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: Gviz
https://packages.ecosyste.ms/registries/bioconductor.org/packages/Gviz
Plotting data and annotation information along genomic coordinates
2 versions
Latest release: about 1 year ago
54 dependent packages
782,714 downloads total
Papers Mentioning Gviz 134
10.15252/msb.20156198
Single‐cell polyadenylation site mapping reveals 3′ isoform choice variabilityCited by: 54
Author(s): Lars Velten, Simon Anders, Aleksandra Pękowska, Aino I Järvelin, Wolfgang Huber, Vicent Pelechano, Lars M. Steinmetz
Software Mentions: 3
Published: over 9 years ago
10.3390/ijms21218383
Trans-Ancestral Fine-Mapping and Epigenetic Annotation as Tools to Delineate Functionally Relevant Risk Alleles at IKZF1 and IKZF3 in Systemic Lupus ErythematosusCited by: 6
Author(s): Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0140077
GATA1 and PU.1 Bind to Ribosomal Protein Genes in Erythroid Cells: Implications for RibosomopathiesCited by: 14
Author(s): Elsa P. Amanatiadou, Giorgio L. Papadopoulos, John Strouboulis, Ioannis S. Vizirianakis
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.ppat.1008666
In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genomeCited by: 19
Author(s): Husam Taher, Eisa Mahyari, Craig N. Kreklywich, Luke S. Uebelhoer, Matthew R. McArdle, Matilda J. Moström, Amruta Bhusari, Michael Nekorchuk, E Xiaofei, Travis Whitmer, Elizabeth A. Scheef, Lesli M. Sprehe, Dawn Roberts, Colette M. Hughes, Kerianne A. Jackson, Andrea N. Selseth, Abigail B. Ventura, Hillary C. Cleveland-Rubeor, Yujuan Yue, Kimberli A. Schmidt, Jason Shao, Paul T. Edlefsen, Jeremy Smedley, Timothy F. Kowalik, Richard J. Stanton, Michael K. Axthelm, Jacob D. Estes, Scott G. Hansen, Amitinder Kaur, Peter A. Barry, Benjamin N. Bimber, Louis J. Picker, Daniel N. Streblow, Klaus Früh, Daniel Malouli
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13058-020-01273-y
Tumor sequencing is useful to refine the analysis of germline variants in unexplained high-risk breast cancer familiesCited by: 6
Author(s): Cédric Van Marcke, Raphaël Helaers, Anne De Leener, Mariam Ahmad, Céline A Schoonjans, Jérôme Ambroise, Christine Galant, P. Delrée, Françoise Rothé, Isabelle Bar, Elsa Khoury, Pascal Brouillard, Jean-Luc Canon, Peter Vuylsteke, Jean‐Pascal Machiels, Martine Berlière, Nisha Limaye, Miikka Vikkula, François P. Duhoux
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-019-5611-7
Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryosCited by: 24
Author(s): Wei Zhu, Xiaocui Xu, Xinxin Wang, Jiang Liu
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-020-06803-8
Replication origin location might contribute to genetic variability in Trypanosoma cruziCited by: 7
Author(s): Christiane B. de Araujo, Júlia Pinheiro Chagas da Cunha, Davi Toshio Inada, Jeziel D. Damasceno, Alex Ranieri Jerônimo Lima, Priscila Mazzocchi Hiraiwa, Catarina A. Marques, Evonnildo Costa Gonçalves, Milton Yutaka Nishiyama-Jr, Richard McCulloch, Maria Carolina Elias
Software Mentions: 2
Published: over 4 years ago
10.7554/eLife.58030
Genome duplication in Leishmania major relies on persistent subtelomeric DNA replicationCited by: 15
Author(s): Jeziel D. Damasceno, Catarina A. Marques, Dario Beraldi, Kathryn Crouch, Craig Lapsley, Ricardo Obonaga, Luíz Ricardo Orsini Tosi, Richard McCulloch
Software Mentions: 2
Published: about 4 years ago
10.3389/fendo.2021.713961
Neuromedins NMU and NMS: An Updated Overview of Their FunctionsCited by: 18
Author(s): Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2020.01288
Structure and Expression of Bud Dormancy-Associated MADS-Box Genes (DAM) in European PlumCited by: 23
Author(s): Carles Quesada-Traver, Brenda Guerrero, M. L. Badenes, Javier Rodrigo, Gabino Ríos, Alba Lloret
Software Mentions: 2
Published: about 4 years ago
10.1038/srep13107
Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genesCited by: 122
Author(s): Liina Tserel, Raivo Kolde, Maia Limbach, Konstantin Tretyakov, Silva Kasela, Kai Kisand, Mario Saare, Jaak Vilo, Andres Metspalu, Lili Milani, Pärt Peterson
Software Mentions: 2
Published: about 9 years ago
10.3390/genes11010096
Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic FetusesCited by: 8
Author(s): Jinsoo Ahn, Huiguang Wu, Joonbum Lee, In-Sul Hwang, Debing Yu, Jin-Seop Ahn, Jeong-Woong Lee, Seongsoo Hwang, Kichoon Lee
Software Mentions: 2
Published: almost 5 years ago
10.1093/gigascience/giy079
Clinker: visualizing fusion genes detected in RNA-seq dataCited by: 16
Author(s): Breon Schmidt, N. Davidson, Anthony D. K. Hawkins, Ray C. Bartolo, Ian J. Majewski, Paul G. Ekert, Alicia Oshlack
Software Mentions: 2
Published: over 6 years ago
10.1534/g3.120.401425
The Landscape of Genomic Imprinting at the Porcine <i>SGCE</i>/<i>PEG10</i> Locus from Methylome and Transcriptome of Parthenogenetic EmbryosCited by: 5
Author(s): Jinsoo Ahn, In-Sul Hwang, Mi-Ryung Park, In-Cheol Cho, Seongsoo Hwang, Kichoon Lee
Software Mentions: 2
Published: about 4 years ago
10.18632/oncotarget.27083
CpG promoter hypo-methylation and up-regulation of microRNA-190b in hormone receptor-positive breast cancerCited by: 2
Author(s): Elisabet Alexandra Frick, Thorkell Gudjonsson, Jórunn E. Eyfjörd, Jón Gunnlaugur Jónasson, Laufey Tryggvadóttír, Olafur A. Stefansson, Stefan Sigurdsson
Software Mentions: 2
Published: over 5 years ago
10.3389/fpls.2020.593692
G4 Structures in Control of Replication and Transcription of rRNA GenesCited by: 12
Author(s): Kateřina Havlová, Jiřı́ Fajkus
Software Mentions: 2
Published: about 4 years ago
10.1038/s41598-018-26112-1
Genome-wide haplotype association analysis of primary biliary cholangitis risk in JapaneseCited by: 5
Author(s): Cindy Im, Yadav Sapkota, Wonjong Moon, M. Kawashima, Minoru Nakamura, Katsushi Tokunaga, Yutaka Yasui
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0128517
Impacts of Chromatin States and Long-Range Genomic Segments on Aging and DNA MethylationCited by: 25
Author(s): Dan Sun, Soojin V. Yi
Software Mentions: 2
Published: over 9 years ago
10.1186/s13029-016-0052-z
A flexible tool to plot a genomic map for single nucleotide polymorphismsCited by: 1
Author(s): Fuquan Zhang
Software Mentions: 2
Published: over 8 years ago
10.3390/v12111264
A Novel Anphevirus in Aedes albopictus Mosquitoes Is Distributed Worldwide and Interacts with the Host RNA Interference PathwayCited by: 8
Author(s): Mosè Manni, Evgeny M. Zdobnov
Software Mentions: 2
Published: about 4 years ago
10.1016/j.ccell.2017.10.004
A Paradoxical Tumor-Suppressor Role for the Rac1 Exchange Factor Vav1 in T Cell Acute Lymphoblastic LeukemiaCited by: 35
Author(s): Javier Robles‐Valero, L. Francisco Lorenzo‐Martín, Mauricio Menacho-Márquez, Isabel Fernández‐Pisonero, Antonio Abad, Mireia Camós, Marı́a L. Toribio, Lluís Espinosa, Anna Bigas, Xosé R. Bustelo
Software Mentions: 2
Published: about 7 years ago
10.1186/s12864-017-4333-y
Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researchesCited by: 21
Author(s): Yuko Makita, Mika Kawashima, Nyok-Sean Lau, Ahmad Sofiman Othman, Minami Matsui
Software Mentions: 1
Published: almost 7 years ago
10.3389/fonc.2021.641184
Identification and Validation of the Prognostic Stemness Biomarkers in Bladder Cancer Bone MetastasisCited by: 4
Author(s): Kang Yao, Xuejun Zhu, Xijun Wang, Shunbao Liao, Mengran Jin, Li Zhang, Xiangyang Wu, Tingxiao Zhao, Jun Zhang, Jun Lee, Danjie Zhu
Software Mentions: 1
Published: over 3 years ago
10.3389/fnins.2018.00119
SP8 Transcriptional Regulation of Cyclin D1 During Mouse Early CorticogenesisCited by: 4
Author(s): Ugo Borello, Barbara Berarducci, Edwige Delahaye, David J. Price, Colette Dehay
Software Mentions: 1
Published: over 6 years ago
10.1161/CIRCGEN.118.002353
High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related PathwaysCited by: 9
Author(s): Örjan Åkerborg, Rapolas Spalinskas, Sailendra Pradhananga, Anandashankar Anil, Pontus Höjer, Flore-Anne Poujade, Lasse Folkersen, Per Eriksson, Pelin Sahlén
Software Mentions: 1
Published: over 5 years ago
10.1038/srep13969
InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCGCited by: 15
Author(s): Min Yang, Chunhui Gao, Jialing Hu, Леи Жао, Qiaoyun Huang, Zheng‐Guo He
Software Mentions: 1
Published: about 9 years ago
10.3390/cells7080102
TNFSF14/LIGHT, a Non-Canonical NF-κB Stimulus, Induces the HIF PathwayCited by: 12
Author(s): Laura D’Ignazio, Michael Batie, Sónia Rocha
Software Mentions: 1
Published: over 6 years ago
10.1098/rstb.2019.0540
The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouseCited by: 13
Author(s): Henry L. North, Pierre Caminade, Dany Séverac, Khalid Belkhir, Carole Smadja
Software Mentions: 1
Published: over 4 years ago
10.7554/eLife.31216
Telomere repeats induce domains of H3K27 methylation in NeurosporaCited by: 31
Author(s): Kirsty Jamieson, Kevin J McNaught, Tereza Ormsby, Neena A. Leggett, Shinji Honda, Eric U. Selker
Software Mentions: 1
Published: almost 7 years ago
10.1128/JVI.01337-19
CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent MechanismsCited by: 48
Author(s): Mattia Ficarelli, Irati Antzin-Anduetza, Rupert Hugh-White, Andrew E. Firth, Helin Sertkaya, Harry Wilson, Stuart J. D. Neil, Reiner Schulz, Chad M. Swanson
Software Mentions: 1
Published: over 4 years ago
10.3390/ijms21083000
HIF-1β Positively Regulates NF-κB Activity via Direct Control of TRAF6Cited by: 10
Author(s): Laura D’Ignazio, Dilem Shakir, Michael Batie, H.‐Arno J. Müller, Sónia Rocha
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-018-4598-9
Mapping QTL for white striping in relation to breast muscle yield and meat quality traits in broiler chickensCited by: 46
Author(s): Eva Pampouille, Cécile Berri, Simon Boitard, Christelle Hennequet-Antier, Stéphane Beauclercq, Estelle Godet, Christophe Praud, Yves Jégo, Elisabeth Le Bihan‐Duval
Software Mentions: 1
Published: over 6 years ago
10.1186/s12864-019-5756-4
Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome sizeCited by: 9
Author(s): Abhijeet Shah, Joseph I. Hoffman, Holger Schielzeth
Software Mentions: 1
Published: over 5 years ago
10.1186/1471-2105-15-306
Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimagesCited by: 10
Author(s): Andreas Dander, Matthias Baldauf, Michael Sperk, Stephan Pabinger, Benjamin Hiltpolt, Zlatko Trajanoski
Software Mentions: 1
Published: about 10 years ago