bioconductor: ArrayExpress | Projects

10.1530/ERC-14-0454

HES5 silencing is an early and recurrent change in prostate tumourigenesis
Cited by: 10
Author(s): Charles E. Massie, Inmaculada Spiteri, Helen Ross-Adams, Hayley J. Luxton, Jonathan Kay, Hayley C. Whitaker, Mark J. Dunning, Alastair Lamb, Antonio Ramos-Montoya, Daniel Brewer, Christopher S. Cooper, Rosalind Eeles, _ _, Anne Y. Warren, Simon Tavaré, David E. Neal, Andy G. Lynch
Software Mentions: 2
Published: over 11 years ago

10.1186/s13326-016-0055-3

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates
Cited by: 7
Author(s): Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson, James Malone
Software Mentions: 2
Published: over 10 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/s13072-018-0232-y

Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains
Cited by: 7
Author(s): Hangnoh Lee, Brian Oliver
Software Mentions: 2
Published: almost 8 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

10.1016/j.dib.2017.11.031

Data on novel DNA methylation changes induced by valproic acid in human hepatocytes
Cited by: 3
Author(s): Jarno E J Wolters, SimoneGJ van Breda, Sandra Claessen, T.D. Kok, J.C.S. Kleinjans
Software Mentions: 2
Published: over 8 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

10.1186/2041-1480-5-31

CSEO – the Cigarette Smoke Exposure Ontology
Cited by: 8
Author(s): Erfan Younesi, Sam Ansari, Michaela Guendel, Shiva Ahmadi, Chris R. E. Coggins, Julia Hoeng, Martin Hofmann‐Apitius, Manuel C. Peitsch
Software Mentions: 2
Published: about 12 years ago

10.1186/2041-1480-5-S1-S3

Semantic Web repositories for genomics data using the eXframe platform
Cited by: 7
Author(s): Emily Merrill, Stéphane Corlosquet, Paolo Ciccarese, Tim W. Clark, Sudeshna Das
Software Mentions: 2
Published: over 12 years ago

10.15252/embr.201846222

Budding yeast Rif1 binds to replication origins and protects <scp>DNA</scp> at blocked replication forks
Cited by: 30
Author(s): Shin‐ichiro Hiraga, Chandre Monerawela, Yuki Katou, Sophie Shaw, Kate Rosalind Mary Clark, Katsuhiko Shirahige, Anne Donaldson
Software Mentions: 2
Published: about 8 years ago

10.1136/gutjnl-2017-314817

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
Cited by: 110
Author(s): Judith Kraiczy, Komal Nayak, Kate J. Howell, Alex Ross, Jessica L. Forbester, Camilla Salvestrini, Roxana C. Mustata, Sally Perkins, Amanda Andersson-Rolf, Esther Leenen, Anke Liebert, Ludovic Vallier, Philip Rosenstiel, Oliver Stegle, Gordon Dougan, Robert Heuschkel, Bon–Kyoung Koo, Matthias Zilbauer
Software Mentions: 2
Published: over 8 years ago

10.1007/s11356-017-0515-z

Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments
Cited by: 7
Author(s): Alexandra Brinke, Georg Reifferscheid, Roland Klein, Ute Feiler, Sebastian Buchinger
Software Mentions: 2
Published: almost 9 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

10.1074/jbc.RA118.006865

Translational regulation contributes to the secretory response of chondrocytic cells following exposure to interleukin-1β
Cited by: 10
Author(s): B.T. McDermott, Mandy J. Peffers, Brian McDonagh, Simon R. Tew
Software Mentions: 2
Published: about 7 years ago

10.1155/2020/9015713

Classification of Thyroid Nodules with Stacked Denoising Sparse Autoencoder
Cited by: 3
Author(s): Zexin Li, Kaiji Yang, Lili Zhang, Chiju Wei, Peixuan Yang, Weilai Xu
Software Mentions: 2
Published: over 5 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

10.1093/database/baaa002

GXD’s RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest
Cited by: 2
Author(s): Cyndi M. Smith, James A. Kadin, Richard M. Baldarelli, Jonathan S Beal, Olin Blodgett, Sharon C Giannatto, Joel E. Richardson, Martin Ringwald
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-021-02215-w

Actin cytoskeleton deregulation confers midostaurin resistance in FLT3-mutant acute myeloid leukemia
Cited by: 11
Author(s): Andoni Garitano‐Trojaola, Ana Sancho, Roland Götz, Patrick Eiring, Susanne Walz, Hardikkumar Jetani, Jesus Gil‐Pulido, Matteo Claudio Da Vià, Eva Teufel, Nadine Rhodes, Larissa Haertle, Estibaliz Arellano-Viera, Raoul Tibes, Andreas Rosenwald, Leo Rasche, Michael Hudecek, Markus Sauer, Jürgen Gröll, Hermann Einsele, Sabrina Kraus, Martin Kortüm
Software Mentions: 2
Published: about 5 years ago

10.1093/database/bav019

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis
Cited by: 75
Author(s): Qing Wan, Hayley Dingerdissen, Fan Yu, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Yan Cheng, Haichen Zhang, Raja Mazumder
Software Mentions: 2
Published: over 11 years ago

10.1167/iovs.61.4.24

The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension
Cited by: 13
Author(s): Ilona Liesenborghs, Lars Eijssen, Martina Kutmon, Theo G. M. F. Gorgels, Chris T. Evelo, Henny J. M. Beckers, Carroll A.B. Webers, Jan S.A.G. Schouten
Software Mentions: 2
Published: over 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

10.3390/genes10080608

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

10.3390/genes10100797

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

10.3390/genes10110864

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

10.1093/database/baab043

The Progenetix oncogenomic resource in 2021
Cited by: 8
Author(s): Qingyao Huang, Paula Carrio-Cordo, Bo Gao, Rahel Paloots, Michael Baudis
Software Mentions: 2
Published: over 5 years ago

10.1038/onc.2015.526

A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer
Cited by: 28
Author(s): Anna Moles, Jacqueline Butterworth, Ana M. Sánchez, Jill E. Hunter, Jack Leslie, Hélène Sellier, Dina Tiniakos, Simon Cockell, Derek A. Mann, Fiona Oakley, Neil D. Perkins
Software Mentions: 2
Published: over 10 years ago

10.1038/s41388-018-0588-2

LCE: an open web portal to explore gene expression and clinical associations in lung cancer
Cited by: 70
Author(s): Ling Cai, Shing-Jong Lin, Luc Girard, Yunyun Zhou, Lin Yang, Bo Ci, Qinbo Zhou, Danni Luo, Bo Yao, Jing Tang, Jeffrey D. Allen, Kenneth E. Huffman, Adi F. Gazdar, John V. Heymach, Ignacio I. Wistuba, Guanghua Xiao, John D. Minna, Yang Xie
Software Mentions: 2
Published: over 7 years ago

10.3390/genes11091108

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

10.1016/j.jmb.2020.10.008

TET1 Interacts Directly with NANOG via Independent Domains Containing Hydrophobic and Aromatic Residues
Cited by: 2
Author(s): Raphaël Pantier, Nicholas P. Mullin, Elisa Hall-Ponselé, Ian Chambers
Software Mentions: 2
Published: almost 6 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

10.3892/or.2014.3579

Human cancer databases (Review)
Cited by: 63
Author(s): Athanasia Pavlopoulou, Demetrios Α. Spandidos, Ioannis Michalopoulos
Software Mentions: 2
Published: almost 12 years ago

10.7554/eLife.44344

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
Cited by: 102
Author(s): Christopher D. Todd, Özgen Deniz, Darren Taylor, Miguel R. Branco
Software Mentions: 2
Published: over 7 years ago

10.1093/hmg/ddx424

Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort
Cited by: 72
Author(s): Ana Viñuela, Andrew Anand Brown, Alfonso Buil, Pei-Chien Tsai, Matthew N. Davies, Jordana T. Bell, Emmanouil T. Dermitzakis, Timothy D. Spector, Kerrin S. Small
Software Mentions: 2
Published: over 8 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: over 8 years ago

10.1128/mSystems.00186-16

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria
Cited by: 34
Author(s): Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
Software Mentions: 2
Published: over 9 years ago

10.1128/mSystems.00014-16

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons
Cited by: 28
Author(s): Mia Urem, Teunke van Rossum, Giselda Bucca, Geri F. Moolenaar, Emma Laing, Magda A. Świątek-Połatyńska, Joost Willemse, Elodie Tenconi, Sébastien Rigali, Nora Goosen, Colin P. Smith, Gilles P. van Wezel
Software Mentions: 2
Published: about 10 years ago

10.1128/mSphere.00579-17

The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315
Cited by: 15
Author(s): Sanne Kiekens, Andrea Saß, Filip Van Nieuwerburgh, Dieter Deforce, Tom Coenye
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.12717

Zeb1 controls neuron differentiation and germinal zone exit by a mesenchymal-epithelial-like transition
Cited by: 58
Author(s): Shalini Singh, Danielle Howell, Niraj Trivedi, Ketty Kessler, Taren Ong, Pedro Rosmaninho, Alexandre A.S.F. Raposo, Giles Robinson, Martine F. Roussel, Diogo S. Castro, David J. Solecki
Software Mentions: 2
Published: over 10 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: over 6 years ago

10.7554/eLife.33506

Epidermal LysM receptor ensures robust symbiotic signalling in Lotus japonicus
Cited by: 48
Author(s): Eiichi Murakami, Jeryl Cheng, Kira Gysel, Zoltán Bozsóki, Yasuyuki Kawaharada, Christian T. Hjuler, Kasper K. Sørensen, Ke Tao, Simon Kelly, Francesco Venice, Andrea Genre, Mikkel B. Thygesen, Noor de Jong, Maria Vinther, Dorthe Bødker Jensen, Knud J. Jensen, Mickaël Blaise, Lene Heegaard Madsen, Kasper R. Andersen, Jens Stougaard, Simona Radutoiu
Software Mentions: 2
Published: about 8 years ago

10.1128/mBio.00465-20

Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump
Cited by: 48
Author(s): Elizabeth Grimsey, Chiara Fais, Robert L. Marshall, Vito Ricci, Maria Laura Ciusa, Jack Stone, Alasdair Ivens, Giuliano Malloci, Paolo Ruggerone, Attilio Vittorio Vargiu, Laura J. V. Piddock
Software Mentions: 2
Published: about 6 years ago

10.1093/database/bav099

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases
Cited by: 7
Author(s): Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, A Namasivayam, Matthew J. Page, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.65722

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Cited by: 18
Author(s): Rong Yu, Egor Vorontsov, Carina Sihlbom, Jens Nielsen
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.18715

A computational interactome and functional annotation for the human proteome
Cited by: 59
Author(s): José Ignacio Garzón, Lei Deng, Diana Murray, Sagi Shapira, Donald Petrey, Barry Honig
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.33761

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair
Cited by: 116
Author(s): Nataša Savić, Femke Ringnalda, Helen Lindsay, Christian Berk, Katja Bargsten, Yizhou Li, Dario Neri, Mark D. Robinson, Constance Ciaudo, Jonathan Hall, Martin Jínek, Gerald Schwank
Software Mentions: 2
Published: about 8 years ago

10.15252/embr.201540476

Abo1, a conserved bromodomain <scp>AAA</scp> ‐ <scp>ATP</scp> ase, maintains global nucleosome occupancy and organisation
Cited by: 20
Author(s): Csenge Gal, Heather E. Murton, Lakxmi Subramanian, Alex J. Whale, Karen Moore, Konrad Paszkiewicz, Sandra Codlin, Jürg Bähler, Kevin M. Creamer, Janet F. Partridge, Robin C. Allshire, Nicholas A. Kent, Simon K. Whitehall
Software Mentions: 2
Published: over 10 years ago

10.1186/s13148-020-00884-8

meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes
Cited by: 19
Author(s): Diana‐Maria Ciuculete, Sarah Voisin, Lara Kular, Jan‐Ingvar Jönsson, Mathias Rask‐Andersen, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 2
Published: about 6 years ago

10.1093/database/baaa111

MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle
Cited by: 2
Author(s): Olof Asplund, Johan Rung, Leif Groop, Rashmi B. Prasad, Ola Hansson
Software Mentions: 2
Published: over 6 years ago

10.1128/mBio.00966-18

cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization
Cited by: 41
Author(s): Jainaba Manneh-Roussel, James R. J. Haycocks, Andrés Magán, Nicolás Pérez-Soto, Kerstin Voelz, Andrew Camilli, Anne Marie Krachler, David C. Grainger
Software Mentions: 2
Published: almost 8 years ago

10.1093/database/bax069

IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes
Cited by: 0
Author(s): I-Man Ng, Jia-Hsin Huang, Shang-Chi Tsai, Huai-Kuang Tsai
Software Mentions: 2
Published: over 9 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

10.3390/ijms141123160

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System
Cited by: 4
Author(s): Paolo Martini, Gabriele Sales, Enrica Calura, Mattia Brugiolo, Gerolamo Lanfranchi, Chiara Romualdi, Stefano Cagnin
Software Mentions: 2
Published: over 12 years ago

10.3390/ijms151017601

Hope for GWAS: Relevant Risk Genes Uncovered from GWAS Statistical Noise
Cited by: 2
Author(s): Catarina Correia, Yoan Diekmann, Astrid M. Vicente, José B. Pereira-Leal
Software Mentions: 2
Published: almost 12 years ago

10.3390/ijms161226148

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders
Cited by: 41
Author(s): Martin Hofmann-Apitius, G. Ball, Stephan Gebel, Shweta Bagewadi, Bernard de Bono, Reinhard Schneider, Matt Page, Alpha Tom Kodamullil, Erfan Younesi, Christian Ebeling, Jesper Tegnér, Luc Canard
Software Mentions: 2
Published: over 10 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: about 8 years ago

10.1016/j.jacbts.2020.09.010

Cardiorenal Tissues Express SARS-CoV-2 Entry Genes and Basigin (BSG/CD147) Increases With Age in Endothelial Cells
Cited by: 30
Author(s): Blerina Ahmetaj‐Shala, Ricky Vaja, Santosh S. Atanur, Peter M. George, Nicholas S. Kirkby, Jane A. Mitchell
Software Mentions: 2
Published: almost 6 years ago

10.1093/database/bau030

'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences
Cited by: 18
Author(s): Julio C. Bolívar, Fabian Machens, Yuri Brill, Artyom Romanov, Lorenz Bülow, Reinhard Hehl
Software Mentions: 2
Published: over 12 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: over 5 years ago

10.3390/ijms20194740

The CXCR4–CXCL12-Axis Is of Prognostic Relevance in DLBCL and Its Antagonists Exert Pro-Apoptotic Effects In Vitro
Cited by: 13
Author(s): Katrin Pansy, Julia Feichtinger, Barbara Ehall, Barbara Uhl, Miriam Sedej, David Roula, Beata Pursche, Axel Wolf, Manuel Zoidl, Elisabeth Steinbauer, Verena Gruber, Hildegard Greinix, Katharina Prochazka, Gerhard G. Thallinger, Ákos Heinemann, Christine Beham–Schmid, Peter Neumeister, Tanja Wrodnigg, Karoline Fechter, Alexander Deutsch
Software Mentions: 2
Published: almost 7 years ago

10.1038/s42003-018-0215-3

Sox9 regulates cell state and activity of embryonic mouse mammary progenitor cells
Cited by: 11
Author(s): Naoko Kogata, Philip Bland, Mandy Tsang, Erik Oliemuller, Anne Lowe, Beatrice A. Howard
Software Mentions: 2
Published: over 7 years ago

10.1093/database/baz149

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans
Cited by: 34
Author(s): L. Basten Snoek, M.G. Sterken, Margi Hartanto, Albert-Jan van Zuilichem, J.E. Kammenga, Dick de Ridder, Harm Nijveen
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-018-0554-4

PRC2 targeting is a therapeutic strategy for EZ score defined high-risk multiple myeloma patients and overcome resistance to IMiDs
Cited by: 32
Author(s): Laurie Herviou, Alboukadel Kassambara, Stéphanie Boireau, Robert Naeije, Guilhem Requirand, Carsten Müller‐Tidow, Laure Vincent, Anja Seckinger, Hartmut Goldschmidt, Guillaume Cartron, Dirk Hose, Giacomo Cavalli, Jérôme Moreaux
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.csbj.2015.10.005

Blood transcriptomics and metabolomics for personalized medicine
Cited by: 66
Author(s): Shuzhao Li, Andrei Todor, Ruiyan Luo
Software Mentions: 2
Published: over 10 years ago

10.1016/j.ydbio.2011.03.003

A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation
Cited by: 3
Author(s): Christopher Sugden, Scott R. Ross, Sarah J. Annesley, Christian Callebaut, Gareth Bloomfield, Alasdair Ivens, Jason Skelton, Paul R. Fisher, Geoffrey J. Barton, Jeffrey Williams
Software Mentions: 2
Published: over 15 years ago

10.1186/s13148-019-0691-4

DNA methylation changes that precede onset of dysplasia in advanced sessile serrated adenomas
Cited by: 15
Author(s): Cheng Liu, Mark Bettington, Neal I. Walker, Joel Dwine, Barbara A. Leggett, Vicki Whitehall
Software Mentions: 2
Published: about 7 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

10.1016/j.devcel.2016.12.023

Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline
Cited by: 72
Author(s): Mahesh N. Sangrithi, Hélène Royo, Shantha K. Mahadevaiah, Obah A. Ojarikre, Leena Bhaw, Abdul Karim Sesay, Antoine H.F.M. Peters, Michael Stadler, James M. A. Turner
Software Mentions: 2
Published: over 9 years ago

10.1186/s12976-015-0017-y

PDON: Parkinson’s disease ontology for representation and modeling of the Parkinson’s disease knowledge domain
Cited by: 27
Author(s): Erfan Younesi, Ashutosh Malhotra, Michaela Gündel, Philip Scordis, Alpha Tom Kodamullil, Matt Page, Burkhard Müller, Stephan Springstubbe, Ullrich Wüllner, D. Scheller, Martin Hofmann‐Apitius
Software Mentions: 2
Published: almost 11 years ago

10.2147/SCCAA.S237361

Informatics Approaches for Harmonized Intelligent Integration of Stem Cell Research
Cited by: 4
Author(s): Joseph Finkelstein, Irena Parvanova, Frederick Zhang
Software Mentions: 2
Published: over 6 years ago

10.1242/dev.157081

Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network
Cited by: 38
Author(s): Simon Scofield, Alex Murison, Angharad Jones, John A. Fozard, Mitsuhiro Aida, Leah R. Band, Malcolm J. Bennett, James A. H. Murray
Software Mentions: 2
Published: over 8 years ago

10.1002/stem.2294

Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency
Cited by: 16
Author(s): Giulia Veluscek, Yaoyong Li, Shen-Hsi Yang, Andrew D. Sharrocks
Software Mentions: 2
Published: over 10 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

10.1007/s00125-020-05107-6

Metabolic alterations in immune cells associate with progression to type 1 diabetes
Cited by: 37
Author(s): Partho Sen, Alex M. Dickens, M.A. López-Bascón, Tuomas Lindeman, Esko Kemppainen, Santosh Lamichhane, Tuukka Rönkkö, Jorma Ilonen, Jorma Toppari, Riitta Veijola, Heikki Hyöty, Tuulia Hyötyläinen, Mikael Knip, Matej Orešič
Software Mentions: 2
Published: over 6 years ago

10.3390/nu11030639

Key Genes of Lipid Metabolism and WNT-Signaling Are Downregulated in Subcutaneous Adipose Tissue with Moderate Weight Loss
Cited by: 9
Author(s): Ruth Schübel, Disorn Sookthai, Judith Greimel, Theron Johnson, Mirja Grafetstätter, Romy Kirsten, Mario Kratz, Cornelia M. Ulrich, Rudolf Kaaks, Tilman Kühn
Software Mentions: 2
Published: over 7 years ago

10.18632/aging.203406

Autophagic flux in cancer cells at the invasive front in the tumor-stroma border
Cited by: 6
Author(s): Fei Yan, Xuexi Zhang, Rongying Tan, Mingchen Li, Zengtuan Xiao, Hao Wang, Zhenfa Zhang, Zhenyi Ma, Liu Zhe
Software Mentions: 2
Published: almost 5 years ago

10.1111/acel.12676

Age‐associated dysregulation of protein metabolism in the mammalian oocyte
Cited by: 80
Author(s): Francesca E. Duncan, Susmita Jasti, Ariel Paulson, John M. Kelsh, Barbara Fegley, Jennifer L. Gerton
Software Mentions: 2
Published: almost 9 years ago

10.1111/acel.13092

Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver
Cited by: 20
Author(s): Andrew Price, Mohan C. Manjegowda, Jessica Kain, Swetha Anandh, Irina M. Bochkis
Software Mentions: 2
Published: over 6 years ago

10.1007/s10456-015-9488-z

ADAMTS3 activity is mandatory for embryonic lymphangiogenesis and regulates placental angiogenesis
Cited by: 73
Author(s): Lauriane Janssen, Laura Dupont, Mourad Bekhouche, Agnès Noël, Cédric Leduc, Marianne Voz, Bernard Peers, Didier Cataldo, Suneel S. Apte, Johanne Dubail, Alain Colige
Software Mentions: 2
Published: almost 11 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

10.3390/antiox5010001

Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression
Cited by: 6
Author(s): Shreya Menon, Chunxia Lü, Rajasree Menon, Jessica Schwartz, Yuanfang Guan
Software Mentions: 2
Published: over 10 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

10.1186/1471-2105-6-192

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/s12859-015-0519-y

Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity
Cited by: 17
Author(s): Xindong Zhang, Lin Gao, Zhiping Liu, Luonan Chen
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-014-0383-1

Efficient prediction of human protein-protein interactions at a global scale
Cited by: 31
Author(s): Andrew Schoenrock, Bahram Samanfar, Sylvain Pitre, M. A. Hooshyar, Ke Jin, Charles Phillips, Hui Wang, Sadhna Phanse, Katayoun Omidi, Yuan Gui, Alamgir, Alex Wong, Fredrik Barrenäs, Mohan Babu, Mikael Benson, Michael A. Langston, James R. Green, Frank Dehne, Ashkan Golshani
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-13-S1-S8

Argudas: lessons for argumentation in biology based on a gene expression use case
Cited by: 2
Author(s): Kenneth McLeod, Gus Ferguson, Albert Burger
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-6-S4-S14

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

10.1186/1471-2105-6-101

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

10.1186/1471-2105-6-264

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
Cited by: 33
Author(s): David G. Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, Andrew J. Wood, Karim Nashar, Douglas B. Kell, Andy Brass
Software Mentions: 2
Published: almost 21 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

10.1186/1471-2105-7-190

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

10.1186/1471-2105-11-576

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

10.1186/1471-2105-8-S1-S21

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

10.1186/1471-2105-13-335

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

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962