bioconductor: ArrayExpress | Projects

10.3390/molecules23071763

Genome Identification of B-BOX Gene Family Members in Seven Rosacea Species and Their Expression Analysis in Response to Flower Induction in Malus domestica
Cited by: 31
Author(s): Abdullah Shalmani, Shiliang Fan, Peng Jia, Guofang Li, Izhar Muhammad, Youmei Li, Rahat Sharif, Feng Dong, Xia Zuo, Ké Li, Kun-Ming Chen, Mingyu Han
Software Mentions: 2
Published: about 8 years ago

10.1016/j.molmet.2019.03.012

Dietary calories and lipids synergistically shape adipose tissue cellularity during postnatal growth
Cited by: 14
Author(s): Irina Meln, Gretchen Wolff, Thomas Gajek, Johanna Koddebusch, Sarah Lerch, Liza Harbrecht, Wujun Hong, Irem Bayindir‐Buchhalter, Damir Krunic, Hellmut G. Augustin, Alexandros Vegiopoulos
Software Mentions: 2
Published: over 7 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

10.1111/j.1365-2958.2009.06883.x

Role of the heat shock transcription factor, Hsf1, in a major fungal pathogen that is obligately associated with warm-blooded animals
Cited by: 89
Author(s): Susan M. Nicholls, Michelle Leach, Claire L. Priest, Alistair J. P. Brown
Software Mentions: 2
Published: almost 17 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: about 11 years ago

10.1002/1878-0261.12068

Gain-of-function p53 activates multiple signaling pathways to induce oncogenicity in lung cancer cells
Cited by: 13
Author(s): Catherine Vaughan, S. K. Singh, Steven R. Grossman, Brad E. Windle, Sumitra Deb, Sumitra Deb
Software Mentions: 2
Published: over 9 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: over 14 years ago

10.1002/1878-0261.12107

Prognostic and functional role of subtype-specific tumor-stroma interaction in breast cancer
Cited by: 5
Author(s): Giuseppe Merlino, Patrizia Miodini, Maurizio Callari, Francesca D'Aiuto, Vera Cappelletti, Maria Grazia Daidone
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0006447

Mining Biological Pathways Using WikiPathways Web Services
Cited by: 107
Author(s): Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Martijn P. van Iersel, Chris T. Evelo, Bruce R. Conklin
Software Mentions: 2
Published: about 17 years ago

10.15252/msb.20145172

Cell cycle population effects in perturbation studies
Cited by: 103
Author(s): Eoghan O’Duibhir, Philip Lijnzaad, Joris J. Benschop, Tineke L. Lenstra, Dik van Leenen, Marian J. A. Groot Koerkamp, Thanasis Margaritis, Mariël Brok, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 2
Published: over 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: almost 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: almost 17 years ago

10.1371/journal.pone.0230822

Characterization of the fungal community in the canopy air of the invasive plant Ageratina adenophora and its potential to cause plant diseases
Cited by: 7
Author(s): Chinho Lin, Kai Fang, Xing-Fan Dong, Ai-Ling Yang, Yuxuan Li, Hanbo Zhang
Software Mentions: 2
Published: over 6 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: over 12 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: almost 18 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: over 15 years ago

10.1371/journal.pone.0121846

Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes
Cited by: 6
Author(s): Avinash M. Veerappa, Sangeetha Vishweswaraiah, Kusuma Lingaiah, Megha Murthy, Raviraj V. Suresh, Dinesh S. Manjegowda, Nallur B. Ramachandra
Software Mentions: 2
Published: over 11 years ago

10.3390/v4101844

miRNA Profiles of Monocyte-Lineage Cells Are Consistent with Complicated Roles in HIV-1 Restriction
Cited by: 31
Author(s): Jeanne M. Sisk, Janice E. Clements, Kenneth W. Witwer
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0256588

Characterization of microRNA expression in B cells derived from Japanese black cattle naturally infected with bovine leukemia virus by deep sequencing
Cited by: 5
Author(s): Chihiro Ochiai, Sonoko Miyauchi, Yuta Kudo, Yuta Naruke, Syuji Yoneyama, Keisuke Tomita, Leng Dongze, Yusuke Chiba, To-ichi Hirata, Toshihiro Ichijo, Kazuya Nagai, Sota Kobayashi, Shinji Yamada, Hirokazu Hikono, Kenji Murakami
Software Mentions: 2
Published: about 5 years ago

10.12688/wellcomeopenres.13119.2

Using mitoribosomal profiling to investigate human mitochondrial translation
Cited by: 2
Author(s): Fei Gao, Maria Wesołowska, Reuven Agami, Koos Rooijers, Fabricio Loayza‐Puch, Conor Lawless, RN Lightowlers, Z. Chrzanowska-Lightowlers
Software Mentions: 2
Published: over 8 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: about 19 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

10.1371/journal.pone.0230802

Detection of novel coronaviruses in bats in Myanmar
Cited by: 66
Author(s): Marc Valitutto, Ohnmar Aung, Kyaw Yan Naing Tun, Megan E. Vodzak, Dawn Zimmerman, Jennifer H. Yu, Ye Tun Win, Min Thein Maw, Wai Zin Thein, Htay Htay Win, Jasjeet K. Dhanota, Victoria Ontiveros, Brett Smith, Alexandre Tremeau-Brevard, Tracey Goldstein, Christine K. Johnson, Suzan Murray, Jonna A. K. Mazet
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-6-192

Storing, linking, and mining microarray databases using SRS
Cited by: 12
Author(s): Antoine Veldhoven, Don de Lange, Marcel Smid, Victor de Jager, Jan A. Kors, Guido Jenster
Software Mentions: 2
Published: about 21 years ago

10.1371/journal.pone.0225873

Dual oxidase Duox and Toll-like receptor 3 TLR3 in the Toll pathway suppress zoonotic pathogens through regulating the intestinal bacterial community homeostasis in Hermetia illucens L.
Cited by: 17
Author(s): Yaqing Huang, Yongqiang Yu, Shuai Zhan, Jeffery K. Tomberlin, Dian Huang, Minmin Cai, Longyu Zheng, Yu Zhou, Jibin Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/s13071-016-1945-z

Immune and biochemical responses in skin differ between bovine hosts genetically susceptible and resistant to the cattle tick Rhipicephalus microplus
Cited by: 32
Author(s): Alessandra Mara Franzin, Sandra Regina Maruyama, Gustavo García, Rosane Oliveira, José M. C. Ribeiro, Richard P. Bishop, Antônio Augusto Mendes Maia, Daniela D. Moré, Beatriz Rossetti Ferreira, Isabel Kinney Ferreira de Miranda Santos
Software Mentions: 2
Published: over 9 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: almost 12 years ago

10.3389/fmicb.2017.01556

Transcriptomic Analyses Reveal Differential Gene Expression of Immune and Cell Death Pathways in the Brains of Mice Infected with West Nile Virus and Chikungunya Virus
Cited by: 21
Author(s): Stephanie M. Lim, Henk-Jan van den Ham, Minoushka Oduber, Eurydice Martina, Fatiha Zaaraoui-Boutahar, Jeroen M. Roose, Wilfred F. J. van IJcken, Albert D. M. E. Osterhaus, Arno C. Andeweg, Penelope Koraka, Byron Martina
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2020.01314

Network-Based Analysis of OMICs Data to Understand the HIV–Host Interaction
Cited by: 13
Author(s): Sergey Ivanov, Alexey Lagunin, Dmitry Filimonov, O. Tarasova
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.618

Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells
Cited by: 2
Author(s): Virginie Mournetas, Quentin Nunes, Patricia Murray, Christopher M. Sanderson, David G. Fernig
Software Mentions: 2
Published: almost 12 years ago

10.3389/fmicb.2018.01955

Active HHV-6 Infection of Cerebellar Purkinje Cells in Mood Disorders
Cited by: 41
Author(s): Bhupesh K. Prusty, Nitish Gulve, Sheila Govind, G. R. F. Krueger, Julia Feichtinger, Lee Larcombe, Richard Aspinall, Dharam V. Ablashi, Carla Toro
Software Mentions: 2
Published: about 8 years ago

10.3389/fmolb.2021.567730

A Novel Nine Apoptosis-Related Genes Signature Predicting Overall Survival for Kidney Renal Clear Cell Carcinoma and its Associations with Immune Infiltration
Cited by: 13
Author(s): Yi Wang, Yinhao Chen, Bingye Zhu
Software Mentions: 2
Published: over 5 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: almost 16 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

10.3389/fnana.2016.00086

HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development
Cited by: 63
Author(s): Susan Lindsay, Yaobo Xu, Steven Lisgo, Lauren F. Harkin, Andrew J. Copp, Dianne Gerrelli, Gavin J. Clowry, Aysha Talbot, Michael J. Keogh, Jonathan Coxhead, Mauro Santibanez‐Koref, Patrick F. Chinnery
Software Mentions: 2
Published: almost 10 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: about 18 years ago

10.3389/fmicb.2017.02676

Transcriptional Modulation of Penicillin-Binding Protein 1b, Outer Membrane Protein P2 and Efflux Pump (AcrAB-TolC) during Heat Stress Is Correlated to Enhanced Bactericidal Action of Imipenem on Non-typeable Haemophilus influenzae
Cited by: 3
Author(s): Abdessalam Cherkaoui, Seydina M. Diène, Adrien Fischer, Stefano Leo, Patrice François, Jacques Schrenzel
Software Mentions: 2
Published: almost 9 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: about 21 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: over 10 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: about 13 years ago

10.3389/fimmu.2017.00557

Predicting RTS,S Vaccine-Mediated Protection from Transcriptomes in a Malaria-Challenge Clinical Trial
Cited by: 49
Author(s): Robert A. van den Berg, Margherita Coccia, W. Ripley Ballou, Kent E. Kester, Christian F. Ockenhouse, Johan Vekemans, Erik Jongert, Arnaud M. Didierlaurent, Robbert G. van der Most
Software Mentions: 2
Published: over 9 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: over 20 years ago

10.3389/fimmu.2021.686795

Circulating and Synovial Pentraxin-3 (PTX3) Expression Levels Correlate With Rheumatoid Arthritis Severity and Tissue Infiltration Independently of Conventional Treatments Response
Cited by: 10
Author(s): Marie-Astrid Boutet, Alessandra Nerviani, Gloria Lliso-Ribera, Roberto Leone, Marina Sironi, Rebecca Hands, Felice Rivellese, Annalisa Del Prete, Katriona Goldmann, Myles Lewis, Alberto Mantovani, Barbara Bottazzi, Costantino Pitzalis
Software Mentions: 2
Published: over 5 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

10.1186/1471-2121-10-87

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: almost 17 years ago

10.3389/fonc.2020.00645

Protective Role of Decorin in Primary Hepatocellular Carcinoma
Cited by: 19
Author(s): Andrea Reszegi, Zsolt Horváth, Hajnalka Fehér, Barnabás Wichmann, Péter Tátrai, Ilona Kovalszky, Kornélia Baghy
Software Mentions: 2
Published: over 6 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: about 15 years ago

10.3389/fimmu.2017.00932

Tumor Necrosis Factor (TNF) Bioactivity at the Site of an Acute Cell-Mediated Immune Response Is Preserved in Rheumatoid Arthritis Patients Responding to Anti-TNF Therapy
Cited by: 12
Author(s): Rachel Byng-Maddick, Chris Turner, Gabriele Pollara, Matthew Ellis, Naomi Guppy, Lucy Bell, Michael R. Ehrenstein, Mahdad Noursadeghi
Software Mentions: 2
Published: about 9 years ago

10.3389/fphar.2019.00561

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR
Cited by: 53
Author(s): Gopal Pawar, Judith C. Madden, David J. Ebbrell, James W. Firman, Mark T.D. Cronin
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2019.01769

Mechanisms Underlying the Functional Cooperation Between PPARα and GRα to Attenuate Inflammatory Responses
Cited by: 11
Author(s): Nadia Bougarne, Viacheslav Mylka, Dariusz Ratman, Ilse Beck, Jonathan Thommis, Lode De Cauwer, Jan Tavernier, Bart Staels, Claude Libert, Karolien De Bosscher
Software Mentions: 2
Published: about 7 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: almost 19 years ago

10.3389/fphys.2017.00253

Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica
Cited by: 41
Author(s): Shiliang Fan, Dong Zhang, Giampiero Cai, Ming Zhao, Haiqin Wu, Youmei Li, Yongming Shen, Mingyu Han
Software Mentions: 2
Published: over 9 years ago

10.3389/fphys.2017.00753

Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference
Cited by: 9
Author(s): Tingting Zheng, Yueqiong Ni, Jun Li, Billy K. C. Chow, Gianni Panagiotou
Software Mentions: 2
Published: about 9 years ago

10.3389/fpls.2015.01124

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress
Cited by: 16
Author(s): Anne-Antonella Serra, Ivan Couée, David Heijnen, Sophie Michon-Coudouel, Cécile Sulmon, Gwenola Gouesbet
Software Mentions: 2
Published: almost 11 years ago

10.1111/acel.13092

Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver
Cited by: 20
Author(s): Andrew Price, Mohan C. Manjegowda, Jessica Kain, Swetha Anandh, Irina M. Bochkis
Software Mentions: 2
Published: almost 7 years ago

10.3389/fpls.2021.604810

Toward Systematic Understanding of Flower Bud Induction in Apple: A Multi-Omics Approach
Cited by: 10
Author(s): Anton Milyaev, Julian Kofler, Iris Klaiber, Stefan Czemmel, Jens Pfannstiel, Henryk Flachowsky, D. Stefanelli, Magda‐Viola Hanke, J. Wünsche
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2020.587756

A Conserved TCRβ Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection
Cited by: 9
Author(s): Natasha L. Smith, Wiebke Nahrendorf, Catherine Sutherland, Jason P. Mooney, Joanne Thompson, Philip J. Spence, Gillian Cowan
Software Mentions: 2
Published: almost 6 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: 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: almost 16 years ago

10.3389/fpls.2017.01640

RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response
Cited by: 23
Author(s): Arjun Krishnan, Chirag Gupta, Madana M.R. Ambavaram, Andy Pereira
Software Mentions: 2
Published: about 9 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: over 20 years ago

10.1534/g3.111.000836

Genome-wide Fitness Profiles Reveal a Requirement for Autophagy During Yeast Fermentation
Cited by: 24
Author(s): Nina Piggott, Michael A. Cook, Mike Tyers, Vivien Measday
Software Mentions: 2
Published: about 15 years ago

10.1534/g3.117.1133

The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster
Cited by: 35
Author(s): Erik Lavington, Andrew D. Kern
Software Mentions: 2
Published: almost 9 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: almost 8 years ago

10.1534/g3.117.1112

Genome-Wide Characterization of DNA Methylation in an Invasive Lepidopteran Pest, the Cotton Bollworm Helicoverpa armigera
Cited by: 21
Author(s): Christopher M. Jones, Koeng Su Lim, Jason W. Chapman, Chris Bass
Software Mentions: 2
Published: over 8 years ago

10.1016/j.placenta.2010.10.010

Genome-wide expression profile of first trimester villous and extravillous human trophoblast cells
Cited by: 114
Author(s): Richard Apps, Andrew Sharkey, Lucy Gardner, Victoria Male, Matthew Trotter, Nigel Miller, Robyn A. North, Sandra A. Founds, Ashley Moffett
Software Mentions: 2
Published: almost 16 years ago

10.3390/genes8100243

Genetic Association between Amyotrophic Lateral Sclerosis and Cancer
Cited by: 20
Author(s): Y-h. Taguchi, Hsiuying Wang
Software Mentions: 2
Published: about 9 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: over 13 years ago

10.3390/genes10070494

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi
Cited by: 16
Author(s): Maria Immacolata Ferrante, Laura Entrambasaguas, Mathias Johansson, Mats Töpel, Anke Kremp, Marina Montresor, Anna Godhe
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10080608

DNILMF-LDA: Prediction of lncRNA-Disease Associations by Dual-Network Integrated Logistic Matrix Factorization and Bayesian Optimization
Cited by: 16
Author(s): Yan Li, Junyi Li, Naizheng Bian
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10100797

Biological Network Approaches and Applications in Rare Disease Studies
Cited by: 22
Author(s): Peng Zhang, Yuval Itan
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10110864

Meta-Analysis of Polymyositis and Dermatomyositis Microarray Data Reveals Novel Genetic Biomarkers
Cited by: 4
Author(s): Jaeseung Song, Daeun Kim, Juyeon Hong, Go Woon Kim, Junghyun Jung, Se Jin Park, Hee Jung Park, Jong Wha J. Joo, Wonhee Jang
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes11091108

Transcriptomic Analysis Revealed an Emerging Role of Alternative Splicing in Embryonal Tumor with Multilayered Rosettes
Cited by: 1
Author(s): Dina Hesham, Shahenda El‐Naggar
Software Mentions: 2
Published: about 6 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: over 5 years ago

10.1093/pcp/pct178

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants
Cited by: 92
Author(s): Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Yosuke Aoki, Matsuyuki Shirota, Kengo Kinoshita
Software Mentions: 2
Published: almost 13 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

10.1186/1753-6561-5-S2-S10

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

10.1016/j.gdata.2014.03.001

Transcriptomic profiling of cartilage ageing
Cited by: 11
Author(s): Mandy J. Peffers, Xuan Li, Peter Clegg
Software Mentions: 2
Published: almost 12 years ago

10.1093/pcp/pcu183

Triticeae Resources in Ensembl Plants
Cited by: 57
Author(s): Dan Bolser, Arnaud Kerhornou, Brandon Walts, Paul J. Kersey
Software Mentions: 2
Published: almost 12 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: almost 8 years ago

10.3389/fgene.2020.626536

Characterization of Genome-Wide DNA Methylation and Hydroxymethylation in Mouse Arcuate Nucleus of Hypothalamus During Puberty Process
Cited by: 13
Author(s): Yihang Shen, Shasha Zhou, Xiaodong Zhao, Hua Li, Jingyong Sun
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.572284

A Transcriptomics-Based Meta-Analysis Combined With Machine Learning Identifies a Secretory Biomarker Panel for Diagnosis of Pancreatic Adenocarcinoma
Cited by: 13
Author(s): Indu Khatri, Manoj Bhasin
Software Mentions: 2
Published: about 6 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: almost 7 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: over 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

10.3389/fgene.2018.00108

Identification and Validation of a Diagnostic and Prognostic Multi-Gene Biomarker Panel for Pancreatic Ductal Adenocarcinoma
Cited by: 41
Author(s): Hagen Klett, Hannah Fuellgraf, Ella Levit‐Zerdoun, Saskia Hussung, Silke Kowar, Simon Küsters, Peter Bronsert, Martin Werner, Uwe A. Wittel, Ralph Fritsch, Hauke Busch, Melanie Boerries
Software Mentions: 2
Published: over 8 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: almost 16 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: over 18 years ago

10.1186/gb-2007-8-11-r249

MADS-complexes regulate transcriptome dynamics during pollen maturation
Cited by: 87
Author(s): Wim Verelst, David Twell, Stefan de Folter, Richard G. H. Immink, Heinz Saedler, Thomas Münster
Software Mentions: 2
Published: almost 20 years ago

10.1186/gb-2007-8-7-r132

Evolutionary conservation of regulated longevity assurance mechanisms
Cited by: 190
Author(s): Joshua McElwee, Eugene F. Schuster, Eric Blanc, Matthew D. W. Piper, James H. Thomas, Dhaval Patel, Colin Selman, Dominic J. Withers, Janet M. Thornton, Linda Partridge, David Gems
Software Mentions: 2
Published: almost 20 years ago

10.1186/gb-2007-8-7-r150

PHIDIAS: a pathogen-host interaction data integration and analysis system
Cited by: 60
Author(s): Zuoshuang Xiang, Yuan Tian, Yongqun He
Software Mentions: 2
Published: almost 20 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: almost 17 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: almost 13 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/gb-2009-10-1-r5

Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon
Cited by: 39
Author(s): Giselda Bucca, Emma Laing, Vassilis Mersinias, Nicholas E. E. Allenby, Douglas Hurd, Jolyon Holdstock, Volker Brenner, Marcus Harrison, Colin P. Smith
Software Mentions: 2
Published: almost 18 years ago

10.3389/fgene.2021.646297

Omics Multi-Layers Networks Provide Novel Mechanistic and Functional Insights Into Fat Storage and Lipid Metabolism in Poultry
Cited by: 8
Author(s): Farzad Ghafouri, Abolfazl Bahrami, Mostafa Sadeghi, S. R. Miraei-Ashtiani, Maryam Bakherad, Herman W. Barkema, Samantha Larose
Software Mentions: 2
Published: over 5 years ago

10.1186/gb-2009-10-9-r97

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
Cited by: 49
Author(s): James C. Costello, Mehmet Dalkılıç, Scott Beason, Jeff R. Gehlhausen, Rupali P Patwardhan, Sumit Middha, Brian D. Eads, Justen Andrews
Software Mentions: 2
Published: almost 18 years ago

10.3389/fgene.2021.680217

Comparative Genomics Identifies Putative Interspecies Mechanisms Underlying Crbn-Sall4-Linked Thalidomide Embryopathy
Cited by: 1
Author(s): Thayne Woycinck Kowalski, Gabriela Barreto Caldas-Garcia, João Luiz Ellera Gomes, Lucas Rosa Fraga, Lavínia Schüler-Faccini, Mariana Recamonde‐Mendoza, Vanessa Rodrigues Paixão‐Côrtes, Fernanda Sales Luiz Vianna
Software Mentions: 2
Published: over 5 years ago

10.1186/gb-2010-11-12-r124

Large scale comparison of global gene expression patterns in human and mouse
Cited by: 110
Author(s): Xiangqun Zheng-Bradley, Johan Rung, Helen Parkinson, Alvis Brāzma
Software Mentions: 2
Published: almost 17 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962