bioconductor: ArrayExpress | Projects

10.1186/1471-2105-6-S4-S14

Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control
Cited by: 20
Author(s): Giacomo Finocchiaro, Francesco Mancuso, Heiko Müller
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2105-6-101

MARS: Microarray analysis, retrieval, and storage system
Cited by: 59
Author(s): Michael Maurer, Robert Molidor, Alexander Sturn, Jürgen Hartler, Hubert Hackl, Gernot Stocker, Andreas Prokesch, Marcel Scheideler, Zlatko Trajanoski
Software Mentions: 2
Published: about 21 years ago

10.1186/1471-2105-6-264

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
Cited by: 33
Author(s): David G. Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, Andrew J. Wood, Karim Nashar, Douglas B. Kell, Andy Brass
Software Mentions: 2
Published: over 20 years ago

10.1186/s12859-020-03836-4

Biological interpretation of deep neural network for phenotype prediction based on gene expression
Cited by: 16
Author(s): Blaise Hanczar, Farida Zehraoui, Tina Issa, Mathieu Arles
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-7-190

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation
Cited by: 15
Author(s): Leandro Hermida, Olivier Schaad, Philippe Demougin, Patrick Descombes, Michael Primig
Software Mentions: 2
Published: about 20 years ago

10.1186/1471-2105-11-576

Validation and characterization of DNA microarray gene expression data distribution and associated moments
Cited by: 15
Author(s): Reuben Thomas, Luís de la Torre, Xiaoqing Chang, Sanjay Mehrotra
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-8-S1-S21

The Genopolis Microarray Database
Cited by: 8
Author(s): Andrea Splendiani, Marco Brandizi, Gaël Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri, Paola Ricciardi‐Castagnoli
Software Mentions: 2
Published: over 19 years ago

10.1186/1471-2105-13-335

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages
Cited by: 132
Author(s): Jonatan Taminau, Stijn Meganck, Cosmin Lazar, David Steenhoff, Alain Coletta, Colin Molter, Robin Duqué, Virginie de Schaetzen, David Solis, Hugues Bersini, Ann Nowé
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-14-70

A novel method for cross-species gene expression analysis
Cited by: 40
Author(s): Erik Kristiansson, Tobias Österlund, Lars Gunnarsson, Gabriella Arne, D. G. Joakim Larsson, Olle Nerman
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-13-S1-S10

A semantic web framework to integrate cancer omics data with biological knowledge
Cited by: 18
Author(s): Matthew Holford, James P. McCusker, Kei‐Hoi Cheung, Michael Krauthammer
Software Mentions: 2
Published: over 14 years ago

10.1186/s12859-021-04359-2

Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders
Cited by: 0
Author(s): Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi, Benoît Ballester
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2105-10-409

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)
Cited by: 89
Author(s): Martin J. Aryee, José A. Gutiérrez‐Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-11-267

A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes
Cited by: 13
Author(s): Guofeng Meng, Axel Mosig, Martin Vingron
Software Mentions: 2
Published: about 16 years ago

10.1186/1471-2105-11-36

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53
Cited by: 16
Author(s): Junbai Wang, Tianhai Tian
Software Mentions: 2
Published: over 16 years ago

10.1186/s12859-020-03932-5

GEOlimma: differential expression analysis and feature selection using pre-existing microarray data
Cited by: 4
Author(s): Liangqun Lu, Kevin Townsend, Bernie J. Daigle
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-12-23

easyDAS: Automatic creation of DAS servers
Cited by: 5
Author(s): Bernat Gel, Andy Jenkinson, Rafael C. Jiménez, Xavier Messeguer, Henning Hermjakob
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-14-131

Eliciting candidate anatomical routes for protein interactions: a scenario from endocrine physiology
Cited by: 2
Author(s): Pierre Grenon, Bernard de Bono
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2105-7-205

SIMAGE: si mulation of DNA-m icroa rray g ene e xpression data
Cited by: 23
Author(s): Casper J. Albers, Ritsert C. Jansen, Jan Kok, Oscar P. Kuipers, Sacha A. F. T. van Hijum
Software Mentions: 2
Published: about 20 years ago

10.1186/1471-2105-11-611

SIDEKICK: Genomic data driven analysis and decision-making framework
Cited by: 4
Author(s): Mark Doderer, Kihoon Yoon, Kay A. Robbins
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-12-46

GCOD - GeneChip Oncology Database
Cited by: 16
Author(s): Fenglong Liu, Joseph A. White, Corina Antonescu, Daniel Gusenleitner, John Quackenbush
Software Mentions: 2
Published: over 15 years ago

10.1186/1741-7007-12-24

Initiating a regenerative response; cellular and molecular features of wound healing in the cnidarian Nematostella vectensis
Cited by: 101
Author(s): Timothy Q. DuBuc, Nikki Traylor-Knowles, Mark Q. Martindale
Software Mentions: 2
Published: about 12 years ago

10.1186/1741-7007-10-90

A gene expression atlas of the domestic pig
Cited by: 145
Author(s): Tom C. Freeman, Alasdair Ivens, J Kenneth Baillie, Dario Beraldi, Mark W. Barnett, David A. Dorward, Alison Downing, Lynsey Fairbairn, Ronan Kapétanovic, Sobia Raza, Andru Tomoiu, Ramiro Alberio, Chunlei Wu, Andrew I. Su, Kim M. Summers, Christopher K. Tuggle, Alan Archibald, David Hume
Software Mentions: 2
Published: over 13 years ago

10.1186/1741-7007-9-29

Lack of global meiotic sex chromosome inactivation, and paucity of tissue-specific gene expression on the Drosophila X chromosome
Cited by: 67
Author(s): Lyudmila Mikhaylova, Dmitry I. Nurminsky
Software Mentions: 2
Published: about 15 years ago

10.1186/s12885-015-1953-y

Consistent gene expression profiles in MexTAg transgenic mouse and wild type mouse asbestos-induced mesothelioma
Cited by: 12
Author(s): Cleo Robinson, Ian M. Dick, Michael J. Wise, Andrew Holloway, Dileepa S. Diyagama, B. W. Robinson, Jenette Creaney, Richard Lake
Software Mentions: 2
Published: over 10 years ago

10.1186/s12885-015-1128-x

Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin
Cited by: 35
Author(s): Jonas Vikeså, Anne Mette Møller, Bogumił Kaczkowski, Rehannah Borup, Ole Winther, Ricardo Henao, Anders Krogh, Katharina Perell, Flemming Jensen, Gedske Daugaard, Finn C. Nielsen
Software Mentions: 2
Published: over 11 years ago

10.1186/s12885-021-08308-3

Identification of significant genes as prognostic markers and potential tumor suppressors in lung adenocarcinoma via bioinformatical analysis
Cited by: 15
Author(s): Mingze Lu, Xiao-Wen Fan, Wei-Lin Liao, Yijiao Li, Li Ma, Man Yuan, Rui Gu, Zhengdao Wei, Chao Wang, Hua Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2121-10-87

Global transcriptional response after exposure of fission yeast cells to ultraviolet light
Cited by: 6
Author(s): Henriette C. Skjølberg, Øyvind Fensgård, Hilde Nilsen, Beáta Grallert, Erik Boye
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-213X-11-2

Targets downstream of Cdk8 in Dictyostelium development
Cited by: 4
Author(s): David Greene, Gareth Bloomfield, Jason Skelton, Alasdair Ivens, Catherine J. Pears
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-7-49

Development of a chicken 5 K microarray targeted towards immune function
Cited by: 31
Author(s): Jacqueline Smith, David Speed, Paul Hocking, Richard Talbot, W.G.J. Degen, Virgil E.J.C. Schijns, Elizabeth J. Glass, David W. Burt
Software Mentions: 2
Published: over 20 years ago

10.1186/s12864-016-2600-y

Gene expression comparison of resistant and susceptible Atlantic salmon fry challenged with Infectious Pancreatic Necrosis virus reveals a marked contrast in immune response
Cited by: 53
Author(s): Diego Robledo, John B. Taggart, J. Ireland, Brendan McAndrew, W. Starkey, Chris Haley, Alastair Hamilton, D. R. Guy, J. C. Mota-Velasco, Almas Gheyas, A. E. Tinch, David W. Verner–Jeffreys, Richard Paley, Georgina S. E. Rimmer, I. Tew, Stephen Bishop, James E. Bron, Ross D. Houston
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-8-452

Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice
Cited by: 55
Author(s): Nicolas Nf Delahaye, Nicolas Coltel, Denis Puthier, Mathieu Barbier, P. Benech, Florence Joly, Fuad Fa Iraqi, Georges E. Grau, Catherine Nguyen, Pascal Rihet
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2164-13-187

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit
Cited by: 32
Author(s): Viviana Lima-Silva, Abel Rosado, Vítor Amorim‐Silva, Antonio Muñoz‐Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta, Miguel A. Botella
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-7-145

Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis
Cited by: 44
Author(s): Ella Palmer, Andrew D. Miller, Tom C. Freeman
Software Mentions: 2
Published: about 20 years ago

10.1186/1471-2164-14-436

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Cited by: 15
Author(s): Katrina Williams, William A Bryant, Victoria A Jenkins, Geraint Barton, Adam A. Witney, John W. Pinney, Brian D. Robertson
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-018-5336-z

Characterization of B-BOX gene family and their expression profiles under hormonal, abiotic and metal stresses in Poaceae plants
Cited by: 48
Author(s): Abdullah Shalmani, Xiu-Qing Jing, Yi Shi, Izhar Muhammad, Meng-Ru Zhou, Xiaoli Wei, Qiongqiong Chen, Wenqiang Li, Wenting Liu, Kun-Ming Chen
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-9-266

Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus
Cited by: 100
Author(s): Jennifer Owen, B Ann Hedley, Claus Svendsen, Jodie F Wren, Martijs J. Jonker, Peter K. Hankard, Linsey J Lister, Stephen R. Stürzenbaum, Andrew Morgan, David J. Spurgeon, Mark Blaxter, Peter Kille
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2164-11-7

Decoding pooled RNAi screens by means of barcode tiling arrays
Cited by: 10
Author(s): Michael Boettcher, Johannes Fredebohm, Amin Moghaddas Gholami, Yafit Hachmo, Iris Dotan, Dan Canaani, Jörg D. Hoheisel
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2164-9-133

A software framework for microarray and gene expression object model (MAGE-OM) array design annotation
Cited by: 1
Author(s): Matloob Qureshi, Alasdair Ivens
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2164-8-383

Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map
Cited by: 19
Author(s): Stefano Campanaro, Simone Picelli, Rossella Torregrossa, Laura Colluto, Monica Ceol, Dorella Del Prete, Angela D’Angelo, Giorgio Valle, Franca Anglani
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2164-11-582

Differential gene expression during the moult cycle of Antarctic krill (Euphausia superba)
Cited by: 43
Author(s): Paul J. Seear, Geraint A. Tarling, Gavin Burns, William P. Goodall‐Copestake, E. Gaten, Özge Özkaya, Ezio Rosato
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-13-59

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens
Cited by: 132
Author(s): Daniel Nätt, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Bélteky, Leif Andersson, Per Jensen
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-15-231

An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation
Cited by: 12
Author(s): Mathieu Lajoie, Yu-Chih Hsu, Richard M. Gronostajski, Timothy L. Bailey
Software Mentions: 2
Published: about 12 years ago

10.1186/s12864-017-3627-4

Exploring the nature of prediagnostic blood transcriptome markers of chronic lymphocytic leukemia by assessing their overlap with the transcriptome at the clinical stage
Cited by: 3
Author(s): Jelle Vlaanderen, Max Leenders, Marc Chadeau‐Hyam, Lützen Portengen, Soterios A. Kyrtopoulos, Ingvar A. Bergdahl, Anders Johansson, Dennie G. A. J. Hebels, Theo M. C. M. de Kok, Paolo Víneis, Roel Vermeulen
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-7-240

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies
Cited by: 5
Author(s): Paul Honoré, Samuel Granjeaud, Rebecca Tagett, S. Deraco, Emmanuel Beaudoing, Jacques Rougemont, Stéphane Debono, Pascal Hingamp
Software Mentions: 2
Published: over 19 years ago

10.1186/1471-2164-10-S3-S15

Improving gene expression similarity measurement using pathway-based analytic dimension
Cited by: 4
Author(s): Changwon Keum, Jung Hoon Woo, Won Seok Oh, Sue-Nie Park, Kyoung Tai No
Software Mentions: 2
Published: over 16 years ago

10.1186/s12864-016-3435-2

Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types
Cited by: 29
Author(s): Bruno Giotti, Anagha Joshi, Tom C. Freeman
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-9-232

Genomic analysis of post-mating changes in the honey bee queen (Apis mellifera)
Cited by: 122
Author(s): Sarah D. Kocher, Freddie-Jeanne Richard, David R. Tarpy, Christina M. Grozinger
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2164-14-922

TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes
Cited by: 1
Author(s): Neelima Chitturi, Govindkumar Balagannavar, Darshan S. Chandrashekar, Sadashivam Abinaya, Vasan S Srini, Kshitish K. Acharya
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-10-411

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery
Cited by: 32
Author(s): Chunlai Feng, Michihiro Araki, Ryo Kunimoto, Akiko Tamon, Hiroki Makiguchi, Satoshi Niijima, Gozoh Tsujimoto, Yasushi Okuno
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2164-13-237

Identification of metagenes and their Interactions through Large-scale Analysis of Arabidopsis Gene Expression Data
Cited by: 12
Author(s): Tyler J. Wilson, Liming Lai, Yuguang Ban, Xijin Ge
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-11-467

A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database
Cited by: 15
Author(s): Kshitish K. Acharya, Darshan S. Chandrashekar, Neelima Chitturi, Hardik Shah, Varun Malhotra, Sreelakshmi Ks, H Deepti, Akhilesh Kumar Bajpai, Sravanthi Davuluri, Pranami Bora, L. Vaikunta Rao
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2164-10-619

The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes
Cited by: 6
Author(s): Fernando Cruz, Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-12-262

GiSAO.db: a database for ageing research
Cited by: 3
Author(s): Edith Hofer, Gerhard Laschober, Matthias Hackl, Gerhard G. Thallinger, Günter Lepperdinger, Johannes Grillari, Pidder Jansen‐Dürr, Zlatko Trajanoski
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2164-8-294

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton
Cited by: 6
Author(s): Jean Muller, André Mehlen, Guillaume Vetter, Mikalai M. Yatskou, Arnaud Muller, Frédéric Chalmel, Olivier Poch, Evelyne Friederich, Laurent Vallar
Software Mentions: 2
Published: almost 19 years ago

10.1186/1471-2164-15-154

Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq
Cited by: 45
Author(s): Jeremy A. Miller, Vilas Menon, Jeff Goldy, Ajamete Kaykas, Chang Kyu Lee, Kimberly A. Smith, Elaine Shen, John W. Phillips, Ed Lein, Mike Hawrylycz
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-15-1181

Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome
Cited by: 13
Author(s): Samoel Renan Mello da Silva, Gabriel C. Perrone, J. Dinis, Rita Maria Cunha de Almeida
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-12-429

Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data
Cited by: 47
Author(s): Gareth R. Howell, David O Walton, Benjamin L. King, Richard T. Libby, Simon W. M. John
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12864-015-1993-3

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
Cited by: 31
Author(s): Andrea Saß, Heleen Van Acker, Konrad U. Förstner, Filip Van Nieuwerburgh, Dieter Deforce, Jörg Vogel, Tom Coenye
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-7-75

Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression
Cited by: 23
Author(s): Karin Richter, Valtteri Wirta, Lina Dahl, Sara Bruce, Joakim Lundeberg, Leif Carlsson, Cecilia Williams
Software Mentions: 2
Published: about 20 years ago

10.1186/1471-2164-11-557

Genome-wide expression patterns in physiological cardiac hypertrophy
Cited by: 17
Author(s): Ignat Drozdov, Sophia Tsoka, Christos A. Ouzounis, Ajay M. Shah
Software Mentions: 2
Published: over 15 years ago

10.1186/s12864-018-5342-1

Genome-wide identification of SERK genes in apple and analyses of their role in stress responses and growth
Cited by: 13
Author(s): Liwei Zheng, Junsheng Ma, Jiangping Mao, Shiliang Fan, Dong Zhang, Caiping Zhao, Na An, Mingyu Han
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-14-297

Genome-wide analysis of the GH3 family in apple (Malus × domestica)
Cited by: 65
Author(s): Hao Yuan, Kai Zhao, Hengjiu Lei, Xinjie Shen, Yun Liu, Xiudong Liao, Tianhong Li
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-13-620

MMpred: functional miRNA – mRNA interaction analyses by miRNA expression prediction
Cited by: 10
Author(s): Przemyslaw Stempor, Michael Cauchi, P. David Wilson
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-14-82

DNA methylation profile dynamics of tissue-dependent and differentially methylated regions during mouse brain development
Cited by: 15
Author(s): Keiji Hirabayashi, Kunio Shiota, Shusuke Yagi
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-019-6283-z

StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis
Cited by: 3
Author(s): Dong‐Won Kang, Hongryul Ahn, Sangseon Lee, Chai-Jin Lee, Jihye Hur, Wi Hoon Jung, Sun Kim
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-12-3

Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis
Cited by: 44
Author(s): Leda Mirbahai, Tim D. Williams, Huiqing Zhan, Zhiyuan Gong, J.K. Chipman
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-13-448

Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar)
Cited by: 92
Author(s): Sofía Morais, Tomé S. Silva, Odete Cordeiro, Pedro M. Rodrigues, D. R. Guy, James E. Bron, John B. Taggart, J. Gordon Bell, Douglas R. Tocher
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-10-596

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis
Cited by: 13
Author(s): Duccio Cavalieri, Enrica Calura, Chiara Romualdi, Emmanuela Marchi, Marijana Radonjić, Ben van Ommen, Michael Müller
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-14-264

Dynamic recruitment of microRNAs to their mRNA targets in the regenerating liver
Cited by: 60
Author(s): Jonathan Schug, Lindsay B. McKenna, G. Brant Walton, Nicholas J. Hand, Sarmistha Mukherjee, Kow Essuman, Zhou Shi, Yan Gao, Karen Markley, Momo Nakagawa, Vasumathi Kameswaran, Anastassios Vourekas, Joshua R. Friedman, Klaus H. Kaestner, Linda E. Greenbaum
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-10-35

Characterization of gene expression profiles for different types of mast cells pooled from mouse stomach subregions by an RNA amplification method
Cited by: 14
Author(s): Soken Tsuchiya, Yuki Tachida, Eri Segi-Nishida, Yasushi Okuno, Shigero Tamba, Gozoh Tsujimoto, Satoshi Tanaka, Yukihiko Sugimoto
Software Mentions: 2
Published: over 17 years ago

10.1186/s12920-018-0414-2

Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk
Cited by: 18
Author(s): Jingpu Zhang, Shuai Zou, Lei Deng
Software Mentions: 2
Published: over 7 years ago

10.1186/1755-8794-3-4

Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma
Cited by: 19
Author(s): Jill C. Rubinstein, Nam Tran, Shuangge Ma, Ruth Halaban, Michael Krauthammer
Software Mentions: 2
Published: over 16 years ago

10.1186/1755-8794-4-73

Quantifying stability in gene list ranking across microarray derived clinical biomarkers
Cited by: 14
Author(s): Sebastian Schneckener, Nilou S Arden, Andreas Schuppert
Software Mentions: 2
Published: over 14 years ago

10.1186/1755-8794-4-57

Identification of transcriptional regulatory networks specific to pilocytic astrocytoma
Cited by: 18
Author(s): Hrishikesh Deshmukh, Jinsheng Yu, Jahangheer Shaik, Tobey J. MacDonald, Arie Perry, Jacqueline E. Payton, David H. Gutmann, Mark A. Watson, Rakesh Nagarajan
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12911-017-0424-6

Orchestrating differential data access for translational research: a pilot implementation
Cited by: 5
Author(s): Marco Brandizi, Olga Melnichuk, Raffael Bild, Florian Kohlmayer, Benedicto Rodriguez-Castro, Helmut Spengler, Klaus A. Kuhn, Wolfgang Kuchinke, Christian Ohmann, Timo Mustonen, Mikael Lindén, Tommi Nyrönen, Ilkka Lappalainen, Alvis Brāzma, Ugis Sarkans
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2180-13-281

Identification of new developmentally regulated genes involved in Streptomyces coelicolorsporulation
Cited by: 18
Author(s): Paola Salerno, Jessica Persson, Giselda Bucca, Emma Laing, Nora Ausmees, Colin P. Smith, Klas Flärdh
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2180-12-22

A comparison of two distinct murine macrophage gene expression profiles in response to Leishmania amazonensisinfection
Cited by: 24
Author(s): Christian M. Probst, Rodrigo A Silva, Juliana Perrone Bezerra de Menezes, Taís Fontoura de Almeida, Ivana Nunes Gomes, Andreia Cristine Dallabona, Luiz Shozo Ozaki, Gregory A. Buck, Daniela Parada Pavoni, Marco Aurélio Krieger, Patrícia Sampaio Tavares Veras
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2180-10-53

Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans
Cited by: 64
Author(s): Sandrine Koechler, Jessica Cleiss-Arnold, Caroline Proux, Odile Sismeiro, Marie‐Agnès Dillies, Florence Goulhen-Chollet, Florence Hommais, Didier Lièvremont, Florence Arsène-Ploetze, Jean‐Yves Coppée, Philippe Bertin
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2202-6-55

Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation
Cited by: 7
Author(s): Maria Sievertzon, Valtteri Wirta, Alex Mercer, Jonas Frisén, Joakim Lundeberg
Software Mentions: 2
Published: almost 21 years ago

10.1186/1471-2210-8-16

Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in Atlantic salmon (Salmo salar L.)
Cited by: 23
Author(s): Pål A. Olsvik, Kai Kristoffer Lie, Eva Mykkeltvedt, Ole Bent Samuelsen, Kjell Petersen, Anne-Kristin Stavrum, Bjørn Tore Lunestad
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2229-13-153

Transcriptome analysis of heat stress response in switchgrass (Panicum virgatumL.)
Cited by: 82
Author(s): Yongfang Li, Yixing Wang, Yuhong Tang, Vijaya Gopal Kakani, Ramamurthy Mahalingam
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2229-11-113

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thalianaseeds
Cited by: 48
Author(s): Peter C. McKeown, Sylvia Laouiellé-Duprat, Pjotr Prins, Philip Wolff, Marc W. Schmid, Mark T.A. Donoghue, Antoine Fort, Dorota Duszynska, Aurélie Comte, Nga T. Lao, Trevor Wennblom, G. Smant, Claudia Köhler, Ueli Grossniklaus, Charles Spillane
Software Mentions: 2
Published: almost 15 years ago

10.1186/1753-6561-5-S2-S10

Managing and querying gene expression data using Curray
Cited by: 3
Author(s): Hasan M. Jamil, Aminul Islam
Software Mentions: 2
Published: about 15 years ago

10.1186/1756-0500-4-157

Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation
Cited by: 10
Author(s): Robab Hakim-Weber, Anne Krogsdam, Claus Jørgensen, Maria Fischer, Andreas Prokesch, Juliane Gertrude Bogner‐Strauß, Stefan R. Bornstein, Jacob B. Hansen, Lise Madsen, Karsten Kristiansen, Zlatko Trajanoski, Hubert Hackl
Software Mentions: 2
Published: about 15 years ago

10.1186/1756-0500-6-72

The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization
Cited by: 2
Author(s): Jaishree Garhyan, Raad Z. Gharaibeh, Stephen J. McGee, Cynthia Gibas
Software Mentions: 2
Published: over 13 years ago

10.1186/1752-0509-8-S2-I1

Data integration in the era of omics: current and future challenges
Cited by: 295
Author(s): David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew E. Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam‐Rudloff, Ana Conesa, Jesper Tegnér
Software Mentions: 2
Published: over 12 years ago

10.1186/1752-0509-8-26

Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions
Cited by: 5
Author(s): Shubhada R. Hegde, Khushbu Pal, Shekhar C. Mande
Software Mentions: 2
Published: over 12 years ago

10.1186/1752-0509-2-36

A logic-based diagram of signalling pathways central to macrophage activation
Cited by: 65
Author(s): Sobia Raza, Kevin A. Robertson, Paul Lacaze, David L. Page, Anton J. Enright, Peter Ghazal, Tom C. Freeman
Software Mentions: 2
Published: about 18 years ago

10.1186/s12918-017-0466-5

Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma
Cited by: 8
Author(s): Xinan Yang, Fangming Tang, Jisu Shin, John M. Cunningham
Software Mentions: 2
Published: over 8 years ago

10.1186/s13040-014-0035-z

Identifying genetic interactions associated with late-onset Alzheimer’s disease
Cited by: 17
Author(s): Charalampos S. Floudas, Nara Um, M. Ilyas Kamboh, M. Michael Barmada, Shyam Visweswaran
Software Mentions: 2
Published: over 11 years ago

10.1093/bioinformatics/btv002

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
Cited by: 11
Author(s): Andrew S. Warren, Cristina Aurrecoechea, Brian P. Brunk, Prerak Desai, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Deborah Hix, Daniel Lawson, Dustin Machi, Chunhong Mao, Michael McClelland, Eric K. Nordberg, Maulik Shukla, Leslie B. Vosshall, Alice R. Wattam, Rebecca Will, Hyun Seung Yoo, Bruno W. S. Sobral
Software Mentions: 2
Published: over 11 years ago

10.1155/2014/170289

Clinic-Genomic Association Mining for Colorectal Cancer Using Publicly Available Datasets
Cited by: 5
Author(s): Fang Liu, Feng Yi, Zhenye Li, Chao Pan, Yuncong Su, Rui Yang, Lei Song, Huilong Duan, Ning Deng
Software Mentions: 2
Published: over 12 years ago

10.1155/2021/8849415

Identification of Multiple Hub Genes and Pathways in Hepatocellular Carcinoma: A Bioinformatics Analysis
Cited by: 8
Author(s): Junwei Liu, Fang Han, Jianyi Ding, Xiaodong Liang, Jie Liu, Dongsheng Huang, Chengwu Zhang
Software Mentions: 2
Published: almost 5 years ago

10.3390/biom9070282

Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray
Cited by: 12
Author(s): Ali Mohamed Alshabi, Basavaraj Vastrad, Ibrahim Ahmed Shaikh, Chanabasayya Vastrad
Software Mentions: 2
Published: almost 7 years ago

10.1002/biot.201100305

Molecular signatures from omics data: From chaos to consensus
Cited by: 103
Author(s): Jaeyun Sung, Yuliang Wang, Sriram Chandrasekaran, Daniela Witten, Nathan D. Price
Software Mentions: 2
Published: about 14 years ago

10.1590/1414-431X2020e10388

Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification
Cited by: 0
Author(s): Lucas Delmonico, John C. Obenauer, Thomas P. Stockfisch, Marcia V. Fournier
Software Mentions: 2
Published: over 5 years ago

10.1186/s13058-015-0539-6

Mouse mammary stem cells express prognostic markers for triple-negative breast cancer
Cited by: 32
Author(s): Kelly Soady, Howard Kendrick, Qiong Gao, Andrew Tutt, Marketa Zvelebil, Liliana Ordonez, Jelmar Quist, David Wei-Min Tan, Clare M. Isacke, Anita Grigoriadis, Matthew J. Smalley
Software Mentions: 2
Published: over 11 years ago

10.1186/bcr3403

Embryonic mammary signature subsets are activated in Brca1 -/- and basal-like breast cancers
Cited by: 47
Author(s): Marketa Zvelebil, Erik Oliemuller, Qiong Gao, Olivia Wansbury, Alan Mackay, Howard Kendrick, Matthew J. Smalley, Jorge S. Reis‐Filho, Beatrice A. Howard
Software Mentions: 2
Published: over 13 years ago

10.1186/bcr2334

Genomic profiling of breast tumours in relation to BRCAabnormalities and phenotypes
Cited by: 131
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Óskar Þór Jóhannsson, Katrín Ólafsdóttir, Margrét Steinarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 2
Published: almost 17 years ago

10.1186/bcr2192

A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer
Cited by: 117
Author(s): Fabien Reyal, Martin H. van Vliet, Nicola J. Armstrong, Hugo M. Horlings, Karin E. de Visser, M Kok, Andrew E. Teschendorff, Stella Mook, Laura van ’t Veer, Carlos Caldas, Rémy Salmon, Marc J. van de Vijver, Lodewyk F.A. Wessels
Software Mentions: 2
Published: over 17 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962