bioconductor: ArrayExpress | Projects

10.1186/gb-2014-15-1-r14

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

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

10.1186/gb-2014-15-4-r62

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

10.1186/s13059-015-0719-9

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

10.1186/gb-2004-5-9-r69

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

10.1186/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: over 8 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: almost 7 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

10.1136/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

10.1016/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: over 5 years ago

10.1172/jci.insight.140785

Neonatal hyperoxia inhibits proliferation and survival of atrial cardiomyocytes by suppressing fatty acid synthesis
Cited by: 15
Author(s): Ethan D. Cohen, Min Yee, George A. Porter, Erin E Ritzer, Andrew McDavid, Paul S. Brookes, Gloria S. Pryhuber, Michael A. O’Reilly
Software Mentions: 2
Published: about 5 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: over 6 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

10.1186/2041-1480-5-31

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: almost 12 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: about 10 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: about 10 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

10.1186/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: over 10 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: over 7 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: almost 6 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: about 8 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: almost 10 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: almost 9 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

10.1155/2020/9015713

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

10.1167/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: almost 6 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: about 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

10.1016/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: over 5 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: over 11 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: almost 7 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: almost 10 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: almost 8 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: about 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: over 9 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: almost 8 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: over 11 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

10.3390/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: over 6 years ago

10.1186/bcr3048

Metastatic breast cancer cells inhibit osteoblast differentiation through the Runx2/CBFβ-dependent expression of the Wnt antagonist, sclerostin
Cited by: 89
Author(s): Daniel Mendoza-Villanueva, Leo Zeef, Paul Shore
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0114627

Altered MicroRNA Expression Profile in Exosomes during Osteogenic Differentiation of Human Bone Marrow-Derived Mesenchymal Stem Cells
Cited by: 184
Author(s): Jiajie Xu, Guangxiao Yang, Xiaohong Pan, Shuijun Zhang, Chen Zhao, Bin-Song Qiu, Haifeng Gu, Jian-fei Hong, Li Cao, Yu Chen, Bing Xia, Qinsheng Bi, Yaping Wang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0171508

A distal intergenic region controls pancreatic endocrine differentiation by acting as a transcriptional enhancer and as a polycomb response element
Cited by: 12
Author(s): Joris van Arensbergen, Sébastien Dussaud, Corinne Pardanaud-Glavieux, Javier García-Hurtado, Claire Sauty, Aline Guerci, Jorge Ferrer, Philippe Ravassard
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0063296

Efferocytosis Promotes Suppressive Effects on Dendritic Cells through Prostaglandin E2 Production in the Context of Autoimmunity
Cited by: 23
Author(s): Irma Pujol‐Autonell, Rosa-Maria Ampudia, Raquel Planas, Sílvia Marín-Gallén, Jorge Carrascal, Álex Sánchez, Ana V. Marín, Manel Puig-Domingo, Ricardo Pujol-Borrell, Joan Verdaguer, Marta Vives-Pi
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0017359

The PI3K p110δ Regulates Expression of CD38 on Regulatory T Cells
Cited by: 71
Author(s): Daniel T. Patton, Marcus D. Wilson, Wendy C. Rowan, Dalya R. Soond, Klaus Okkenhaug
Software Mentions: 1
Published: about 15 years ago

10.1186/s12915-019-0725-6

Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans
Cited by: 35
Author(s): Katharina Jovic, Jacopo Grilli, M.G. Sterken, L. Basten Snoek, J.A.G. Riksen, Stefano Allesina, J.E. Kammenga
Software Mentions: 1
Published: over 6 years ago

10.1186/bcr3191

Preclinical and clinical studies of estrogen deprivation support the PDGF/Abl pathway as a novel therapeutic target for overcoming endocrine resistance in breast cancer
Cited by: 39
Author(s): Marion T. Weigel, Zara Ghazoui, Anita K. Dunbier, Sunil Pancholi, Mitch Dowsett, Lesley-Ann Martin
Software Mentions: 1
Published: almost 14 years ago

10.1155/2018/1270483

Kynurenic Acid Protects against Thioacetamide-Induced Liver Injury in Rats
Cited by: 24
Author(s): Sebastian Marciniak, Artur Wnorowski, Katarzyna Smolińska, Beata Walczyna, Waldemar A. Turski, Tomasz Kocki, Piotr Paluszkiewicz, Jolanta Parada-Turska
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0011066

Contrasting Transcriptional Responses of a Virulent and an Attenuated Strain of Mycobacterium tuberculosis Infecting Macrophages
Cited by: 43
Author(s): Alice H. Li, Simon J. Waddell, Jason Hinds, Chad A. Malloff, Manjeet Bains, Robert E. W. Hancock, Wan L. Lam, Philip D. Butcher, Richard W. Stokes
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0030960

Role of Position 627 of PB2 and the Multibasic Cleavage Site of the Hemagglutinin in the Virulence of H5N1 Avian Influenza Virus in Chickens and Ducks
Cited by: 61
Author(s): K. A. Schat, John Bingham, Jeff Butler, Li Mei Chen, Sue Lowther, Tamsyn M. Crowley, Robert J. Moore, Ruben O. Donis, John W. Lowenthal
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0112399

Protein Interaction Networks Reveal Novel Autism Risk Genes within GWAS Statistical Noise
Cited by: 15
Author(s): Catarina Correia, Guiomar Oliveira, Astrid M. Vicente
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0052232

Interaction of Salmonella Typhimurium with Dendritic Cells Derived from Pluripotent Embryonic Stem Cells
Cited by: 10
Author(s): Raffaella Rossi, Christine Hale, David Goulding, Robert Andrews, Zarah Abdellah, Paul J. Fairchild, Gordon Dougan
Software Mentions: 1
Published: over 13 years ago

10.1186/bcr3328

Low levels of Stat5a protein in breast cancer are associated with tumor progression and unfavorable clinical outcomes
Cited by: 64
Author(s): Amy R. Peck, Agnieszka K. Witkiewicz, Chengbao Liu, Alexander C. Klimowicz, Ginger A. Stringer, Edward Pequignot, Boris Freydin, Ning Yang, Adam Ertel, Thai H. Tran, Melanie A. Girondo, Anne Rosenberg, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, David L. Rimm, Anthony M. Magliocco, Terry Hyslop, Hallgeir Rui
Software Mentions: 1
Published: over 13 years ago

10.1186/s12915-018-0555-y

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0
Cited by: 37
Author(s): Alberto Santos-Zavaleta, Mishael Sánchez-Pérez, Heladia Salgado, David Alberto Velázquez-Ramírez, Socorro Gama-Castro, Víctor H. Tierrafría, Stephen J. W. Busby, Patricia Aquino, Xin Fang, Bernhard Ø. Palsson, James E. Galagan, Julio Collado‐Vides
Software Mentions: 1
Published: over 7 years ago

10.1186/2041-1480-1-S1-S1

Building a biomedical ontology recommender web service
Cited by: 68
Author(s): Clément Jonquet, Mark A. Musen, Nigam H. Shah
Software Mentions: 1
Published: over 16 years ago

10.1186/s12915-014-0060-x

Developmental stage-dependent metabolic regulation during meiotic differentiation in budding yeast
Cited by: 9
Author(s): Thomas Walther, Fabien Létisse, Lindsay Peyriga, Ceren Alkım, Yuchen Liu, Aurélie Lardenois, Hélène Martin-Yken, Jean‐Charles Portais, Michael Primig, Jean François
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0084611

TFPI1 Mediates Resistance to Doxorubicin in Breast Cancer Cells by Inducing a Hypoxic-Like Response
Cited by: 14
Author(s): Gerald F. Davies, Arnie Berg, Spike D. L. Postnikoff, Heather L. Wilson, Terra Arnason, Anthony Kusalik, Troy A. A. Harkness
Software Mentions: 1
Published: about 12 years ago

10.1186/2041-1480-5-25

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
Cited by: 60
Author(s): James Malone, Andy Brown, Allyson L. Lister, Jon C. Ison, Duncan Hull, Helen Parkinson, Robert Stevens
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13058-017-0897-3

SPEN, a new player in primary cilia formation and cell migration in breast cancer
Cited by: 28
Author(s): Stéphanie Légaré, Catherine Chabot, Mark Basik
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0011429

Revealing New Mouse Epicardial Cell Markers through Transcriptomics
Cited by: 59
Author(s): Lars Bochmann, Padmini Sarathchandra, Frederica Mori, Enrique Lara‐Pezzi, Domenico Lazzaro, Nadia Rosenthal
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0019077

miR-132 Mediates the Integration of Newborn Neurons into the Adult Dentate Gyrus
Cited by: 140
Author(s): Bryan W. Luikart, Ae Soon L. Bensen, Eric K. Washburn, Julia V. Perederiy, Kimmy Su, Yun Li, Steven G. Kernie, Luis F. Parada, Gary L. Westbrook
Software Mentions: 1
Published: almost 15 years ago

10.1186/s40478-014-0093-y

Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases
Cited by: 80
Author(s): Matthew Li, Terry C. Burns, Alexander A. Morgan, Purvesh Khatri
Software Mentions: 1
Published: over 11 years ago

10.1186/bcr3154

Functional characterization of the 19q12 amplicon in grade III breast cancers
Cited by: 61
Author(s): Rachael Natrajan, Alan Mackay, Paul M. Wilkerson, Maryou B. Lambros, Daniel Wetterskog, Mónica Arnedos, K-K. Shiu, Felipe C. Geyer, Anita Langerød, Bas Kreike, Fabien Reyal, Hugo M. Horlings, Marc J. van de Vijver, José Palacios, Britta Weigelt, Jorge S. Reis‐Filho
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0044206

MiR-214 Targets β-Catenin Pathway to Suppress Invasion, Stem-Like Traits and Recurrence of Human Hepatocellular Carcinoma
Cited by: 142
Author(s): Hongping Xia, London Lucien Ooi, Kam M. Hui
Software Mentions: 1
Published: over 13 years ago

10.1038/s41416-018-0125-7

Transcriptomic immune profiling of ovarian cancers in paraneoplastic cerebellar degeneration associated with anti-Yo antibodies
Cited by: 12
Author(s): Clément Vialatte de Pémille, Giulia Berzero, Mathilde Small, Dimitri Psimaras, Marine Giry, Maïlys Daniau, Marc Sanson, Jean‐Yves Delattre, Jérôme Honnorat, Virginie Desestret, Agustí Alentorn
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13195-014-0070-5

PLD3 is accumulated on neuritic plaques in Alzheimer’s disease brains
Cited by: 35
Author(s): Jun‐ichi Satoh, Yoshihiro Kino, Yoji Yamamoto, Natsuki Kawana, Tsuyoshi Ishida, Yuko Saito, Kunimasa Arima
Software Mentions: 1
Published: over 11 years ago

10.1186/2041-1480-5-37

CLO: The cell line ontology
Cited by: 84
Author(s): Sirarat Sarntivijai, Yuling Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew Brush, Melissa Haendel, Jie Zheng, Christian J. Stoeckert, Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms20133173

Meta-Analysis of Microarray Expression Studies on Metformin in Cancer Cell Lines
Cited by: 8
Author(s): Hans-Juergen Schulten, Sherin Bakhashab
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0200716

Identification of serum miR-1915-3p and miR-455-3p as biomarkers for breast cancer
Cited by: 45
Author(s): Jian Guo, Chen Liu, Wei Wang, Yan Liu, Huiwen He, Chong Chen, Rong Xiang, Yunping Luo
Software Mentions: 1
Published: over 7 years ago

10.1186/s13068-019-1489-5

The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16
Cited by: 16
Author(s): Christian Arenas-López, Jessica Locker, Diego Orol, Frederik Walter, Tobias Busche, Jörn Kalinowski, Nigel P. Minton, Kármen Kovács, Klaus Winzer
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13068-019-1446-3

Combining loss of function of FOLYLPOLYGLUTAMATE SYNTHETASE1 and CAFFEOYL-COA 3-O-METHYLTRANSFERASE1 for lignin reduction and improved saccharification efficiency in Arabidopsis thaliana
Cited by: 17
Author(s): Hong-Li Xie, Nancy L. Engle, Sivasankari Venketachalam, Chang Geun Yoo, Jaime Barros, Mitch Lecoultre, Nikki Howard, Guifen Li, Liang Sun, Ashutosh Srivastava, Sivakumar Pattathil, Yunqiao Pu, Michael G. Hahn, Arthur J. Ragauskas, Richard S. Nelson, Richard A. Dixon, Timothy J. Tschaplinski, Elison B. Blancaflor, Yuhong Tang
Software Mentions: 1
Published: almost 7 years ago

10.3390/biomedicines9091251

Ladostigil Attenuates Induced Oxidative Stress in Human Neuroblast-like SH-SY5Y Cells
Cited by: 4
Author(s): Keren Zohar, Elyad Lezmi, Tsiona Eliyahu, Michal Linial
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0014672

Estrogen-Dependent Gene Expression in the Mouse Ovary
Cited by: 9
Author(s): Seng H. Liew, Mai A. Sarraj, Ann E. Drummond, Jock K. Findlay
Software Mentions: 1
Published: about 15 years ago

10.1155/2021/6529255

Synthetic Evaluation of MicroRNA-1-3p Expression in Head and Neck Squamous Cell Carcinoma Based on Microarray Chips and MicroRNA Sequencing
Cited by: 1
Author(s): Yubing Chen, Mingjiang Liu, Jin Hu, Bo Peng, Luo Dai, Sifan Wang, H. Rosie Xing, Baoju Wang, Zhan He Wu
Software Mentions: 1
Published: over 4 years ago

10.1186/s12859-016-1106-6

Gene expression prediction using low-rank matrix completion
Cited by: 40
Author(s): Arnav Kapur, Kshitij Marwah, Gil Alterovitz
Software Mentions: 1
Published: almost 10 years ago

10.1155/2017/9614596

Detecting the Candidate Gender Determinants by Bioinformatic Prediction of miRNAs and Their Targets from Transcriptome Sequences of the Male and Female Flowers in Salix suchowensis
Cited by: 1
Author(s): Suyun Wei, Ning Ye, Tongming Yin
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0106706

Research Resources: Comparative MicroRNA Profiles in Human Corona Radiata Cells and Cumulus Oophorus Cells Detected by Next-Generation Small RNA Sequencing
Cited by: 23
Author(s): Xianhong Tong, Bo Xu, Yuan‐Wei Zhang, Yusheng Liu, Chao Ma
Software Mentions: 1
Published: over 11 years ago

10.1155/2015/724715

Detecting Key Genes Regulated by miRNAs in Dysfunctional Crosstalk Pathway of Myasthenia Gravis
Cited by: 11
Author(s): Yuze Cao, Jianjian Wang, Huixue Zhang, Qinghua Tian, Lixia Chen, Shangwei Ning, Peifang Liu, Xiang Sun, Xiaoyu Lu, Chang Eun Song, Shuai Zhang, Bo Xiao, Lihua Wang
Software Mentions: 1
Published: over 11 years ago

10.1242/bio.047530

Forcing contacts between mitochondria and the endoplasmic reticulum extends lifespan in a Drosophila model of Alzheimer's disease
Cited by: 25
Author(s): Juan Garrido-Maraver, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 1
Published: over 7 years ago

10.1093/bioinformatics/btz959

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
Cited by: 41
Author(s): Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie-Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo López, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Elixir Core Data Resource Forum, Niklas Blomberg, Christine Durinx, Johanna McEntyre
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0145696

Correction: Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury
Cited by: 3
Author(s): Marialbert Acosta‐Herrera, Fabián Lorenzo-Díaz, Maria Pino‐Yanes, Almudena Corrales, Francisco Valladares, Tilman E. Klassert, Basilio Valladares, Hortense Slevogt, Shwu‐Fan Ma, Jesús Villar, Carlos Flores
Software Mentions: 1
Published: over 10 years ago

10.1093/bioinformatics/btw545

PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations
Cited by: 12
Author(s): Jamie Soul, Sara Dunn, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 1
Published: over 9 years ago

10.7150/jca.29293

Clinical Significance of microRNA-196b-5p in Hepatocellular Carcinoma and its Potential Molecular Mechanism
Cited by: 11
Author(s): Lu Zhang, Bin Luo, Yi‐Wu Dang, Rong‐Quan He, Zhigang Peng, Gang Chen, Zhaoyong Feng
Software Mentions: 1
Published: over 7 years ago

10.1093/bioinformatics/btt019

CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data
Cited by: 841
Author(s): Gabriela Bindea, Jérôme Galon, Bernhard Mlecnik
Software Mentions: 1
Published: over 13 years ago

10.1093/bioinformatics/btt108

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
Cited by: 13
Author(s): George Y. Wu, Jason T. Yustein, Matthew N. McCall, Michael J. Zilliox, Rafael A. Irizarry, Karen Zeller, Chi V. Dang, Hongkai Ji
Software Mentions: 1
Published: about 13 years ago

10.7150/jca.34693

Distinct Roles of VEGFA and ANGPT2 in Lung Adenocarcinoma and Squamous Cell Carcinoma
Cited by: 20
Author(s): Shuang Qin, Ming Yi, Dechao Jiao, An‐Ping Li, Zeyu Wu
Software Mentions: 1
Published: over 6 years ago

10.1093/bioinformatics/btx739

SATORI: a system for ontology-guided visual exploration of biomedical data repositories
Cited by: 9
Author(s): Fritz Lekschas, Nils Gehlenborg
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0017259

GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets
Cited by: 27
Author(s): John Patrick Mpindi, Henri Sara, Saija Haapa-Paananen, Sami Kilpinen, Tommi Pisto, Elmar Bucher, K. Ojala, Kristiina Iljin, Paula Vainio, Mari Björkman, Santosh Gupta, Pekka Kohonen, Matthias Nees, Olli Kallioniemi
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0073817

Wild Type p53 Transcriptionally Represses the SALL2 Transcription Factor under Genotoxic Stress
Cited by: 10
Author(s): Carlos Farkas, Carla P. Martins, D. E. Escobar, Matías I. Hepp, David B. Donner, Ariel F. Castro, Gérard I. Evan, José L. Gutiérrez, Robert S. Warren, Roxana Pincheira
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0057329

Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)
Cited by: 116
Author(s): Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0177278

The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.)
Cited by: 23
Author(s): Bart Verwaaijen, Daniel Wibberg, Magdalena Kröber, Anderson M. Winkler, Rita Zrenner, Hanna Bednarz, Karsten Niehaus, Rita Grosch, Alfred Pühler, Andreas Schlüter
Software Mentions: 1
Published: almost 9 years ago

10.1093/bioinformatics/btz731

Metric learning on expression data for gene function prediction
Cited by: 10
Author(s): Stavros Makrodimitris, Marcel J. T. Reinders, Roeland C. H. J. van Ham
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0062456

Age-Mediated Transcriptomic Changes in Adult Mouse Substantia Nigra
Cited by: 12
Author(s): Lin Gao, María Hidalgo-Figueroa, Luis Escudero, Juan Díaz‐Martín, José López‐Barneo, Alberto Pascual
Software Mentions: 1
Published: almost 13 years ago

10.1186/1756-0381-7-18

ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions
Cited by: 20
Author(s): Philip Zimmermann, Stefan Bleuler, Oliver Laule, Florian Martin, Nikolai V. Ivanov, Prisca Campanoni, Karen K. Oishi, Nicolas Lugon-Moulin, Markus Wyss, Tomás Hrúz, Wilhelm Gruissem
Software Mentions: 1
Published: over 11 years ago

10.1186/1756-0381-1-9

Fast approximate hierarchical clustering using similarity heuristics
Cited by: 18
Author(s): Meelis Kull, Jaak Vilo
Software Mentions: 1
Published: over 17 years ago

10.1186/1756-0381-4-15

Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation
Cited by: 13
Author(s): Pablo Christian Echeverria, Fedor Forafonov, Deo Prakash Pandey, Guillaume Mühlebach, Didier Picard
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0008939

The Transcriptional Programme of Human Heart Valves Reveals the Natural History of Infective Endocarditis
Cited by: 29
Author(s): Marie Benoit, Franck Thuny, Yannick Le Priol, Hubert Lépidi, Sonia Bastonero, Jean‐Paul Casalta, Frédéric Collart, Christian Capo, Didier Raoult, Jean‐Louis Mège
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0020063

Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
Cited by: 72
Author(s): Masayuki Murata, Hiroko Fujimoto, Kaori Nishimura, Kannikar Charoensuk, Hiroshi Nagamitsu, Satish Raina, Tomoyuki Kosaka, Taku Oshima, Nagahisa Ogasawara, Mamoru Yamada
Software Mentions: 1
Published: almost 15 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962