bioconductor: ArrayExpress | Projects

10.1186/s40001-018-0328-7

Membrane-bound estrogen receptor alpha initiated signaling is dynamin dependent in breast cancer cells
Cited by: 9
Author(s): István Marczell, Petra Balogh, G Nyírő, Anna L. Kiss, Balázs Kovács, Gábor Békési, Kàroly Rácz, Attila Patócs
Software Mentions: 2
Published: over 7 years ago

10.12688/f1000research.28449.1

Recommendations for the FAIRification of genomic track metadata
Cited by: 7
Author(s): Sveinung Gundersen, Sanjay Boddu, Salvador Capella-Gutierrez, Finn Drabløs, José Marı́a Fernández, Radmila Kompova, Kieron Taylor, Dmytro Titov, Daniel R. Zerbino, Eivind Hovig
Software Mentions: 2
Published: almost 5 years ago

10.12688/f1000research.15119.1

Norwegian e-Infrastructure for Life Sciences (NeLS)
Cited by: 10
Author(s): Kidane Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Zhang Wei, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen
Software Mentions: 2
Published: over 7 years ago

10.1111/febs.15261

Data libraries – the missing element for modeling biological systems
Cited by: 3
Author(s): Anastasia Baryshnikova
Software Mentions: 2
Published: almost 6 years ago

10.1002/2211-5463.12354

The clinical value of miR-193a-3p in non-small cell lung cancer and its potential molecular mechanism exploredin silicousing RNA-sequencing and microarray data
Cited by: 11
Author(s): Xiang Gao, Rongjiang Tang, Qiongni Xie, Jiaying Lin, Hong-lan Shi, Gang Chen, Zu‐Yun Li
Software Mentions: 2
Published: about 8 years ago

10.3389/fbioe.2019.00106

Cyberbiosecurity Challenges of Pathogen Genome Databases
Cited by: 15
Author(s): Boris A. Vinatzer, Lenwood S. Heath, Hussain M. J. Almohri, Michael J. Stulberg, Christopher J. Lowe, Song Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fcvm.2019.00165

Single Cell Analysis of Endothelial Cells Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features
Cited by: 64
Author(s): Wei Feng, Lyuqin Chen, Patricia K. Nguyen, Sean M. Wu, Guang Li
Software Mentions: 2
Published: about 6 years ago

10.3389/fcell.2020.629030

Dynamic Expression of m6A Regulators During Multiple Human Tissue Development and Cancers
Cited by: 8
Author(s): Ya Zhang, Sicong Xu, Gang Xu, Yueying Gao, Si Li, Ke Zhang, Zhanyu Tian, Jing Guo, Xia Li, Juan Xu, Yongsheng Li
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2020.630492

Human Bile Contains Cholangiocyte Organoid-Initiating Cells Which Expand as Functional Cholangiocytes in Non-canonical Wnt Stimulating Conditions
Cited by: 9
Author(s): Floris J.M. Roos, Monique M A Verstegen, Laura Muñoz Albarinos, Henk P. Roest, Jan‐Werner Poley, G. W. M. Tetteroo, Jan N.M. IJzermans, Luc J. W. van der Laan
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2021.642681

Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction
Cited by: 4
Author(s): Þóra Björg Sigmarsdóttir, Sarah McGarrity, James T. Yurkovich, Óttar Rolfsson, Ólafur E. Sigurjónsson
Software Mentions: 2
Published: over 4 years ago

10.3389/fcell.2021.671838

Epigenetic Deregulation of the Histone Methyltransferase KMT5B Contributes to Malignant Transformation in Glioblastoma
Cited by: 6
Author(s): Virginia López, Juan Ramón Tejedor, Antonella Carella, María González García, Pablo Santamarina‐Ojeda, Raúl Fernández Pérez, Cristina Mangas, Rocío G. Urdinguio, A.I. Aranburu, Daniel de la Nava, María D. Corte‐Torres, Aurora Astudillo, Manuela Mollejo, Bárbara Meléndez, Agustín F. Fernández, Mario F. Fraga
Software Mentions: 2
Published: over 4 years ago

10.3389/fcell.2014.00039

Fingerprints of a message: integrating positional information on the transcriptome
Cited by: 1
Author(s): Erik Dassi, Alessandro Quattrone
Software Mentions: 2
Published: over 11 years ago

10.3389/fcell.2017.00012

The Importance of REST for Development and Function of Beta Cells
Cited by: 21
Author(s): David Martín, Anne Grapin-Botton
Software Mentions: 2
Published: almost 9 years ago

10.3389/fncel.2019.00461

Transcranial Current Stimulation Alters the Expression of Immune-Mediating Genes
Cited by: 20
Author(s): Monika Rabenstein, Marcus Unverricht-Yeboah, Meike Hedwig Keuters, Anton Pikhovych, Joerg Hucklenbroich, Sabine Ulrike Vay, Stefan Blaschke, Anne Ladwig, Henrik Walter, Magdalena Beiderbeck, Gereon R. Fink, Michael Schroeter, Ralf Kriehuber, Maria Adele Rueger
Software Mentions: 2
Published: over 6 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

10.3389/fgene.2021.649764

Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study
Cited by: 1
Author(s): Yesid Cuesta-Astroz, Guilherme Gischkow Rucatti, Leandro Murgas, Carol D. SanMartín, Mario Sanhueza, Alberto J. M. Martin
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2021.625797

Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework
Cited by: 4
Author(s): Yiqian Zhang, Michiaki Hamada
Software Mentions: 2
Published: almost 5 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 4 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 4 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: almost 8 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: over 5 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: about 5 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

10.3389/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: about 5 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

10.3389/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: over 6 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: over 8 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 4 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 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: over 10 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: about 8 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: about 8 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: over 8 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 5 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: over 7 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: almost 5 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: over 9 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

10.3389/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: almost 6 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

10.3389/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 6 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: about 16 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

10.1186/1476-4598-10-29

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

10.3389/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: almost 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: over 8 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: about 10 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

10.3389/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: almost 5 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: over 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: over 8 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: 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: 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: over 5 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: almost 8 years ago

10.1111/jcmm.15429

Bioinformatics analysis of the biological changes involved in the osteogenic differentiation of human mesenchymal stem cells
Cited by: 16
Author(s): Tao Fan, Rongmei Qu, Qinghe Yu, Bing Sun, Xin Jiang, Yuchao Yang, Xiaolan Huang, Zhaoxi Zhou, Jun Ouyang, Shizhen Zhang, Jingxing Dai
Software Mentions: 2
Published: over 5 years ago

10.1242/jcs.226969

An essential role for dNTP homeostasis following CDK-induced replication stress
Cited by: 15
Author(s): Chen Chun Pai, Kuo–Feng Hsu, Samuel C. Durley, Andrea Keszthelyi, Stephen Kearsey, Charalampos Rallis, Lisa K. Folkes, Rachel S. Deegan, Sarah E. Wilkins, Sophia X. Pfister, Nagore de León, Christopher J. Schofield, Jürg Bähler, Antony Carr, Timothy C. Humphrey
Software Mentions: 2
Published: about 7 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: over 15 years ago

10.1371/journal.ppat.0010045

Bordetella pertussis, the Causative Agent of Whooping Cough, Evolved from a Distinct, Human-Associated Lineage of B. bronchiseptica
Cited by: 238
Author(s): Dimitri A. Diavatopoulos, Craig Cummings, Leo M. Schouls, Mary M. Brinig, David A. Relman, Frits R. Mooi
Software Mentions: 2
Published: about 20 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

10.1371/journal.ppat.1000105

Anti-Fungal Innate Immunity in C. elegans Is Enhanced by Evolutionary Diversification of Antimicrobial Peptides
Cited by: 215
Author(s): Nathalie Pujol, Olivier Zugasti, Daniel Wong, Carole Couillault, C. Léopold Kurz, Hinrich Schulenburg, Jonathan J. Ewbank
Software Mentions: 2
Published: over 17 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

10.1371/journal.ppat.1002027

Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival
Cited by: 133
Author(s): Hebert Echenique-Rivera, Alessandro Muzzi, Elena Del Tordello, Kate L. Seib, Patrice François, Rino Rappuoli, Mariagrazia Pizza, Davide Serruto
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.ppat.1002046

Transition of Plasmodium Sporozoites into Liver Stage-Like Forms Is Regulated by the RNA Binding Protein Pumilio
Cited by: 88
Author(s): Carina S. S. Gomes-Santos, Joanna A. M. Braks, Miguel Prudêncio, Céline Carret, Ana Gomes, Arnab Pain, Theresa Feltwell, Shahid M. Khan, Andrew P. Waters, Chris J. Janse, Gunnar R. Mair, Maria M. Mota
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.ppat.1004609

Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1
Cited by: 77
Author(s): Luis Apolonia, Reiner Schulz, Tomaž Curk, Paula Rocha, Chad M. Swanson, Torsten Schaller, Jernej Ule, Michael H. Malim
Software Mentions: 2
Published: about 11 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: about 16 years ago

10.1371/journal.ppat.1007729

Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution
Cited by: 16
Author(s): Audrey M. V. Ah‐Fong, Meenakshi S. Kagda, Melania Abrahamian, Howard S. Judelson
Software Mentions: 2
Published: almost 7 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

10.1098/rsos.150402

Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts
Cited by: 21
Author(s): Brett Trost, Catherine A. Moir, Zoe E. Gillespie, Anthony Kusalik, Jennifer A. Mitchell, Christopher H. Eskiw
Software Mentions: 2
Published: over 10 years ago

10.1016/j.redox.2020.101450

Mitochondrial complex I derived ROS regulate stress adaptation in Drosophila melanogaster
Cited by: 37
Author(s): Filippo Scialò, Ashwin Sriram, Rhoda Stefanatos, Ruth V. Spriggs, Samantha H. Y. Loh, L. Miguel Martins, Alberto Sanz
Software Mentions: 2
Published: almost 6 years ago

10.1186/1477-7827-7-94

A cross-study gene set enrichment analysis identifies critical pathways in endometriosis
Cited by: 20
Author(s): Hang Zhao, Qishan Wang, Chen Bai, Kan He, Yuchun Pan
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

10.1186/1471-2164-13-237

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/s12958-015-0088-y

The rat placental renin-angiotensin system - a gestational gene expression study
Cited by: 14
Author(s): Kanchan Vaswani, Hsiu‐Wen Chan, Pali Verma, Marloes Dekker Nitert, Hassendrini N. Peiris, Ryan J Wood-Bradley, James A. Armitage, Gregory E. Rice, Murray D. Mitchell
Software Mentions: 2
Published: over 10 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

10.1093/rheumatology/kez358

Interleukin-36 family dysregulation drives joint inflammation and therapy response in psoriatic arthritis
Cited by: 29
Author(s): Marie-Astrid Boutet, Alessandra Nerviani, Gloria Lliso-Ribera, Davide Lucchesi, Edoardo Prediletto, Giulia Maria Ghirardi, Katriona Goldmann, Myles Lewis, Costantino Pitzalis
Software Mentions: 2
Published: over 6 years ago

10.1186/1939-8433-5-17

The Rice Oligonucleotide Array Database: an atlas of rice gene expression
Cited by: 156
Author(s): Peijian Cao, Ki‐Hong Jung, Daeseok Choi, Daehee Hwang, Jun Zhu, Pamela C. Ronald
Software Mentions: 2
Published: over 13 years ago

10.1038/sdata.2014.11

Genomes and phenomes of a population of outbred rats and its progenitors
Cited by: 28
Author(s): Amelie Baud, Victor Guryev, Oliver Hummel, Martina Johannesson, Amelie Baud, Victor Guryev, Oliver Hummel, Martina Johannesson, Roel Hermsen, Pernilla Stridh, Delyth Graham, Martin W. McBride, Tatiana Foroud, Sophie Caldérari, Margarita Diez, Johan Öckinger, Amennai Daniel Beyeen, Alan Gillett, Nada Abdelmagid, André Ortlieb Guerreiro-Cacais, Maja Jagodic, Jonatan Tuncel, Ulrika Norin, Elisabeth Beattie, Ngan Huynh, William H. Miller, Daniel L. Koller, Imranul Alam, Samreen Falak, Mary Osborne-Pellegrin, Esther Martínez-Membrives, Toni Cañete, Gloria Blázquez, Elia Vicens-Costa, Carme Mont-Cardona, Sira Díaz-Morán, Adolf Tobeña, Diana Zélénika, Kathrin Saar, Giannino Patone, Anja Bauerfeind, Marie-Thérèse Bihoreau, Matthias Heinig, Youngae Lee, Carola Rintisch, Herbert Schulz, David A. Wheeler, Kim C. Worley, Donna M. Muzny, Richard A. Gibbs, Mark Lathrop, Nico Lansu, Pim W. Toonen, Frans Paul Ruzius, Ewart de Bruijn, Heidi Hauser, David J. Adams, Thomas Keane, Santosh S. Atanur, Tim Aitman, Paul Flicek, Tomas Malinauskas, Elizabeth Jones, Diana Ekman, Regina López-Aumatell, Anna F. Dominiczak, Rikard Holmdahl, Tomas Olsson, Dominique Guyader, Norbert Hübner, Alberto Fernández-Teruel, Edwin Cuppen, Richard Mott, Jonathan Flint, Jonathan Flint
Software Mentions: 2
Published: over 11 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

10.1038/sdata.2018.13

Single cell RNA sequencing of stem cell-derived retinal ganglion cells
Cited by: 41
Author(s): Maciej Daniszewski, Anne Senabouth, Quan Nguyen, Duncan E. Crombie, Samuel W. Lukowski, Tejal Kulkarni, Valentin M. Sluch, Jafar S. Jabbari, Xitiz Chamling, Donald J. Zack, Alice Pébay, Joseph E. Powell, Alex W. Hewitt
Software Mentions: 2
Published: almost 8 years ago

10.1038/sdata.2018.158

The REMBRANDT study, a large collection of genomic data from brain cancer patients
Cited by: 101
Author(s): Yuriy Gusev, Krithika Bhuvaneshwar, Lei Song, Jean-Claude Zenklusen, Howard A. Fine, Subha Madhavan
Software Mentions: 2
Published: over 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: about 16 years ago

10.1038/s41597-020-00636-6

Cross-sectional study of human coding- and non-coding RNAs in progressive stages of Helicobacter pylori infection
Cited by: 1
Author(s): Sergio Lario, María José Ramírez‐Lázaro, Aintzane González-Lahera, José L. Lavín, María Vila-Casadesús, María Elisa Quílez, Anna Brunet-Vega, Juan José Lozano, Ana M. Aransay, Xavier Calvet
Software Mentions: 2
Published: over 5 years ago

10.1038/s41597-021-00808-y

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials
Cited by: 17
Author(s): Laura Aliisa Saarimäki, Antonio Federico, Iseult Lynch, Anastasios G. Papadiamantis, Andreas Tsoumanis, Georgia Melagraki, Antreas Afantitis, Angela Serra, Dario Greco
Software Mentions: 2
Published: about 5 years ago

10.1038/srep13113

Human cell dedifferentiation in mesenchymal condensates through controlled autophagy
Cited by: 34
Author(s): Rebecca Rose Pennock, Elen Bray, Paul R. Pryor, Sally James, Paul J. McKeegan, Roger G. Sturmey, Paul G. Genever
Software Mentions: 2
Published: over 10 years ago

10.1038/srep17470

Fine-tuned SRF activity controls asymmetrical neuronal outgrowth: implications for cortical migration, neural tissue lamination and circuit assembly
Cited by: 14
Author(s): Marilyn Scandaglia, Eva Benito, Cruz Morenilla‐Palao, Anna Fiorenza, Beatriz del Blanco, Yaiza Coca, Eloı́sa Herrera, Ángel Barco
Software Mentions: 2
Published: about 10 years ago

10.1038/srep19729

Nucleosome architecture throughout the cell cycle
Cited by: 27
Author(s): Özgen Deniz, Oscar Flores, Martí Aldea, Montserrat Soler-López, Modesto Orozco
Software Mentions: 2
Published: about 10 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

10.3390/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

10.1038/srep31209

Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation
Cited by: 69
Author(s): Marpe Bam, Xiaoming Yang, Elizabeth E. Zumbrun, Zhimin Yin, Juhua Zhou, J. P. Ginsberg, Quinne Leyden, Jiajia Zhang, Prakash Nagarkatti, Mitzi Nagarkatti
Software Mentions: 2
Published: over 9 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

10.1186/1471-2164-8-294

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/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: about 5 years ago

10.1038/srep37988

Global gene regulation during activation of immunoglobulin class switching in human B cells
Cited by: 22
Author(s): Youming Zhang, David Fear, Saffron A.G. Willis‐Owen, William Cookson, Miriam F. Moffatt
Software Mentions: 2
Published: about 9 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: over 20 years ago

10.1038/s41598-017-01141-4

The yeast osmostress response is carbon source dependent
Cited by: 52
Author(s): Roja Babazadeh, Petri‐Jaan Lahtvee, Caroline B. Adiels, Mattias Goksör, Jens Nielsen, Stefan Hohmann
Software Mentions: 2
Published: almost 9 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962