cran: TopDom | Projects | Ecosyste.ms: Papers

10.1186/s12864-016-3387-6

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking
Cited by: 64
Author(s): Charalampos Lazaris, Stephen M. Kelly, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
Software Mentions: 28
Published: almost 8 years ago

10.1186/s13072-021-00390-y

Molecular and computational approaches to map regulatory elements in 3D chromatin structure
Cited by: 7
Author(s): Beoung Hun Lee, Suhn Kyong Rhie
Software Mentions: 21
Published: over 3 years ago

10.3389/fgene.2019.01079

HiCeekR: A Novel Shiny App for Hi-C Data Analysis
Cited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: about 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

10.1093/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/s13059-020-01992-7

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
Cited by: 5
Author(s): Guangyu Wang, Qingshu Meng, Bo Xia, Shuo Zhang, Jie Lv, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao, Kaifu Chen
Software Mentions: 7
Published: over 4 years ago

10.1186/s12915-018-0608-2

Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells
Cited by: 35
Author(s): Elsie C. Jacobson, Jo K. Perry, David S. Long, Ada L. Olins, Bryon E. Wright, Mark H. Vickers, Justin M. O’Sullivan
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-021-02435-7

DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
Cited by: 15
Author(s): Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giz037

GenPipes: an open-source framework for distributed and scalable genomic analyses
Cited by: 107
Author(s): Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Létourneau, Joël Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, François Lefebvre, Gary Leveque, Eloi Mercier, David Bujold, Pascale Marquis, Patrick Tran Van, David Anderson de Lima Morais, Julien Tremblay, Xiaojian Shao, Édouard Henrion, Emmanuel González, Pierre-Olivier Quirion, B. Caron, Guillaume Bourque
Software Mentions: 6
Published: over 5 years ago

10.1186/s13072-021-00417-4

Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C
Cited by: 2
Author(s): Ning Liu, Wai Yee Low, Hamid Alinejad‐Rokny, Stephen Pederson, Timothy Sadlon, Simon C. Barry, James Breen
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-019-1860-7

CRUP: a comprehensive framework to predict condition-specific regulatory units
Cited by: 26
Author(s): Anna Ramisch, Verena Heinrich, Laura V. Glaser, Alisa Fuchs, Xinyi Yang, Philipp Benner, Robert Schöpflin, Na Li, Sarah Kinkley, Anja Römer-Hillmann, John Longinotto, Steffen Heyne, Beate Czepukojc, Sonja M. Kessler, Alexandra K. Kiemer, Cristina Cadenas, Laura Arrigoni, Nina Gasparoni, Thomas Manke, Thomas Pap, J. Andrew Pospisilik, Jan G. Hengstler, Jörn Walter, Sebastiaan H. Meijsing, Ho‐Ryun Chung, Martin Vingron
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-021-02378-z

GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
Cited by: 14
Author(s): Da-Inn Lee, Sushmita Roy
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.35788

A promoter interaction map for cardiovascular disease genetics
Cited by: 111
Author(s): Lindsey Montefiori, Débora R. Sobreira, Noboru Jo Sakabe, Ivy Aneas, Amelia C Joslin, Grace Hansen, Grazyna Bozek, Ivan P. Moskowitz, Elizabeth M. McNally, Marcelo A. Nóbrega
Software Mentions: 5
Published: over 6 years ago

10.3389/fcvm.2018.00186

Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation
Cited by: 15
Author(s): Douglas J. Chapski, Manuel Rosa‐Garrido, Haiyang Nan, Frank Alber, Thomas M. Vondriska
Software Mentions: 4
Published: almost 6 years ago

10.3390/epigenomes3020011

Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors
Cited by: 11
Author(s): Diana L. Gerrard, Joseph R. Boyd, Gary S. Stein, Victor X. Jin, Seth Frietze
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-020-02183-0

Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage
Cited by: 19
Author(s): Yasutaka Kakui, Christopher Barrington, David J. Barry, Tereza Gerguri, Xiao Fu, Paul A. Bates, Bhavin S. Khatri, Frank Uhlmann
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-021-02455-3

Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization
Cited by: 29
Author(s): Xinyi Liu, Shaoshuai Jiang, Lin Ma, Jiale Qu, Longying Zhao, Xing Zhu, Junjun Ding
Software Mentions: 4
Published: over 3 years ago

10.1038/s41438-021-00494-2

Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication
Cited by: 15
Author(s): Le Zhang, Jingtian Zhao, Hao Bi, Xiangyu Yang, Zhiyang Zhang, Yutao Su, Zhenghao Li, Lei Zhang, Brian J. Sanderson, Jianquan Liu, Tao Ma
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1007467

Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae
Cited by: 73
Author(s): David J. Winter, Austen R. D. Ganley, Carolyn A. Young, Ivan Liachko, Christopher L. Schardl, Pierre‐Yves Dupont, Daniel Berry, Arvina Ram, Barry Scott, Murray P. Cox
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1005708

Analysis of the relationship between coexpression domains and chromatin 3D organization
Cited by: 46
Author(s): María E. Soler-Oliva, José A. Guerrero-Martínez, Valentina Bachetti, José Carlos Castañeda Reyes
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-021-04113-8

Deciphering hierarchical organization of topologically associated domains through change-point testing
Cited by: 11
Author(s): Haipeng Xing, Yingru Wu, Michael Q. Zhang, Yong Chen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008278

Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates
Cited by: 63
Author(s): Ittai Eres, Kaixuan Luo, Chiaowen Joyce Hsiao, Lauren E. Blake, Yoav Gilad
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.3000004

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development
Cited by: 25
Author(s): Nayuta Yakushiji-Kaminatsui, Lucille Lopez-Delisle, Christopher Chase Bolt, Guillaume Andrey, Léonardo Beccari, Denis Duboule
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-021-02436-6

Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers
Cited by: 3
Author(s): Marie Zufferey, Yuanlong Liu, Daniele Tavernari, Marco Mina, Giovanni Ciriello
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-017-1931-2

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data
Cited by: 35
Author(s): Oluwatosin Oluwadare, Jianlin Cheng
Software Mentions: 2
Published: about 7 years ago

10.3390/genes11030276

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing
Cited by: 14
Author(s): Daniela C. Soto, Colin J. Shew, Mira Mastoras, Joshua M. Schmidt, Ruta Sahasrabudhe, Gulhan Kaya, Aida M. Andrés, Megan Y. Dennis
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pmed.1003132

Distinct subtypes of polycystic ovary syndrome with novel genetic associations: An unsupervised, phenotypic clustering analysis
Cited by: 106
Author(s): Matthew Dapas, Frederick Lin, Girish N. Nadkarni, Ryan Sisk, Richard S. Legro, Margrit Urbanek, M. Geoffrey Hayes, Andrea Dunaif
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-019-1893-y

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
Cited by: 44
Author(s): Lin An, Tao Yang, Jingquan Yang, Johannes Nuebler, Guanjue Xiang, R Hardison, Qunhua Li, Yu Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13148-021-01167-6

Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance
Cited by: 10
Author(s): Jingwei Li, Kun Fang, Lavanya Choppavarapu, Ke Yang, Yilin Yang, Junbai Wang, Ruifeng Cao, Ismail Jatoi, Victor X. Jin
Software Mentions: 2
Published: about 3 years ago

10.3390/genes8090223

Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction
Cited by: 6
Author(s): Binhua Tang, Xiaolong Cheng, Yunlong Xi, Zixin Chen, Yufan Zhou, Victor X. Jin
Software Mentions: 1
Published: about 7 years ago

Ecosyste.ms: Papers

Projects: cran: TopDom

Papers Mentioning TopDom 31