bioconductor: ArrayExpress | Projects

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: almost 11 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: over 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: over 10 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: almost 10 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: over 9 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: about 9 years ago

10.1038/s41598-017-03986-1

Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks
Cited by: 70
Author(s): Yun Xiao, Jingpu Zhang, Lei Deng
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-05451-5

Loss of Usp9x disrupts cell adhesion, and components of the Wnt and Notch signaling pathways in neural progenitors
Cited by: 26
Author(s): Susitha Premarathne, Mariyam Murtaza, Nicholas Matigian, Lachlan A. Jolly, Stephen A. Wood
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-09430-8

Cerium oxide nanoparticles inhibit differentiation of neural stem cells
Cited by: 59
Author(s): Anda R. Gliga, Karin Edoff, Fanny Caputo, Thomas Källman, Hans Blom, Hanna Karlsson, Lina Ghibelli, Enrico Traversa, Sandra Ceccatelli, Bengt Fadeel
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-18043-0

Aedes aegypti microRNA miR-2b regulates ubiquitin-related modifier to control chikungunya virus replication
Cited by: 21
Author(s): Sunil Kumar Dubey, Jatin Shrinet, Jaspreet Jain, Shakir Ali, Sujatha Sunil
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-19357-3

TPGLDA: Novel prediction of associations between lncRNAs and diseases via lncRNA-disease-gene tripartite graph
Cited by: 73
Author(s): Liang Ding, Minghui Wang, Dongdong Sun, Ao Li
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-44235-x

Cynomolgus macaque IL37 polymorphism and control of SIV infection
Cited by: 3
Author(s): Takashi Shiina, Shingo Suzuki, Nicolas Congy-Jolivet, Alice Aarnink, Henri‐Jean Garchon, Nathalie Dereuddre‐Bosquet, Bruno Vaslin, Nicolas Tchitchek, Delphine Desjardins, Brigitte Autran, Olivier Lambotte, Ioannis Théodorou, Roger Le Grand, Antoine Blancher
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-57076-5

The ETS transcription factor ETV5 is a target of activated ALK in neuroblastoma contributing to increased tumour aggressiveness
Cited by: 19
Author(s): Liselot Mus, Irina Lambertz, Shana Claeys, Candy Kumps, Wouter Van Loocke, Christophe Van Neste, Ganesh Umapathy, Marica Vaapil, Christoph Bartenhagen, Geneviève Laureys, Olivier De Wever, Daniel Bexell, Matthias Fischer, Bengt Hållberg, Johannes H. Schulte, Bram De Wilde, Kaat Durinck, Geertrui Denecker, Katleen De Preter, Frank Speleman
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59514-1

Combined HER3-EGFR score in triple-negative breast cancer provides prognostic and predictive significance superior to individual biomarkers
Cited by: 24
Author(s): Angela Ogden, Shristi Bhattarai, Bikram Sahoo, Nigel P. Mongan, Mansour Alsaleem, Andrew Green, Mohammed A. Aleskandarany, Ian O. Ellis, Sonal Pattni, Xiaoxian Bill Li, Carlos S. Moreno, Uma Krishnamurti, Emiel A. M. Janssen, Kristín Jónsdóttir, Emad A. Rakha, Padmashree C.G. Rida, Ritu Aneja
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-60235-8

Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction
Cited by: 8
Author(s): Jessica Gliozzo, Paolo Perlasca, Marco Mesiti, Elena Casiraghi, Viviana Vallacchi, Elisabetta Vergani, Giuliano Grossi, Alessandro Petrini, Matteo Ré, Alberto Paccanaro, Giorgio Valentini
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-74417-x

Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)
Cited by: 9
Author(s): Ying Li, Qilu Song, Yamin Zhang, Zheng Li, Jialin Guo, Xinhong Chen, Gaisheng Zhang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-74288-2

Cell-free DNA in plasma as an essential immune system regulator
Cited by: 19
Author(s): Marie Korabečná, Alžběta Zinková, Iva Brynychova, Blanka Chylíková, Petr Přikryl, Lucie Šedová, Pavel Neužil, Ondřej Šeda
Software Mentions: 2
Published: over 5 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

10.2147/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: almost 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: 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: over 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: about 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: about 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: 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

10.1016/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: about 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: about 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: 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: 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: about 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

10.1038/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: about 8 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: over 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: about 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: over 15 years ago

10.1186/1471-2407-9-409

Impact of biospecimens handling on biomarker research in breast cancer
Cited by: 84
Author(s): Loris De Cecco, Valeria Musella, Silvia Veneroni, Vera Cappelletti, Italia Bongarzone, Maurizio Callari, Barbara Valeri, Marco A. Pierotti, Maria Grazia Daidone
Software Mentions: 1
Published: over 16 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

10.3390/ani10101924

Ovarian Transcriptomic Analysis Reveals Differential Expression Genes Associated with Cell Death Process after Selection for Ovulation Rate in Rabbits
Cited by: 0
Author(s): Marta Serna-García, Rosa Peiró, Eva Serna, M. A. Santacreu
Software Mentions: 1
Published: over 5 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: about 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: over 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/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: about 7 years ago

10.1038/s41598-019-43795-2

Replication termination without a replication fork trap
Cited by: 20
Author(s): Elisa Galli, Jean-Luc Ferat, Jean-Michel Desfontaines, Marie-Eve Val, Ove Skovgaard, François‐Xavier Barre, Christophe Possoz
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-46664-0

Virus Genotype-Dependent Transcriptional Alterations in Lipid Metabolism and Inflammation Pathways in the Hepatitis C Virus-infected Liver
Cited by: 18
Author(s): W. d’Avigdor, Magdalena A. Budzinska, M Lee, Roselind S. Lam, James G. Kench, Michael Stapelberg, Susan V. McLennan, Geoffrey C. Farrell, Jacob George, Geoffrey W. McCaughan, Thomas Tu, Nicholas Shackel
Software Mentions: 1
Published: almost 7 years ago

10.1186/1472-6750-5-5

Cited by: 5
Author(s): Valtteri Wirta, Anders Holmberg, Morten Lukacs, Peter Nilsson, Pierre Hilson, Mathias Uhlén, Rishikesh P. Bhalerao, Joakim Lundeberg
Software Mentions: 1
Published: over 21 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: over 12 years ago

10.1186/1472-6750-13-2

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Cited by: 67
Author(s): Dennis Thomas, Sharon Gaheen, Stacey L. Harper, M. J. Fritts, Fred Klaessig, Elizabeth Hahn-Dantona, David S. Paik, Sue Pan, Grace A. Stafford, Elaine T. Freund, Juli Klemm, Nathan A. Baker
Software Mentions: 1
Published: over 13 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.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: about 15 years ago

10.1038/s41598-019-49124-x

Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis
Cited by: 8
Author(s): Perumal Gnanakkumaar, Ram Murugesan, Shiek S. S. J. Ahmed
Software Mentions: 1
Published: almost 7 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: almost 5 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: almost 14 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

10.1186/1472-6750-7-24

Comparison of target labeling methods for use with Affymetrix GeneChips
Cited by: 3
Author(s): William Lonergan, Toni Whistler, Suzanne D. Vernon
Software Mentions: 1
Published: about 19 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

10.7554/eLife.58374

SOX11 promotes epithelial/mesenchymal hybrid state and alters tropism of invasive breast cancer cells
Cited by: 24
Author(s): Erik Oliemuller, Richard Newman, Siu Man Tsang, Shane Foo, Gareth Muirhead, Farzana Noor, Syed Haider, Iskander Aurrekoetxea-Rodríguez, María dM Vivanco, Beatrice A. Howard
Software Mentions: 1
Published: almost 6 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: almost 8 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: over 6 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: over 15 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: almost 10 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

10.1093/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

10.1371/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: almost 12 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: over 13 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

10.1093/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.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

10.1186/1756-0381-7-18

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: almost 12 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: almost 12 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: about 15 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: almost 8 years ago

10.1186/1746-6148-6-44

Feasibility of a liver transcriptomics approach to assess bovine treatment with the prohormone dehydroepiandrosterone (DHEA)
Cited by: 19
Author(s): Jeroen C.W. Rijk, Ad Peijnenburg, Peter J.M. Hendriksen, Johan M. Van Hende, M.J. Groot, Michel W. F. Nielen
Software Mentions: 1
Published: over 16 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: over 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: almost 13 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: over 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: about 9 years ago

10.1186/s12894-015-0056-z

An online tool for evaluating diagnostic and prognostic gene expression biomarkers in bladder cancer
Cited by: 14
Author(s): Garrett M. Dancik
Software Mentions: 1
Published: almost 11 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: about 13 years ago

10.1186/1752-0509-2-58

Short time-series microarray analysis: Methods and challenges
Cited by: 43
Author(s): Xuewei Wang, Ming Tsang Wu, Lirong Zheng, Christina Chan
Software Mentions: 1
Published: almost 18 years ago

10.1186/1752-0509-4-164

ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work
Cited by: 69
Author(s): Gregor Warsow, Boris Greber, Steffi Falk, Clemens Harder, Marcin Siatkowski, Sandra Schordan, Anup Som, Nicole Endlich, Hans R. Schöler, Dirk Repsilber, Karlhans Endlich, Georg Fuellen
Software Mentions: 1
Published: over 15 years ago

10.1186/1752-0509-4-62

Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis
Cited by: 51
Author(s): Elizabeth Allen, Annick Moing, Timothy M. D. Ebbels, Mickaël Maucourt, A. D. Tomos, Dominique Rolin, Mark A. Hooks
Software Mentions: 1
Published: about 16 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: over 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: about 15 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962