bioconductor: ArrayExpress | Projects

10.1186/s12903-019-0738-0

Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO)
Cited by: 26
Author(s): Asami Suzuki, Tetsuro Horie, Yukihiro Numabe
Software Mentions: 1
Published: about 7 years ago

10.1016/j.tranon.2021.101132

ViBiBa: Virtual BioBanking for the DETECT multicenter trial program - decentralized storage and processing
Cited by: 0
Author(s): Hannah Asperger, Jan-Philipp Cieslik, Barbara Alberter, Cäcilia Köstler, Bernhard Polzer, Volkmar Müller, Klaus Pantel, Sabine Riethdorf, André Koch, Andreas D. Hartkopf, Lisa Wiesmüller, Wolfgang Janni, Fabienne Schochter, A Franken, Dieter Niederacher, Tanja Fehm, Hans Neubauer
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0056681

SGLT5 Reabsorbs Fructose in the Kidney but Its Deficiency Paradoxically Exacerbates Hepatic Steatosis Induced by Fructose
Cited by: 30
Author(s): Taku Fukuzawa, Motoharu Fukazawa, Otoya Ueda, Hideaki Shimada, Kito Aki, Mami Kakefuda, Yoshiaki Kawase, Naoko Wada, Chisato Goto, Naoshi Fukushima, Kou-ichi Jishage, Kazuo Honda, George L. King, Yojiro Kawabe
Software Mentions: 1
Published: over 13 years ago

10.1016/j.trecan.2020.10.011

Expanding and Remixing the Metadata Landscape
Cited by: 5
Author(s): Ariel A. Hippen, Casey S. Greene
Software Mentions: 1
Published: about 5 years ago

10.1016/j.tube.2012.12.003

Adenylylation of mycobacterial Glnk (PII) protein is induced by nitrogen limitation
Cited by: 11
Author(s): Katrina Williams, Mark H. Bennett, Geraint Barton, Victoria A Jenkins, Brian D. Robertson
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0074923

FHOD1, a Formin Upregulated in Epithelial-Mesenchymal Transition, Participates in Cancer Cell Migration and Invasion
Cited by: 49
Author(s): Maria Gardberg, Katja Kaipio, Laura Lehtinen, Piia Mikkonen, Vanina D. Heuser, Kati Talvinen, Kristiina Iljin, Caroline Kampf, Mathias Uhlén, Reidar Grénman, Mari Koivisto, Olli Carpén
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0070862

A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae
Cited by: 17
Author(s): Layla K. Mahdi, Esmaeil Ebrahimie, David L. Adelson, James C. Paton, Abiodun D. Ogunniyi
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2202-6-28

Transcriptome analysis in primary neural stem cells using a tag cDNA amplification method
Cited by: 12
Author(s): Maria Sievertzon, Valtteri Wirta, Alex Mercer, Konstantinos Meletis, Rikard Erlandsson, Lilian Wikström, Jonas Frisén, Joakim Lundeberg
Software Mentions: 1
Published: about 21 years ago

10.1371/journal.pone.0046744

Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon
Cited by: 89
Author(s): Lihong Chen, Wei Hu, Shenglong Tan, Min Wang, Zhanbing Ma, Shiyi Zhou, Xianwen Deng, Yang Zhang, Chao Huang, Guangxiao Yang, Guoqing He
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0038351

A Novel Strategy for Selection and Validation of Reference Genes in Dynamic Multidimensional Experimental Design in Yeast
Cited by: 49
Author(s): Ayca Cankorur-Cetinkaya, Elif Dereli, Serpil Eraslan, Muhammed Erkan Karabekmez, Duygu Dikicioglu, Betül Kırdar
Software Mentions: 1
Published: about 14 years ago

10.1016/j.tube.2013.05.004

Overexpression of the Rv0805 phosphodiesterase elicits a cAMP-independent transcriptional response
Cited by: 12
Author(s): Nishad Matange, Debbie M. Hunt, Roger S. Buxton, Sandhya S. Visweswariah
Software Mentions: 1
Published: almost 13 years ago

10.1016/j.tube.2013.05.005

Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: Its operon and regulon
Cited by: 14
Author(s): Alison Gaudion, Lisa F. Dawson, E. A. Davis, Katherine Smollett
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0021907

NRF2 Activation Restores Disease Related Metabolic Deficiencies in Olfactory Neurosphere-Derived Cells from Patients with Sporadic Parkinson's Disease
Cited by: 82
Author(s): Anthony Cook, Alejandra Vitale, Sugandha Ravishankar, Nicholas Matigian, Greg T. Sutherland, Jianguo Shan, Ratneswary Sutharsan, Christopher Perry, Peter A. Silburn, George D. Mellick, Murray L. Whitelaw, Christine A. Wells, Alan Mackay‐Sim, Stephen A. Wood
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0077263

Non-Specific dsRNA-Mediated Antiviral Response in the Honey Bee
Cited by: 113
Author(s): Michelle L. Flenniken, Raul Andino
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2202-11-14

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
Cited by: 365
Author(s): Tim R. Mercer, Irfan A. Qureshi, Şölen Gokhan, Marcel E. Dinger, Guangyu Li, John S. Mattick, Mark F. Mehler
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0018902

Deciphering the Role of RND Efflux Transporters in Burkholderia cenocepacia
Cited by: 67
Author(s): Silvia Bazzini, Claudia Udine, Andrea Saß, Maria Rosalia Pasca, Francesca Longo, Giovanni Emiliani, Marco Fondi, Elena Perrin, Francesca Decorosi, Carlo Viti, Luciana Giovannetti, Livia Leoni, Renato Fani, Giovanna Riccardi, Eshwar Mahenthiralingam, Silvia Buroni
Software Mentions: 1
Published: about 15 years ago

10.4274/tjh.2015.0145

Expression Profiles of the Individual Genes Corresponding to the Genes Generated by Cytotoxicity Experiments with Bortezomib in Multiple Myeloma
Cited by: 3
Author(s): Mehdi Ghasemi, Semih Alpsoy, Seyhan Türk, Ümi̇t Yavuz Malkan, Şükrü Atakan, İbrahim C. Haznedaroğlu, Gülsen Güneş, Mehmet Gündüz, Burak Yılmaz, Sezgin Etgül, Seda Aydın, Tuncay Aslan, Nilgün Sayınalp, Salih Aksu, Halûk Demiroğlu, Osman Özcebe, Yahya Büyükaşık, Hakan Göker
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0142688

Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice
Cited by: 23
Author(s): Thaís A. Fornari, Paula B. Donate, Amanda Freire Assis, Cristiana Santos de Macedo, Elza T. Sakamoto-Hojo, Eduardo Antônio Donadi, Geraldo A. S. Passos
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2202-8-34

Reduced expression of TAC1, PENK and SOCS2 in Hcrtr-2 mutated narcoleptic dog brain
Cited by: 7
Author(s): Julia Hedlund Lindberg, Peter Saetre, Seiji Nishino, Emmanuel Mignot, Elena Jazin
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pone.0116404

Protein Interactome of Muscle Invasive Bladder Cancer
Cited by: 12
Author(s): Akshay Bhat, Andreas Heinzel, Bernd Mayer, Paul Perco, Irmgard Mühlberger, Holger Husi, Axel S. Merseburger, Jérôme Zoidakis, Antonia Vlahou, Joost P. Schanstra, Harald Mischak, Vera Jankowski
Software Mentions: 1
Published: over 11 years ago

10.1128/mBio.01334-14

Mechanisms Underlying the Exquisite Sensitivity of Candida albicans to Combinatorial Cationic and Oxidative Stress That Enhances the Potent Fungicidal Activity of Phagocytes
Cited by: 63
Author(s): Despoina Kaloriti, Martin Jacobsen, Zhikang Yin, Miranda Patterson, Anna Tillmann, Deborah A. Smith, Emily A. Cook, Tao You, Melissa Grimm, Iryna Bohovych, Celso Grebogi, Brahm H. Segal, Neil A. R. Gow, Ken Haynes, Janet Quinn, Alistair J. P. Brown
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0099822

Underpinning Sustainable Vector Control through Informed Insecticide Resistance Management
Cited by: 50
Author(s): Edward Thomsen, Clare Strode, Kay Hemmings, Angela Hughes, Emmanuel Chanda, Mulenga Musapa, Mulakwa Kamuliwo, Faustina N. Phiri, Lucy Muzia, Javan Chanda, Alister Kandyata, Brian Chirwa, Kathleen Poer, Janet Hemingway, Charles S. Wondji, Hilary Ranson, Michael Coleman
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0103618

Gene Expression Analysis Suggests Bone Development-Related Genes GDF5 and DIO2 Are Involved in the Development of Kashin-Beck Disease in Children Rather than Adults
Cited by: 10
Author(s): Yan Wen, Na Zhang, Chunyan Li, Shulan He, Wenfeng Tan, Yanxia Lei, Zhang Qiang, Yu Sun, Jingjing Zheng, Xiong Guo
Software Mentions: 1
Published: almost 12 years ago

10.1128/mBio.00430-16

The Acinetobacter baumannii Two-Component System AdeRS Regulates Genes Required for Multidrug Efflux, Biofilm Formation, and Virulence in a Strain-Specific Manner
Cited by: 95
Author(s): Grace E. Richmond, Laura P. Evans, Michael Anderson, Matthew E. Wand, Laura C. Bonney, Alasdair Ivens, Kim Lee Chua, Mark A. Webber, J. Mark Sutton, Marnie L. Peterson, Laura J. V. Piddock
Software Mentions: 1
Published: about 10 years ago

10.1128/mBio.00642-16

DamX Controls Reversible Cell Morphology Switching in Uropathogenic Escherichia coli
Cited by: 43
Author(s): Surabhi Khandige, Cecilie Antoinette Asferg, Karina Juhl Rasmussen, Martin Jakob Larsen, Martin Overgaard, Thomas Emil Andersen, Jakob Møller‐Jensen
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2474-13-130

Expression profile analysis of mycotoxin-related genes in cartilage with endemic osteochondropathy kashin-beck disease
Cited by: 7
Author(s): Na Zhang, Xiong Guo, Weizhuo Wang, Shixun Wu, Wei-Juan Ma, Yan Hua
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0063210

Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage
Cited by: 49
Author(s): Chih‐Jung Chen, Clemens Unger, W. H. Hoffmann, Jodi A. Lindsay, Yhu-Chering Huang, Friedrich Götz
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2199-8-112

Checkpoint independence of most DNA replication origins in fission yeast
Cited by: 36
Author(s): Katie L Mickle, Sunita Ramanathan, Adam P. Rosebrock, Anna Maria Oliva, Amna Chaudari, Chulee Yompakdee, David Scott, Janet Leatherwood, Joel A. Huberman
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pone.0148936

Expression of cagA, virB/D Complex and/or vacA Genes in Helicobacter pylori Strains Originating from Patients with Gastric Diseases
Cited by: 7
Author(s): Andrzej Szkaradkiewicz, Tomasz M. Karpiński, Krzysztof Linke, Przemysław Majewski, Dorota I. Rożkiewicz, Olga Goślińska-Kuźniarek
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0086643

Transcriptomic Meta-Analysis of Multiple Sclerosis and Its Experimental Models
Cited by: 27
Author(s): Barbara B. Raddatz, Florian Hansmann, Ingo Spitzbarth, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2199-8-119

Checkpoint effects and telomere amplification during DNA re-replication in fission yeast
Cited by: 10
Author(s): Katie L Mickle, Anna Maria Oliva, Joel A. Huberman, Janet Leatherwood
Software Mentions: 1
Published: over 18 years ago

10.1128/mBio.00968-17

Lack of AcrB Efflux Function Confers Loss of Virulence on <i>Salmonella enterica</i> Serovar Typhimurium
Cited by: 92
Author(s): Xuan Wang-Kan, Jessica M A Blair, Barbara Chirullo, Jonathan W. Betts, Roberto M. La Ragione, Alasdair Ivens, Vito Ricci, Timothy J. Opperman, Laura J. V. Piddock
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2199-11-95

Overexpression of miR-128 specifically inhibits the truncated isoform of NTRK3 and upregulates BCL2 in SH-SY5Y neuroblastoma cells
Cited by: 78
Author(s): Monia Guidi, Margarita Muiños‐Gimeno, Birgit Kagerbauer, Eulàlia Martı́, Xavier Estivill, Yolanda Espinosa‐Parrilla
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2180-7-88

Comparative gene expression profiling in two congenic mouse strains following Bordetella pertussis infection
Cited by: 7
Author(s): Sander Banus, Rob J. Vandebriel, Jeroen L. A. Pennings, Eric R. Gremmer, Piet W. Wester, Henk J. van Kranen, Timo M. Breit, Peter Démant, Frits R. Mooi, Barbara Hoebee, Tjeerd G. Kimman
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2180-12-104

The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated
Cited by: 120
Author(s): Alex J. McCarthy, Jodi A. Lindsay
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2180-13-224

Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions
Cited by: 8
Author(s): Yared H. Kidane, Christopher B. Lawrence, T. M. Murali
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2180-9-246

Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Cited by: 7
Author(s): J. F. Yuan, Zhang Sj, Osman Jafer, RA Furlong, OE Chausiaux, Carole A. Sargent, Zhang Gh, Nabeel A. Affara
Software Mentions: 1
Published: over 16 years ago

10.1111/acel.12080

<scp>TORC</scp>1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast
Cited by: 113
Author(s): Charalampos Rallis, Sandra Codlin, Jürg Bähler
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0012667

Claudin 13, a Member of the Claudin Family Regulated in Mouse Stress Induced Erythropoiesis
Cited by: 16
Author(s): Pamela Thompson, Hannah Tipney, Andy Brass, Harry Noyes, Stephen J. Kemp, Jan Naessens, May Tassabehji
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2180-8-73

Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni
Cited by: 20
Author(s): Sandra Rodin, Anders F. Andersson, Valtteri Wirta, Lena Eriksson, Marianne Ljungström, Britta Björkholm, Hans Lindmark, Lars Engstrand
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0148308

Disruption of STAT5b-Regulated Sexual Dimorphism of the Liver Transcriptome by Diverse Factors Is a Common Event
Cited by: 41
Author(s): Keiyu Oshida, Naresh Vasani, David J. Waxman, J. Christopher Corton
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2180-12-212

Insight into the bacterial gut microbiome of the North American moose (Alces alces)
Cited by: 45
Author(s): Suzanne L. Ishaq, André‐Denis G. Wright
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-10-330

BASE - 2nd generation software for microarray data management and analysis
Cited by: 50
Author(s): Johan Vallon‐Christersson, Nicklas Nordborg, Martin Svensson, Jari Häkkinen
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2180-10-106

The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori
Cited by: 3
Author(s): François P. Douillard, Kevin Ryan, Michael Lane, Delphine L. Caly, Stanley A. Moore, Charles W. Penn, Jason Hinds, Paul W. O’Toole
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2105-11-433

Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization
Cited by: 10
Author(s): Ming Zhang, Yudong Zhang, Li Liu, Lijuan Yu, Shirley Tsang, Jian Tan, Wenhua Yao, Manjit S. Kang, Yong-Qiang An, Xing Fan
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12911-021-01634-3

A framework for validating AI in precision medicine: considerations from the European ITFoC consortium
Cited by: 18
Author(s): Rosy Tsopra, Xose M Fernandez-Suarez, Claudio Luchinat, Lilia Alberghina, Hans Lehrach, Marco Vanoni, Felix Dreher, Osman Uğur Sezerman, Marc Cuggia, Marie de Tayrac, Edvīns Miklaševičs, Lucian Mihai Itu, Marius Geantă, Lesley A. Ogilvie, Florence Godey, C. Boldisor, Boris Campillo‐Gimenez, Cosmina Cioroboiu, Costin Florian Ciușdel, Simona M. Coman, Oliver Hijano Cubelos, Alexandru Itu, Bodo Lange, Matthieu Le Gallo, Alexandra Lespagnol, Giancarlo Mauri, H Okan Soykam, Bastien Rance, Paola Turano, Leonardo Tenori, Alessia Vignoli, Christoph Wierling, Nora Benhabilès, Anita Burgun
Software Mentions: 1
Published: over 4 years ago

10.1186/s12920-017-0293-y

Differential gene expression in disease: a comparison between high-throughput studies and the literature
Cited by: 52
Author(s): Raul Rodriguez‐Esteban, Xiaoyu Jiang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12920-014-0063-z

Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS)
Cited by: 22
Author(s): Maria Chiara Pelleri, Allison Piovesan, Maria Caracausi, Anna C. Berardi, Lorenza Vitale, Pierluigi Strippoli
Software Mentions: 1
Published: over 11 years ago

10.3390/cancers12092450

Sustained Inflammatory Signalling through Stat1/Stat2/IRF9 Is Associated with Amoeboid Phenotype of Melanoma Cells
Cited by: 3
Author(s): Aneta Gandalovičová, Anna-Marie Šůchová, Vladimı́r Čermák, Ladislav Merta, Daniel Rösel, Jan Brábek
Software Mentions: 1
Published: almost 6 years ago

10.3390/cancers12071790

Induction of Lysosome Membrane Permeabilization as a Therapeutic Strategy to Target Pancreatic Cancer Stem Cells
Cited by: 7
Author(s): Timothy P. Cash, Sonia Alcalá, María del Rosario Rico-Ferreira, Elena Hernández-Encinas, Jennifer García, María I. Albarrán, Sandra Valle, Javier Muñoz, Sonia Martínez-González, Carmen Blanco‐Aparicio, Joaquı́n Pastor, Manuel Serrano, Bruno Sáinz
Software Mentions: 1
Published: almost 6 years ago

10.1111/acel.12160

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging
Cited by: 40
Author(s): Erik B. van den Akker, Willemijn M. Passtoors, Ritsert C. Jansen, Erik W. van Zwet, Jelle J. Goeman, Marc Hulsman, Valur Emilsson, Markus Perola, Gonneke Willemsen, Brenda W. J. H. Penninx, B.T. Heijmans, Andrea B. Maier, Dorret I. Boomsma, Joost N. Kok, P. Eline Slagboom, Marcel J. T. Reinders, Marian Beekman
Software Mentions: 1
Published: over 12 years ago

10.3390/cancers12020469

Personalized Assessment of Normal Tissue Radiosensitivity via Transcriptome Response to Photon, Proton and Carbon Irradiation in Patient-Derived Human Intestinal Organoids
Cited by: 8
Author(s): Ali Nowrouzi, Mathieu Sertorio, Mahdi Akbarpour, Maximilian Knoll, Damir Krunic, Matthew Kuhar, Christian Schwager, Stephan Brons, Jürgen Debus, Susanne I. Wells, James M. Wells, Amir Abdollahi
Software Mentions: 1
Published: over 6 years ago

10.1128/mBio.00109-21

Metabolomics Reveal Potential Natural Substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium
Cited by: 14
Author(s): Xuan Wang-Kan, Giovanny Rodrı́guez-Blanco, Andrew D. Southam, Catherine Winder, Warwick B. Dunn, Alasdair Ivens, Laura J. V. Piddock
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers12051133

Multi-Gene Prognostic Signatures and Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy in ER-Positive, HER2-Negative Breast Cancer Patients
Cited by: 13
Author(s): Claudia Mazo, Stephen Barron, Catherine Mooney, William M. Gallagher
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-8-447

Application of a correlation correction factor in a microarray cross-platform reproducibility study
Cited by: 7
Author(s): Kellie J. Archer, Catherine I. Dumur, G. Scott Taylor, Michael D. Chaplin, Anthony Guiseppi‐Elie, Geraldine M. Grant, Andrea Ferreira‐Gonzalez, Carleton T. Garrett
Software Mentions: 1
Published: over 18 years ago

10.3390/cancers12102738

Schlafen 12 Is Prognostically Favorable and Reduces C-Myc and Proliferation in Lung Adenocarcinoma but Not in Lung Squamous Cell Carcinoma
Cited by: 8
Author(s): Sarmad Al-Marsoummi, Jonathan Pacella, Kaylee Dockter, Matthew Soderberg, Sandeep K. Singhal, Emilie E. Vomhof-DeKrey, Marc D. Basson
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-015-0854-z

Evaluation of O2PLS in Omics data integration
Cited by: 91
Author(s): Said el Bouhaddani, Jeanine J. Houwing-Duistermaat, Perttu Salo, Markus Perola, Geurt Jongbloed, Hae‐Won Uh
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-8-343

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model
Cited by: 12
Author(s): Ryoko Morioka, Shigehiko Kanaya, Masami Yokota Hirai, Mitsuru Yano, Nagahisa Ogasawara, Kazuki Saito
Software Mentions: 1
Published: over 18 years ago

10.1186/1755-8794-6-35

Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers
Cited by: 34
Author(s): Adam L. Cohen, Stephen R. Piccolo, Luis Cheng, Rafaella Soldi, Bing Han, W. Evan Johnson, Andrea Bild
Software Mentions: 1
Published: over 12 years ago

10.1016/j.cell.2013.07.007

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
Cited by: 148
Author(s): Klara Stefflova, David Thybert, Michael D. Wilson, Ian Streeter, J. Aleksić, Panagiota Karagianni, Alvis Brāzma, David J. Adams, Iannis Talianidis, John C. Marioni, Paul Flicek, Duncan T. Odom
Software Mentions: 1
Published: almost 13 years ago

10.1186/1755-8794-2-18

PrognoScan: a new database for meta-analysis of the prognostic value of genes
Cited by: 698
Author(s): Hideaki Mizuno, Koji Kitada, Katsunori Nakai, Akinori Sarai
Software Mentions: 1
Published: about 17 years ago

10.1186/1755-8794-2-41

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus
Cited by: 12
Author(s): Yaomin Hu, Pamela J. Kaisaki, Karène Argoud, Steven P. Wilder, Karin J. Wallace, Peng Yeong Woon, Christine Blancher, Lise Tarnow, Per‐Henrik Groop, Samy Hadjadj, Michel Marre, Hans‐Henrik Parving, Martin Farrall, Roger D. Cox, Mark Lathrop, Nathalie Vionnet, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 1
Published: almost 17 years ago

10.1038/cddis.2017.109

Convergence and divergence between the transcriptional responses to Zika virus infection and prenatal irradiation
Cited by: 5
Author(s): Roel Quintens
Software Mentions: 1
Published: over 9 years ago

10.1186/1755-8794-3-5

Insight in modulation of inflammation in response to diclofenac intervention: a human intervention study
Cited by: 34
Author(s): Marjan J. van Erk, Suzan Wopereis, Carina M. Rubingh, T. van Vliet, Elwin Verheij, N.H.P. Cnubben, Theresa L. Pedersen, John W. Newman, Age K. Smilde, J. van der Greef, H. Hendriks, Ben van Ommen
Software Mentions: 1
Published: over 16 years ago

10.1038/s41419-019-1496-2

Enhancing folic acid metabolism suppresses defects associated with loss of Drosophila mitofusin
Cited by: 11
Author(s): Juan Garrido-Maraver, Ivana Celardo, Ana Carolina Oliveira Costa, Susann Lehmann, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 1
Published: about 7 years ago

10.1038/s41419-018-0681-z

CD24 regulates sorafenib resistance via activating autophagy in hepatocellular carcinoma
Cited by: 83
Author(s): Shan Lü, Yao Yao, Guolong Xu, Chao Zhou, Yuan Zhang, Jie Sun, Runqiu Jiang, Qing Shao, Yun Chen
Software Mentions: 1
Published: about 8 years ago

10.1038/s41419-020-2449-5

Enhanced fatty acid oxidation provides glioblastoma cells metabolic plasticity to accommodate to its dynamic nutrient microenvironment
Cited by: 59
Author(s): Shri Kant, Pravin Kesarwani, Antony Prabhu, Stewart F. Graham, Katie L. Buelow, Ichiro Nakano, Prakash Chinnaiyan
Software Mentions: 1
Published: about 6 years ago

10.1038/s41419-018-0933-y

The bHLH transcription factor DEC1 promotes thyroid cancer aggressiveness by the interplay with NOTCH1
Cited by: 25
Author(s): Cristina Gallo, Valentina Fragliasso, Benedetta Donati, Federica Torricelli, Annalisa Tameni, Simonetta Piana, Alessia Ciarrocchi
Software Mentions: 1
Published: almost 8 years ago

10.1186/1755-8794-2-12

Impaired immune function in Gulf War Illness
Cited by: 71
Author(s): Toni Whistler, Mary A Fletcher, William Lonergan, Xiao Rong Zeng, Jin Mann S. Lin, A. LaPerriere, Suzanne D. Vernon, Nancy G. Klimas
Software Mentions: 1
Published: over 17 years ago

10.1038/s41419-020-03129-x

Suppression of poised oncogenes by ZMYND8 promotes chemo-sensitization
Cited by: 10
Author(s): Shravanti Mukherjee, Santanu Adhikary, Shrikanth S. Gadad, Payel Mondal, Sabyasachi Sen, Ramesh Choudhari, Vipin Kumar Singh, Swagata Adhikari, Pratiti Mandal, Soumi Chaudhuri, Aditi Sengupta, Rajkumar Lakshmanaswamy, Partha Chakrabarti, Siddhartha Roy, Chandrima Das
Software Mentions: 1
Published: over 5 years ago

10.1111/j.1462-5822.2007.01099.x

During infection of epithelial cells Salmonella enterica serovar Typhimurium undergoes a time-dependent transcriptional adaptation that results in simultaneous expression of three type 3 secretion systems
Cited by: 230
Author(s): Isabelle Hautefort, Arthur R. Thompson, Sofia Eriksson-Ygberg, Mary L. Parker, Sacha Lucchini, Vittoria Danino, Roy J. Bongaerts, Norazah Ahmad, Mikael Rhen, Jay C. D. Hinton
Software Mentions: 1
Published: about 18 years ago

10.1111/cpr.13015

TSP50 promotes hepatocyte proliferation and tumour formation by activating glucose‐6‐phosphate dehydrogenase (G6PD)
Cited by: 12
Author(s): Xiaojun Zhang, Feng Gao, Huihan Ai, Shuyue Wang, Zhenbo Song, Lihua Zheng, Guannan Wang, Yu Sun, Yongli Bao
Software Mentions: 1
Published: over 5 years ago

10.1186/1755-8794-1-33

An approach to analyse the specific impact of rapamycin on mRNA-ribosome association
Cited by: 16
Author(s): Raphaël Genolet, Tanguy Araud, Laetitia Maillard, Pascale Jaquier-Gubler, Joseph Curran
Software Mentions: 1
Published: almost 18 years ago

10.1016/j.celrep.2016.03.007

G9a/GLP Complex Maintains Imprinted DNA Methylation in Embryonic Stem Cells
Cited by: 90
Author(s): Tuo Zhang, Ausma Termanis, Burak Özkan, Xun X. Bao, Jayne Culley, Flávia de Lima Alves, Juri Rappsilber, Bernard Ramsahoye, Irina Stancheva
Software Mentions: 1
Published: about 10 years ago

10.1186/1755-8794-2-11

Promoter methylation correlates with reduced NDRG2expression in advanced colon tumour
Cited by: 36
Author(s): Ada Piepoli, Rosa Cotugno, Giuseppe Merla, Annamaria Gentile, Bartolomeo Augello, M. Quitadamo, Antonio Merla, Anna Panza, Massimo Carella, Rosalia Maglietta, A. D’Addabbo, Nicola Ancona, Saverio Fusilli, Francesco Perri, Angelo Andriulli
Software Mentions: 1
Published: over 17 years ago

10.1186/s12920-016-0227-0

A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without
Cited by: 10
Author(s): Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner, Nicki Tiffin
Software Mentions: 1
Published: over 9 years ago

10.1016/j.crmeth.2021.100054

Retrospective cell lineage reconstruction in humans by using short tandem repeats
Cited by: 7
Author(s): Liming Tao, Ofir Raz, Zipora Marx, Manjusha Ghosh, Sandra Huber, Julia Greindl-Junghans, Tamir Biezuner, Shiran Amir, Lilach Milo, R Adar, Ronald Levy, Amos Onn, Noa Chapal-Ilani, Veronika Berman, Asaf Ben Arie, Guy Rom, Barak Oron, Ruth Halaban, Zbigniew T. Czyż, Melanie Werner-Klein, Christoph Klein, Ehud Shapiro
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2350-8-36

Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets
Cited by: 110
Author(s): ChaRandle Jordan, Hong Hua Li, Helen H. Kwan, Uta Francke
Software Mentions: 1
Published: almost 19 years ago

10.1186/s12916-017-0929-y

A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes
Cited by: 40
Author(s): Jean‐Philippe Foy, Louis Bazire, Sandra Ortiz-Cuàran, Sophie Deneuve, Janice Kielbassa, Emilie Thomas, Alain Viari, Alain Puisieux, P. Goudot, Chloé Bertolus, Nicolas Foray, Youlia Kirova, Pierre Verrelle, Pierre Saintigny
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12916-016-0609-3

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy
Cited by: 45
Author(s): Isobella Honeyborne, Timothy D. McHugh, Iitu Kuittinen, Anna Cichońska, Dimitrios Evangelopoulos, Katharina Ronacher, Paul D. van Helden, Stephen H. Gillespie, Delmiro Fernández-Reyes, Gerhard Walzl, Juho Rousu, Philip D. Butcher, Simon J. Waddell
Software Mentions: 1
Published: about 10 years ago

10.1186/s12879-016-1533-z

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
Cited by: 13
Author(s): Steven T. Pullan, Jon C. Allnutt, Rebecca Devine, Kim A. Hatch, Rose E. Jeeves, Charlotte L. Hendon-Dunn, Philip Marsh, Joanna Bacon
Software Mentions: 1
Published: about 10 years ago

10.3390/cells9010142

Dissecting Mechanisms of Melanoma Resistance to BRAF and MEK Inhibitors Revealed Genetic and Non-Genetic Patient- and Drug-Specific Alterations and Remarkable Phenotypic Plasticity
Cited by: 41
Author(s): Mariusz L. Hartman, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Małgorzata Czyż
Software Mentions: 1
Published: over 6 years ago

10.3390/cells8121554

Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study
Cited by: 9
Author(s): Enrica Calura, Matteo Ciciani, Andrea Sambugaro, Lara Paracchini, Giuseppe Benvenuto, Salvatore Milite, Paolo Martini, Luca Beltrame, Flaminia Zane, Robert Fruscio, Martina Delle Marchette, Fulvio Borella, Germana Tognon, Antonella Ravaggi, Dionyssios Katsaros, Eliana Bignotti, Franco Odicino, Maurizio D’Incalci, Sergio Marchini, Chiara Romualdi
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.03743

The transcription factor Pitx2 positions the embryonic axis and regulates twinning
Cited by: 33
Author(s): Angela Torlopp, Mohsin A.F. Khan, Nidia M M Oliveira, Ingrid Lekk, Luz Mayela Soto‐Jiménez, Alona Sosinsky, Claudio D. Stern
Software Mentions: 1
Published: over 11 years ago

10.3390/cells10030674

Acyl–Acyl Carrier Protein Desaturases and Plant Biotic Interactions
Cited by: 11
Author(s): Sami Kazaz, Romane Miray, Sébastien Baud
Software Mentions: 1
Published: about 5 years ago

10.1186/s12865-017-0238-4

Cattle infection response network and its functional modules
Cited by: 5
Author(s): Hamid Beiki, A. Pakdel, A Nejati Javaremi, Ali Masoudi‐Nejad, James M. Reecy
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-13-49

Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice
Cited by: 29
Author(s): Rumdeep K Grewal, S. K. Gupta, Sampa Das
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-15-438

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Cited by: 26
Author(s): Marta Vergara-Irigaray, María Fookes, Nicholas R. Thomson, Christoph M. Tang
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-12-S10-S2

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
Cited by: 14
Author(s): Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 1
Published: over 14 years ago

10.7554/eLife.09886

Protein kinase C coordinates histone H3 phosphorylation and acetylation
Cited by: 13
Author(s): Zoulfia Darieva, Aaron Webber, Stacey Warwood, Andrew D. Sharrocks
Software Mentions: 1
Published: over 10 years ago

10.18632/aging.101078

Human exceptional longevity: transcriptome from centenarians is distinct from septuagenarians and reveals a role of Bcl-xL in successful aging
Cited by: 37
Author(s): Consuelo Borrás, Kheira M. Abdelaziz, Juan Gambini, Eva Serna, Marta Inglés, Mónica De la Fuente, Idoia García, Ander Matheu, Paula Sanchís, Ángel Belenguer, Alessandra Errigo, Juan A. Avellana, Ana Barettino, Carla Lloret-Fernández, Nuria Flames, Giovanni Mario Pes, Leocadio Rodríguez‐Mañas, José Viña
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-016-2771-6

Transcriptomic response of yeast cells to ATX1 deletion under different copper levels
Cited by: 12
Author(s): Ayca Cankorur-Cetinkaya, Serpil Eraslan, Betül Kırdar
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13148-018-0542-8

Epigenetic regulation of ID4 in breast cancer: tumor suppressor or oncogene?
Cited by: 20
Author(s): Daniela Nasif, Emanuel Campoy, Sergio Laurito, Richard L. Branham, Guillermo Urrutia, María Roqué, Marı́a Teresita Branham
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-10-215

Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays
Cited by: 29
Author(s): Minjie Wang, Xiaoli Qi, Shutang Zhao, Shougong Zhang, Mengzhu Lu
Software Mentions: 1
Published: about 17 years ago

10.1186/s13148-020-00851-3

Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma
Cited by: 32
Author(s): Fan Jian, Jun Li, Shicheng Guo, Chengcheng Tao, Haikun Zhang, Wenjing Wang, Ying Zhang, Dake Zhang, Shigang Ding, Changqing Zeng
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-11-682

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Cited by: 40
Author(s): Richard A. Lewis, Emma Laing, Nicholas E. E. Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M. Kierzek, Colin P. Smith
Software Mentions: 1
Published: over 15 years ago

10.1007/s10585-016-9810-1

Prognostic value of 5-microRNA based signature in T2-T3N0 colon cancer
Cited by: 49
Author(s): Maciej Bobowicz, Marcin Skrzypski, Piotr Czapiewski, Michał Marczyk, Agnieszka Maciejewska, Michał Jankowski, Anna Szulgo-Paczkowska, Wojciech Zegarski, Ryszard Pawłowski, Joanna Polańska, Wojciech Biernat, Janusz Jaśkiewicz, Jacek Jassem
Software Mentions: 1
Published: almost 10 years ago

10.1093/cid/ciaa503

The Current Status of Enteric Fever Diagnostics and Implications for Disease Control
Cited by: 2
Author(s): Stephen Baker, Christoph J. Blohmke, Mailis Maes, Peter I Johnston, Thomas C. Darton
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2105-12-137

Assessing affymetrix GeneChip microarray quality
Cited by: 70
Author(s): Matthew N. McCall, Peter Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry
Software Mentions: 1
Published: about 15 years ago

10.1038/cti.2015.17

Expression profiling pre‐diabetic mice to uncover drugs with clinical application to type 1 diabetes
Cited by: 2
Author(s): Dimeng Pang, Katharine M. Irvine, Ahmed M. Mehdi, Helen E. Thomas, Mark Harris, Emma E. Hamilton‐Williams, Ranjeny Thomas
Software Mentions: 1
Published: almost 11 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962