bioconductor: ArrayExpress | Projects

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: almost 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: about 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: about 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: over 17 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: about 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: over 16 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 13 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: about 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: about 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: over 14 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: over 18 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: almost 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: about 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: over 14 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: almost 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: about 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: almost 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: about 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: about 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: about 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: about 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: about 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: about 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: almost 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: about 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: about 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: over 14 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: almost 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: about 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: about 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: about 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: over 20 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: over 17 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: over 14 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: almost 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: over 14 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: almost 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: about 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: almost 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: almost 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: about 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: about 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: about 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: over 4 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: over 6 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: almost 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: about 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: almost 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: almost 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: over 16 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: about 17 years ago

10.1186/bcr2109

PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Cited by: 25
Author(s): Anna Git, Inmaculada Spiteri, Cherie Blenkiron, Mark J. Dunning, Jessica C. Pole, Suet-Feung Chin, Yanzhong Wang, James Smith, Frederick J. Livesey, Carlos Caldas
Software Mentions: 2
Published: over 17 years ago

10.1186/bcr2256

Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression
Cited by: 46
Author(s): Cecilia Williams, Luísa A. Helguero, Karin Edvardsson, Lars Arne Haldosén, Jan‐Åke Gustafsson
Software Mentions: 2
Published: almost 17 years ago

10.1093/bib/bbw044

Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned
Cited by: 9
Author(s): Gerald Li, Peter Bankhead, Philip D. Dunne, Paul G. O’Reilly, Jacqueline James, Manuel Salto-Tellez, Peter Hamilton, Darragh G. McArt
Software Mentions: 2
Published: over 9 years ago

10.26508/lsa.201900356

Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO
Cited by: 15
Author(s): So Yeon Kwon, Karen A. Massey, Mark A. Watson, Tayab Hussain, Giacomo Volpe, Christopher D. Buckley, Anna Nicolaou, Paul Badenhorst
Software Mentions: 2
Published: about 6 years ago

10.3390/metabo8040084

An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction
Cited by: 12
Author(s): Amornpan Klanchui, Sudarat Dulsawat, Kullapat Chaloemngam, Supapon Cheevadhanarak, Peerada Prommeenate, Asawin Meechai
Software Mentions: 2
Published: about 7 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: over 10 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: over 8 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: over 11 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: almost 15 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: about 18 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: about 16 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: about 13 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: over 5 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: over 7 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 6 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: over 16 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: almost 9 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: over 8 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 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: over 13 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: about 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: about 9 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: over 11 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: about 15 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: about 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: about 11 years ago

10.1007/s00497-015-0261-7

A decade of pollen transcriptomics
Cited by: 113
Author(s): Nicholas Rutley, David Twell
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pbio.0060225

A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth
Cited by: 200
Author(s): Todd P. Michael, Ghislaı̀n Breton, Samuel P. Hazen, Henry D. Priest, Todd C. Mockler, Steve A. Kay, Joanne Chory
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pcbi.1005873

A FAIR guide for data providers to maximise sharing of human genomic data
Cited by: 24
Author(s): Manuel Corpas, Nadezda V. Kovalevskaya, Amanda McMurray, Fiona Nielsen
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1000779

A Quick Guide to Large-Scale Genomic Data Mining
Cited by: 38
Author(s): Curtis Huttenhower, Oliver Hofmann
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pgen.1007440

Antimicrobial peptides modulate long-term memory
Cited by: 45
Author(s): Raquel Barajas-Azpeleta, Jianping Weng, Jason Gill, Ryan Welte, Chris Seidel, Sean A. McKinney, Stephane Dissel, Kausik Si
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1005251

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding
Cited by: 34
Author(s): Xin Xie, Michael J. T. Stubbington, Jesper K. Nissen, Kristian G. Andersen, Daniel Hebenstreit, Sarah A. Teichmann, Alexander G. Betz
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1009297

Dis3L2 regulates cell proliferation and tissue growth through a conserved mechanism
Cited by: 12
Author(s): Benjamin P. Towler, Amy L. Pashler, Hope J. Haime, Katarzyna M. Przybyl, Sandra C. Viegas, Rute G. Matos, Simon Morley, Cecília M. Arraiano, Sarah F. Newbury
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1004288

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip
Cited by: 188
Author(s): Yujia Alina Chan, Maria J. Aristizabal, Phoebe Y. T. Lu, Zongli Luo, Akil Hamza, Michæl S. Kobor, Peter C. Stirling, Philip Hieter
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1000663

Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis
Cited by: 137
Author(s): Aleksandra Erilova, Lynette Brownfield, Vivien Exner, Marisa Rosa, David Twell, Ortrun Mittelsten Scheid, Lars Hennig, Claudia Köhler
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pgen.1002505

Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes
Cited by: 56
Author(s): Josine L. Min, George Nicholson, Ingileif Halgrimsdottir, Kristian Almstrup, Andreas Petri, Amy Barrett, Mary E. Travers, Nigel W. Rayner, Reedik Mägi, Fredrik Pettersson, John Broxholme, Matt J. Neville, Quin F. Wills, Jane Cheeseman, Maxine Allen, Chris Holmes, Tim D. Spector, Jan Fleckner, Mark I. McCarthy, Fredrik Karpe, Cecilia M. Lindgren, Krina T. Zondervan
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pgen.1004684

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability
Cited by: 65
Author(s): Ayesha Hasan, Cristina Cotobal, Caia D. S. Duncan, Juan Mata
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1008837

Control of mRNA translation by dynamic ribosome modification
Cited by: 12
Author(s): Lucia Grenga, Richard Little, Govind Chandra, Stuart Daniel Woodcock, Gerhard Saalbach, Richard J. Morris, Jacob G. Malone
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1004112

Transcriptomics and Functional Genomics of ROS-Induced Cell Death Regulation by RADICAL-INDUCED CELL DEATH1
Cited by: 83
Author(s): Mikael Brosché, Tiina Blomster, Jarkko Salojärvi, Fuqiang Cui, Nina Sipari, Johanna Leppälä, Airi Lamminmäki, Gloria Tomai, Shaman Narayanasamy, Ramesha A. Reddy, Markku Keinänen, Kirk Overmyer, Jaakko Kangasjärvi
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1000161

Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms
Cited by: 186
Author(s): Björn Schumacher, Ingrid van der Pluijm, Michael Moorhouse, Theodoros Kosteas, Andria Rasile Robinson, Yousin Suh, Timo M. Breit, Harry van Steeg, Laura J. Niedernhofer, Wilfred F. J. van IJcken, Andrzej Bartke, Stephen R. Spindler, Jan H.J. Hoeijmakers, Gijsbertus T. J. van der Horst, George A. Garinis
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pgen.1006682

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus
Cited by: 37
Author(s): Anchel de Jaime-Soguero, Francesco Aulicino, Gökhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, María Pía Cosma, Frederic Lluı́s
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1000605

CHD3 Proteins and Polycomb Group Proteins Antagonistically Determine Cell Identity in Arabidopsis
Cited by: 151
Author(s): Ernst Aichinger, Corina Belle R. Villar, Sara Farrona, José Carlos Castañeda Reyes, Lars Hennig, Claudia Köhler
Software Mentions: 2
Published: over 16 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962