Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: HiTC

https://packages.ecosyste.ms/registries/bioconductor.org/packages/HiTC

High Throughput Chromosome Conformation Capture analysis
1 version
Latest release: about 1 year ago
1 dependent package
37,874 downloads total

Papers Mentioning HiTC 21

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

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Cited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Software Mentions: 15
Published: about 9 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

10.12688/f1000research.8759.2

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments
Cited by: 16
Author(s): Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons
Software Mentions: 10
Published: over 8 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/s13059-020-01998-1

Wheat chromatin architecture is organized in genome territories and transcription factories
Cited by: 89
Author(s): Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Séverine Domenichini, Natalia Y. Rodriguez Granados, Soon-Kap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza‐Mianza, Caroline Juéry, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martín Crespi, Magdy M. Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse, Moussa Benhamed
Software Mentions: 8
Published: over 4 years ago

10.1186/s12915-019-0726-5

Multi-species annotation of transcriptome and chromatin structure in domesticated animals
Cited by: 80
Author(s): Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kévin Muret, Diane Esquerré, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cédric Cabau, Elisa Crisci, Sophie Dhorne–Pollet, Françoise Drouet, Thomas Faraut, Ignacio González, Adeline Goubil, Sonia Lacroix‐Lamandé, Fabrice Laurent, Sylvain Marthey, Maria Marti-Marimon, Raphaëlle Momal-Leisenring, Florence Mompart, Pascale Quéré, David Robelin, Magali San Cristobal, Gwenola Tosser‐Klopp, Silvia Vincent‐Naulleau, Stéphane Fabre, Marie-Hélène Pinard van der Laan, Christophe Klopp, Michèle Tixier‐Boichard, Hervé Acloque, Sandrine Lagarrigue, Elisabetta Giuffra
Software Mentions: 8
Published: almost 5 years ago

10.1186/s13015-019-0157-4

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics
Cited by: 17
Author(s): Christophe Ambroise, Alia Dehman, Pierre Neuvial, Guillem Rigaill, Nathalie Vialaneix
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-015-0678-x

HiCdat: a fast and easy-to-use Hi-C data analysis tool
Cited by: 45
Author(s): Marc W. Schmid, Stefan Grob, Ueli Grossniklaus
Software Mentions: 5
Published: about 9 years ago

10.1038/s41375-020-0856-3

Contribution of CTCF binding to transcriptional activity at the HOXA locus in NPM1-mutant AML cells
Cited by: 19
Author(s): Reza Ghasemi, Heidi Struthers, Elisabeth R. Wilson, David H. Spencer
Software Mentions: 5
Published: over 4 years ago

10.1186/s13578-020-00399-y

Alternative splicing signatures in preimplantation embryo development
Cited by: 12
Author(s): Geng Tian, Jing Li, Ji Wu
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-017-1281-4

Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid
Cited by: 77
Author(s): Weiren Zhu, Bo Hu, Claude Becker, Ezgi Sueheyla Dogan, Kenneth W. Berendzen, Detlef Weigel, Chang Liu
Software Mentions: 5
Published: over 7 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

10.1186/s13072-020-00358-4

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes
Cited by: 11
Author(s): Parna Saha, Divya Tej Sowpati, Mamilla Soujanya, Ishanee Srivastava, Rakesh K. Mishra
Software Mentions: 3
Published: about 4 years ago

10.1186/s12915-021-01041-0

Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence
Cited by: 13
Author(s): Zhaoen Yang, Xiaoyang Ge, Weinan Li, Yang Jin, Lisen Liu, Wei Hu, Fuyan Liu, Yanli Chen, Shaoliang Peng
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-020-0715-x

A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons
Cited by: 29
Author(s): Sergio Espeso-Gil, Tobias B. Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan K. 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 K. Lipska, Nadejda M. Tsankova, Laura Huckins, Yan Jiang, Schahram Akbarian
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-018-1430-4

OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks
Cited by: 46
Author(s): Tingting Li, Lumeng Jia, Yong Cao, Qing Chen, Cheng Li
Software Mentions: 3
Published: over 6 years ago

10.1093/bioinformatics/btz808

HiCBricks: building blocks for efficient handling of large Hi-C datasets
Cited by: 5
Author(s): Koustav Pal, Ilario Tagliaferri, Carmen Maria Livi, Francesco Ferrari
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-019-1694-3

Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery
Cited by: 77
Author(s): Bo Hu, Nan Wang, Xiuli Bi, Ezgi Süheyla Karaaslan, Anna-Lena Weber, Weiren Zhu, Kenneth W. Berendzen, Chang Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-017-1161-y

Software tools for visualizing Hi-C data
Cited by: 49
Author(s): Galip Gürkan Yardımcı
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-015-0806-y

HiFive: a tool suite for easy and efficient HiC and 5C data analysis
Cited by: 55
Author(s): Michael E.G. Sauria, Jennifer E. Phillips-Cremins, Victor G. Corcés, James Taylor
Software Mentions: 1
Published: about 9 years ago