bioconductor: regioneR | Projects

10.1111/tpj.14784

Segmental duplications are hot spots of copy number variants affecting barley gene content
Cited by: 4
Author(s): Gianluca Bretani, Laura Rossini, Chiara Ferrandi, Joanne Russell, Robbie Waugh, Benjamin Kilian, Paolo Bagnaresi, Luigi Cattivelli, Agostino Fricano
Software Mentions: 11
Published: over 4 years ago

10.1038/s41598-019-41601-7

Characteristics and homogeneity of N6-methylation in human genomes
Cited by: 13
Author(s): Clare Pacini, Charles R. Bradshaw, Nigel Garrett, Magdalena J. Koziol
Software Mentions: 11
Published: almost 6 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: about 7 years ago

10.3389/fnmol.2021.664912

Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition
Cited by: 9
Author(s): Sergio Espeso‐Gil, Aliaksei Z. Holik, Sarah Bonnin, Shalu Jhanwar, Sandhya Chandrasekaran, Roger Piqué-Regi, Júlia Albaigès-Ràfols, Michael P. Maher, Jon Permanyer, Manuel Irimia, Marc R. Friedländer, Meritxell Pons-Espinal, Schahram Akbarian, Mara Dierssen, Philipp G. Maass, Charlotte N. Hor, Stephan Ossowski
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0212248

Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti
Cited by: 17
Author(s): Ruvini V. Lelwala, Pasi K. Korhonen, Neil D. Young, Jason B. Scott, Peter K. Ades, Robin B. Gasser, P. W. J. Taylor
Software Mentions: 8
Published: over 5 years ago

10.1093/bioinformatics/btx346

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
Cited by: 451
Author(s): Bernat Gel, Eduard Serra
Software Mentions: 7
Published: over 7 years ago

10.1186/s13059-021-02450-8

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
Cited by: 3
Author(s): Chenyang Dong, Shane P. Simonett, Sun‐Young Shin, Donnie S. Stapleton, Kathryn L. Schueler, Gary A. Churchill, Leina Lu, Huan Liu, Fulai Jin, Yan Li, Alan D. Attie, Mark P. Keller, Sündüz Keleş
Software Mentions: 7
Published: over 3 years ago

10.1186/s13059-021-02440-w

Bedshift: perturbation of genomic interval sets
Cited by: 5
Author(s): Aaron Gu, Hyun-Jae Cho, Nathan C. Sheffield
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1006940

CNEr: A toolkit for exploring extreme noncoding conservation
Cited by: 15
Author(s): Ge Tan, Dimitris Polychronopoulos, Boris Lenhard
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1009432

Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans
Cited by: 12
Author(s): Chenglin Li, Mintie Pu, Wenke Wang, Amaresh Chaturbedi, Felicity J Emerson, Siu Sylvia Lee
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.66524

Extracellular signal-regulated kinase mediates chromatin rewiring and lineage transformation in lung cancer
Cited by: 14
Author(s): Yusuke Inoue, Ana Nikolić, Dylan Farnsworth, Rocky Shi, Fraser Johnson, Alvin Liu, Marc Ladanyi, Romel Somwar, Marco Gallo, William W. Lockwood
Software Mentions: 6
Published: over 3 years ago

10.1016/j.immuni.2021.08.011

Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses
Cited by: 58
Author(s): Qingli Tang, Rachel E. Rigby, George R. Young, Astrid Korning Hvidt, Tanja Davis, Tiong Kit Tan, Anne Bridgeman, Alain Townsend, George Kassiotis, Jan Rehwinkel
Software Mentions: 6
Published: over 3 years ago

10.1093/gbe/evz108

Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish
Cited by: 8
Author(s): Carmelo Fruciano, Axel Meyer, Paolo Franchini
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.50541

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Cited by: 62
Author(s): Rita A Batista, Jordi Moreno‐Romero, Yue Qiu, Joram van Boven, Juan Santos‐González, Duarte D. Figueiredo, Claudia Köhler
Software Mentions: 5
Published: about 5 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.53459

The histone modification reader ZCWPW1 links histone methylation to PRDM9-induced double-strand break repair
Cited by: 28
Author(s): Tao Huang, Shenli Yuan, Lei Gao, Mengjing Li, Xiaochen Yu, Jianhong Zhan, Yingying Yin, Chao Liu, Chuanxin Zhang, Gang Lü, Wei Li, Jiang Liu, Zi‐Jiang Chen, Hongbin Liu
Software Mentions: 4
Published: over 4 years ago

10.1128/MCB.00668-17

The <i>Caenorhabditis elegans</i> Ortholog of TDP-43 Regulates the Chromatin Localization of the Heterochromatin Protein 1 Homolog HPL-2
Cited by: 12
Author(s): Tassa Saldi, Patrick Gonzales, Alfonso Garrido-Lecca, Vishantie Dostal, Christine M. Roberts, Leonard Petrucelli, Christopher D. Link
Software Mentions: 4
Published: over 6 years ago

10.26508/lsa.201900331

Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis
Cited by: 18
Author(s): Florian Noack, Abhijeet Pataskar, Martin Schneider, Frank Buchholz, Vijay Tiwari, Federico Calegari
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0213278

A common genomic code for chromatin architecture and recombination landscape
Cited by: 17
Author(s): Kamel Jabbari, Johannes Wirtz, Martina Rauscher, Thomas Wiehe
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13059-019-1635-1

Modeling double strand break susceptibility to interrogate structural variation in cancer
Cited by: 11
Author(s): Tracy Ballinger, Britta A. M. Bouwman, Reza Mirzazadeh, Silvano Garnerone, Nicola Crosetto, Colin A. Semple
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-6414-6

Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family
Cited by: 26
Author(s): Sivasubramanian Rajarammohan, Kumar Paritosh, Deepak Pental, Jagreet Kaur
Software Mentions: 3
Published: about 5 years ago

10.1186/s12711-021-00664-9

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes
Cited by: 14
Author(s): Elaheh Rostamzadeh Mahdabi, Ali Esmailizadeh, Ahmad Ayatollahi Mehrgardi, Masood Asadi Fozi
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-020-0932-2

Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate
Cited by: 18
Author(s): Agnieszka A. Golicz, Prem L. Bhalla, David Edwards, Mohan B. Singh
Software Mentions: 3
Published: over 4 years ago

10.1111/eva.13210

Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive
Cited by: 18
Author(s): Kevin P. Oh, Aaron B. Shiels, Laura Shiels, Dimitri V. Blondel, Karl J. Campbell, J. Royden Saah, Alun L. Lloyd, Paul Q. Thomas, Fred Gould, Zaid Abdo, John Godwin, Antoinette J. Piaggio
Software Mentions: 2
Published: almost 4 years ago

10.1093/bioinformatics/btv562

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests
Cited by: 330
Author(s): Bernat Gel, Anna Díez-Villanueva, Eduard Serra, Marcus Buschbeck, Miguel A. Peinado, Roberto Malinverni
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0168023

An Isochore Framework Underlies Chromatin Architecture
Cited by: 57
Author(s): Kamel Jabbari, Giorgio Bernardi
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-018-4871-y

Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Cited by: 33
Author(s): Aline Silva Mello Cesar, Luciana Correia de Almeida Regitano, James M. Reecy, Mirele Daiana Poleti, P. S. N. Oliveira, Guilherme Bueno de Oliveira, Gabriel Costa Monteiro Moreira, Maurício A. Mudadu, P. C. Tizioto, James E. Koltes, Eric R. Fritz-Waters, Luke M. Kramer, Dorian J. Garrick, Hamid Beiki, Ludwig Geistlinger, Gérson Barreto Mourão, Adhemar Zerlotini
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-021-02279-1

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues
Cited by: 12
Author(s): Pawel F. Przytycki, Katherine S. Pollard
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-018-19782-4

Widespread modulation of gene expression by copy number variation in skeletal muscle
Cited by: 16
Author(s): Ludwig Geistlinger, Vinícius da Silva, Aline Silva Mello Cesar, P. C. Tizioto, Levi Waldron, Ralf Zimmer, Luciana Correia de Almeida Regitano
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-30335-7

Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
Cited by: 61
Author(s): Andrew D. Armitage, Andrew Taylor, Maria K. Sobczyk, Laura Baxter, Bethany P. J. Greenfield, Helen Bates, Frank J. Wilson, Alison C. Jackson, Sascha Ott, Richard J. Harrison, John P. Clarkson
Software Mentions: 2
Published: over 6 years ago

Ecosyste.ms: Papers

Projects: bioconductor: regioneR

Papers Mentioning regioneR 30