bioconductor: baySeq | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-11-422

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
Cited by: 677
Author(s): Thomas J. Hardcastle, Krystyna A. Kelly
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pgen.1003820

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
Cited by: 80
Author(s): Stefanie Traeger, Florian Altegoer, Michael Freitag, Toni Gabaldón, Frank Kempken, Abhishek Kumar, Marina Marcet‐Houben, Stefanie Pöggeler, Jason E. Stajich, Minou Nowrousian
Software Mentions: 3
Published: about 11 years ago

10.1093/bioinformatics/btu205

ReadXplorer—visualization and analysis of mapped sequences
Cited by: 94
Author(s): Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
Software Mentions: 3
Published: over 10 years ago

10.1093/bioinformatics/btv425

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Cited by: 72
Author(s): Marek Gierliński, Christian Callebaut, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0116941

RNA-Seq Reveals a Role for NFAT-Signaling in Human Retinal Microvascular Endothelial Cells Treated with TNFα
Cited by: 16
Author(s): Sara R. Savage, Colin A. Bretz, John S. Penn
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2105-14-S9-S1

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Cited by: 84
Author(s): Xiao Xu, Yuanhao Zhang, Jennie L. Williams, Eric Antoniou, W. Richard McCombie, Song Wu, Wei Zhu, Nicholas O. Davidson, Paula Denoya, Ellen Li
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0097821

PIWI Proteins Are Dispensable for Mouse Somatic Development and Reprogramming of Fibroblasts into Pluripotent Stem Cells
Cited by: 22
Author(s): Elaine Cheng, Dongwan Kang, Zhong Wang, Haifan Lin
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-018-23069-z

Enterobacter bugandensis: a novel enterobacterial species associated with severe clinical infection
Cited by: 46
Author(s): Niladri Bhusan Pati, Swapnil Doijad, Tilman Schultze, Gopala Krishna Mannala, Yancheng Yao, Sangeeta Jaiswal, Daniel Ryan, Mrutyunjay Suar, Konrad Gwozdzinski, Boyke Bunk, Mobarak Abu Mraheil, Mohamed A. Marahiel, Julian D. Hegemann, Cathrin Spröer, Alexander Goesmann, Linda Falgenhauer, Torsten Hain, Can Imirzalioglu, Stephen E. Mshana, Jörg Overmann, Trinad Chakraborty
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms19123789

Differentially-Expressed miRNAs in Ectopic Stromal Cells Contribute to Endometriosis Development: The Plausible Role of miR-139-5p and miR-375
Cited by: 32
Author(s): Kadri Rekker, Tõnis Tasa, Merli Saare, Külli Samuel, Ülle Kadastik, Helle Karro, Martin Götte, Andres Salumets, Maire Peters
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcimb.2018.00416

Changes in Transcriptome of Yersinia pseudotuberculosis IP32953 Grown at 3 and 28°C Detected by RNA Sequencing Shed Light on Cold Adaptation
Cited by: 6
Author(s): Jussa-Pekka Virtanen, Riikka Keto-Timonen, Kaisa Jaakkola, Noora Salin, Hannu Korkeala
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0115597

Long-Term Quiescent Fibroblast Cells Transit into Senescence
Cited by: 39
Author(s): Shiva Marthandan, Stefan Priebe, Peter Hemmerich, Karolin Klement, Stephan Diekmann
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0037118

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton
Cited by: 63
Author(s): Frank J. Stewart, Tage Dalsgaard, Charles W. Young, Bo Thamdrup, Niels Peter Revsbech, Osvaldo Ulloa, Donald E. Canfield, Edward F. DeLong
Software Mentions: 2
Published: over 12 years ago

10.3389/fbioe.2015.00077

Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques
Cited by: 58
Author(s): Dario Veneziano, Giovanni Nigita, Alfredo Ferro
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-14-135

Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution
Cited by: 29
Author(s): Thomas J. Hardcastle, Krystyna A. Kelly
Software Mentions: 2
Published: over 11 years ago

10.3389/fmicb.2016.01668

Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum
Cited by: 62
Author(s): Frederike S. Haack, Anja Poehlein, Cathrin Kröger, Christian A. Voigt, Meike Piepenbring, Helge B. Bode, Rolf Daniel, Wilhelm Schäfer, Wolfgang R. Streit
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-017-1836-0

Methods for discovering genomic loci exhibiting complex patterns of differential methylation
Cited by: 1
Author(s): Thomas J. Hardcastle
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-014-0356-6

Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis
Cited by: 17
Author(s): R. Petersen, Haris Djozgic, Benjamin Rieger, Steffen Rapp, Erwin R. Schmidt
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-015-1929-y

Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes
Cited by: 38
Author(s): Yan Guo, Amma Bosompem, Sanjay Mohan, Begüm Erdoğan, Fei Ye, Kasey C. Vickers, Quanhu Sheng, Shilin Zhao, Chung I. Li, Pei Fang Su, Madan Jagasia, Stephen A. Strickland, Elizabeth A. Griffiths, Annette S. Kim
Software Mentions: 2
Published: about 9 years ago

10.1186/s12859-018-2354-4

Detecting differentially expressed genes for syndromes by considering change in mean and dispersion simultaneously
Cited by: 2
Author(s): Chenchen Ma, Tieming Ji
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-016-3441-4

The transcriptome of the mosquito Aedes fluviatilis (Diptera: Culicidae), and transcriptional changes associated with its native Wolbachia infection
Cited by: 38
Author(s): Eric P. Caragata, Fabiano Sviatopolk-Mirsky Pais, Luke Anthony Baton, J. B. L. Silva, Marcos Henrique Ferreira Sorgine, Luciano Andrade Moreira
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1006942

miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence
Cited by: 15
Author(s): Malak Haidar, Zineb Rchiad, Hifzur Rahman Ansari, Fathia Ben Rached, Shahin Tajeri, Perle Latré de Laté, Gordon Langsley, Arnab Pain
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-017-1706-9

dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond
Cited by: 24
Author(s): Miha Štajdohar, Rafael D. Rosengarten, Janez Kokošar, Luka Jeran, Domen Blenkus, Gad Shaulsky, Blaž Zupan
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-23601-1

Palmitic Acid Induces Müller Cell Inflammation that is Potentiated by Co-treatment with Glucose
Cited by: 20
Author(s): Megan E. Capozzi, Meredith J. Giblin, John S. Penn
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0067019

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq
Cited by: 471
Author(s): Andrew D. Fernandes, Jean M. Macklaim, Thomas Linn, Gregor Reid, Gregory B. Gloor
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0157244

Overexpression of OsSAP16 Regulates Photosynthesis and the Expression of a Broad Range of Stress Response Genes in Rice (Oryza sativa L.)
Cited by: 14
Author(s): Fei Wang, Robert A. Coe, Shanta Karki, Samart Wanchana, Vivek Thakur, Amelia Henry, Hsiang-Chun Lin, Jikun Huang, Shaobing Peng, W. Paul Quick
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0093677

TraV: A Genome Context Sensitive Transcriptome Browser
Cited by: 21
Author(s): Sascha Dietrich, Sandra Wiegand, Heiko Liesegang
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-017-3540-x

Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system
Cited by: 38
Author(s): Kristin E. Gribble, David Welch
Software Mentions: 1
Published: over 7 years ago

10.1038/srep13965

Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects
Cited by: 41
Author(s): Alice B. Dennis, Luke T. Dunning, Brent J. Sinclair, Thomas R. Buckley
Software Mentions: 1
Published: about 9 years ago

10.3389/fmicb.2015.00547

Standard filtration practices may significantly distort planktonic microbial diversity estimates
Cited by: 41
Author(s): Cory C. Padilla, Sangita Ganesh, Shelby E. Gantt, Alex Huhman, Darren J. Parris, Neha Sarode, Frank J. Stewart
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-07226-4

Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma
Cited by: 16
Author(s): Kirill Batmanov, Wei Wang, Magnar Bjørås, Jan Delabie, Junbai Wang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-021-03141-z

Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress
Cited by: 3
Author(s): Pau Boher, Marçal Soler, Sandra Fernández-Piñán, Xènia Torrent, Sebastian Müller, Krystyna A. Kelly, Olga Serra, Mercè Figueras
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0118214

A Transcriptome Derived Female-Specific Marker from the Invasive Western Mosquitofish (Gambusia affinis)
Cited by: 25
Author(s): Dunja K. Lamatsch, Sofia Adolfsson, Alistair M. Senior, Guntram Christiansen, Maria Pichler, Yuichi Ozaki, Linnéa Smeds, Manfred Schartl, Shinichi Nakagawa
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1003565

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding
Cited by: 151
Author(s): Kevin S. Myers, Huirong Yan, Irene M. Ong, Dongjun Chung, Kun Liang, Frances Tran, Sündüz Keleş, Robert Landick, Patricia J. Kiley
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-14-667

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation
Cited by: 40
Author(s): Sandra Wiegand, Sascha Dietrich, Robert Hertel, Johannes Bongaerts, Stefan Evers, Sonja Volland, Rolf Daniel, Heiko Liesegang
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-13-592

Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses
Cited by: 26
Author(s): Arimantas Lionikas, Caroline Meharg, Jonathan M.J. Derry, Aivaras Ratkevičius, Andrew M. Carroll, David J. Vandenbergh, David A. Blizard
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12870-021-03086-3

Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot
Cited by: 4
Author(s): Eleni Tente, Nelzo C. Ereful, Anyela Camargo Rodriguez, Paul K. Grant, Donal M. O’Sullivan, Lesley A. Boyd, Anna Gordon
Software Mentions: 1
Published: over 3 years ago

10.1186/s12870-014-0301-8

Flavonoid supplementation affects the expression of genes involved in cell wall formation and lignification metabolism and increases sugar content and saccharification in the fast-growing eucalyptus hybrid E. urophylla x E. grandis
Cited by: 8
Author(s): Jorge Lepikson-Neto, Leandro Costa do Nascimento, Marcela Salazar, Eduardo Leal Oliveira Camargo, João P F Cairo, Paulo José Pereira Lima Teixeira, Wesley Leoricy Marques, Fábio M. Squina, Piotr A. Mieczkowski, Ana Carolina Deckmann, Gonçalo Amarante Guimarães Pereira
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-13-511

Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development
Cited by: 66
Author(s): Ines Teichert, Gabriele Wolff, Ulrich Kück, Minou Nowrousian
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0045242

Metastable Differentially Methylated Regions within Arabidopsis Inbred Populations Are Associated with Modified Expression of Non-Coding Transcripts
Cited by: 19
Author(s): Ericka R. Havecker, Laura M. Wallbridge, Paola Fedito, Thomas J. Hardcastle, David C. Baulcombe
Software Mentions: 1
Published: about 12 years ago

Projects: bioconductor: baySeq

Papers Mentioning baySeq 139