bioconductor: DEXSeq | Projects | Ecosyste.ms: Papers

10.1186/s12859-015-0698-6

CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements
Cited by: 3
Author(s): Eman Badr, Lenwood S. Heath
Software Mentions: 1
Published: about 9 years ago

Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors
Cited by: 23
Author(s): Jennifer L. Caswell, Roman Camarda, Alicia Y. Zhou, Scott Huntsman, Donglei Hu, Steven E. Brenner, Noah Zaitlen, Andrei Goga, Elad Ziv
Software Mentions: 1
Published: about 9 years ago

10.3389/fgene.2020.00586

Intron Retention as a Mode for RNA-Seq Data Analysis
Cited by: 24
Author(s): Juanjuan Zheng, Cui-Xiang Lin, Zhao-Yu Fang, Hongdong Li
Software Mentions: 1
Published: over 4 years ago

10.1007/s12035-020-02258-w

Directly Reprogrammed Neurons Express MAPT and APP Splice Variants Pertinent to Ageing and Neurodegeneration
Cited by: 11
Author(s): Mette Habekost, Per Qvist, Mark Denham, Ida E. Holm, Arne Lund Jørgensen
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13059-019-1756-6

Alternative splicing is required for stage differentiation in malaria parasites
Cited by: 29
Author(s): Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Emma McHugh, V Vern Lee, Angelika Sturm, Anton Cozijnsen, Geoffrey I. McFadden, Stuart A. Ralph
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07669-0

Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation
Cited by: 6
Author(s): Fernando Dı́az, Carson W. Allan, Therese A. Markow, Jeremy M. Bono, Luciano M. Matzkin
Software Mentions: 1
Published: over 3 years ago

10.1093/biostatistics/kxt053

Differential expression analysis of RNA-seq data at single-base resolution
Cited by: 59
Author(s): Alyssa C. Frazee, Sarven Sabunciyan, Kasper D. Hansen, Rafael A. Irizarry, Jeffrey T. Leek
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-017-05537-0

Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma
Cited by: 27
Author(s): Sunniva Bjørklund, Anshuman Panda, Surendra Kumar, Michael Seiler, Doug Robinson, Jinesh Gheeya, Ming Yao, Grethe I.G. Alnæs, Deborah Toppmeyer, Margit Riis, Bjørn Naume, Anne Lise Børresen-Dale, Vessela N. Kristensen, Shridar Ganesan, Gyan Bhanot
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-017-1687-8

A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays
Cited by: 2
Author(s): Marijke Van Moerbeke, Adetayo Kasim, Willem Talloen, Joke Reumers, Hinrick W. H. Göhlmann, Ziv Shkedy
Software Mentions: 1
Published: over 7 years ago

10.3390/vaccines7040160

Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts
Cited by: 4
Author(s): Diwakar Santhakumar, Mohammed A. Rohaim, Muhammad Munir
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0163590

Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation
Cited by: 7
Author(s): Stephen W. Hartley, James C. Mullikin, David C. Klein, Morgan Park, Nisc Comparative Sequencing Program, Steven L. Coon
Software Mentions: 1
Published: about 8 years ago

10.1038/tpj.2015.93

Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
Cited by: 23
Author(s): Aparna Chhibber, Courtney French, Sook Wah Yee, Eric R. Gamazon, Elizabeth Theusch, Xiang Qin, Amy Webb, Audrey C. Papp, Ann Wang, Christine Q. Simmons, Anuar Konkashbaev, Amarjit S. Chaudhry, Katrina Mitchel, Doug Stryke, Thomas E. Ferrin, Scott T. Weiss, Deanna L. Kroetz, Wolfgang Sadée, Deborah A. Nickerson, Ronald M. Krauss, AlfredL. George, Erin G. Schuetz, Marisa W. Medina, Nancy J. Cox, Steven E. Scherer, Kathleen M. Giacomini, Steven E. Brenner
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep42790

Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain
Cited by: 34
Author(s): Tian-Lin Cheng, Jingqi Chen, Huida Wan, Bin Tang, Weidong Tian, Lujian Liao, Zilong Qiu
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep28210

Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39
Cited by: 14
Author(s): Noel Faherty, Matthew A. Benson, Eshita Sharma, Angela Lee, Alison Howarth, Helen Lockstone, Daniel Ebner, Shoumo Bhattacharya
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1006660

TDRD6 mediates early steps of spliceosome maturation in primary spermatocytes
Cited by: 14
Author(s): Müge Akpınar, Mathias Lesche, Grigorios Fanourgakis, Jun Fu, Konstantinos Anastassiadis, Andreas Dahl, Rolf Jessberger
Software Mentions: 1
Published: over 7 years ago

10.1038/srep24545

Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2′-deoxycytidine
Cited by: 13
Author(s): Xiaolei Ding, Xiaojing Yang, Gangning Liang, Kai Wang
Software Mentions: 1
Published: over 8 years ago

10.1038/srep18741

Exon-centric regulation of ATM expression is population-dependent and amenable to antisense modification by pseudoexon targeting
Cited by: 5
Author(s): Jana Královičová, Marcin Knut, Nicholas C. P. Cross, Igor Vořechovský
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.ppat.1006355

Generational distribution of a Candida glabrata population: Resilient old cells prevail, while younger cells dominate in the vulnerable host
Cited by: 27
Author(s): Tejas Bouklas, Luz Alonso-Crisóstomo, T. Székely, Elizabeth Diago-Navarro, Erika P. Orner, Kalie Smith, Mansa Munshi, Maurizio Del Poeta, Gábor Balázsi, Bettina C. Fries
Software Mentions: 1
Published: over 7 years ago

10.1038/s41419-020-03055-y

Splicing factor SF3B1 promotes endometrial cancer progression via regulating KSR2 RNA maturation
Cited by: 26
Author(s): Pooja Popli, Megan M. Richters, Sangappa B. Chadchan, Tae Hoon Kim, Eric Tycksen, Malachi Griffith, Premal H. Thaker, Ramakrishna Kommagani
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0166978

Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data
Cited by: 17
Author(s): Eman Badr, Mahmoud ElHefnawi, Lenwood S. Heath
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-015-1740-9

Common and specific downstream signaling targets controlled by Tlr2 and Tlr5 innate immune signaling in zebrafish
Cited by: 29
Author(s): Shuxin Yang, Rubén Marín-Juez, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 1
Published: over 9 years ago

10.1016/j.ebiom.2016.05.009

Decreased Usage of Specific Scrib Exons Defines a More Malignant Phenotype of Breast Cancer With Worsened Survival
Cited by: 3
Author(s): Gergana Metodieva, Samson Adoki, Berthold Lausen, Metodi V. Metodiev
Software Mentions: 1
Published: over 8 years ago

10.1016/j.celrep.2017.07.025

Impact of Alternative Splicing on the Human Proteome
Cited by: 137
Author(s): Yansheng Liu, Mar Gonzàlez-Porta, Susana Santos, Alvis Brāzma, John C. Marioni, Ruedi Aebersold, Ashok R. Venkitaraman, Vihandha O. Wickramasinghe
Software Mentions: 1
Published: over 7 years ago

10.1186/s13073-021-00949-0

Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain
Cited by: 16
Author(s): Lindsay Liang, Siavash Fazel Darbandi, Sirisha Pochareddy, Forrest O. Gulden, Michael C. Gilson, Brooke Sheppard, Atehsa Sahagun, Joon Yong An, Donna M. Werling, John L.R. Rubenstein, Nenad Šestan, Kevin J. Bender, Stephan J. Sanders
Software Mentions: 1
Published: about 3 years ago

10.1186/s13059-020-02039-7

SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins
Cited by: 5
Author(s): Chen Fan, Sündüz Keleş
Software Mentions: 1
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: DEXSeq

Papers Mentioning DEXSeq 226