Shane A. McCarthy, Kerstin Howe, James Torrance, Jonathan Wood, Sarah Pelan, Ying Sims, Richard Challis, Jonathan Threlfall, Daniel Mead, Mark Blaxter

The complete sequence of a human genome⟶

Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G. S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Yumi Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sovic, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Francoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O'Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, Adam M. Phillippy

3’HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression⟶

Pamela Himadewi, Xue Qing David Wang, Fan Feng, Haley Gore, Yushuai Liu, Lei Yu, Jie Liu, Ryo Kurita, Yukio Nakamura, Gerd Pfeifer, and Xiaotian Zhang

Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci⟶

Stephanie Sungalee, Yuanlong Liu, Ruxandra A. Lambuta, Natalya Katanayeva, Maria Donaldson Collier, Daniele Tavernari, Sandrine Roulland, Giovanni Ciriello & Elisa Oricchio

Sex-specific multi-level 3D genome dynamics in the mouse brain⟶

Devin Rocks, Mamta Shukla, Silvia C. Finnemann, Achyuth Kalluchi, M. Jordan Rowley, Marija Kundakovic

Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma⟶

Konstantin Okonechnikov, Aylin Camgoz, Donglim Esther Park, Owen Chapman, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Edwin F. Juarez, James T. Robinson, Kristian W. Pajtler, Monika Mauermann, Till Milde, Nicole G. Coufal, Michael Levy, Denise Malicki, Shareef Nahas, Matija Snuderl, John Crawford, Robert J. Wechsler-Reya, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michaelraj, Sachin A. Kumar, Michael D. Taylor, Jeremy Rich, Frank Buchholz, Jill P. Mesirov, Stefan M. Pfister, Ferhat Ay, Jesse R. Dixon, Marcel Kool, Lukas Chavez

Altered 3D chromatin structure permits inversional recombination at the IgH locus⟶

Xiang Qiu, Fei Ma, Mingming Zhao, Yaqiang Cao, Lillian Shipp, Angela Liu, Arun Dutta, Amit Singh, Fatima Zohra Braikia, Supriyo De, William H Wood 3rd, Kevin G Becker, Weiqiang Zhou, Hongkai Ji, Keji Zhao, Michael L Atchison, Ranjan Sen.

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C⟶

Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, David Porubsky, Kristen Kuhn, Kathryn A. Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo, Ivan Liachko, Richard J. Hall, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Timothy P. L. Smith, Erich D. Jarvis, Shawn T. Sullivan & Sarah B. Kingan

Evolutionary and biomedical insights from a marmoset diploid genome assembly⟶

Chentao Yang, Yang Zhou, Stephanie Marcus, Giulio Formenti, Lucie A. Bergeron, Zhenzhen Song, Xupeng Bi, Juraj Bergman, Marjolaine Marie C. Rousselle, Chengran Zhou, Long Zhou, Yuan Deng, Miaoquan Fang, Duo Xie, Yuanzhen Zhu, Shangjin Tan, Jacquelyn Mountcastle, Bettina Haase, Jennifer Balacco, Jonathan Wood, William Chow, Arang Rhie, Martin Pippel, Margaret M. Fabiszak, Sergey Koren, Olivier Fedrigo, Winrich A. Freiwald, Kerstin Howe, Huanming Yang, Adam M. Phillippy, Mikkel Heide Schierup, Erich D. Jarvis & Guojie Zhang

Universal nomenclature for oxytocin–vasotocin ligand and receptor families⟶

Constantina Theofanopoulou, Gregory Gedman, James A. Cahill, Cedric Boeckx & Erich D. Jarvis

A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush)⟶

Seth Smith, Eric Normandeau, Haig Djambazian, Pubudu Nawarathna, Pierre Berube, Andrew Muir, Jiannis Ragoussis, Chantelle Penney, Kim Scribner, Gordon Luikart, Chris Wilson, Louis Bernatchez

Alterations in chromosome spatial compartmentalization classify prostate cancer progression⟶

Rebeca San Martin, Priyojit Das, Renata Dos Reis Marques, Yang Xu, Rachel Patton McCord

Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia⟶

Benny Wang, Lingshi Kong, Deepak Babu, Ruchi Choudhary, Winnie Fam, Jia Qi Tng, Yufen Goh, Bertrand Wong Jern Han, Xin Liu, Fang Fang Song, Priscella Chia, Ming Chun Chan, Omer An, Cheng Yong Tham, Touati Benoukraf, Henry Yang, Wilson Wang, Wee Joo Chng, Daniel Tenen, Melissa Jane Fullwood

Widespread false gene gains caused by duplication errors in genome assemblies⟶

Byung June Ko, Chul Lee, Juwan Kim, Arang Rhie, DongAhn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis, Heebal Kim

False gene and chromosome losses affected by assembly and sequence errors⟶

Juwan Kim, Chul Lee, Byung June Ko, DongAhn Yoo, Sohyoung Won, Adam Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V. Mello, Seoae Cho, Arang Rhie, Heebal Kim, Erich D. Jarvis

A noncatalytic activity of the H4K20 demethylase DPY-21 regulates condensin DC binding⟶

Laura Breimann, Ana Karina Morao, Jun Kim, David Jimenez, Nina Maryn, Krishna Bikkasani, Michael J Carrozza, Sarah Elizabeth Albritton, Maxwell Kramer, Lena Annika Street, Kustrim Cerimi, Vic Fabienne Schumann, Ella Bahry, Stephan Preibisch, Andrew Woehler, Sevinc Ercan

The Lithuanian reference genome LT1 - a human de novo genome assembly with short and long read sequence and Hi-C data⟶

Hui-Su Kim, Asta Blazyte, Sungwon Jeon, Changhan Yoon, Yeonkyung Kim, Changjae Kim, Dan Bolser, Ji-Hye Ahn, Jeremy S. Edwards, Jong Bhak

Chromatin architecture in addiction circuitry elucidates biological mechanisms underlying cigarette smoking and alcohol use traits⟶

Nancy Y.A Sey, Benxia Hu, Marina Iskhakova, Huaigu Sun, Neda Shokrian, Gabriella Ben Hutta, Jesse Marks, Bryan C. Quach, Eric O. Johnson, Dana B. Hancock, Schahram Akbarian, Hyejung Won

A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression⟶

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

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans⟶

David Sebastian Jimenez, Jun Kim, Bhavana Ragipani, Bo Zhang, Lena Annika Street, Maxwell Kramer, Sarah E Albritton, Lara Winterkorn, Sevinç Ercan

A UVB-responsive common variant at chr7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor gene (AHR) ⟶

Mai Xu, Lindsey Mehl, Tongwu Zhang, Rohit Thakur, Hayley Sowards, Timothy Myers, Lea Jessop, Alessandra Chesi, Matthew E Johnson, Andrew D Wells, Helen T Michael, Patricia Bunda, Kristine Jones, Herbert Higson, Rebecca C Hennessey, Ashley Jermusyk, Michael A Kovacs, Maria Teresa Landi, Mark M Iles, Alisa M Goldstein, Melanoma Meta-Analysis Consortium, Jiyeon Choi, Stephen J Chanock, Struan F A Grant, Raj Chari, Glenn Merlino, Matthew H Law, Kevin M Brown

H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization⟶

Bobbie Pelham-Webb, Alexander Polyzos, Luke Wojenski, Andreas Kloetgen, Jiexi Li, Dafne Campigli Di Giammartino, Theodore Sakellaropoulos, Aristotelis Tsirigos, Leighton Core & Effie Apostolous

Interferons Reshape the 3D Conformation and Accessibility of Macrophage Chromatin⟶

Ekaterini Platanitis, Stephan Grüner, Aarathy Ravi Sundar Jose Geetha, Laura Boccuni, Alexander Vogt, Maria Novachkova, Andreas Sommer, Mathias Müller & Thomas Decker

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck)⟶

Ralf C Mueller, Patrik Ellström, Kerstin Howe, Marcela Uliano-Silva, Richard I Kuo, Katarzyna Miedzinska, Amanda Warr, Olivier Fedrigo, Bettina Haase, Jacquelyn Mountcastle, William Chow, James Torrance, Jonathan Wood, Josef D Järhult, Mahmoud M Naguib, Björn Olsen, Erich D Jarvis, Jacqueline Smith, Lél Eöry & Robert HS Krau

Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly⟶

Marios Gavrielatos, Konstantinos Kyriakidis, Demetrios A. Spandidos & Ioannis Michalopoulos

A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries in Hox Clusters⟶

Havva Ortabozkoyun-Kara, Pin-Yao Huang, Hyunwoo Cho, Varun Narendra, Gary Leroy, Jane A. Skok, Aristotelis Tsirigos, Esteban O. Mazzoni & Danny Reinberg

Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples⟶

Sambhavi Animesh, Ruchi Choudhary, Xin Yi Ng, Joshua Kai Xun Tay, Wan-Qin Chong, Boon Cher Goh & Melissa Jane Fullwood

Chromatin Interaction Neural Network (ChINN): A machine learning-based method for predicting chromatin interactions from DNA sequences⟶

Fan Cao, Yu Zhang, Yichao Cai, Sambhavi Animesh, Ying Zhang, Semih Akincilar, Yan Ping Loh, Wee Joo Chng, Vinay Tergaonkar, Chee Keong Kwoh & Melissa J. Fullwood

Genomic instability is an early event driving chromatin reorganization and escape from oncogene-induced senescence⟶

C Zampetidis, P Galanos, A Angelopoulou, Y Zhu, T Karamitros, A Polyzou, I Mourkioti, N Lagopati, R Mirzazadeh, A Polyzos,
S Garnerone, EG Gusmao, K Sofiadis, DE Pefani, M Demaria, N Crosetto, A Maya‑Mendoza, K Evangelou, J Bartek, A Papantonis & VG Gorgoulis

MYC overexpression leads to increased chromatin interactions at superenhancers and c-Myc binding sites⟶

Yi Xiang See, Kaijing Chen & Melissa J. Fullwood

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout⟶

Guangtu Gao, Susana Magadan, Geoffrey C. Waldbieser, Ramey C. Youngblood, Paul A. Wheeler, Brian E. Scheffler, Gary H. Thorgaard & Yniv Palti

Molecular basis of CTCF binding polarity in genome folding⟶

Elphège P. Nora, Laura Caccianini, Geoffrey Fudenberg, Kevin So, Vasumathi Kameswaran, Abigail Nagle, Alec Uebersohn, Bassam Hajj, Agnès Le Saux, Antoine Coulon, Leonid A. Mirny, Katherine S. Pollard, Maxime Dahan & Benoit G. Bruneau

De novo assembly of a chromosome-scale reference genome for the northern flicker Colaptes auratus⟶

Jack P. Hruska & Joseph D. Manthey

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis⟶

Shu Zhang, Nadine Übelmesser, Natasa Josipovic, Giada Forte, Johan A. Slotman, Michael Chiang, Henrike Gothe, Eduardo Gade Gusmao, Christian Becker, JanineAltmüller, Adriaan B. Houtsmuller, Vassilis Roukos, Kerstin S. Wendt, DavideMarenduzzo, Argyris Papantonis

The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861)⟶

Iliana Bista, Shane A McCarthy, Jonathan Wood, Zemin Ning, H William Detrich Iii, Thomas Desvignes, John Postlethwait, William Chow, Kerstin Howe, James Torrance, Michelle Smith, Karen Oliver, Vertebrate Genomes Project Consortium, Eric A Miska & Richard Durbin

Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis Strain SH1⟶

Simo Sun, Ryoji Shinya, Mehmet Dayi, Akemi Yoshida, Paul W. Sternberg, Taisei Kikuchi

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?⟶

Mitsutaka Kadota, Osamu Nishimura, Hisashi Miura, Kaori Tanaka, Ichiro Hiratani, Shigehiro Kuraku

Stress-induced RNA–chromatin interactions promote endothelial dysfunction⟶

Riccardo Calandrelli, Lixia Xu, Yingjun Luo, Weixin Wu, Xiaochen Fan, Tri Nguyen, Chien-Ju Chen, Kiran Sriram, Xiaofang Tang, Andrew B. Burns, Rama Natarajan, Zhen Bouman Chen & Sheng Zhong

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity⟶

Qian Du, Grady C. Smith, Phuc Loi Luu, James M. Ferguson, Nicola J. Armstrong, C. Elizabeth Caldon, Elyssa Campbell, Shalima S. Nair, Elena Zotenko, Cathryn M. Gould, Michael Buckley, Dominik Kaczorowski, Kirston Barton, Ira W. Deveson, Martin A.Smith, Joseph E. Powell, Ksenia Skvortsova, Clare Stirzaker, Joanna Achinger-Kawecka, Susan J. Clark

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines⟶

Mikhail G. Dozmorov, Katarzyna M. Tyc, Nathan C. Sheffield, David C. Boyd, Amy L.Olex, Jason Reed, J. Chuck Harrell

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis⟶

Anton Zamyatin, Pavel Avdeyev, Jiangtao Liang, Atashi Sharma, Chujia Chen, Varvara Lukyanchikova, Nikita Alexeev, Zhijian Tu, Max A. Alekseyev, Igor V. Sharakhov

Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)⟶

Prashant Shingate, Vydianathan Ravi, Aravind Prasad, Boon‐Hui Tay & Byrappa Venkatesh

Cross-species chromatin interactions drive transcriptional rewiring in Epstein–Barr virus–positive gastric adenocarcinoma⟶

Atsushi Okabe, Kie Kyon Huang, Keisuke Matsusaka, Masaki Fukuyo, Manjie Xing, Xuewen Ong, Takayuki Hoshii, Genki Usui, Motoaki Seki, Yasunobu Mano, Bahityar Rahmutulla, Teru Kanda, Takayoshi Suzuki, Sun Young Rha, Tetsuo Ushiku, Masashi Fukayama, Patrick Tan & Atsushi Kaneda

Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation⟶

Deblina Banerjee, Berkley Gryder, Sukriti Bagchi, Zhihui Liu, Hsien-Chao Chen, Man Xu, Ming Sun, Zalman Vaksman, Sharon J. Diskin, Javed Khan & Carol J Thiele

Six reference-quality genomes reveal 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 K. N. Dechmann, Andrea G. Locatelli, Sébastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Michael Hiller, Sonja C. Vernes, Eugene W. Myers & Emma C. Teeling

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, Amy B. Wilfert, 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, Jennifer L. Gerton, Beth A. Sullivan, Evan E. Eichler & Adam M. Phillippy

HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding⟶

Edwin A. Solares, Yuan Tao, Anthony D. Long & Brandon S. Gaut

Chromosome-scale, haplotype-resolved assembly of human genomes⟶

Shilpa Garg, Arkarachai 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 M Li

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder⟶

Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho & Romain Koszul

β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture⟶

Syed Raza Mahmood, Xin Xie, Nadine Hosny El Said, Kristin C Gunsalus & Piergiorgio Percipalle

Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype⟶

Wilson Lek Wen Tan, Chukwuemeka George Anene-Nzelu, Eleanor Wong, Mick Lee, Hui San Tan, Sze Jing Tang, Arnaud Michel Yvon Perrin, Kan Xing Wu, Wen Hao Zheng, Robert John Ashburn, Bangfen Pan, May Yin Lee, Matias I Autio, Michael Morley, Wai Leong Tam, Christine Cheung, Kenneth B Margulies, Leilei Chen, Thomas P Cappola, Marie Loh, John Chambers, Shyam Prabhakar & Roger SY Foo

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly⟶

Mahul Chakraborty, Arunachalam Ramaiah, Adriana Adolfi, Paige Halas, Bhagyashree Kaduskar, Luna Thanh Ngo, Suvratha Jayaprasad, Kiran Paul, Saurabh Whadgar, Subhashini Srinivasan, Suresh Subramani, Ethan Bier, Anthony A. James & J.J. Emerson

Reference genome and demographic history of the most endangered marine mammal, the vaquita⟶

Phillip A. Morin, Frederick I. Archer, Catherine D. Avila, Jennifer R. Balacco, Yury V. Bukhman, William Chow, Olivier Fedrigo, Giulio Formenti, Julie A. Fronczek, Arkarachai Fungtammasan, Frances M.D. Gulland, Bettina Haase, Mads Peter Heide-Jorgensen, Marlys L. Houck, Kerstin Howe, Ann C. Misuraca, Jacquelyn Mountcastle, Whitney Musser, Sadye Paez, Sarah Pelan, Adam Phillippy, Arang Rhie, Jacqueline Robinson, Lorenzo Rojas-Bracho, Teri K. Rowles, Oliver A. Ryder, Cynthia R. Smith, Sacha Stevenson, Barbara L. Taylor, Jonas Teilmann, James Torrance, Randall S. Wells, Andrew Westgate & Erich D. Jarvis

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 & Erich D. Jarvis

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

Yi Liao, Xinwen Zhang, Mahul Chakraborty & 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

Chromatin looping links target genes with 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 & 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 formation of DNA damage repair foci⟶

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

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

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 & 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

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 & 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

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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