bioconductor: DEXSeq | Projects | Ecosyste.ms: Papers

10.1016/j.molcel.2021.05.023

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection
Cited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 3 years ago

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: almost 10 years ago

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago

10.12688/f1000research.12223.1

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
Cited by: 47
Author(s): Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe
Software Mentions: 14
Published: about 7 years ago

10.1371/journal.ppat.1008653

Genome-wide transcriptomics identifies an early preclinical signature of prion infection
Cited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: over 4 years ago

10.1186/s12920-017-0274-1

Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Cited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: over 7 years ago

10.12688/f1000research.8900.2

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
Cited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: almost 8 years ago

10.1186/s13059-020-02071-7

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Cited by: 56
Author(s): Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W. K. Ho, Richard P. Harvey, Kitty Lo
Software Mentions: 13
Published: over 4 years ago

10.1186/s12859-019-3029-5

CAGEfightR: analysis of 5′-end data using R/Bioconductor
Cited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: about 5 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: almost 9 years ago

10.12688/f1000research.17082.2

Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk)
Cited by: 4
Author(s): Christophe D. Chabbert, Tanja Eberhart, Ilaria Guccini, Wilhelm Krek, Werner J. Kovacs
Software Mentions: 12
Published: over 5 years ago

10.1186/gb-2012-13-8-r77

ggbio: an R package for extending the grammar of graphics for genomic data
Cited by: 265
Author(s): Tao Yin, Dianne Cook, Michael C. Lawrence
Software Mentions: 11
Published: almost 13 years ago

10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: over 7 years ago

10.1038/s41598-017-06110-5

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
Cited by: 10
Author(s): Brian Gloss, Bethany Signal, Seth W. Cheetham, Franziska Gruhl, Dominik C. Kaczorowski, Andrew C. Perkins, Marcel E. Dinger
Software Mentions: 10
Published: about 7 years ago

10.1371/journal.pone.0240895

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef
Cited by: 9
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, Chad Carr, Raluca G. Mateescu
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13059-018-1414-4

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
Cited by: 140
Author(s): Kevin C.H. Ha, Benjamin J. Blencowe, Quaid Morris
Software Mentions: 9
Published: over 6 years ago

10.7554/eLife.65537

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
Cited by: 32
Author(s): Matthew T Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel F. A. Tomé, Xuhong Yu, Pascal G.P. Martin, Jim Beynon, Scott D. Michaels, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: about 6 years ago

10.1186/s13059-015-0862-3

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
Cited by: 107
Author(s): Charlotte Soneson, Katarina L. Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson
Software Mentions: 8
Published: over 8 years ago

10.3389/fgene.2019.00182

Detection of Differentially Expressed Cleavage Site Intervals Within 3′ Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs
Cited by: 9
Author(s): Benjamin J. Harrison, Juw Won Park, Cynthia Gomes, Jeffrey C. Petruska, Matthew R. Sapio, Michael J. Iadarola, Julia H. Chariker, Eric C. Rouchka
Software Mentions: 8
Published: over 5 years ago

10.7554/eLife.19545

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution
Cited by: 52
Author(s): Jan Attig, Igor Ruiz de los Mozos, Nejc Haberman, Zhen Wang, Warren Emmett, Kathi Zarnack, Julian König, Jernej Ule
Software Mentions: 8
Published: almost 8 years ago

10.3390/ijms22073296

Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases
Cited by: 5
Author(s): Markus Kwik, Stefan Hainzl, Jan Oppelt, Boris Tichý, Ulrich Koller, Emanuele Bernardinelli, Markus J. Steiner, Greta Zara, Charity Nofziger, Serge Weis, Markus Paulmichl, Silvia Dossena, Wolfgang Patsch, Selma M. Soyal
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.58331

An essential role for MEF2C in the cortical response to loss of sleep in mice
Cited by: 19
Author(s): Theresa E. Bjorness, Ashwinikumar Kulkarni, Volodymyr Rybalchenko, Ayako Suzuki, Catherine Bridges, Adam J. Harrington, Christopher W. Cowan, Joseph S. Takahashi, Genevieve Konopka, Robert Greene
Software Mentions: 8
Published: about 4 years ago

10.1186/s12859-021-04114-7

Streamlining differential exon and 3′ UTR usage with diffUTR
Cited by: 3
Author(s): Stefan Gerber, Gerhard Schratt, Pierre-Luc Germain
Software Mentions: 8
Published: over 3 years ago

10.1186/1471-2105-14-219

TCC: an R package for comparing tag count data with robust normalization strategies
Cited by: 394
Author(s): Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota
Software Mentions: 8
Published: about 11 years ago

10.18632/oncotarget.24506

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data
Cited by: 13
Author(s): Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Software Mentions: 8
Published: over 6 years ago

10.3390/genes11101165

OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
Cited by: 21
Author(s): Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu
Software Mentions: 7
Published: about 4 years ago

10.1186/s12859-021-04198-1

Comparative evaluation of full-length isoform quantification from RNA-Seq
Cited by: 12
Author(s): Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens, Gregory R. Grant
Software Mentions: 7
Published: over 3 years ago

10.1038/sdata.2016.90

Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice
Cited by: 5
Author(s): Tonatiuh Peña Centeno, Orr Shomroni, Magali Hennion, Rashi Halder, Ramón Vidal, Raza-Ur Rahman, Stefan Bonn
Software Mentions: 7
Published: almost 8 years ago

10.3389/fnbeh.2019.00157

Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated With Altered Stress Responses in Adulthood
Cited by: 37
Author(s): Jordan Marrocco, Jason D. Gray, Joshua F. Kogan, Nathan R. Einhorn, Emma M. O’Cinneide, Todd G. Rubin, Thomas Carroll, Eric F. Schmidt, Bruce S. McEwen
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0232646

Two-step mixed model approach to analyzing differential alternative RNA splicing
Cited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: almost 4 years ago

10.1093/bib/bbz126

Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: almost 5 years ago

10.1186/1471-2105-16-S9-S2

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis
Cited by: 17
Author(s): Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Calogero, Francesca Zolezzi
Software Mentions: 7
Published: over 9 years ago

10.1038/s41598-021-84693-w

Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells
Cited by: 12
Author(s): Shang Liu, Biaofeng Zhou, Liang Wu, Yan Sun, Jie Chen, Shiping Liu
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-019-41940-5

The ciliary Frizzled-like receptor Tmem67 regulates canonical Wnt/β-catenin signalling in the developing cerebellum via Hoxb5
Cited by: 15
Author(s): Zakia Abdelhamed, Dina Abdelmottaleb, Mohammed E. El‐Asrag, Subaashini Natarajan, Gabrielle Wheway, Chris F. Inglehearn, Carmel Toomes, Colin A. Johnson
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-016-1180-9

Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
Cited by: 21
Author(s): Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, Ping Ma
Software Mentions: 7
Published: about 8 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: over 8 years ago

10.7554/eLife.47809

Free circular introns with an unusual branchpoint in neuronal projections
Cited by: 11
Author(s): Harleen Saini, Alicia A. Bicknell, Sean R. Eddy, Melissa J. Moore
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13059-017-1286-z

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy
Cited by: 68
Author(s): Matthias Heinig, Michiel E. Adriaens, Sebastian Schäfer, Hanneke W. M. van Deutekom, Elisabeth M. Lodder, James S. Ware, Valentin Schneider, Leanne E. Felkin, Esther E. Creemers, Benjamin Meder, Hugo A. Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, András Varró, Nanette H. Bishopric, Alfred L. George, Cristobal dos Remedios, Aida Moreno‐Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J.R. Barton, Stuart A. Cook, Yigal M. Pinto, Connie R. Bezzina, Norbert Hübner
Software Mentions: 7
Published: about 7 years ago

10.12688/f1000research.17916.1

Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
Cited by: 19
Author(s): Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-14-262

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Cited by: 30
Author(s): Yingtao Bi, Ramana V. Davuluri
Software Mentions: 7
Published: about 11 years ago

10.15252/msb.20199195

Improved detection of differentially represented DNA barcodes for high‐throughput clonal phenomics
Cited by: 12
Author(s): Yevhen Akimov, Daria Bulanova, Sanna Timonen, Krister Wennerberg, Tero Aittokallio
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-020-06831-4

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure
Cited by: 13
Author(s): Shubha Suresh, Teresa J. Crease, Melania E. Cristescu, Frédéric J. J. Chain
Software Mentions: 6
Published: over 4 years ago

10.1111/mec.15047

Caste‐ and pesticide‐specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees
Cited by: 53
Author(s): Thomas J. Colgan, Isabel Fletcher, Andres N. Arce, Richard J. Gill, Ana Ramos Rodrigues, Eckart Stolle, Lars Chittka, Yannick Wurm
Software Mentions: 6
Published: over 5 years ago

10.15252/embr.202051289

LncRNA <i>Ctcflos</i> orchestrates transcription and alternative splicing in thermogenic adipogenesis
Cited by: 16
Author(s): Andrea Bast‐Habersbrunner, Christoph Kiefer, Peter Weber, Tobias Fromme, Anna Schießl, Petra Schwalie, Bart Deplancke, Yongguo Li, Martin Klingenspor
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-94442-8

Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
Cited by: 1
Author(s): Sebastian Friedrich, Hannah Müller, Caroline Riesterer, Hannah Schüller, Katja Friedrich, Carlotta Leonie Wörner, Tilman Busch, Amandine Viau, E. Wolfgang Kuehn, Michael Köttgen, Alexis Hofherr
Software Mentions: 6
Published: about 3 years ago

10.1186/1471-2105-14-370

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
Cited by: 36
Author(s): Hubert Rehrauer, Lennart Opitz, Ge Tan, Lina Sieverling, Ralph Schlapbach
Software Mentions: 6
Published: almost 11 years ago

10.1038/s41598-019-57214-z

5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation
Cited by: 14
Author(s): Santiago Uribe-Lewis, Thomas Carroll, Suraj Menon, Anna M. Nicholson, Piotr J. Manasterski, Douglas J. Winton, Simon Buczacki, Adele Murrell
Software Mentions: 6
Published: over 4 years ago

10.1186/1471-2105-14-320

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
Cited by: 40
Author(s): David Sturgill, John H. Malone, Xia Sun, Harold E. Smith, Léonard Rabinow, Marie-Laure Samson, Brian Oliver
Software Mentions: 6
Published: almost 11 years ago

10.1038/s41398-021-01561-x

Comparison of mouse models reveals a molecular distinction between psychotic illness in PWS and schizophrenia
Cited by: 5
Author(s): Simona Zahova, Trevor Humby, Jennifer R. Davies, Joanne Morgan, Anthony R Isles
Software Mentions: 6
Published: about 3 years ago

10.1038/srep34220

Widespread DNA hypomethylation and differential gene expression in Turner syndrome
Cited by: 99
Author(s): Christian Trolle, Morten Muhlig Nielsen, Anne Skakkebæk, Philippe Lamy, Søren Vang, Jakob Hedegaard, Iver Nordentoft, Torben F. Ørntoft, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0092111

Transcriptome Analysis Reveals Differential Splicing Events in IPF Lung Tissue
Cited by: 69
Author(s): Tracy Nance, Kevin S. Smith, Vanessa Anaya, Rhea Richardson, Lawrence Ho, Mauro Pala, Sara Mostafavi, Alexis Battle, Carol Feghali‐Bostwick, Glenn D. Rosen, Stephen B. Montgomery
Software Mentions: 6
Published: over 10 years ago

10.1038/s41598-021-85256-9

Creation and validation of models to predict response to primary treatment in serous ovarian cancer
Cited by: 11
Author(s): Jesús González Bosquet, Eric J. Devor, A.M. Newtson, Brian J. Smith, David Bender, Michael J. Goodheart, Megan McDonald, Terry A. Braun, Kristina W. Thiel, Kimberly K. Leslie
Software Mentions: 6
Published: over 3 years ago

10.3390/jcm9051499

Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy
Cited by: 10
Author(s): Weng‐Tein Gi, Jan Haas, Farbod Sedaghat‐Hamedani, Elham Kayvanpour, Rewati Tappu, David Lehmann, Omid Shirvani Samani, Michael Wisdom, Andreas Keller, Hugo A. Katus, Benjamin Meder
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-018-37397-7

Temporal dynamics in meta longitudinal RNA-Seq data
Cited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-020-01967-8

BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty
Cited by: 16
Author(s): Simone Tiberi, Mark D. Robinson
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms22105322

The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers
Cited by: 4
Author(s): Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David Powell, Traude H. Beilharz
Software Mentions: 6
Published: over 3 years ago

10.1534/genetics.116.195008

A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation
Cited by: 12
Author(s): Owen J. L. Rackham, Sarah R. Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K. Srivastava, Jacques Behmoaras, Πέτρος Δελλαπόρτας, Leonardo Bottolo, Enrico Petretto
Software Mentions: 6
Published: over 7 years ago

10.1186/s13059-017-1284-1

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
Cited by: 75
Author(s): N. Davidson, Anthony D. K. Hawkins, Alicia Oshlack
Software Mentions: 6
Published: about 7 years ago

10.1534/g3.113.006742

The Developmental Transcriptome of the Mosquito <i>Aedes aegypti</i>, an Invasive Species and Major Arbovirus Vector
Cited by: 184
Author(s): Omar S. Akbari, Igor Antoshechkin, Henry Amrhein, Brian A. Williams, Rose DiLoreto, Jeremy E. Sandler, Bruce A. Hay
Software Mentions: 6
Published: about 11 years ago

10.1038/s41598-017-17407-w

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation
Cited by: 37
Author(s): Mariana Fontes, Ayşegül Güvenek, Riki Kawaguchi, Dinghai Zheng, Alden Huang, Victoria M. Ho, Patrick B. Chen, Xiaochuan Liu, Thomas J. O’Dell, Giovanni Coppola, Bin Tian, Kelsey C. Martin
Software Mentions: 6
Published: almost 7 years ago

10.1186/s13059-018-1419-z

Gene-level differential analysis at transcript-level resolution
Cited by: 97
Author(s): Lynn Yi, Harold Pimentel, Nicolas Bray, Lior Pachter
Software Mentions: 6
Published: over 6 years ago

10.1186/s13045-020-01005-x

RNA sequencing: new technologies and applications in cancer research
Cited by: 187
Author(s): Mingye Hong, Shuangping Tao, Ling Zhang, Li-Ting Diao, Xuanmei Huang, Shaohui Huang, Shu‐Juan Xie, Zhilong Xiao, Hua Zhang
Software Mentions: 5
Published: almost 4 years ago

10.3892/or.2015.4023

Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome
Cited by: 20
Author(s): Jie Du, Lin Zhang
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-015-0670-5

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
Cited by: 211
Author(s): Stephen W. Hartley, James C. Mullikin
Software Mentions: 5
Published: about 9 years ago

10.1186/1744-8069-10-7

A Comparison of RNA-Seq and Exon Arrays for Whole Genome Transcription Profiling of the L5 Spinal Nerve Transection Model of Neuropathic Pain in the Rat
Cited by: 72
Author(s): James R. Perkins, Ana Antunes-Martins, Margarita Calvo, John Grist, Werner Rust, RM Schmid, Tobias Hildebrandt, Matthias Kohl, Christine A. Orengo, Stephen B. McMahon, David L.H. Bennett
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12943-017-0653-4

Human germ/stem cell-specific gene TEX19 influences cancer cell proliferation and cancer prognosis
Cited by: 18
Author(s): Vicente Planells-Palop, Ali Hazazi, Julia Feichtinger, Jana Jezkova, Gerhard G. Thallinger, Naif Alsiwiehri, Mikhlid H. Almutairi, Lee Parry, Jane A. Wakeman, Ramsay J. McFarlane
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0160925

The 4p16.3 Parkinson Disease Risk Locus Is Associated with GAK Expression and Genes Involved with the Synaptic Vesicle Membrane
Cited by: 16
Author(s): Michael W. Nagle, Jeanne C. Latourelle, Adam Labadorf, Alexandra Dumitriu, Tiffany C. Hadzi, Thomas G. Beach, Richard H. Myers
Software Mentions: 5
Published: about 8 years ago

10.1186/s13059-020-02028-w

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Cited by: 34
Author(s): Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue‐Agudo, Pablo Bonilla, Jeremy R.B. Newman, Shunichi Kosugi, Lauren McIntyre, Victoria Moreno‐Manzano, Ana Conesa
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-2947-6

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
Cited by: 3
Author(s): Mohamed K. Gunady, Stephen M. Mount, Héctor Corrada Bravo
Software Mentions: 5
Published: about 5 years ago

10.18632/aging.101341

Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Cited by: 45
Author(s): Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale Alessandro Puca, Alessandra Magenta, Fabio Martelli
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pgen.1007559

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
Cited by: 141
Author(s): Rachel Kaletsky, Victoria Yao, April Williams, Alexi Runnels, Alicja Tadych, Shaoqiang Zhou, Olga G. Troyanskaya, Coleen T. Murphy
Software Mentions: 5
Published: about 6 years ago

10.12688/f1000research.18276.2

Using equivalence class counts for fast and accurate testing of differential transcript usage
Cited by: 9
Author(s): Marek Cmero, N. Davidson, Alicia Oshlack
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-018-2122-5

IntEREst: intron-exon retention estimator
Cited by: 18
Author(s): Ali Oghabian, Dario Greco, Mikko J. Frilander
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1005952

Evolution of Social Insect Polyphenism Facilitated by the Sex Differentiation Cascade
Cited by: 46
Author(s): Antonia Klein, Eva Schultner, Helena Lowak, Lukas Schrader, Juergen Heinze, Luke Holman, Jan Oettler
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pcbi.1004105

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers
Cited by: 173
Author(s): Christopher DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Z. Rassenti, Christian Barrett, Kristen Jepsen, Catriona Jamieson, Dennis A. Carson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 5
Published: over 9 years ago

10.1007/s00424-021-02582-7

Abnormal neonatal sodium handling in skin precedes hypertension in the SAME rat
Cited by: 2
Author(s): L. J. Mullins, Jessica R. Ivy, Mairi Ward, Olav Tenstad, Helge Wiig, Kento Kitada, Jonathan Manning, Natalia Rakova, Dominik N. Müller, John J. Mullins
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22168451

Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data
Cited by: 8
Author(s): Christian Vahlensieck, Cora S. Thiel, Jan Andreas Adelmann, Béatrice Lauber, Jennifer Polzer, Oliver Ullrich
Software Mentions: 5
Published: about 3 years ago

10.1186/s12711-016-0257-2

Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Cited by: 31
Author(s): Harald Olsen, Tim Martin Knutsen, Anna Lewandowska-Sabat, Harald Grove, Torfinn Nome, Mathias Tiedemann Svendsen, Mariann Árnyasi, Marte Sodeland, Kristil Kindem Sundsaasen, Sandra Rinne Dahl, B. Heringstad, Hanne Hellerud Hansen, I. Olsaker, Matthew Kent, Sigbjørn Lien
Software Mentions: 4
Published: almost 8 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

10.1038/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/s12864-015-2321-7

Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits
Cited by: 16
Author(s): Chiara Biselli, Paolo Bagnaresi, Daniela Cavalluzzo, Simona Urso, Francesca Desiderio, G. Orasen, Alberto Gianinetti, Federico Righettini, M. C. Gennaro, Rosaria Perrini, Manel Ben Hassen, Gian Attilio Sacchi, Luigi Cattivelli, Giampiero Valè
Software Mentions: 4
Published: almost 9 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: over 5 years ago

10.15252/embr.201847592

CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes
Cited by: 57
Author(s): Anil Paul Chirackal Manavalan, Květa Pilařová, Michael Kluge, Koen Bartholomeeusen, Michal Rájecký, Jan Oppelt, Prashant Khirsariya, Kamil Paruch, Lumír Krejčí, Caroline C. Friedel, Dalibor Blažek
Software Mentions: 4
Published: about 5 years ago

10.1016/j.ajhg.2015.11.018

Autosomal-Dominant Corneal Endothelial Dystrophies CHED1 and PPCD1 Are Allelic Disorders Caused by Non-coding Mutations in the Promoter of OVOL2
Cited by: 65
Author(s): Alice E. Davidson, Petra Lišková, Cerys J. Evans, Ľubica Ďuďáková, Lenka Nosková, Nikolas Pontikos, Hana Hartmannová, Kateřina Hodaňová, Viktor Stránecký, Zbyněk Kozmík, Hannah J. Levis, Nwamaka Juliana Idigo, Noriaki Sasai, Geoffrey J. Maher, James Bellingham, Neyme Veli, Neil D. Ebenezer, Michael E. Cheetham, Julie T. Daniels, Caroline Thaung, Kateřina Jirsová, Vincent Plagnol, Martin Filipec, Stanislav Kmoch, Stephen Tuft, Alison J. Hardcastle
Software Mentions: 4
Published: almost 9 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/s12864-019-5793-z

Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera
Cited by: 7
Author(s): Xinlei Gao, Yating Fu, Olugbenga Emmanuel Ajayi, Dongyang Guo, Liqin Zhang, Qingfa Wu
Software Mentions: 4
Published: over 5 years ago

10.1038/bcj.2017.71

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma
Cited by: 13
Author(s): Suvi‐Katri Leivonen, M.-R. Taskinen, Alejandra Cervera, Marja‐Liisa Karjalainen‐Lindsberg, Jan Delabie, Harald Holte, Rainer Lehtonen, Sampsa Hautaniemi, Sirpa Leppä
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2020.566320

Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection
Cited by: 11
Author(s): Hongmei Li-Byarlay, Humberto Boncristiani, Gary W. Howell, Jacob Herman, Lindsay V. Clark, Micheline K. Strand, David R. Tarpy, Olav Rueppell
Software Mentions: 4
Published: about 4 years ago

10.3389/fpls.2021.653183

Transcriptome Analysis of Tetraploid and Octoploid Common Reed (Phragmites australis)
Cited by: 5
Author(s): Cui Wang, Tong Wang, Meiqi Yin, Franziska Eller, Lele Liu, Hans Brix, Weihua Guo
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0201690

Strap associates with Csde1 and affects expression of select Csde1-bound transcripts
Cited by: 5
Author(s): Kat Moore, Nurcan Yağcı, Floris van Alphen, Alexander B. Meijer, Peter A.C. ’t Hoen, Marieke von Lindern
Software Mentions: 4
Published: about 6 years ago

10.1016/j.ydbio.2015.04.010

Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern
Cited by: 7
Author(s): Tomasz M. Kuliński, M. Rita T. Casari, Philipp M. Guenzl, D. Wenzel, Daniel Andergassen, Anastasiya Hladik, Paul Datlinger, Matthias Farlik, Hans-Christian Theussl, Josef Penninger, Sylvia Knapp, Christoph Bock, Denise P. Barlow, Quanah J. Hudson
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0177739

Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid
Cited by: 15
Author(s): Wang Hai, Shengyan Li, Shouzhen Teng, Haisheng Liang, Hongjia Xin, Hongjiang Gao, Dafang Huang, Zhihong Lang
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2017.00175

Smooth, an hnRNP-L Homolog, Might Decrease Mitochondrial Metabolism by Post-Transcriptional Regulation of Isocitrate Dehydrogenase (Idh) and Other Metabolic Genes in the Sub-Acute Phase of Traumatic Brain Injury
Cited by: 21
Author(s): Arko Sen, Katherine Gurdziel, Jenney Liu, Qian Wen, Oluwademi O Nuga, Rayanne B. Burl, Maik Hüttemann, Roger Piqué-Regi, Douglas M. Ruden
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13062-015-0071-8

Experiences with workflows for automating data-intensive bioinformatics
Cited by: 51
Author(s): Ola Spjuth, Erik Bongcam‐Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimerà, Aleksi Kallio, Eija Korpelainen, Maciej M. Kańduła, Milko Krachunov, David P. Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr, Alexey Siretskiy, Dimitar Vassilev
Software Mentions: 4
Published: about 9 years ago

10.1093/bioinformatics/btx143

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
Cited by: 26
Author(s): Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brāzma
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0115964

A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
Cited by: 12
Author(s): Asta Laiho, Laura L. Elo
Software Mentions: 4
Published: almost 10 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: almost 6 years ago

10.3389/fpls.2016.00889

PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants
Cited by: 19
Author(s): Xiaohui Wu, Yumin Zhang, Qingshun Quinn Li
Software Mentions: 4
Published: over 8 years ago

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: about 7 years ago

Projects: bioconductor: DEXSeq

Papers Mentioning DEXSeq 226