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: MBASED

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

Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
1 version
Latest release: about 1 year ago
14,671 downloads total

Papers Mentioning MBASED 18

10.1093/molbev/msaa218

Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate<i>Cis</i>-Regulatory Alleles Underlying Rapid Craniofacial Divergence
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 10
Published: about 4 years ago

10.1186/s12864-018-4835-2

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)
Cited by: 15
Author(s): Julien Richard Albert, Takao Koike, Hamid Younesy, Iain Thompson, Aaron B. Bogutz, Mehdi Karimi, Matthew C. Lorincz
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.48476

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
Cited by: 29
Author(s): Matteo D’Antonio, Joaquin Reyna, David Jakubosky, Maureen D. Donovan, Marc Jan Bonder, Hiroko Matsui, Oliver Stegle, Naoki Nariai, Agnieszka D’Antonio‐Chronowska, Kelly A. Frazer
Software Mentions: 5
Published: about 5 years ago

10.1016/j.stemcr.2019.04.012

Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci
Cited by: 31
Author(s): Erin N. Smith, Agnieszka D’Antonio‐Chronowska, William W. Greenwald, Victor Borja, Lana Ribeiro Aguiar, Robert Pogue, Hiroko Matsui, Paola Benaglio, Shyamanga Borooah, Matteo D’Antonio, Radha Ayyagari, Kelly A. Frazer
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0218899

Hybrid gene misregulation in multiple developing tissues within a recent adaptive radiation of Cyprinodon pupfishes
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2542-4

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA
Cited by: 6
Author(s): Matt R. Paul, Nicholas P. Levitt, David E. Moore, Patricia M. Watson, Robert Wilson, Chadrick E. Denlinger, Dennis K. Watson, Paul E. Anderson
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.12206

Pseudoexons provide a mechanism for allele-specific expression of <i>APC</i> in familial adenomatous polyposis
Cited by: 17
Author(s): Taina T. Nieminen, Walter Hernán Pavicic, Noora Porkka, Matti Kankainen, Heikki Järvinen, Anna Lepistö, Païvi Peltomäki
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1008786

ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing
Cited by: 37
Author(s): Jiaxin Fan, Jian Hu, Chenyi Xue, Hanrui Zhang, Katalin Suszták, Muredach P Reilly, Rui Xiao, Mingyao Li
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-017-4261-x

Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis
Cited by: 12
Author(s): Dejian Zhao, Mingyan Lin, Erika Pedrosa, Herbert M. Lachman, Deyou Zheng
Software Mentions: 3
Published: about 7 years ago

10.1128/mSystems.00466-21

Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity
Cited by: 7
Author(s): Carlos A. Villarroel, Macarena Bastías, Paulo Canessa, Francisco A. Cubillos
Software Mentions: 2
Published: about 3 years ago

10.1186/s13059-017-1363-3

Intergenic disease-associated regions are abundant in novel transcripts
Cited by: 38
Author(s): Nenad Bartoniček, Michael B. Clark, Xiu Cheng Quek, James R. Torpy, Antonia L. Pritchard, Jesper L.V. Mååg, Brian Gloss, Joanna Crawford, Ryan J. Taft, Nicholas K. Hayward, Grant W. Montgomery, John S. Mattick, Tim R. Mercer, Marcel E. Dinger
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12920-015-0084-2

ASEQ: fast allele-specific studies from next-generation sequencing data
Cited by: 49
Author(s): Alessandro Romanel, Sara Lago, Davide Prandi, Andrea Sboner, Francesca Demichelis
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0214346

Genetic and genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep
Cited by: 6
Author(s): Georgios Banos, Emily L. Clark, Stephen J. Bush, P. K. Dutta, D. Georgios Bramis, G. Arsenos, David Hume, Androniki Psifidi
Software Mentions: 2
Published: almost 5 years ago

10.18632/oncotarget.27468

Tumor suppressor genes and allele-specific expression: mechanisms and significance
Cited by: 5
Author(s): Evan Clayton, Shareef Khalid, Dongjo Ban, Lu Wang, I. King Jordan, John F. McDonald
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13059-014-0405-3

MBASED: allele-specific expression detection in cancer tissues and cell lines
Cited by: 116
Author(s): Oleg Mayba, Houston Gilbert, Jinfeng Liu, Peter M. Haverty, Suchit Jhunjhunwala, Zhaoshi Jiang, Colin Watanabe, Zemin Zhang
Software Mentions: 1
Published: over 10 years ago

10.1186/s13073-017-0464-7

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
Cited by: 13
Author(s): Zeynep Kalender Atak, Hana Imrichová, Dmitry Svetlichnyy, Gert Hulselmans, Valerie Christiaens, Joke Reumers, Hugo Ceulemans, Stein Aerts
Software Mentions: 1
Published: about 7 years ago

10.1038/srep21134

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information
Cited by: 44
Author(s): Daniel Edsgärd, María Jesús Iglesias, Sarah-Jayne Reilly, Anders Hamsten, Per Tornvall, Jacob Odeberg, Olof Emanuelsson
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12859-019-3141-6

Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model
Cited by: 5
Author(s): Jing Xie, Tieming Ji, Marco A. R. Ferreira, Yahan Li, Bhaumik Narendrabhai Patel
Software Mentions: 1
Published: about 5 years ago