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: GenomicRanges
https://packages.ecosyste.ms/registries/bioconductor.org/packages/GenomicRanges
Representation and manipulation of genomic intervals
3 versions
Latest release: about 1 year ago
570 dependent packages
5,558,893 downloads total
Papers Mentioning GenomicRanges 323
10.1186/s13059-015-0668-3
Inferring regulatory element landscapes and transcription factor networks from cancer methylomesCited by: 163
Author(s): Lijing Yao, Hui Shen, Peter W. Laird, Peggy J. Farnham, Benjamin P. Berman
Software Mentions: 2
Published: over 9 years ago
10.1186/gb-2012-13-10-r87
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profilesCited by: 1,321
Author(s): Altuna Akalin, Matthías Kormáksson, Sheng Li, Francine E. Garrett-Bakelman, María E. Figueroa, Ari Melnick, Christopher E. Mason
Software Mentions: 2
Published: almost 13 years ago
10.7554/eLife.20148
Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesisCited by: 135
Author(s): Shelby A. Blythe, Eric Wieschaus
Software Mentions: 2
Published: almost 8 years ago
10.3390/ijms19113609
Causal Transcription Regulatory Network Inference Using Enhancer Activity as a Causal AnchorCited by: 4
Author(s): Deepti Vipin, Lingfei Wang, Guillaume Devailly, Tom Michoel, Anagha Joshi
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pbio.3000464
Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutationCited by: 33
Author(s): Cynthia J. Sakofsky, Natalie Saini, Leszek J. Klimczak, Kin Chan, Ewa Malc, Piotr A. Mieczkowski, Adam Burkholder, David C. Fargo, Dmitry A. Gordenin
Software Mentions: 2
Published: about 5 years ago
10.1016/j.cell.2017.01.019
UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same GeneCited by: 148
Author(s): Laura Williamson, Marco Saponaro, Stefan Boeing, Philip East, Richard Mitter, Theodoros Kantidakis, Gavin Kelly, Anna Lobley, Jane Walker, Bradley Spencer–Dene, Michael Howell, Aengus Stewart, Jesper Q. Svejstrup
Software Mentions: 2
Published: almost 8 years ago
10.1038/s41598-018-32712-8
Lymphocyte activation gene 3 (Lag3) expression is increased in prion infections but does not modify disease progressionCited by: 44
Author(s): Yingjun Liu, Silvia Sorce, Mario Nuvolone, Julie Domange, Adriano Aguzzi
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-017-05878-w
Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cellsCited by: 8
Author(s): John Blischak, Ludovic Tailleux, Marsha Myrthil, Cécile Charlois, Emmanuel Bergot, Aurélien Dinh, Gloria Morizot, Olivia Chény, Cassandre Von Platen, Jean-Louis Herrmann, Roland Brosch, Luis B. Barreiro, Yoav Gilad
Software Mentions: 2
Published: over 7 years ago
10.1186/s12864-018-5314-5
Fine mapping chromatin contacts in capture Hi-C dataCited by: 16
Author(s): Chris Eijsbouts, Oliver S. Burren, Paul Newcombe, Chris Wallace
Software Mentions: 2
Published: almost 6 years ago
10.1186/s12885-019-6394-6
Clonal relationship of synchronous head and neck cancer and esophageal cancer assessed by single nucleotide polymorphism-based loss of heterozygosity analysisCited by: 8
Author(s): Somkiat Sunpaweravong, Sacarin Bunbanjerdsuk, Tanjitti Pongrujikorn, Chaiwat Naktang, Patrapim Sunpaweravong, Anupong Nitiruangjaras, Tanadech Dechaphankul, Natini Jinawath
Software Mentions: 1
Published: almost 5 years ago
10.3389/fgene.2014.00075
Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo dataCited by: 176
Author(s): Thomas Carroll, Ziwei Liang, Rafik Salama, Rory Stark, Inês de Santiago
Software Mentions: 1
Published: over 10 years ago
10.3389/fcell.2021.651145
An ATAC-seq Dataset Uncovers the Regulatory Landscape During Axolotl Limb RegenerationCited by: 8
Author(s): Xiaoyü Wei, Hanbo Li, Yang Guo, Xiqian Zhao, Yang Liu, Xudong Zou, Li Zhou, Yue Yuan, Yating Qin, Chunyan Mao, Guodong Huang, Yeya Yu, Qiuting Deng, Weimin Feng, Jiangshan Xu, Mingyue Wang, Shanshan Liu, Huanming Yang, Longqi Liu, Chuanyu Liu, Ying Gu
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-018-24755-8
Galactic Cosmic Radiation Induces Persistent Epigenome Alterations Relevant to Human Lung CancerCited by: 20
Author(s): Elizabeth M. Kennedy, Doris R. Powell, Z. Li, Jason D. Bell, Benjamin G. Barwick, Hao Feng, Myles R. McCrary, Bhakti Dwivedi, Jeanne Kowalski, William S. Dynan, Karen N. Conneely, Paula M. Vertino
Software Mentions: 1
Published: over 6 years ago
10.18632/oncotarget.7450
Glucose-regulated protein 94 deficiency induces squamous cell metaplasia and suppresses PTEN-null driven endometrial epithelial tumor developmentCited by: 9
Author(s): Jiang-Cheng Shen, Lijing Yao, Yvonne G. Lin, Francesco J. DeMayo, John P. Lydon, Louis Dubeau, Amy Lee
Software Mentions: 1
Published: almost 9 years ago
10.3389/fgene.2013.00229
A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibilityCited by: 53
Author(s): Brian K. Meredith, D.P. Berry, F. Kearney, Emma K. Finlay, Alan G. Fahey, Daniel G. Bradley, David J. Lynn
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pone.0073627
Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344T during Growth in BeerCited by: 21
Author(s): Vanessa Pittet, Trevor G. Phister, Barry Ziola
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0159028
A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-SeqCited by: 11
Author(s): Tianyuan Wang, Janine H. Santos, Jian Feng, David C. Fargo, Ли Шен, Gonzalo Riadi, Elizabeth Keeley, Zachary S. Rosh, Eric J. Nestler, Richard P. Woychik
Software Mentions: 1
Published: over 8 years ago
10.1186/1756-8935-6-4
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip arrayCited by: 419
Author(s): E. Magda Price, Allison M. Cotton, Lucia L.C. Lam, Pau Farré, Eldon Emberly, Carolyn J. Brown, Wendy P. Robinson, Michæl S. Kobor
Software Mentions: 1
Published: over 11 years ago
10.1080/15592294.2015.1127479
Tissue-specific patterns of allelically-skewed DNA methylationCited by: 21
Author(s): Sarah Marzi, Emma L. Meaburn, Emma Dempster, Katie Lunnon, Jose Luis Paya-Cano, Rebecca Smith, Manuela Volta, Claire Troakes, Leonard C. Schalkwyk, Jonathan Mill
Software Mentions: 1
Published: almost 9 years ago
10.7554/eLife.51810
Attacks on genetic privacy via uploads to genealogical databasesCited by: 25
Author(s): Michael D. Edge, Graham Coop
Software Mentions: 1
Published: almost 5 years ago
10.1016/j.xcrm.2020.100002
Modeling Human Cytomegalovirus-Induced Microcephaly in Human iPSC-Derived Brain OrganoidsCited by: 60
Author(s): Guoqiang Sun, Flavia Chiuppesi, Xianwei Chen, Cheng Wang, Erpo Tian, Jenny Nguyen, Mindy Kha, Daniel Trinh, Hannah Zhang, Maria C. Marchetto, Hongjun Song, Guo‐li Ming, Fred H. Gage, Don J. Diamond, Felix Wussow, Yanhong Shi
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0174032
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancerCited by: 8
Author(s): Rebecca F. Lowdon, Ting Wang
Software Mentions: 1
Published: over 7 years ago