pypi: HiCExplorer | Projects | Ecosyste.ms: Papers

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.1093/bioinformatics/btaa073

<i>Coolpup.py:</i> versatile pile-up analysis of Hi-C data
Cited by: 86
Author(s): Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13059-018-1596-9

Comparison of computational methods for the identification of topologically associating domains
Cited by: 155
Author(s): Marie Zufferey, Daniele Tavernari, Elisa Oricchio, Giovanni Ciriello
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12915-021-01123-z

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation
Cited by: 12
Author(s): Jana Sperschneider, Ashley Jones, Jamila Nasim, Bo Xu, Silke Jacques, Chengcheng Zhong, Narayana M. Upadhyaya, Rohit Mago, Yiheng Hu, Melania Figueroa, Karam B. Singh, Eric A. Stone, Ming-Bo Wang, Jennifer Taylor, Peter N. Dodds
Software Mentions: 9
Published: about 3 years ago

10.3390/ijms22179426

Gravitational Force—Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells
Cited by: 14
Author(s): Christian Vahlensieck, Cora S. Thiel, Ye Zhang, Andreas Huge, Oliver Ullrich
Software Mentions: 8
Published: about 3 years ago

10.1007/s12551-018-0489-1

Hi-C analysis: from data generation to integration
Cited by: 62
Author(s): Koustav Pal, Mattia Forcato, Francesco Ferrari
Software Mentions: 8
Published: almost 6 years ago

10.1093/bioinformatics/btaa555

Benchmark of software tools for prokaryotic chromosomal interaction domain identification
Cited by: 3
Author(s): Mikhail D. Magnitov, Veronika S Kuznetsova, Sergey V. Ulianov, Sergey V. Razin, Alexander Tyakht
Software Mentions: 8
Published: about 4 years ago

10.1186/s12859-020-03652-w

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
Cited by: 22
Author(s): Kellen Garrison Cresswell, John C. Stansfield, Mikhail G. Dozmorov
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-020-02049-5

Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping
Cited by: 13
Author(s): Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B. Fraser, Thomas Quertermous
Software Mentions: 7
Published: over 4 years ago

10.7554/eLife.59889

Cohesin residency determines chromatin loop patterns
Cited by: 45
Author(s): Lorenzo Costantino, Hsieh Ts, Rebecca Lamothe, Xavier Darzacq, Douglas Koshland
Software Mentions: 7
Published: about 4 years ago

10.1111/cgf.13727

Tasks, Techniques, and Tools for Genomic Data Visualization
Cited by: 48
Author(s): Sabrina Nusrat, Theresa Harbig, Nils Gehlenborg
Software Mentions: 6
Published: over 5 years ago

10.15252/embj.2021108345

Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci
Cited by: 4
Author(s): Yuka W. Iwasaki, Sira Sriswasdi, Yasuha Kinugasa, Jun Adachi, Yasunori Horikoshi, Aoi Shibuya, Wataru Iwasaki, Satoshi Tashiro, Takeshi Tomonaga, Haruhiko Siomi
Software Mentions: 6
Published: over 3 years ago

10.1186/s13073-021-00938-3

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability
Cited by: 9
Author(s): Jennifer Derrien, Catherine Guérin‐Charbonnel, Victor Gaborit, Loı̈c Campion, Martine Devic, Elise Douillard, Nathalie Roi, Hervé Avet‐Loiseau, Olivier Decaux, Thierry Facon, Jan‐Philipp Mallm, Roland Eils, Nikhil C. Munshi, Philippe Moreau, Carl Herrmann, Florence Magrangeas, Stέphane Minvielle
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-021-00996-4

Reorganization of the 3D chromatin architecture of rice genomes during heat stress
Cited by: 39
Author(s): Zhe Liang, Qian Zhang, Changmian Ji, Guihua Hu, Pingxian Zhang, Yifan Wang, Liwen Yang, Xiaofeng Gu
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-020-00793-5

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Cited by: 28
Author(s): Yang Zhou, Shuli Liu, Yan Hu, Lingzhao Fang, Yahui Gao, Han Xia, Steven G. Schroeder, Benjamin D. Rosen, Erin E. Connor, Congjun Li, R.L. Baldwin, John B. Cole, Curtis P. Van Tassell, Liguo Yang, Li Ma, George E. Liu
Software Mentions: 4
Published: over 4 years ago

10.1186/s13148-019-0690-5

ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells
Cited by: 34
Author(s): Madhobi Sen, Xin Wang, Feda H. Hamdan, Jacobe Rapp, Jessica Eggert, Robyn Laura Kosinsky, Florian Wegwitz, Ana P. Kutschat, Fereshteh Younesi, Jochen Gaedcke, Marian Grade, Elisabeth Heßmann, Argyris Papantonis, Philipp Ströbel, Steven A. Johnsen
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07615-0

Identification of the conserved long non-coding RNAs in myogenesis
Cited by: 0
Author(s): Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh, Soumyadeep Nandi
Software Mentions: 4
Published: over 3 years ago

10.1186/s12915-021-00963-z

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly
Cited by: 64
Author(s): 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
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-020-02215-9

FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
Cited by: 79
Author(s): Kai Kruse, Clemens B. Hug, Juan M. Vaquerizas
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-020-02063-7

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
Cited by: 57
Author(s): Yonghao Sun, Liang Dong, Ying Zhang, Dazhen Lin, Weize Xu, Changxiong Ke, Linqian Han, Lulu Deng, Guoliang Li, David Jackson, Xingwang Li, Fang Yang
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giaa142

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals
Cited by: 29
Author(s): Jing Li, Jilin Zhang, Jing Liu, Yang Zhou, Changqing Cai, Luohao Xu, Xuelei Dai, Shaohong Feng, Chunxue Guo, Jiahui Rao, Kai Wei, Erich D. Jarvis, Yu Jiang, Zhengkui Zhou, Guojie Zhang, Qi Zhou
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1009229

3D genome evolution and reorganization in the Drosophila melanogaster species group
Cited by: 24
Author(s): Nicole S. Torosin, Aparna Anand, Tirupathi Rao Golla, Weihuan Cao, Chris Ellison
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.27024

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Cited by: 113
Author(s): Jason C. Bell, David Jukam, Nicole A Teran, Viviana I. Risca, Owen K. Smith, Whitney L. Johnson, Jan M. Skotheim, William J. Greenleaf, Aaron F. Straight
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btz436

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
Cited by: 92
Author(s): Vivek Bhardwaj, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S. Richter, Devon P. Ryan, Thomas Manke
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1009778

IGSF11 is required for pericentric heterochromatin dissociation during meiotic diplotene
Cited by: 5
Author(s): Bin Chen, Gengzhen Zhu, An Yan, Jing He, Yang Liu, Lin Li, Xuerui Yang, Dong Chen, Kehkooi Kee
Software Mentions: 3
Published: about 3 years ago

10.1186/s13059-018-1510-5

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains
Cited by: 65
Author(s): Abdulrahman Salhab, Karl Nordström, Gilles Gasparoni, Kathrin Kattler, Peter Ebert, Fidel Ramírez, Laura Arrigoni, Fabian Müller, Julia K. Polansky, Cristina Cadenas, Jan G. Hengstler, Thomas Lengauer, Thomas Manke, Jörn Walter
Software Mentions: 3
Published: about 6 years ago

10.1186/s12920-018-0437-8

Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma
Cited by: 9
Author(s): Luís Augusto Eijy Nagai, Sung‐Joon Park, Kenta Nakai
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83903-9

Erythrocytes 3D genome organization in vertebrates
Cited by: 10
Author(s): Anastasia Ryzhkova, Alena Taskina, А. А. Хабарова, Veniamin Fishman, Nariman Battulin
Software Mentions: 2
Published: over 3 years ago

10.1093/bioinformatics/btaa692

pyGenomeTracks: reproducible plots for multivariate genomic datasets
Cited by: 179
Author(s): Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn Grüning, Fidel Ramírez, Thomas Manke
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btab272

EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework
Cited by: 8
Author(s): Yue Hu, Wenxiu Ma
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.57212

Large domains of heterochromatin direct the formation of short mitotic chromosome loops
Cited by: 11
Author(s): Giacomo Cavalli, Pin Tong, Alison L. Pidoux, Hakan Özadam, Liyan Yang, Sharon A. White, Job Dekker, Robin C. Allshire
Software Mentions: 1
Published: about 4 years ago

10.1128/mBio.00148-21

The Architectural Factor HMGB1 Is Involved in Genome Organization in the Human Malaria Parasite Plasmodium falciparum
Cited by: 12
Author(s): Binbin Lu, Meng Liu, Liang Gu, Ying Liu, Shijun Shen, Gangqiang Guo, Fei Wang, Xiaohong He, Yuge Zhao, Xianwen Shang, Liping Wang, Guang Yang, Qianshu Zhu, Jun Cao, Cizhong Jiang, Richard Culleton, Gang Wei, Qingfeng Zhang
Software Mentions: 1
Published: over 3 years ago

10.1186/s13059-020-02232-8

Compacting a synthetic yeast chromosome arm
Cited by: 21
Author(s): Zhong‐Zhen Luo, Yu Kang, Shuang Xie, Marco Monti, Daniel Schindler, Fang Yuan, Shijun Zhao, Zong Liang-gang, Shuangying Jiang, Meiwei Luan, Chuan-Le Xiao, Yizhi Cai, Junbiao Dai
Software Mentions: 1
Published: almost 4 years ago

Ecosyste.ms: Papers

Projects: pypi: HiCExplorer

Papers Mentioning HiCExplorer 33