bioconductor: DEXSeq | Projects | Ecosyste.ms: Papers

10.1186/s13059-017-1277-0

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
Cited by: 72
Author(s): Koen Van den Berge, Charlotte Soneson, Mark D. Robinson
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-018-1551-9

Alternative polyadenylation factors link cell cycle to migration
Cited by: 21
Author(s): Mithun Mitra, Elizabeth L. Johnson, Vinay Swamy, Lois E Nersesian, David C. Corney, David G. Robinson, Daniel Taylor, Aaron M. Ambrus, David Jelínek, Wei Wang, Sandra Batista, Hilary A. Coller
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-36912-0

DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patients
Cited by: 10
Author(s): Alessandro Corti, Raina Sota, Matteo Dugo, Raffaele Calogero, Benedetta Terragni, Massimo Mantegazza, Silvana Franceschetti, Michela Restelli, Patrizia Gasparini, Daniele Lecis, Krystyna Chrzanowska, Domenico Delia
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-78997-6

Genes associated with cognitive performance in the Morris water maze: an RNA-seq study
Cited by: 18
Author(s): Vasiliy V. Reshetnikov, Polina E. Kisaretova, Nikita I. Ershov, Anastasia S. Shulyupova, Dmitry Oshchepkov, Н. В. Климова, Anna V. Ivanchihina, T. I. Merkulova, Natalia P. Bondar
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13045-014-0089-x

Splicing factor 3b subunit 1 (Sf3b1) haploinsufficient mice display features of low risk Myelodysplastic syndromes with ring sideroblasts
Cited by: 20
Author(s): Valeria Visconte, Ali Tabarroki, Li Zhang, Yvonne Parker, Edy Hasrouni, R. Mahfouz, Kyoichi Isono, Haruhiko Koseki, Mikkael A. Sekeres, Yogen Saunthararajah, John Barnard, Daniel J. Lindner, Heesun J. Rogers, Ramon V. Tiu
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.46919

FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
Cited by: 63
Author(s): Kirsty Sawicka, Caryn Hale, Christopher Y. Park, John Fak, Jodi Gresack, Sarah J. Van Driesche, Jaw Jou Kang, Jennifer C. Darnell, Robert B. Darnell
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13227-017-0069-7

Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus
Cited by: 50
Author(s): Amie L. Romney, Jason E. Podrabsky
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0178281

Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma
Cited by: 18
Author(s): Mikaela Miller, Thomas Danhorn, Charmion Cruickshank‐Quinn, Sonia M. Leach, Sean Jacobson, Matthew Strand, Nichole Reisdorph, Russell P. Bowler, Irina Petrache, Katerina Kechris
Software Mentions: 3
Published: over 7 years ago

10.1098/rstb.2017.0073

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing
Cited by: 12
Author(s): Clare Pacini, Magdalena J. Koziol
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-015-0749-3

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength
Cited by: 77
Author(s): Vihandha O. Wickramasinghe, Mar Gonzàlez-Porta, David Perera, Arthur R. Bartolozzi, Christopher R. Sibley, Martina Hallegger, Jernej Ule, John C. Marioni, Ashok R. Venkitaraman
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-15-1031

Differential gene expression and alternative splicing in insect immune specificity
Cited by: 38
Author(s): Carolyn Riddell, Juan David Lobaton Garces, Sally Adams, Seth M. Barribeau, David Twell, Eamonn B. Mallon
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-017-1184-4

IRFinder: assessing the impact of intron retention on mammalian gene expression
Cited by: 184
Author(s): Robert Middleton, Dadi Gao, Aubin Thomas, Babita Singh, Amy Y M Au, Justin Wong, Alexandra Bomane, Bertrand Cosson, Eduardo Eyras, John E.J. Rasko, William Ritchie
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.33070

Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice
Cited by: 67
Author(s): Roman M. Stilling, Gerard M. Moloney, Feargal J. Ryan, Alan E. Hoban, Thomaz F.S. Bastiaanssen, Fergus Shanahan, Gerard Clarke, Marcus J. Claesson, Timothy G. Dinan, John F. Cryan
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.02313

Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion
Cited by: 32
Author(s): Patricia Sieber, Kerstin Voigt, Philipp Kämmer, Sascha Brunke, Stefan Schuster, Jörg Linde
Software Mentions: 3
Published: about 6 years ago

10.15252/msb.20199367

Pan‐tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation
Cited by: 4
Author(s): Yisheng Li, Bernhard Schaefke, Xudong Zou, Min Zhang, Florian Heyd, Wei Sun, Bin Zhang, Guipeng Li, Weizheng Liang, Yuhao He, Juexiao Zhou, Yunfei Li, Liang Fang, Yuhui Hu, Wei Chen
Software Mentions: 3
Published: over 4 years ago

10.1186/s12876-020-01288-x

Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer
Cited by: 23
Author(s): Haifeng Lian, Aili Wang, Yuanyuan Shen, Qian Wang, Zijun Zhou, Ranran Zhang, Kun Li, Chengxia Liu, Huiying Jia
Software Mentions: 3
Published: over 4 years ago

10.3389/fonc.2021.699594

Identification of Gender-Specific Molecular Differences in Glioblastoma (GBM) and Low-Grade Glioma (LGG) by the Analysis of Large Transcriptomic and Epigenomic Datasets
Cited by: 12
Author(s): Tipu Khan, Bharat Prajapati, Simran Lakhina, Mridula B Sharma, Suneel Prajapati, Kunzang Chosdol, Subrata Sinha
Software Mentions: 3
Published: about 3 years ago

10.1186/s13024-021-00475-y

SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis
Cited by: 11
Author(s): Lydia M. Castelli, Luisa Cutillo, Catiane Souza, Álvaro Sánchez-Martínez, Ilaria Granata, Ya-Hui Lin, Monika A. Myszczynska, Paul R. Heath, Matthew R. Livesey, Ke Ning, Mimoun Azzouz, Pamela J. Shaw, Mario Rosario Guarracino, Alexander J. Whitworth, Laura Ferraiuolo, Marta Milo, Guillaume M. Hautbergue
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-15-S3-S1

Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers
Cited by: 19
Author(s): Federica Riccardo, Maddalena Arigoni, Genny Buson, Elisa Zago, Manuela Iezzi, Dario Livio Longo, Matteo Carrara, Alessandra Fiore, Simona Nuzzo, Silvio Bicciato, Patrizia Nanni, Lorena Landuzzi, Federica Cavallo, Raffaele Calogero, Elena Quaglino
Software Mentions: 3
Published: over 10 years ago

10.18632/oncotarget.27406

Characterization of unique PMEPA1 gene splice variants (isoforms d and e) from RNA Seq profiling provides novel insights into prognostic evaluation of prostate cancer
Cited by: 7
Author(s): Shashwat Sharad, Allissa Dillman, Zsófia Sztupinszki, Zoltán Szállási, Inger L. Rosner, Jennifer Cullen, Shiv Srivastava, Alagarsamy Srinivasan, Hua Li
Software Mentions: 3
Published: almost 5 years ago

10.1155/2015/206937

Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects
Cited by: 52
Author(s): Woo Jin Kim, Jae Hyun Lim, Jae Seung Lee, Sang Do Lee, Ju Han Kim, Yeon Mok Oh
Software Mentions: 3
Published: almost 10 years ago

10.3389/fgene.2021.623861

Transcriptome Analysis Reveals a Potential Role of Benzoxazinoid in Regulating Stem Elongation in the Wheat Mutant qd
Cited by: 4
Author(s): Daxing Xu, Yi Xie, Huijun Guo, Weiwei Zeng, Hui Xiong, Liyan Zhao, Jun Gu, Shirong Zhao, Yuping Ding, Luxiang Liu
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-018-4925-1

Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data
Cited by: 5
Author(s): Huijuan Feng, Tingting Li, Xuegong Zhang
Software Mentions: 3
Published: over 6 years ago

10.1016/j.molcel.2019.01.027

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination
Cited by: 87
Author(s): Kinga Kamieniarz-Gdula, Michal R. Gdula, Karin Panser, Takayuki Nojima, Joan Monks, Jacek R. Wiśniewski, Joey Riepsaame, Neil Brockdorff, Andrea Pauli, Nick J. Proudfoot
Software Mentions: 3
Published: over 5 years ago

10.1038/s41398-021-01256-3

Functional brain defects in a mouse model of a chromosomal t(1;11) translocation that disrupts DISC1 and confers increased risk of psychiatric illness
Cited by: 3
Author(s): Marion Bonneau, Shane T. O’ Sullivan, Miguel A. Gonzalez‐Lozano, Paul Baxter, Phillippe Gautier, Elena Marchisella, Neil Robert Hardingham, Robert Chesters, Helen S. Torrance, David M. Howard, Maurits A. Jansen, Melanie McMillan, Yasmin Singh, Michel Didier, Frank Koopmans, Colin A. Semple, Hansjürgen Volkmer, Maarten Loos, Kevin Fox, Giles E. Hardingham, Anthony C. Vernon, David J. Porteous, August B. Smit, David J. Price, J. Kirsty Millar
Software Mentions: 3
Published: almost 4 years ago

10.1007/s00251-014-0820-3

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics
Cited by: 15
Author(s): Wouter J. Veneman, Jan de Sonneville, Kees-Jan van der Kolk, Anita Ordas, Zaid Al-Ars, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.molcel.2019.04.034

Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome
Cited by: 66
Author(s): Nicolas Viphakone, Ian Sudbery, Llywelyn Griffith, Catherine G. Heath, David Sims, Stuart A. Wilson
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-1695-x

QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation
Cited by: 66
Author(s): Prerana Wagle, Miloš Nikolić, Peter Frommolt
Software Mentions: 3
Published: over 9 years ago

10.1007/s00335-016-9663-6

Genome characterization of the selected long- and short-sleep mouse lines
Cited by: 4
Author(s): Robin D. Dowell, Aaron Odell, Phillip A. Richmond, Daniel Malmer, Eitan Halper-Stromberg, Beth Bennett, Colin Larson, Sonia M. Leach, Richard A. Radcliffe
Software Mentions: 3
Published: about 8 years ago

10.1038/leu.2014.331

Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells
Cited by: 154
Author(s): Hamid Dolatshad, Andrea Pellagatti, Marta Fernández-Mercado, Bon Ham Yip, Luca Malcovati, Martin Attwood, B. Przychodzen, Natasha Sahgal, Alexander Kanapin, Helen Lockstone, L Scifo, Peter Vandenberghe, Elli Papaemmanuil, Christopher W. Smith, Peter J. Campbell, Shimpei Ogawa, Jaroslaw P. Maciejewski, Mario Cazzola, Kienan I. Savage, Jacqueline Boultwood
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41597-019-0014-9

Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells
Cited by: 14
Author(s): Xiaoyong Li, Geng Tian, Yue Zhao, Ji Wu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-018-0453-8

Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus
Cited by: 17
Author(s): Seonggyun Han, Jason E. Miller, Seyoun Byun, Dokyoon Kim, Shannon L. Risacher, Andrew J. Saykin, Younghee Lee, Kwangsik Nho
Software Mentions: 3
Published: almost 6 years ago

10.18632/oncotarget.17813

Transcriptome profiling in preadipocytes identifies long noncoding RNAs as Sam68 targets
Cited by: 13
Author(s): Naomi Li, Steven C. Hebert, Jingwen Song, Claudia L. Kleinman, Stéphane Richard
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-32310-8

The m6A-methylase complex recruits TREX and regulates mRNA export
Cited by: 82
Author(s): Simon Lesbirel, Nicolas Viphakone, Matthew T Parker, Jacob Parker, Catherine G. Heath, Ian Sudbery, Stuart A. Wilson
Software Mentions: 3
Published: about 6 years ago

10.2174/1389202911314030004

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity
Cited by: 75
Author(s): Bishakha Roy, Larisa M. Haupt, Lyn R. Griffiths
Software Mentions: 3
Published: over 11 years ago

10.1093/bioinformatics/btaa854

flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data
Cited by: 0
Author(s): Krzysztof J. Szkop, David S. Moss, Irene Nobeli
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-06211-1

Transcriptome profiling of mouse brains with qkI-deficient oligodendrocytes reveals major alternative splicing defects including self-splicing
Cited by: 22
Author(s): Lama Darbelli, Karine Choquet, Stéphane Richard, Claudia L. Kleinman
Software Mentions: 3
Published: over 7 years ago

10.1186/s13578-021-00546-z

Alterations of RNA splicing patterns in esophagus squamous cell carcinoma
Cited by: 10
Author(s): Jiyu Ding, Chunquan Li, Yin-Wei Cheng, Zhifeng Du, Qiuyu Wang, Zhidong Tang, Chao Song, Qiaoxi Xia, Wenjing Bai, Gang Li, Wei Liu, Li‐Yan Xu, En‐Min Li, Bingli Wu
Software Mentions: 3
Published: almost 4 years ago

10.1534/g3.114.012351

A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegans
Cited by: 138
Author(s): Marco Antonio Ortiz, Daniel Noble, Elena P. Sorokin, Judith Kimble
Software Mentions: 3
Published: about 10 years ago

10.1534/g3.118.200297

Key Transport and Ammonia Recycling Genes Involved in Aphid Symbiosis Respond to Host-Plant Specialization
Cited by: 17
Author(s): Dohyup Kim, Bushra Fazal Minhas, Hongmei Li-Byarlay, Allison K. Hansen
Software Mentions: 3
Published: over 6 years ago

10.15252/embj.201899016

miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the <scp>RNA</scp> ‐binding protein Quaking
Cited by: 75
Author(s): Katherine A. Pillman, C. Phillips, Suraya Roslan, John Toubia, B Kate Dredge, Andrew G. Bert, Rachael Lumb, Daniel Neumann, Xiaochun Li, Simon J. Conn, Dawei Liu, Cameron P. Bracken, David Lawrence, Nataly Stylianou, Andreas W. Schreiber, Wayne D. Tilley, Brett G. Hollier, Yeesim Khew‐Goodall, Luke A. Selth, Gregory J. Goodall, Philip A. Gregory
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0094646

Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain
Cited by: 12
Author(s): David N. Hauser, Allissa Dillman, Jinhui Ding, Li Yan, Mark Cookson
Software Mentions: 3
Published: over 10 years ago

10.1186/s12915-020-00873-6

Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate
Cited by: 15
Author(s): Girish Beedessee, Takaaki Kubota, Asuka Arimoto, Koki Nishitsuji, Ross F. Waller, Kanako Hisata, Shin‐ichi Yamasaki, Noriyuki Satoh, Jun’ichi Kobayashi, Eiichi Shoguchi
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0136653

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq
Cited by: 42
Author(s): Yafang Li, Xiayu Rao, William Mattox, Christopher I. Amos, Bin Liu
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pgen.1007617

Tudor-domain containing protein 5-like promotes male sexual identity in the Drosophila germline and is repressed in females by Sex lethal
Cited by: 21
Author(s): Shekerah Primus, Caitlin Pozmanter, Kelly Baxter, Mark Van Doren
Software Mentions: 3
Published: over 5 years ago

10.3390/genes12040545

A Complex Gene Network Mediated by Ethylene Signal Transduction TFs Defines the Flower Induction and Differentiation in Olea europaea L.
Cited by: 2
Author(s): Amelia Salimonti, Ivano Forgione, Tiziana Maria Sirangelo, Guglielmo Puccio, Antonio Mauceri, Francesco Mercati, Francesco Sunseri, Fabrizio Carbone
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0191096

Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds
Cited by: 11
Author(s): Shanshan Xie, Xiufen Yang, Dehe Wang, Feng Zhu, Ning Yang, Zhuocheng Hou, Zhonghua Ning
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1009182

Differential transcript usage in the Parkinson’s disease brain
Cited by: 12
Author(s): Fiona Dick, Gonzalo S. Nido, Guido Alves, Ole‐Bjørn Tysnes, Gry Hilde Nilsen, Christian Dölle, Charalampos Tzoulis
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0234710

Integrative analysis of gene expression and alternative splicing in microalgae grown under heterotrophic condition
Cited by: 5
Author(s): Bahman Panahi, Mohammad Amin Hejazi
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.48788

Lmx1b is required at multiple stages to build expansive serotonergic axon architectures
Cited by: 30
Author(s): Lauren J. Donovan, W. Clay Spencer, Meagan M. Kitt, Brent A Eastman, Katherine J Lobur, Kexin Jiao, Jerry Silver, Evan S. Deneris
Software Mentions: 2
Published: over 5 years ago

10.1242/dmm.043174

Drosophila model to study Retinitis pigmentosa pathology associated with mutations in the core splicing factor Prp8
Cited by: 7
Author(s): Dimitrije Stanković, Ann-Katrin Claudius, Thomas Schertel, Tina Bresser, Mirka Uhlířová
Software Mentions: 2
Published: almost 5 years ago

10.15252/embj.201798684

Mice with endogenous <scp>TDP</scp> ‐43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis
Cited by: 116
Author(s): Pietro Fratta, Prasanth Sivakumar, Jack Humphrey, Kitty Lo, Thomas C. Ricketts, Hugo M De Oliveira, José M. Brito-Armas, Bernadett Kalmár, Agnieszka M Ule, Yichao Yu, Nicol Birsa, Cristian Bodo, Toby Collins, Alexander E. Conicella, Alan Mejia Maza, Alessandro Marrero‐Gagliardi, Michelle Stewart, Joffrey Mianné, Silvia Corrochano, Warren Emmett, Gemma Codner, Michael J. Groves, Ryutaro Fukumura, Yoichi Gondo, Mark F. Lythgoe, Erwin Pauws, Emma Peskett, Philip Stanier, Lydia Teboul, Martina Hallegger, Andrea Calvo, Adriano Chiò, Adrian M. Isaacs, Nicolas L. Fawzi, Eric Wang, David E. Housman, Francisco E. Baralle, Linda Greensmith, Emanuele Buratti, Vincent Plagnol, Elizabeth Fisher, Abraham Acevedo‐Arozena
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0156040

Deciphering the Molecular Variations of Pine Wood Nematode Bursaphelenchus xylophilus with Different Virulence
Cited by: 33
Author(s): Xiaolei Ding, Jian‐Ren Ye, Sixi Lin, Xiao‐Qin Wu, Dewei Li, Bo Nian
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0164164

Neuronal Splicing Regulator RBFOX3 (NeuN) Regulates Adult Hippocampal Neurogenesis and Synaptogenesis
Cited by: 42
Author(s): Yi‐Wen Lin, Hanying Wang, De-Fong Huang, Pei-Fen Hsieh, Min Lin, Chih-Hsuan Chou, Wu I-Ju, Guo-Jen Huang, Susan Shur‐Fen Gau, Hsiang‐Po Huang
Software Mentions: 2
Published: about 8 years ago

10.1111/eva.12404

Loss of genetic diversity as a consequence of selection in response to high <scp>pCO</scp>2
Cited by: 17
Author(s): Melanie M. Lloyd, April D. Makukhov, Melissa H. Pespeni
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0208526

Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response
Cited by: 7
Author(s): Isabel Carrascoso, José Alcalde, Daniel Tabas-Madrid, Juan Carlos Oliveros, José M. Izquierdo
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0196590

Transcriptome reprogramming of resistant and susceptible peach genotypes during Xanthomonas arboricola pv. pruni early leaf infection
Cited by: 11
Author(s): F. Gervasi, Patrizia Ferrante, Maria Teresa Dettori, M. Scortichini, Ignazio Verde
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2021.683408

PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes
Cited by: 22
Author(s): Ali R. Ali, Gary H. Thorgaard, Mohamed Salem
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-014-0364-4

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems
Cited by: 85
Author(s): Ruolin Liu, Ann E. Loraine, Julie A. Dickerson
Software Mentions: 2
Published: almost 10 years ago

10.3389/fgene.2018.00402

Ethanol-Induced Behavioral Sensitization Alters the Synaptic Transcriptome and Exon Utilization in DBA/2J Mice
Cited by: 8
Author(s): Megan A. O’Brien, Rory M. Weston, Nihar U. Sheth, Steven Bradley, John W. Bigbee, Ashutosh Kumar Pandey, Robert W. Williams, Jennifer T. Wolstenholme, Michael F. Miles
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2021.689892

Splicing in the Diagnosis of Rare Disease: Advances and Challenges
Cited by: 31
Author(s): Jenny Lord, Diana Baralle
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.63982

Fruitless mutant male mosquitoes gain attraction to human odor
Cited by: 32
Author(s): Nipun S. Basrur, Maria Elena De Obaldia, Takeshi Morita, Margaret Herre, Ricarda K von Heynitz, Yael N. Tsitohay, Leslie B. Vosshall
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2020.00408

Retinoic Acid Exerts Disease Stage-Dependent Effects on Pristane-Induced Lupus
Cited by: 14
Author(s): Leila Abdelhamid, Xavier Cabana-Puig, Brianna Swartwout, Jiyoung Lee, Song Li, Sha Sun, Yaqi Li, A. Catharine Ross, Thomas E. Cecere, Tanya LeRoith, Stephen R. Werre, Haifeng Wang, Christopher M. Reilly, Xin Luo
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2020.02131

Genome-Wide Characterization of Host Transcriptional and Epigenetic Alterations During HIV Infection of T Lymphocytes
Cited by: 5
Author(s): Xi Zeng, J Tsui, Mai Shi, Jie Peng, Cyanne Ye Cao, Lea Ling-Yu Kan, Carol Lau, Yonghao Liang, Lingyi Wang, Li Liu, Zhiwei Chen, Stephen Kwok-Wing Tsui
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2017.00098

Modulation of Replicative Lifespan in Cryptococcus neoformans: Implications for Virulence
Cited by: 19
Author(s): Tejas Bouklas, Neena Jain, Bettina C. Fries
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms21124465

The Splicing Factor SF2 Is Critical for Hyperproliferation and Survival in a TORC1-Dependent Model of Early Tumorigenesis in Drosophila
Cited by: 3
Author(s): Malgorzata Maria Parniewska, Hugo Stocker
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22010169

OsMre11 Is Required for Mitosis during Rice Growth and Development
Cited by: 5
Author(s): Miaomiao Shen, Yanshen Nie, Yueyue Chen, Xiufeng Zhang, Zhao Jie
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1004932

Regulation of Toll-like Receptor Signaling by the SF3a mRNA Splicing Complex
Cited by: 36
Author(s): Brian P. O’Connor, Thomas Danhorn, Lesly De Arras, Brenna R. Flatley, Randall E. Marcus, Eveline Farias-Hesson, Sonia M. Leach, Scott Alper
Software Mentions: 2
Published: almost 10 years ago

10.1534/g3.119.400935

Inflammation-Induced Alternative Pre-mRNA Splicing in Mouse Alveolar Macrophages
Cited by: 16
Author(s): William J. Janssen, Thomas Danhorn, Chelsea Harris, Kara J. Mould, Frank Fang‐Yao Lee, Brenna R. Hedin, Angelo D’Alessandro, Sonia M. Leach, Scott Alper
Software Mentions: 2
Published: almost 5 years ago

10.1534/g3.120.401515

cnd-1/NeuroD1 Functions with the Homeobox Geneceh-5/Vax2 and Hox Geneceh-13/labial To Specify Aspects of RME and DD Neuron Fate inCaenorhabditis elegans
Cited by: 6
Author(s): Wendy Aquino-Nunez, Zachery Mielko, Trae Dunn, Elise M Santorella, Ciara N. Hosea, Lauren Leitner, Derrica McCalla, Claire Simms, Wendy M Verola, Sharanya Vijaykumar, Martin L. Hudson
Software Mentions: 2
Published: about 4 years ago

10.3390/genes11010096

Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses
Cited 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

10.3390/genes11040410

Gallop Racing Shifts Mature mRNA towards Introns: Does Exercise-Induced Stress Enhance Genome Plasticity?
Cited by: 6
Author(s): Katia Cappelli, Samanta Mecocci, Silvia Gioiosa, Andrea Giontella, Maurizio Silvestrelli, Raffaele Cherchi, Alessio Valentini, Giovanni Chillemi, Stefano Capomaccio
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1007925

Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
Cited by: 19
Author(s): Yu Hu, Kai Wang, Mingyao Li
Software Mentions: 2
Published: over 4 years ago

10.1186/gb-2013-14-7-r70

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene
Cited by: 220
Author(s): Mar Gonzàlez-Porta, Adam Frankish, Johan Rung, Jennifer Harrow, Alvis Brāzma
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2014-15-1-r26

The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA
Cited by: 44
Author(s): Vicky Cho, Mei Yan, Arleen Sanny, S.M.T. Chan, Anselm Enders, Edward M. Bertram, Andy Hee-Meng Tan, Christopher C. Goodnow, T. Daniel Andrews
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-017-1548-5

Manananggal - a novel viewer for alternative splicing events
Cited by: 7
Author(s): Matthias Barann, Ralf Zimmer, Fabian Birzele
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-018-1417-1

SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
Cited by: 330
Author(s): Juan L. Trincado, Juan Carlos Entizne, Gerald Hysenaj, Babita Singh, Miha Škalič, David Elliott, Eduardo Eyras
Software Mentions: 2
Published: over 6 years ago

10.15252/msb.20167375

Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation
Cited by: 22
Author(s): Mei-Sheng Xiao, Bin Zhang, Yi-Sheng Li, Qingsong Gao, Wei Sun, Wei Chen
Software Mentions: 2
Published: almost 8 years ago

10.1128/MCB.00651-17

Multilevel Differential Control of Hormone Gene Expression Programs by hnRNP L and LL in Pituitary Cells
Cited by: 6
Author(s): Lei Lei, Wenguang Cao, Ling Liu, Urmi Das, Yujia Wu, Guodong Liu, Muhammad Sohail, Yi Jen Chen, Jiuyong Xie
Software Mentions: 2
Published: over 6 years ago

10.1186/s13058-017-0802-0

Insulin-like growth factor 1 receptor activation promotes mammary gland tumor development by increasing glycolysis and promoting biomass production
Cited by: 23
Author(s): Bas ter Braak, Christine L. E. Siezen, Joo S. Lee, Pooja Rao, Charlotte Voorhoeve, Eytan Ruppin, Jan Willem van der Laan, Bob van de Water
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-09191-4

Bi-directional and shared epigenomic signatures following proton and 56Fe irradiation
Cited by: 28
Author(s): Soren Impey, Timothy Jopson, Carl Pelz, Amanuel Tafessu, Fatema Fareh, Damian G. Zuloaga, Tessa Marzulla, Lara Kirstie Riparip, Blair Stewart, Susanna Rosi, Mitchell S. Turker, Jacob Raber
Software Mentions: 2
Published: about 7 years ago

10.3390/biology2041311

Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos
Cited by: 16
Author(s): Delasa Aghamirzaie, Mahdi Nabiyouni, Yihui Fang, Curtis Klumas, Lenwood S. Heath, Ruth Grene, Eva Collakova
Software Mentions: 2
Published: about 11 years ago

10.1038/s41598-018-20738-x

Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid
Cited by: 28
Author(s): Niege Silva Mendes, Tamires Aparecida Bitencourt, Pablo Rodrigo Sanches, Rafael Silva‐Rocha, Nilce Maria Martinez-Rossi, Antônio Rossi
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-26695-9

The Usage of Exon-Exon Splice Junctions for the Detection of Alternative Splicing using the REIDS model
Cited by: 4
Author(s): Marijke Van Moerbeke, Adetayo Kasim, Ziv Shkedy
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-015-0128-7

RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states
Cited by: 47
Author(s): Kaiyu Jiang, Xiaoyun Sun, Yanmin Chen, Yufeng Shen, James N. Jarvis
Software Mentions: 2
Published: about 9 years ago

10.1111/acel.12999

PGC‐1a integrates a metabolism and growth network linked to caloric restriction
Cited by: 21
Author(s): Karl Miller, Josef P. Clark, Stephen A. Martin, Porsha R. Howell, Maggie S. Burhans, Spencer A. Haws, Nathan B. Johnson, Timothy W. Rhoads, Derek M. Pavelec, Kevin W. Eliceiri, Avtar Roopra, James M. Ntambi, John M. Denu, Brian W. Parks, Rozalyn M. Anderson
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-017-3697-3

Inter- and intra-species variation in genome-wide gene expression of Drosophila in response to parasitoid wasp attack
Cited by: 32
Author(s): Laura Salazar-Jaramillo, Kirsten M. Jalvingh, Ammerins de Haan, Ken Kraaijeveld, Henk P.J. Buermans, Bregje Wertheim
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-15-592

Identification of tissue-enriched novel transcripts and novel exons in mice
Cited by: 13
Author(s): Su Young Hong, Heesang Song, Do Han Kim
Software Mentions: 2
Published: over 10 years ago

10.1038/s41398-018-0228-1

DISC1 regulates N-methyl-D-aspartate receptor dynamics: abnormalities induced by a Disc1 mutation modelling a translocation linked to major mental illness
Cited by: 17
Author(s): Elise L.V. Malavasi, Kyriakos D. Economides, Ellen Grünewald, Paraskevi Makedonopoulou, Philippe Gautier, Shaun Mackie, Laura C. Murphy, Hannah Murdoch, Darragh K. Crummie, Fumiaki Ogawa, Daniel L. McCartney, Shane O’Sullivan, Karen Burr, Helen S. Torrance, Jonathan Phillips, Marion Bonneau, Susan M. Anderson, Paul Perry, Matthew Pearson, Costas Constantinides, Hazel Davidson‐Smith, Mostafa Kabiri, Barbara Duff, Mandy Johnstone, H. Greg Polites, Stephen M. Lawrie, Douglas Blackwood, Colin A. Semple, Kathryn Evans, Michel Didier, Siddharthan Chandran, Andrew M. McIntosh, David J. Price, Miles D. Houslay, David J. Porteous, J. Kirsty Millar
Software Mentions: 2
Published: about 6 years ago

10.1186/1479-7364-8-3

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data
Cited by: 63
Author(s): Joan E. Hooper
Software Mentions: 2
Published: almost 11 years ago

10.1093/hmg/ddv471

Deficiency of the zinc finger protein ZFP106 causes motor and sensory neurodegeneration
Cited by: 17
Author(s): Peter Joyce, Pietro Fratta, Allison Landman, Philip McGoldrick, Henning Wackerhage, Michael J. Groves, Bharani Shiva Busam, Jorge Galino, Silvia Corrochano, Olga A. Beskina, Christopher T. Esapa, Edward Ryder, Sarah Carter, Michelle Stewart, Gemma Codner, Helen Hilton, Lydia Teboul, Jennifer Tucker, Arimantas Lionikas, Jeanne Estabel, Ramiro Ramirez-Solis, Jacqueline K. White, Sebastian Brandner, Vincent Plagnol, David L. H. Bennet, Andrey Y. Abramov, Linda Greensmith, Elizabeth Fisher, Abraham Acevedo-Arozena
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.07938

Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing
Cited by: 114
Author(s): Li Zhang, Ngoc Tung Tran, Hairui Su, Rui Wang, Yuheng Lu, Haiping Tang, Sakae Aoyagi, Ailan Guo, Alireza Khodadadi‐Jamayran, Dewang Zhou, Kun Qian, Todd Hricik, Jocelyn Côté, Xiaosi Han, Wenping Zhou, Suparna Laha, Omar Abdel‐Wahab, Ross L. Levine, Glen D. Raffel, Yanyan Liu, Dongquan Chen, Haitao Li, Tim M. Townes, Hengbin Wang, Haiteng Deng, Y. George Zheng, Christina Leslie, Minkui Luo, Xinyang Zhao
Software Mentions: 2
Published: about 9 years ago

10.1242/dev.199754

The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection
Cited by: 10
Author(s): Ching‐In Lau, Jasmine Rowell, Diana C. Yánez, Anisha Solanki, Scott R. Ross, Masahiro Ono, Tessa Crompton
Software Mentions: 2
Published: over 3 years ago

10.1002/path.4483

<scp>SF3B1</scp> mutations constitute a novel therapeutic target in breast cancer
Cited by: 156
Author(s): Sarah Maguire, Andreas Leonidou, Patty T. Wai, Caterina Marchiò, Charlotte K.Y. Ng, Anna Sapino, Anne Vincent‐Salomon, Jorge S. Reis‐Filho, Britta Weigelt, Rachael Natrajan
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0141836

Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin
Cited by: 40
Author(s): Alexandre Amlie‐Wolf, Paul Ryvkin, Rui Tong, Isabelle Dragomir, EunRan Suh, Yan Xu, Vivianna M. Van Deerlin, Brian D. Gregory, Linda K. Kwong, John Q. Trojanowski, Virginia Man-Yee Lee, Li-San Wang, Edward B. Lee
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0146107

Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii
Cited by: 20
Author(s): Stephen A. Bell, Chien-Hua Shen, A. Brown, Arthur G. Hunt
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.cell.2012.12.023

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements
Cited by: 365
Author(s): Kathi Zarnack, Julian König, Mojca Tajnik, Iñigo Martincorena, Sebastian Eustermann, Isabelle Stévant, Alejandro Reyes, Simon Anders, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 2
Published: almost 12 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 Gene
Cited 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/s41419-021-03906-2

Impaired stem cell differentiation and somatic cell reprogramming in DIDO3 mutants with altered RNA processing and increased R-loop levels
Cited by: 5
Author(s): Agnes Fütterer, Amaia Talavera-Gutiérrez, Tirso Pons, Jésus de Celis, Julio Gutiérrez, Verónica Plaza, Carlos Martínez‐A
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.02866-18

Alternative Splicing in Apicomplexan Parasites
Cited by: 15
Author(s): Lee M. Yeoh, V Vern Lee, Geoffrey I. McFadden, Stuart A. Ralph
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: DEXSeq

Papers Mentioning DEXSeq 226