bioconductor: ArrayExpress | Projects

10.1186/1472-6750-7-24

Comparison of target labeling methods for use with Affymetrix GeneChips
Cited by: 3
Author(s): William Lonergan, Toni Whistler, Suzanne D. Vernon
Software Mentions: 1
Published: over 17 years ago

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Cited by: 67
Author(s): Dennis Thomas, Sharon Gaheen, Stacey L. Harper, M. J. Fritts, Fred Klaessig, Elizabeth Hahn-Dantona, David S. Paik, Sue Pan, Grace A. Stafford, Elaine T. Freund, Juli Klemm, Nathan A. Baker
Software Mentions: 1
Published: almost 12 years ago

10.1186/1472-6750-5-5

Cited by: 5
Author(s): Valtteri Wirta, Anders Holmberg, Morten Lukacs, Peter Nilsson, Pierre Hilson, Mathias Uhlén, Rishikesh P. Bhalerao, Joakim Lundeberg
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2407-9-409

Impact of biospecimens handling on biomarker research in breast cancer
Cited by: 84
Author(s): Loris De Cecco, Valeria Musella, Silvia Veneroni, Vera Cappelletti, Italia Bongarzone, Maurizio Callari, Barbara Valeri, Marco A. Pierotti, Maria Grazia Daidone
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2407-8-18

Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation
Cited by: 11
Author(s): Olivier Gevaert, Frank De Smet, Toon Van Gorp, Nathalie Pochet, Kristof Engelen, Frédéric Amant, Bart De Moor, Dirk Timmerman, Ignace Vergote
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2407-12-608

Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon
Cited by: 16
Author(s): Rosalia Maglietta, Vania C. Liuzzi, Elisa Cattaneo, Endre Laczkó, Ada Piepoli, Anna Panza, Massimo Carella, Orazio Palumbo, Teresa Staiano, Federico Buffoli, Angelo Andriulli, Giancarlo Marra, Nicola Ancona
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2407-10-482

Differential detection of alternatively spliced variants of Ciz1 in normal and cancer cells using a custom exon-junction microarray
Cited by: 22
Author(s): Faisal Rahman, Naveed Aziz, Dawn Coverley
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2407-10-176

Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells
Cited by: 12
Author(s): Michael St.Pierre, Benoît DeHertogh, Anthoula Gaigneaux, Bertrand DeMeulder, Fabrice Berger, Eric Bareke, Carine Michiels, Eric Depiereux
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2407-14-871

Estrogen independent gene expression defines clinically relevant subgroups of estrogen receptor positive breast cancer
Cited by: 4
Author(s): Robin Hallett, John A. Hassell
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2407-13-184

Expressional alterations in functional ultra-conserved non-coding rnas in response to all-transretinoic acid - induced differentiation in neuroblastoma cells
Cited by: 34
Author(s): Karen M. Watters, Kenneth Bryan, Niamh H. Foley, Maria Meehan, Raymond L. Stallings
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2407-12-260

Colon cancer molecular subtypes identified by expression profiling and associatedto stroma, mucinous type and different clinical behavior
Cited by: 112
Author(s): Beatriz Pérez-Villamil, Alejandro Romera Lopez, Susana Prieto, Guillermo López–Campos, Antonio Calles, J. A. Asenjo, Julián Sanz-Ortega, Cristina Fernández Pérez, Javier Sastre, Rosario Alfonso, Trinidad Caldés, Fernando Martín-Sánchez, Eduardo Díaz-Rubio
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-213X-10-54

Analysis of the asymmetrically expressed Ablim1 locus reveals existence of a lateral plate Nodal-independent left sided signal and an early, left-right independent role for nodal flow
Cited by: 11
Author(s): Jonathan L. Stevens, А. Н. Ермаков, José Bragança, Helen Hilton, Peter A. Underhill, Shoumo Bhattacharya, Nigel A. Brown, Dominic P. Norris
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-213X-7-129

Gene array identification of Ipf1/Pdx1-/-regulated genes in pancreatic progenitor cells
Cited by: 26
Author(s): Per H. Svensson, Cecilia Williams, Joakim Lundeberg, Patrik Rydén, Ingela Bergqvist, Helena Edlund
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2148-9-59

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation
Cited by: 53
Author(s): Arne W. Nolte, Sébastien Renaut, Louis Bernatchez
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-7-224

Development and validation of a bovine macrophage specific cDNA microarray
Cited by: 38
Author(s): Kirsty Jensen, Richard Talbot, Edith Paxton, David Waddington, Elizabeth J. Glass
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-11-389

Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile
Cited by: 24
Author(s): Gemma Marsden, Ian J. Davis, Victoria Wright, Mohammed Sebaihia, Ed J. Kuijper, Nigel P. Minton
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-8-377

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards
Cited by: 4
Author(s): Torunn Bruland, Endre Anderssen, Berit Doseth, Hallgeir Bergum, Vidar Beisvåg, Astrid Lægreid
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-11-93

Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis
Cited by: 65
Author(s): Stephanus J. Ferreira, Melanie Senning, Sophia Sonnewald, Petra-Maria Keßling, Ralf Goldstein, Uwe Sonnewald
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-11-361

Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background
Cited by: 11
Author(s): Harry Noyes, Morris Agaba, Stuart Anderson, Alan Archibald, Andy Brass, John P. Gibson, Laurence S. Hall, Helen Hulme, Sung Jong Oh, Stephen J. Kemp
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-016-2803-2

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana
Cited by: 9
Author(s): Robert Hoffmann, Michael G. Palmgren
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-12-12

Mesenteric lymph node transcriptome profiles in BALB/c mice sensitized to three common food allergens
Cited by: 12
Author(s): Mainul Husain, Herman J. Boermans, Niel A. Karrow
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-017-4200-x

Genes for asparagine metabolism in Lotus japonicus: differential expression and interconnection with photorespiration
Cited by: 8
Author(s): Margarita García‐Calderón, Carmen M. Pérez-Delgado, Alfredo Credali, José M. Vega, Marco Betti, Antonio J. Márquez
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-020-6712-z

Lung transcriptomic clock predicts premature aging in cigarette smoke-exposed mice
Cited by: 12
Author(s): Mohamed-Amin Choukrallah, Julia Hoeng, Manuel C. Peitsch, Florian Martin
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-14-710

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression
Cited by: 26
Author(s): Paul Golby, Javier Nuñez, Adam A. Witney, Jason Hinds, Michael A. Quail, Stephen D. Bentley, Simon R. Harris, Noel H. Smith, R. Glyn Hewinson, Stephen V. Gordon
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-8-450

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance
Cited by: 75
Author(s): Fanny Ramel, Cécile Sulmon, Francisco Cabello‐Hurtado, Ludivine Taconnat, Marie‐Laure Martin‐Magniette, Jean-Pierre Renou, Abdelhak El Amrani, Ivan Couée, Gwenola Gouesbet
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis
Cited by: 53
Author(s): Victoria A Jenkins, Geraint Barton, Brian D. Robertson, Katrina Williams
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-7-113

Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes
Cited by: 41
Author(s): Maud Vallée, Claude Robert, S. Méthot, Marie‐France Palin, Marc‐André Sirard
Software Mentions: 1
Published: over 18 years ago

10.1186/s12864-018-4954-9

Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression
Cited by: 13
Author(s): Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs, Susanne E. Ulbrich
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-016-2562-0

Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq
Cited by: 44
Author(s): Shaofeng Li, Chengming Fan, Yán Li, Jianhui Zhang, Jie Sun, Yuhong Chen, Tian Chen, Xiaohua Su, Mengzhu Lu, Chengzhi Liang, Zhongliang Hu
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-8-387

BMDExpress: a software tool for the benchmark dose analyses of genomic data
Cited by: 160
Author(s): Longlong Yang, Bruce C. Allen, Russell S. Thomas
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-8-181

Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni
Cited by: 34
Author(s): Michael Waisberg, Francisco Pereira Lobo, Gustavo C. Cerqueira, Liana Konovaloff Jannotti Passos, Omar S. Carvalho, Glória Regina Franco, Najib M. El-Sayed
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-14-169

Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes
Cited by: 38
Author(s): Meagan J Gillespie, Tamsyn M. Crowley, Volker Häring, Susanne Wilson, Jennifer Harper, Jean Payne, Diane Green, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-8-202

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees
Cited by: 48
Author(s): Moushumi Sen Sarma, Charles W. Whitfield, Gene E. Robinson
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-9-3

Switch-like genes populate cell communication pathways and are enriched for extracellular proteins
Cited by: 36
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-7-319

Systematic interpretation of microarray data using experiment annotations
Cited by: 17
Author(s): Kurt Fellenberg, Christian Busold, Olaf Witt, Andrea S. Bauer, Boris Beckmann, Nicole Hauser, Marcus Frohme, Stefan Winter, Jürgen Dippon, Jörg D. Hoheisel
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12864-019-5464-0

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes
Cited by: 3
Author(s): Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny, Krzysztof Fujarewicz
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-11-418

Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)
Cited by: 124
Author(s): Samuel Martín, Alex Douglas, D.F. Houlihan, Christopher J. Secombes
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-13-33

Transcriptional ontogeny of the developing liver
Cited by: 41
Author(s): Janice S. Lee, William O. Ward, Geremy W. Knapp, Hongzu Ren, Beena Vallanat, Barbara D. Abbott, Karen J. Ho, Seth J. Karp, J. Christopher Corton
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-9-221

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA
Cited by: 5
Author(s): Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A. Setterquist, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-6-178

GPX-Macrophage Expression Atlas: A database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
Cited by: 16
Author(s): Graeme R. Grimes, Stuart Moodie, John S. Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D. Livingston, Muriel Mewissen, Kevin A. Robertson, Alan J. Ross, Garwin K. Sing, Peter Ghazal
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-9-340

Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
Cited by: 87
Author(s): Marcel Scheideler, Christian Elabd, Laure‐Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fátima Sánchez‐Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gérard Ailhaud, Christian Dani, Ez-Zoubir Amri, Zlatko Trajanoski
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-12-620

An expression map for Anopheles gambiae
Cited by: 27
Author(s): Robert M. MacCallum, Seth Redmond, George K. Christophides
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-10-42

Positive correlation between gene coexpression and positional clustering in the zebrafish genome
Cited by: 28
Author(s): Yen Kaow Ng, Wei Wu, Louxin Zhang
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-8-401

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
Cited by: 12
Author(s): Santiago P. Aubourg, Marie‐Laure Martin‐Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E. Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, Jean-Pierre Renou
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-10-306

Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Cited by: 30
Author(s): Jin Hwan, Rui Yamaguchi, Satoru Miyano
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-10-153

Learning from microarray interlaboratory studies: measures of precision for gene expression
Cited by: 9
Author(s): David L. Duewer, Wendell Jones, Laura Reid, Marc Salit
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-10-560

ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles
Cited by: 1
Author(s): Weizhong Li, Andrew Y. Gracey, Luciane V. Mello, Andy Brass, Andrew R. Cossins
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-7-78

Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity
Cited by: 34
Author(s): Vattipally B Sreenu, Pankaj Kumar, Javaregowda Nagaraju, Hampapathalu A. Nagarajaram
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-8-210

Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state
Cited by: 1
Author(s): Daniel Y L Yap, David K. Smith, Xue W Zhang, Jeffrey Hill
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12864-016-2814-z

A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease
Cited by: 20
Author(s): Helgi B. Schiöth, Adrian Boström, Susan K. Murphy, Wiebke Erhart, Jochen Hampe, Cynthia A. Moylan, Jessica Mwinyi
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-8-208

Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits
Cited by: 22
Author(s): Carl-Johan Rubin, Johan Lindberg, Carolyn Fitzsimmons, Peter Savolainen, Per Jensen, Joakim Lundeberg, Leif C. Andersson, Andreas Kindmark
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-15-315

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach
Cited by: 66
Author(s): Tommy Bengtsson, Deborah Weighill, Estelle Proux‐Wéra, Fredrik Levander, Svante Resjö, Dharani Dhar Burra, Laith Ibrahim Moushib, Pete E. Hedley, Erland Liljeroth, Dan Jacobson, Erik Alexandersson, Erik Andréasson
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-016-2537-1

On the genome base composition of teleosts: the effect of environment and lifestyle
Cited by: 14
Author(s): Andrea Tarallo, Claudia Angelini, Remo Sanges, Mitsuharu Yagi, Claudio Agnisola, Giuseppe D’Onofrio
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-16-S1-S11

Transcriptomics profiling study of breast cancer from Kingdom of Saudi Arabia revealed altered expression of Adiponectin and Fatty Acid Binding Protein4: Is lipid metabolism associated with breast cancer?
Cited by: 25
Author(s): Adnan Merdad, Sajjad Karim, Hans-Juergen Schulten, Jayapal Manikandan, Ashraf Dallol, Abdelbaset Buhmeida, Fatima Al-Thubaity, Mamdooh A GariI, Adeel Chaudhary, Adel M. Abuzenadah, Mohammed Al‐Qahtani
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-336

A simple and reproducible breast cancer prognostic test
Cited by: 47
Author(s): Luigi Marchionni, Bahman Afsari, Donald Geman, Jeffrey T. Leek
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-14-376

Time-dependent changes in gene expression induced by secreted amyloid precursor protein-alpha in the rat hippocampus
Cited by: 35
Author(s): Margaret M. Ryan, Gary P. Morris, Bruce G. Mockett, Katie Bourne, Wickliffe C. Abraham, Warren P. Tate, Joanna M. Williams
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-015-1342-6

The recent escalation in strength of pyrethroid resistance in Anopheles coluzzi in West Africa is linked to increased expression of multiple gene families
Cited by: 80
Author(s): Hyacinthe K. Toé, N’Falé Sagnon, Roch K. Dabiré, Hilary Ranson, Christopher M. Jones
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-7-266

Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™
Cited by: 14
Author(s): Carole L. Yauk, Andrew Williams, Sherri E. Boucher, Lynn Berndt, Gu Zhou, Jiangxia Zheng, Andrea Rowan-Carroll, Hongyan Dong, Iain B. Lambert, George R. Douglas, Craig L.J. Parfett
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-9-121

Transcriptome analysis of grain development in hexaploid wheat
Cited by: 183
Author(s): Yongfang Wan, Rebecca L Poole, Alison K. Huttly, C. Toscano-Underwood, Kevin A. Feeney, S. J. Welham, M. J. Gooding, Clare Mills, Keith J. Edwards, Peter R. Shewry, R. A. C. Mitchell
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-10-324

Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues
Cited by: 28
Author(s): Anita Grigoriadis, Gavin R. Oliver, Austin Tanney, Howard Kendrick, Matthew J. Smalley, Parmjit Jat, A. Munro Neville
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-9-375

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability
Cited by: 76
Author(s): Martin H. van Vliet, Fabien Reyal, Hugo M. Horlings, Marc J. van de Vijver, Marcel J. T. Reinders, Lodewyk Wessels
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-8-70

Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation
Cited by: 338
Author(s): Birgit Kulterer, Gerald Friedl, Anita Jandrositz, Fátima Sánchez‐Cabo, Andreas Prokesch, Christine Paar, Marcel Scheideler, Reinhard Windhager, Karl‐Heinz Preisegger, Zlatko Trajanoski
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-11-709

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans
Cited by: 62
Author(s): Jessica Cleiss-Arnold, Sandrine Koechler, Caroline Proux, Marie‐Laure Fardeau, Marie‐Agnès Dillies, Jean‐Yves Coppée, Florence Arsène-Ploetze, Philippe Bertin
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-11-343

Regulation of the cardiomyocyte transcriptome vs translatome by endothelin-1 and insulin: translational regulation of 5' terminal oligopyrimidine tract (TOP) mRNAs by insulin
Cited by: 15
Author(s): Thomais Markou, Andrew Keith Marshall, Timothy E. Cullingford, El Li Tham, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-11-142

TobEA: an atlas of tobacco gene expression from seed to senescence
Cited by: 61
Author(s): Kieron D. Edwards, Aureliano Bombarely, Geraint W. Story, F H Allen, Lukas A. Mueller, Steve Coates, Louise Jones
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-15-649

Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation
Cited by: 28
Author(s): Alison F. Richard, Paul Lyons, James E. Peters, Daniele Biasci, Shaun Flint, James C. Lee, Eoín McKinney, Richard M. Siegel, Kenneth G. C. Smith
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-13-407

Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins
Cited by: 75
Author(s): David Peris, Christian A. Lopes, Carmela Belloch, Amparo Querol, Eladio Barrio
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-12-452

Histological and global gene expression analysis of the 'lactating' pigeon crop
Cited by: 43
Author(s): Meagan J Gillespie, Volker Häring, Kenneth A. McColl, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-11-714

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources
Cited by: 22
Author(s): Camille Rustenholz, Pete E. Hedley, Jenny Morris, Frédéric Choulet, Catherine Feuillet, Robbie Waugh, Etienne Paux
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-9-628

Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality
Cited by: 13
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-14-799

Chronic parasitization by Nosema microsporidia causes global expression changes in core nutritional, metabolic and behavioral pathways in honey bee workers (Apis mellifera)
Cited by: 85
Author(s): Holly L. Holt, Katherine A. Aronstein, Christina M. Grozinger
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-6-174

Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species of different survival strategies
Cited by: 137
Author(s): Heenam Stanley Kim, Mark A. Schell, Yan Yu, Ricky L. Ulrich, Saul Sarria, William C. Nierman, David DeShazer
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-10-119

Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes
Cited by: 58
Author(s): José Osorio y Fortéa, Emilie de La Llave, Béatrice Regnault, Jean‐Yves Coppée, Geneviève Milon, Thierry Lang, Éric Prina
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-15-333

MicroRNA profiling of rats with ochratoxin A nephrotoxicity
Cited by: 47
Author(s): Dai Qiu, Jingbo Zhao, Xiaozhe Qi, Wentao Xu, Xiaoyun He, Mingzhang Guo, Harsh Dweep, Wen‐Hsing Cheng, Yunbo Luo, Kai Xia, Norbert Gretz, Kunlun Huang
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-9-324

Topoisomerase II inhibition involves characteristic chromosomal expression patterns
Cited by: 7
Author(s): Susanne Reymann, Jürgen Borlak
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-13-146

Meta-analysis of Chicken – Salmonella infection experiments
Cited by: 11
Author(s): M.F.W. te Pas, Ina Hulsegge, Dirkjan Schokker, M.A. Smits, Mark Fife, Rima Zoorob, Marie-Laure Endale, Johanna M.J. Rebel
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-8-22

Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population
Cited by: 73
Author(s): Chun Shi, Anna Użarowska, Milena Ouzunova, Matthias Landbeck, G. Wenzel, Thomas Lübberstedt
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-12-113

Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns
Cited by: 21
Author(s): Daniel Báron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péreón, Reiner A. Veitia, Frédérique Savagner, Gérard Ramstein, Rémi Houlgatte
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-15-S10-S4

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation
Cited by: 2
Author(s): Alexis Vandenbon, Shunsuke Teraguchi, Osamu Takeuchi, Yutaka Suzuki, Daron M. Standley
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-10-350

Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo
Cited by: 17
Author(s): Matthijs Raaben, Marian J. A. Groot Koerkamp, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-9-171

Transcriptional regulation by Poly(ADP-ribose) polymerase-1 during T cell activation
Cited by: 41
Author(s): Luis Sáenz, Juan José Lozano, Rut Valdor, Alberto Baroja‐Mazo, Pablo Ramı́rez, Pascual Parrilla, Pedro Aparicio, Lauro Sumoy, José Yélamos
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-9-285

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
Cited by: 78
Author(s): Michael Boedigheimer, Russell D. Wolfinger, Michael Bass, Pierre R. Bushel, Jeff W. Chou, Matthew N. Cooper, J. Christopher Corton, Jennifer Fostel, Susan Hester, Janice S. Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, Karol L. Thompson
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-11-478

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes
Cited by: 11
Author(s): Michael Klutstein, Zahava Siegfried, Ariel Gispan, Shlomit Farkash-Amar, Guy Zinman, Ziv Bar‐Joseph, Giora Simchen, Itamar Simon
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-9-291

Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium
Cited by: 66
Author(s): Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, Salvatore Bozzaro
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-11-S1-S6

Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha
Cited by: 116
Author(s): Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir A. Kuznetsov, Lim Sai Kiang, Vivek Tanavde
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-16-S1-S2

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data
Cited by: 41
Author(s): Anna L Swan, Dov J. Stekel, Charlie Hodgman, David Allaway, Mohammed Hussein Al-Qahtani, Ali Mobasheri, Jaume Bacardit
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-5-68

PEDRo: A database for storing, searching and disseminating experimental proteomics data
Cited by: 66
Author(s): Kevin Garwood, Thomas J. McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen M. Carroll, Caroline A. Evans, Anthony D. Whetton, Sarah R. Hart, David Stead, Zhikang Yin, Alistair J. P. Brown, Andrew Hesketh, Keith F. Chater, Lena Hansson, Muriel Mewissen, Peter Ghazal, Julie A. Howard, Kathryn S. Lilley, Simon J. Gaskell, Andy Brass, Simon J. Hubbard, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2164-10-575

Using transcriptome profiling to characterize QTL regions on chicken chromosome 5
Cited by: 13
Author(s): Guillaume Le Mignon, Colette Désert, Frédérique Pitel, Sophie Leroux, Olivier Demeure, Grégory Guernec, Behnam Abasht, Madeleine Douaire, Pascale Le Roy, Sandrine Lagarrigue
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-9-208

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina
Cited by: 14
Author(s): Ravi Kiran Reddy Kalathur, Nicolas Gagnière, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, Olivier Poch
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-11-682

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Cited by: 40
Author(s): Richard A. Lewis, Emma Laing, Nicholas E. E. Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M. Kierzek, Colin P. Smith
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-10-215

Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays
Cited by: 29
Author(s): Minjie Wang, Xiaoli Qi, Shutang Zhao, Shougong Zhang, Mengzhu Lu
Software Mentions: 1
Published: over 15 years ago

10.1186/s12864-016-2771-6

Transcriptomic response of yeast cells to ATX1 deletion under different copper levels
Cited by: 12
Author(s): Ayca Cankorur-Cetinkaya, Serpil Eraslan, Betül Kırdar
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-15-438

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Cited by: 26
Author(s): Marta Vergara-Irigaray, María Fookes, Nicholas R. Thomson, Christoph M. Tang
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-13-49

Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice
Cited by: 29
Author(s): Rumdeep K Grewal, S. K. Gupta, Sampa Das
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12865-017-0238-4

Cattle infection response network and its functional modules
Cited by: 5
Author(s): Hamid Beiki, A. Pakdel, A Nejati Javaremi, Ali Masoudi‐Nejad, James M. Reecy
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12879-016-1533-z

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
Cited by: 13
Author(s): Steven T. Pullan, Jon C. Allnutt, Rebecca Devine, Kim A. Hatch, Rose E. Jeeves, Charlotte L. Hendon-Dunn, Philip Marsh, Joanna Bacon
Software Mentions: 1
Published: over 8 years ago

10.1186/s12916-016-0609-3

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy
Cited by: 45
Author(s): Isobella Honeyborne, Timothy D. McHugh, Iitu Kuittinen, Anna Cichońska, Dimitrios Evangelopoulos, Katharina Ronacher, Paul D. van Helden, Stephen H. Gillespie, Delmiro Fernández-Reyes, Gerhard Walzl, Juho Rousu, Philip D. Butcher, Simon J. Waddell
Software Mentions: 1
Published: over 8 years ago

10.1186/s12916-017-0929-y

A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes
Cited by: 40
Author(s): Jean‐Philippe Foy, Louis Bazire, Sandra Ortiz-Cuàran, Sophie Deneuve, Janice Kielbassa, Emilie Thomas, Alain Viari, Alain Puisieux, P. Goudot, Chloé Bertolus, Nicolas Foray, Youlia Kirova, Pierre Verrelle, Pierre Saintigny
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2350-8-36

Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets
Cited by: 110
Author(s): ChaRandle Jordan, Hong Hua Li, Helen H. Kwan, Uta Francke
Software Mentions: 1
Published: over 17 years ago

10.1186/s12920-016-0227-0

A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without
Cited by: 10
Author(s): Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner, Nicki Tiffin
Software Mentions: 1
Published: about 8 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962