bioconductor: ArrayExpress | Projects

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: almost 21 years ago

10.1371/journal.pone.0244755

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya
Cited by: 8
Author(s): Samuel Mwangangi Muturi, Lucy Muthui, Paul Njogu, Justus M. Onguso, Francis N. Wachira, Stephen O. Opiyo, Roger Pellé
Software Mentions: 2
Published: over 5 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

10.1371/journal.pone.0034158

Coexpression of Nuclear Receptors and Histone Methylation Modifying Genes in the Testis: Implications for Endocrine Disruptor Modes of Action
Cited by: 18
Author(s): Alison Anderson, Kim W. Carter, Denise Anderson, Michael J. Wise
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0166520

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii
Cited by: 38
Author(s): Shahid Manzoor, Erik Bongcam‐Rudloff, Anna Schnürer, Bettina Müller
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0166991

dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees
Cited by: 2
Author(s): Michael J. Wise
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0236424

Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock
Cited by: 22
Author(s): Birsen Aydemir, Canan Yüksel Özmen, Umut Kibar, Filiz Mutaf, Pelin Burcu Büyük, Melike Bakır, Ali Ergül
Software Mentions: 2
Published: about 6 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: over 18 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: over 11 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: about 7 years ago

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

10.1371/journal.pone.0159934

Nutritional Evaluation of an EPA-DHA Oil from Transgenic Camelina sativa in Feeds for Post-Smolt Atlantic Salmon (Salmo salar L.)
Cited by: 63
Author(s): Mónica B. Betancor, Matthew Sprague, Olga Sayanova, Sarah Usher, Christoforos Metochis, Patrick Campbell, Johnathan A. Napier, Douglas R. Tocher
Software Mentions: 2
Published: about 10 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/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

10.3390/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: almost 6 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

10.3390/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/genes10100797

Biological Network Approaches and Applications in Rare Disease Studies
Cited by: 22
Author(s): Peng Zhang, Yuval Itan
Software Mentions: 2
Published: almost 7 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: about 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: almost 9 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: over 19 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: over 19 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: over 19 years ago

10.1371/journal.pone.0181365

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice
Cited by: 6
Author(s): Olusegun Oshota, Max Conway, María Fookes, Fernanda Schreiber, Roy R. Chaudhuri, Lu Yu, Fiona J. E. Morgan, Simon Clare, Jyoti S. Choudhary, Nicholas R. Thomson, Píetro Lió, Duncan J. Maskell, Pietro Mastroeni, A. Grant
Software Mentions: 2
Published: about 9 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

10.15252/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: about 12 years ago

10.1371/journal.pone.0237245

Increasing temperature can modify the effect of straw mulching on soil C fractions, soil respiration, and microbial community composition
Cited by: 10
Author(s): Xin Fu, Jun Wang, Meng-Yi Xie, Fazhu Zhao, Russell Doughty
Software Mentions: 2
Published: about 6 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: about 7 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/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: over 17 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: almost 9 years ago

10.1371/journal.pone.0243065

Differential plasma exosomal long non-coding RNAs expression profiles and their emerging role in E-cigarette users, cigarette, waterpipe, and dual smokers
Cited by: 16
Author(s): Gagandeep Kaur, K. R. P. Singh, Krishna Prahlad Maremanda, Dongmei Li, Hitendra S. Chand, Irfan Rahman
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: over 17 years ago

10.1371/journal.pone.0044800

Mining Gene Expression Signature for the Detection of Pre-Malignant Melanocytes and Early Melanomas with Risk for Metastasis
Cited by: 21
Author(s): Cláudia Souza, Patrícia Xander, Ana Carolina Monteiro, Amanda Gonçalves dos Santos Silva, Débora Castanheira Pereira da Silva, Sabine Mai, Viviane Bernardo, José Daniel Lopes, Miriam Galvonas Jasiulionis
Software Mentions: 2
Published: almost 14 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: almost 6 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: over 16 years ago

10.1186/gb-2010-11-12-r125

Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
Cited by: 83
Author(s): Peter L. Chang, Brian P. Dilkes, Michelle M. McMahon, Luca Comai, Sergey V. Nuzhdin
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0058992

Spatio-Temporal Expression Patterns of Arabidopsis thaliana and Medicago truncatula Defensin-Like Genes
Cited by: 55
Author(s): Mesfin Tesfaye, Kevin A.T. Silverstein, Sumitha Nallu, Lin Wang, Christopher Botanga, S. Karen Gomez, Liliana M. Costa, Maria J. Harrison, Deborah A. Samac, Jane Glazebrook, Fumiaki Katagiri, José Gutierrez-Marcos, Kathryn A. VandenBosch
Software Mentions: 2
Published: over 13 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

10.1186/s12943-020-01217-2

LINC00173.v1 promotes angiogenesis and progression of lung squamous cell carcinoma by sponging miR-511-5p to regulate VEGFA expression
Cited by: 85
Author(s): Jia‐Rong Chen, Aibin Liu, Zhihui Wang, Bin Wang, Xingxing Chai, Wenjie Lu, Ting Cao, Ronggang Li, Mingyan Wu, Zhuming Lu, Wei Pang, Lin Xiao, Xiangmeng Chen, Yan Zheng, Qiong Chen, Jincheng Zeng, Jun Li, Xin Zhang, Dong Ren, Yanming Huang
Software Mentions: 2
Published: about 6 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

10.1186/1755-8794-3-4

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

10.1371/journal.pone.0241098

Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis
Cited by: 7
Author(s): Prateek Dey, Sanjeev Kumar Sharma, Indrani Sarkar, Swapna Devi Ray, Padmanabhan Pramod, Venkata Hanumat Sastry Kochiganti, Goldin Quadros, Saurabh Singh Rathore, Vikram Singh, Ram Pratap Singh
Software Mentions: 2
Published: over 5 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: almost 15 years ago

10.1186/gb-2012-13-8-r67

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Cited by: 197
Author(s): Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule
Software Mentions: 2
Published: over 14 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/gb-2014-15-1-r14

Dissecting the expression landscape of RNA-binding proteins in human cancers
Cited by: 195
Author(s): Bobak D. Kechavarzi, Sarath Chandra Janga
Software Mentions: 2
Published: over 12 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: almost 15 years ago

10.1186/gb-2013-14-12-r138

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution
Cited by: 43
Author(s): Dina Raats, Zeev Frenkel, Tamar Krugman, Itay Dodek, Hanan Sela, Hana Šimková, Federica Magni, Federica Cattonaro, Sonia Vautrin, Hélène Bergès, Thomas Wicker, Beat Keller, Philippe Leroy, Romain Philippe, Etienne Paux, Jaroslav Doležel, Catherine Feuillet, Abraham B. Korol, Tzion Fahima
Software Mentions: 2
Published: over 13 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: almost 9 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: almost 14 years ago

10.1186/1471-2105-10-214

Construction and use of gene expression covariation matrix
Cited by: 3
Author(s): Jérôme Hennetin, Petri Pehkonen, Michel Bellis
Software Mentions: 2
Published: about 17 years ago

10.1186/gb-2014-15-4-r62

Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes
Cited by: 54
Author(s): Huan Shu, Miyuki Nakamura, Alexey Siretskiy, Loris Borghi, Izabel Cristina Freitas Moraes, Thomas Wildhaber, Wilhelm Gruissem, Lars Hennig
Software Mentions: 2
Published: over 12 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

10.12688/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: almost 19 years ago

10.1186/1476-4598-12-130

miR-125b targets erythropoietin and its receptor and their expression correlates with metastatic potential and ERBB2/HER2 expression
Cited by: 74
Author(s): Manuela Ferracin, Cristian Bassi, Massimo Pedriali, Sara Pagotto, Lucilla D’Abundo, Barbara Zagatti, Fabio Corrà, Gentian Musa, Elisa Callegari, Laura Lupini, Stefano Volpato, Patrizia Querzoli, Massimo Negrini
Software Mentions: 2
Published: over 13 years ago

10.1186/1476-4598-9-115

Determination of genes and microRNAs involved in the resistance to fludarabine in vivo in chronic lymphocytic leukemia
Cited by: 73
Author(s): Etienne Moussay, Valérie Palissot, Laurent Vallar, Hélène Poirel, Thomas Wenner, Victoria El Khoury, Nasséra Aouali, Kris Van Moer, Bernadette Leners, François Bernardin, Arnaud Muller, Pascale Cornillet‐Lefèbvre, Alain Delmer, Caroline Duhem, F. Ries, Eric Van Dyck, Guy Berchem
Software Mentions: 2
Published: over 16 years ago

10.1186/s13059-015-0719-9

Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer
Cited by: 42
Author(s): Sehrish Rafique, Jeremy Thomas, Duncan Sproul, Wendy A. Bickmore
Software Mentions: 2
Published: about 11 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: over 10 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: almost 9 years ago

10.1186/s13059-016-0957-5

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
Cited by: 62
Author(s): Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew N. J. McKenzie, Ruddy Montandon, Oliver Billker, Steven Woodhouse, Pietro Cicuta, Mario Nicodemi, Sarah A. Teichmann
Software Mentions: 2
Published: over 10 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: about 15 years ago

10.1371/journal.pone.0249757

Genome-wide identification and expression analysis of late embryogenesis abundant protein-encoding genes in rye (Secale cereale L.)
Cited by: 7
Author(s): Mengyue Ding, Lijian Wang, Weimin Zhan, Guanghua Sun, Xiaolin Jia, Shizhan Chen, Wusi Ding, Jianping Yang
Software Mentions: 2
Published: over 5 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

10.3389/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

10.1186/1476-4598-7-6

Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile
Cited by: 69
Author(s): Ingrid Cifola, Roberta Spinelli, Luca Beltrame, Clelia Peano, Ester Fasoli, Stefano Ferrero, Silvano Bòsari, Stefano Signorini, Francesco Rocco, R Perego, Vanessa Proserpio, Francesca Raimondo, Paolo Mocarelli, Cristina Battaglia
Software Mentions: 2
Published: over 18 years ago

10.1186/s13059-016-1070-5

Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Cited by: 1,710
Author(s): Étienne Becht, Nicolás A. Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Sèlves, Pierre Laurent‐Puig, Catheriné Sautès-Fridman, Wolf H. Fridman, Aurélien de Reyniès
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2004-5-9-r69

Cited by: 199
Author(s): Jingjing Wang, Laura Kean, Jingli Yang, Adrian K. Allan, Shireen A. Davies, Paweł Herzyk, Julian A. T. Dow
Software Mentions: 2
Published: over 22 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

10.1186/s13059-017-1338-4

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses
Cited by: 34
Author(s): Joseph L. Costello, Christopher J. Kershaw, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Simon J. Hubbard, Graham D. Pavitt
Software Mentions: 2
Published: almost 9 years ago

10.1186/1476-4598-10-29

miR-449 inhibits cell proliferation and is down-regulated in gastric cancer
Cited by: 199
Author(s): Tony Bou Kheir, Ewa Futoma-Kazmierczak, Anders Jacobsen, Anders Krogh, Linda Bardram, Christoffer Hother, Kirsten Grønbæk, Birgitte Federspiel, Anders H. Lund, Lennart Friis‐Hansen
Software Mentions: 2
Published: over 15 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

10.1186/1752-0509-8-26

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

10.1186/1471-2105-10-409

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

10.3389/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: about 7 years ago

10.1093/molbev/msu226

Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila
Cited by: 51
Author(s): Carlo G. Artieri, Hunter B. Fraser
Software Mentions: 2
Published: about 12 years ago

10.1186/s13229-017-0136-x

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder—implications of a copy number variation involving DPP10
Cited by: 12
Author(s): A. Mak, Annie Ting Gee Chiu, Gordon Leung, Christopher Chun Yu Mak, Yoyo Wing Yiu Chu, Gary Tsz Kin Mok, Wing Fai Tang, Kelvin Y.K. Chan, Mary Hoi Yin Tang, Elizabeth Tak-Kwong Lau Yim, Kin Wai So, Victoria Qinchen Tao, Cheuk Wing Fung, Virginia Wong, Mohammed Uddin, So Lun Lee, Christian R. Marshall, Stephen W. Scherer, Anita Sik Yau Kan, Brian Hon Yin Chung
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0200004

Activation of Nrf2 in the liver is associated with stress resistance mediated by suppression of the growth hormone-regulated STAT5b transcription factor
Cited by: 36
Author(s): John P. Rooney, Keiyu Oshida, Naresh Vasani, Beena Vallanat, Natalia Ryan, Brian N. Chorley, Xuting Wang, Douglas A. Bell, Kai Wu, Lauren M. Aleksunes, Curtis D. Klaassen, Thomas W. Kensler, J. Christopher Corton
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0232972

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet
Cited by: 17
Author(s): Lei Chen, Liangyu Zhang, Wendong Wang, Wei Qiu, Lei Liu, Anhong Ning, Jing Cao, Min Huang, Ming-Chao Zhong
Software Mentions: 2
Published: about 6 years ago

10.1093/gbe/evz103

The Role of Chromatin Accessibility in cis-Regulatory Evolution
Cited by: 14
Author(s): Pei-Chen Peng, Pierre Khoueiry, Charles Girardot, James P. Reddington, David Garfield, Eileen E. M. Furlong, Saurabh Sinha
Software Mentions: 2
Published: about 7 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

10.1186/1471-2164-14-922

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

10.3389/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/s13073-014-0097-z

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer’s disease
Cited by: 7
Author(s): Ashutosh Malhotra, Erfan Younesi, Shweta Bagewadi, Martin Hofmann‐Apitius
Software Mentions: 2
Published: over 11 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/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

10.3389/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: almost 8 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

10.3389/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: about 6 years ago

10.1371/journal.pone.0235551

An iron-dependent metabolic vulnerability underlies VPS34-dependence in RKO cancer cells
Cited by: 7
Author(s): M.J. Kobylarz, Jonathan M. Goodwin, Kang Zhao, John W. Annand, Sarah Hevi, Ellen O’Mahony, Gregory McAllister, John S. Reece‐Hoyes, Qiong Wang, John Alford, Carsten Russ, Alicia Lindeman, Martin Beibel, Guglielmo Roma, Walter Carbone, Judith Knehr, Joseph Loureiro, Christophe Antczak, Dmitri Wiederschain, Leon O. Murphy, Suchithra Menon, Beat Nyfeler
Software Mentions: 2
Published: almost 6 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: almost 9 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: over 8 years ago

10.1136/annrheumdis-2017-212603

Stratification of knee osteoarthritis: two major patient subgroups identified by genome-wide expression analysis of articular cartilage
Cited by: 82
Author(s): Jamie Soul, Sara Dunn, Sanjay Anand, Ferdinand Serracino‐Inglott, Jean-Marc Schwartz, Raymond P. Boot-Handford, Timothy E. Hardingham
Software Mentions: 2
Published: over 8 years ago

10.1007/s11306-015-0810-y

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
Cited by: 122
Author(s): Reza M. Salek, Steffen Neumann, Daniel Schober, Jan Hummel, Kenny Billiau, Joachim Kopka, Elon Correa, Theo H. Reijmers, Antonio Rosato, Leonardo Tenori, Paola Turano, Silvia Marín, Catherine Deborde, Daniel Jacob, Dominique Rolin, Benjamin Dartigues, Pablo Conesa, Kenneth Haug, Philippe Rocca-Serra, Steve O’Hagan, Jie Hao, Michael Van Vliet, Marko Sysi-Aho, Christian Ludwig, Jildau Bouwman, Marta Cascante, Timothy M. D. Ebbels, Julian L. Griffin, Annick Moing, Macha Nikolski, Matej Orešič, Susanna-Assunta Sansone, Mark R. Viant, Royston Goodacre, Ulrich L. Günther, Thomas Hankemeier, Claudio Luchinat, Dirk Walther, Christoph Steinbeck
Software Mentions: 2
Published: about 11 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: about 9 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: about 5 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962