bioconductor: ArrayExpress | Projects

10.1186/1471-2105-7-489

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Cited by: 197
Author(s): Tim Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert, Joseph A. White, Patricia L. Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brāzma
Software Mentions: 1
Published: about 18 years ago

10.3389/fgene.2014.00191

Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
Cited by: 19
Author(s): Miguel A. Hernández‐Prieto, T. A. Semeniuk, Matthias E. Futschik
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-8-210

Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state
Cited by: 1
Author(s): Daniel Y L Yap, David K. Smith, Xue W Zhang, Jeffrey Hill
Software Mentions: 1
Published: almost 18 years ago

10.1002/path.5335

Overactivity or blockade of transforming growth factor‐β each generate a specific ureter malformation
Cited by: 11
Author(s): Filipa Lopes, Neil Roberts, Leo Zeef, Natalie J. Gardiner, Adrian S. Woolf
Software Mentions: 1
Published: about 5 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: over 5 years ago

10.3389/fgene.2018.00125

Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells
Cited by: 32
Author(s): Maria Chiara Pelleri, Chiara Cattani, Lorenza Vitale, Francesca Antonaros, Pierluigi Strippoli, Chiara Locatelli, Guido Cocchi, Allison Piovesan, Maria Caracausi
Software Mentions: 1
Published: over 6 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: over 5 years ago

10.1186/1471-2164-7-78

Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity
Cited by: 34
Author(s): Vattipally B Sreenu, Pankaj Kumar, Javaregowda Nagaraju, Hampapathalu A. Nagarajaram
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-10-560

ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles
Cited by: 1
Author(s): Weizhong Li, Andrew Y. Gracey, Luciane V. Mello, Andy Brass, Andrew R. Cossins
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2105-11-150

Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes
Cited by: 41
Author(s): Sigrid Rouam, Thierry Moreau, Philippe Broët
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-9-183

Data capture in bioinformatics: requirements and experiences with Pedro
Cited by: 16
Author(s): Daniel Jameson, Kevin Garwood, Christopher Garwood, Tim Booth, Pinar Alper, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: over 16 years ago

10.3389/fgene.2014.00206

Evolutionary analysis of the cystatin family in three Schistosoma species
Cited by: 13
Author(s): Yesid Cuesta-Astroz, Larissa Lopes Silva Scholte, Fabiano Sviatopolk-Mirsky Pais, Guilherme Oliveira, Laila Alves Nahum
Software Mentions: 1
Published: over 10 years ago

10.3389/fimmu.2013.00353

MicroRNA-Mediated Down-Regulation of M-CSF Receptor Contributes to Maturation of Mouse Monocyte-Derived Dendritic Cells
Cited by: 28
Author(s): Joey Riepsaame, A. Van Oudenaren, Berlinda J. H. den Broeder, Wilfred F. J. van IJcken, Joris Pothof, Pieter J. M. Leenen
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-10-153

Learning from microarray interlaboratory studies: measures of precision for gene expression
Cited by: 9
Author(s): David L. Duewer, Wendell Jones, Laura Reid, Marc Salit
Software Mentions: 1
Published: almost 16 years ago

10.3389/fimmu.2021.653110

Endothelial Immunity Trained by Coronavirus Infections, DAMP Stimulations and Regulated by Anti-Oxidant NRF2 May Contribute to Inflammations, Myelopoiesis, COVID-19 Cytokine Storms and Thromboembolism
Cited by: 37
Author(s): Ying Shao, Jason Saredy, Keman Xu, Yu Sun, Fatma Saaoud, Charles Drummer, Yifan Lu, Jin Jun Luo, Jahaira Lopez-Pastraña, Eric T. Choi, Xiaohua Jiang, Hong Wang, Xiaofeng Yang
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-10-306

Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Cited by: 30
Author(s): Jin Hwan, Rui Yamaguchi, Satoru Miyano
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-8-401

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
Cited by: 12
Author(s): Santiago P. Aubourg, Marie‐Laure Martin‐Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E. Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, Jean-Pierre Renou
Software Mentions: 1
Published: almost 18 years ago

10.3389/fimmu.2021.631044

An Immunological Perspective: What Happened to Pregnant Women After Recovering From COVID-19?
Cited by: 12
Author(s): Sijia Zhao, Ting Xie, Li Shen, Hong Liu, Liling Wang, Xixiang Ma, Jiankang Wu, Shuiqiao Yuan, Gil Mor, Aihua Liao
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-10-42

Positive correlation between gene coexpression and positional clustering in the zebrafish genome
Cited by: 28
Author(s): Yen Kaow Ng, Wei Wu, Louxin Zhang
Software Mentions: 1
Published: almost 16 years ago

10.3389/fimmu.2018.01425

Chromatin Binding of c-REL and p65 Is Not Limiting for Macrophage IL12B Transcription During Immediate Suppression by Ovarian Carcinoma Ascites
Cited by: 11
Author(s): Annika Unger, Florian Finkernagel, Nathalie Hoffmann, Felix Neuhaus, Barbara Joos, Andrea Nist, Thorsten Stiewe, Alexander Visekruna, Uwe Wagner, Silke Reinartz, Sabine Müller‐Brüsselbach, Rolf Müller, Till Adhikary
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2016.00272

Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging
Cited by: 22
Author(s): Jeffrey L. Ebersole, Sreenatha Kirakodu, M. John Novak, Luis Orraca, Janis Gonzalez Martinez, Larry L. Cunningham, Mark V. Thomas, Arnold J. Stromberg, Subramanya Pandruvada, Octavio A. González
Software Mentions: 1
Published: over 8 years ago

10.3389/fimmu.2018.00032

Induction of Short NFATc1/αA Isoform Interferes with Peripheral B Cell Differentiation
Cited by: 4
Author(s): Khalid Muhammad, Ronald Rudolf, Duong Anh Thuy Pham, Stefan Klein-Heßling, Katsuyoshi Takata, Nobuko Matsushita, Volker Ellenrieder, Eisaku Kondo, Edgar Serfling
Software Mentions: 1
Published: almost 7 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: about 5 years ago

10.3389/fimmu.2017.00479

Co-Inflammatory Roles of TGFβ1 in the Presence of TNFα Drive a Pro-inflammatory Fate in Mesenchymal Stem Cells
Cited by: 25
Author(s): Shalom Lerrer, Yulia Liubomirski, Alexander Bott, Khalid Abnaof, Nino Oren, Afsheen Yousaf, Cindy Körner, Tsipi Meshel, Stefan Wiemann, Adit Ben‐Baruch
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-12-620

An expression map for Anopheles gambiae
Cited by: 27
Author(s): Robert M. MacCallum, Seth Redmond, George K. Christophides
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-9-340

Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
Cited by: 87
Author(s): Marcel Scheideler, Christian Elabd, Laure‐Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fátima Sánchez‐Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gérard Ailhaud, Christian Dani, Ez-Zoubir Amri, Zlatko Trajanoski
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-10-S12-S10

Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
Cited by: 4
Author(s): Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-6-178

GPX-Macrophage Expression Atlas: A database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
Cited by: 16
Author(s): Graeme R. Grimes, Stuart Moodie, John S. Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D. Livingston, Muriel Mewissen, Kevin A. Robertson, Alan J. Ross, Garwin K. Sing, Peter Ghazal
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2105-14-8

XperimentR: painless annotation of a biological experiment for the laboratory scientist
Cited by: 7
Author(s): Christopher Tomlinson, Geraint Barton, Mark Woodbridge, Sarah Butcher
Software Mentions: 1
Published: almost 12 years ago

10.3389/fimmu.2020.585414

Oral Microbiome and Gingival Tissue Apoptosis and Autophagy Transcriptomics
Cited by: 10
Author(s): Jeffrey L. Ebersole, Sreenatha Kirakodu, Elliot Neumann, Luis Orraca, Janis Gonzalez Martinez, Octavio A. González
Software Mentions: 1
Published: about 4 years ago

10.3389/fimmu.2020.00438

Dual Pro- and Anti-Inflammatory Features of Monocyte-Derived Dendritic Cells
Cited by: 12
Author(s): Waqas Azeem, Ragnhild Maukon Bakke, Silke Appel, Anne Margrete Øyan, Karl‐Henning Kalland
Software Mentions: 1
Published: over 4 years ago

10.1002/cjp2.138

High immune cytolytic activity in tumor‐free tongue tissue confers better prognosis in patients with squamous cell carcinoma of the oral tongue
Cited by: 13
Author(s): Xiaolian Gu, Linda Boldrup, Philip J. Coates, Robin Fåhræus, Lixiao Wang, Torben Wilms, Lena Norberg‐Spaak, Nicola Sgaramella, Karin Nylander
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-9-221

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA
Cited by: 5
Author(s): Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A. Setterquist, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 16 years ago

10.3389/fimmu.2020.00380

Development of a Bioinformatics Framework for Identification and Validation of Genomic Biomarkers and Key Immunopathology Processes and Controllers in Infectious and Non-infectious Severe Inflammatory Response Syndrome
Cited by: 14
Author(s): Dong Tong, Karen E. Kempsell, Tamás Szakmány, Graham Ball
Software Mentions: 1
Published: over 4 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: over 11 years ago

10.1186/1471-2164-13-33

Transcriptional ontogeny of the developing liver
Cited by: 41
Author(s): Janice S. Lee, William O. Ward, Geremy W. Knapp, Hongzu Ren, Beena Vallanat, Barbara D. Abbott, Karen J. Ho, Seth J. Karp, J. Christopher Corton
Software Mentions: 1
Published: almost 13 years ago

10.3389/fmed.2020.527433

Distinct miRNA Gene Expression Profiles Among the Nodule Tissues of Lung Sarcoidosis, Tuberculous Lymphadenitis and Normal Healthy Control Individuals
Cited by: 2
Author(s): Yunan Zhao, Wei Li, Qin Zhang, Yan Yin, Chuanjia Yang, Wen-Xiang Xu, Jian Kang, Ruiqun Qi, Gang Hou
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2019.01157

Inactivation of farR Causes High Rhodomyrtone Resistance and Increased Pathogenicity in Staphylococcus aureus
Cited by: 13
Author(s): Minh Thu Nguyen, Jongkon Saising, Paula María Tribelli, Mulugeta Nega, Seydina M. Diène, Patrice François, Jacques Schrenzel, Cathrin Spröer, Boyke Bunk, Patrick Ebner, Tobias Hertlein, Nimerta Kumari, Thomas Härtner, Dorothee Wistuba, Supayang Piyawan Voravuthikunchai, Ulrike Mäder, Knut Ohlsen, Friedrich Götz
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2017.02039

A Novel TetR-Like Transcriptional Regulator Is Induced in Acid-Nitrosative Stress and Controls Expression of an Efflux Pump in Mycobacteria
Cited by: 9
Author(s): Filomena Perrone, Barbara De Siena, Lidia Muscariello, Sharon L. Kendall, Simon J. Waddell, Margherita Sacco
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2016.00759

The Chromatin of Candida albicans Pericentromeres Bears Features of Both Euchromatin and Heterochromatin
Cited by: 13
Author(s): Verónica Freire-Benéitez, R. Jordan Price, Alessia Buscaino
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-11-418

Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)
Cited by: 124
Author(s): Samuel Martín, Alex Douglas, D.F. Houlihan, Christopher J. Secombes
Software Mentions: 1
Published: almost 15 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: about 11 years ago

10.3389/fmicb.2018.01952

Coumarin Reduces Virulence and Biofilm Formation in Pseudomonas aeruginosa by Affecting Quorum Sensing, Type III Secretion and C-di-GMP Levels
Cited by: 53
Author(s): Yunhui Zhang, Andrea Saß, Heleen Van Acker, Jasper Wille, Bruno Verhasselt, Filip Van Nieuwerburgh, Volkhard Kaever, Aurélie Crabbé, Tom Coenye
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-8-360

Linking microarray reporters with protein functions
Cited by: 12
Author(s): Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. Evelo
Software Mentions: 1
Published: about 17 years ago

10.1186/ar1903

Cited by: 51
Author(s): Johan Lindberg, Erik af Klint, Ann‐Kristin Ulfgren, André Stark, T. Andersson, Peter Nilsson, Lars Klareskog, Joakim Lundeberg
Software Mentions: 1
Published: almost 19 years ago

10.1186/s12864-019-5464-0

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes
Cited by: 3
Author(s): Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny, Krzysztof Fujarewicz
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-69254-x

Identification of potential biomarkers for predicting the early onset of diabetic cardiomyopathy in a mouse model
Cited by: 8
Author(s): Rabia Johnson, Xolisa Nxele, Martin Cour, Nonhlakanipho F. Sangweni, Tracey Jooste, Nkanyiso Hadebe, Ebrahim Samodien, Mongi Benjeddou, Mikateko Mazino, Johan Louw, Sandrine Lecour
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.00763

An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA
Cited by: 12
Author(s): Marta Garrido, Jan-Philip Schlüter, Lars O. Loehr, Uwe Linne, Stefan P. Albaum, Josè I. Jiménez-Zurdo, Anke Becker
Software Mentions: 1
Published: over 6 years ago

10.1098/rsob.120091

Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations
Cited by: 27
Author(s): Matthew D. Rolfe, Andrea Ocone, Melanie R. Stapleton, Simon T.E. Hall, Eleanor W. Trotter, Robert K. Poole, Guido Sanguinetti, Jeffrey Green
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-7-319

Systematic interpretation of microarray data using experiment annotations
Cited by: 17
Author(s): Kurt Fellenberg, Christian Busold, Olaf Witt, Andrea S. Bauer, Boris Beckmann, Nicole Hauser, Marcus Frohme, Stefan Winter, Jürgen Dippon, Jörg D. Hoheisel
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-9-3

Switch-like genes populate cell communication pathways and are enriched for extracellular proteins
Cited by: 36
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-8-202

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees
Cited by: 48
Author(s): Moushumi Sen Sarma, Charles W. Whitfield, Gene E. Robinson
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-14-169

Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes
Cited by: 38
Author(s): Meagan J Gillespie, Tamsyn M. Crowley, Volker Häring, Susanne Wilson, Jennifer Harper, Jean Payne, Diane Green, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-8-181

Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni
Cited by: 34
Author(s): Michael Waisberg, Francisco Pereira Lobo, Gustavo C. Cerqueira, Liana Konovaloff Jannotti Passos, Omar S. Carvalho, Glória Regina Franco, Najib M. El-Sayed
Software Mentions: 1
Published: almost 18 years ago

10.1186/1743-7075-7-56

Identification of the Eph receptor pathway as a novel target for eicosapentaenoic acid (EPA) modification of gene expression in human colon adenocarcinoma cells (HT-29)
Cited by: 5
Author(s): Joanne F. Doleman, John J. Eady, Ruan Elliott, Robert J. Foxall, John Seers, Ian T. Johnson, Elizabeth K. Lund
Software Mentions: 1
Published: almost 15 years ago

10.3389/fninf.2014.00051

Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool
Cited by: 11
Author(s): Andrew Zaldivar, Jeffrey L. Krichmar
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-8-387

BMDExpress: a software tool for the benchmark dose analyses of genomic data
Cited by: 160
Author(s): Longlong Yang, Bruce C. Allen, Russell S. Thomas
Software Mentions: 1
Published: about 17 years ago

10.1186/s12864-016-2562-0

Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq
Cited by: 44
Author(s): Shaofeng Li, Chengming Fan, Yán Li, Jianhui Zhang, Jie Sun, Yuhong Chen, Tian Chen, Xiaohua Su, Mengzhu Lu, Chengzhi Liang, Zhongliang Hu
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-018-4954-9

Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression
Cited by: 13
Author(s): Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs, Susanne E. Ulbrich
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-7-113

Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes
Cited by: 41
Author(s): Maud Vallée, Claude Robert, S. Méthot, Marie‐France Palin, Marc‐André Sirard
Software Mentions: 1
Published: over 18 years ago

10.3389/fonc.2019.01515

CXCL1 as an Unfavorable Prognosis Factor Negatively Regulated by DACH1 in Non-small Cell Lung Cancer
Cited by: 24
Author(s): Shengnan Yu, Ming Yi, Lei Xu, Shuang Qin, An‐Ping Li, Kongming Wu
Software Mentions: 1
Published: almost 5 years ago

10.3389/fonc.2017.00332

Human Epididymis Protein 4 Promotes Events Associated with Metastatic Ovarian Cancer via Regulation of the Extracelluar Matrix
Cited by: 19
Author(s): Jennifer Ribeiro, Hilary Gaudet, Mehreen Ali Khan, Christoph Schorl, Nicole James, M. Oliver, Paul DiSilvestro, Richard G. Moore, Naohiro Yano
Software Mentions: 1
Published: almost 7 years ago

10.3389/fonc.2019.00026

EYA2 Correlates With Clinico-Pathological Features of Breast Cancer, Promotes Tumor Proliferation, and Predicts Poor Survival
Cited by: 16
Author(s): Hanxiao Xu, Yanmei Jiao, Ming Yi, Wei Zhao, Zeyu Wu
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis
Cited by: 53
Author(s): Victoria A Jenkins, Geraint Barton, Brian D. Robertson, Katrina Williams
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-8-450

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance
Cited by: 75
Author(s): Fanny Ramel, Cécile Sulmon, Francisco Cabello‐Hurtado, Ludivine Taconnat, Marie‐Laure Martin‐Magniette, Jean-Pierre Renou, Abdelhak El Amrani, Ivan Couée, Gwenola Gouesbet
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-14-710

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression
Cited by: 26
Author(s): Paul Golby, Javier Nuñez, Adam A. Witney, Jason Hinds, Michael A. Quail, Stephen D. Bentley, Simon R. Harris, Noel H. Smith, R. Glyn Hewinson, Stephen V. Gordon
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-020-6712-z

Lung transcriptomic clock predicts premature aging in cigarette smoke-exposed mice
Cited by: 12
Author(s): Mohamed-Amin Choukrallah, Julia Hoeng, Manuel C. Peitsch, Florian Martin
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-017-4200-x

Genes for asparagine metabolism in Lotus japonicus: differential expression and interconnection with photorespiration
Cited by: 8
Author(s): Margarita García‐Calderón, Carmen M. Pérez-Delgado, Alfredo Credali, José M. Vega, Marco Betti, Antonio J. Márquez
Software Mentions: 1
Published: about 7 years ago

10.3389/fonc.2021.605884

Exosomal LncRNA LBX1-AS1 Derived From RBPJ Overexpressed-Macrophages Inhibits Oral Squamous Cell Carcinoma Progress via miR-182-5p/FOXO3
Cited by: 17
Author(s): Yilong Ai, Haigang Wei, Si-Pei Wu, Zhe Tang, Xia Li, Chen Zou
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-12-12

Mesenteric lymph node transcriptome profiles in BALB/c mice sensitized to three common food allergens
Cited by: 12
Author(s): Mainul Husain, Herman J. Boermans, Niel A. Karrow
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-016-2803-2

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana
Cited by: 9
Author(s): Robert Hoffmann, Michael G. Palmgren
Software Mentions: 1
Published: over 8 years ago

10.1186/ar2294

Expression and regulation of CCL18 in synovial fluid neutrophils of patients with rheumatoid arthritis
Cited by: 49
Author(s): Judith Auer, Bläss Markus, Hendrik Schulze‐Koops, Stefan Rußwurm, Thomas Nagel, Joachim R. Kalden, Martin Röllinghoff, H U Beuscher
Software Mentions: 1
Published: almost 18 years ago

10.3389/fonc.2020.00044

Clinical Significance of Circulating miR-1273g-3p and miR-122-5p in Pancreatic Cancer
Cited by: 19
Author(s): Tommaso Mazza, Domenica Gioffreda, Andrea Fontana, Tommaso Biagini, Massimo Carella, Orazio Palumbo, Evaristo Maiello, Francesca Bazzocchi, Angelo Andriulli, Francesca Tavano
Software Mentions: 1
Published: almost 5 years ago

10.3389/fonc.2020.00068

Comprehensive Review of Web Servers and Bioinformatics Tools for Cancer Prognosis Analysis
Cited by: 70
Author(s): Hong Zheng, Guosen Zhang, Lu Zhang, Qiang Wang, Huimin Li, Yali Han, Longxiang Xie, Zhongyi Yan, Yongqiang Li, Yang An, H. Dong, Wan Zhu, Xiangqian Guo
Software Mentions: 1
Published: almost 5 years ago

10.3389/fonc.2019.00145

Spheroid-Induced Epithelial-Mesenchymal Transition Provokes Global Alterations of Breast Cancer Lipidome: A Multi-Layered Omics Analysis
Cited by: 29
Author(s): Yun Pyo Kang, Jung-ho Yoon, Nguyen Phuoc Long, Gi‐Bang Koo, Hyunjin Noh, Seung-Jae Oh, Sae Bom Lee, Hyung Min Kim, Ji Yeon Hong, Wonjun Lee, Seul Ji Lee, Soon‐Sun Hong, Sung Won Kwon, You‐Sun Kim
Software Mentions: 1
Published: over 5 years ago

10.3389/fphar.2018.00847

UBE2C Is a Potential Biomarker of Intestinal-Type Gastric Cancer With Chromosomal Instability
Cited by: 43
Author(s): Jun Zhang, Xinyu Liu, Guanzhen Yu, Lei Liu, Jiejun Wang, Xiaoyu Chen, Yuhai Bian, Yuan Ji, Xiaoyan Zhou, Yinan Chen, Jun Ji, Zhen Xiang, Li Guo, Jing‐Yuan Fang, Yihong Sun, Hui Cao, Zhenggang Zhu, Yingyan Yu
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-11-361

Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background
Cited by: 11
Author(s): Harry Noyes, Morris Agaba, Stuart Anderson, Alan Archibald, Andy Brass, John P. Gibson, Laurence S. Hall, Helen Hulme, Sung Jong Oh, Stephen J. Kemp
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-11-93

Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis
Cited by: 65
Author(s): Stephanus J. Ferreira, Melanie Senning, Sophia Sonnewald, Petra-Maria Keßling, Ralf Goldstein, Uwe Sonnewald
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1003594

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts
Cited by: 38
Author(s): Daria V. Zhernakova, Eleonora de Klerk, Harm-Jan Westra, Anastasios Mastrokolias, Shoaib Amini, Yavuz Ariyürek, Ritsert C. Jansen, Brenda W. J. H. Penninx, Jouke Jan Hottenga, Gonneke Willemsen, Eco J. C. de Geus, Dorret I. Boomsma, Jan H. Veldink, Leonard H van den Berg, Cisca Wijmenga, Johan T. den Dunnen, Gert‐Jan B. van Ommen, Peter A C ‘t Hoen, Lude Franke
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1004243

The Membrane-Associated Transcription Factor NAC089 Controls ER-Stress-Induced Programmed Cell Death in Plants
Cited by: 160
Author(s): Zhenle Yang, Mei-Jing Wang, Ling Sun, Sun-Jie Lu, Dongling Bi, Li‐Zhong Sun, Ze‐Ting Song, Shuang-Shuang Zhang, Shun-Fan Zhou, Jian‐Xiang Liu
Software Mentions: 1
Published: over 10 years ago

10.1186/ar2002

Cited by: 54
Author(s): Betti Giusti, Gabriella Fibbi, Francesca Margheri, Simona Serratì, Luciana Rossi, Filippo Poggi, Ilaria Lapini, Alberto Magi, Angela Del Rosso, Marina Cinelli, Serena Guiducci, Bashar Kahaleh, Laura Bazzichi, Stefano Bombardieri, Marco Matucci‐Cerinic, Gian Franco Gensini, Mario Del Rosso, Rosanna Abbate
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pcbi.1002126

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
Cited by: 80
Author(s): Tim D. Williams, Nahid Turan, Amer Diab, Huifeng Wu, Carolynn Mackenzie, Kerry L. Bartie, Olga Hrydziuszko, Brett P. Lyons, Grant D. Stentiford, John Herbert, Kuruvilla Joseph Abraham, Ioanna Katsiadaki, Michael J. Leaver, John B. Taggart, Stephen George, Mark R. Viant, Kevin Chipman, Francesco Falciani
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pgen.1002362

Caenorhabditis elegans Cyclin D/CDK4 and Cyclin E/CDK2 Induce Distinct Cell Cycle Re-Entry Programs in Differentiated Muscle Cells
Cited by: 32
Author(s): Jerome Korzelius, Suzan Ruijtenberg, Martine B.W. Prinsen, Vincent Portegijs, Teije C. Middelkoop, Marian J. A. Groot Koerkamp, Frank C. P. Holstege, Mike Boxem, Sander van den Heuvel
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pgen.1000599

A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene
Cited by: 290
Author(s): Chris Church, Sheena Lee, Eleanor A. L. Bagg, James S. McTaggart, Robert M. J. Deacon, Thomas A. Gerken, Angela Lee, Lee Moir, Jasmin Mecinović, Mohamed M. Quwailid, Christopher J. Schofield, Frances M. Ashcroft, Roger D. Cox
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pgen.1003160

Insulin and IGF1 Receptors Are Essential for XX and XY Gonadal Differentiation and Adrenal Development in Mice
Cited by: 110
Author(s): Jean-Luc Pitetti, Pierre Calvel, Yannick Romero, Béatrice Conne, Vy Truong, Marilena D. Papaioannou, Olivier Schaad, Mylène Docquier, Pedro Luis Herrera, Dagmar Wilhelm, Serge Nef
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1000851

Large-Scale Analysis of Network Bistability for Human Cancers
Cited by: 75
Author(s): Tetsuya Shiraishi, Shinako Matsuyama, Hiroaki Kitano
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1008549

Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs
Cited by: 15
Author(s): Satesh Ramdhani, Elisa Navarro, Evan Udine, Anastasia G. Efthymiou, Brian M Schilder, Madison Parks, Alison M. Goate, Towfique Raj
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pcbi.1000940

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions
Cited by: 63
Author(s): Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel T. Dudley, Szu Chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush, Minnie M. Sarwal, Atul J. Butte
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pcbi.1003597

Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation
Cited by: 10
Author(s): Marcus J. Tindall, Angela Clerk
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1002278

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Cited by: 65
Author(s): Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1000846

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome
Cited by: 220
Author(s): Juan M. Vaquerizas, Ritsuko Suyama, Jop Kind, Kota Miura, Nicholas M. Luscombe, Asifa Akhtar
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pbio.3001311

MHC class I H2-Kb negatively regulates neural progenitor cell proliferation by inhibiting FGFR signaling
Cited by: 12
Author(s): Karin Lin, Gregor Bieri, Géraldine Gontier, Sören Müller, Lucas K. Smith, Cedric E Snethlage, Charles White, Sun Y. Maybury-Lewis, Saul Villeda
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pbio.0030297

Bioinformatics and Data Management Support for Environmental Genomics
Cited by: 23
Author(s): Dawn Field, Bela Tiwari, Jason Snape
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pbio.0030384

Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning
Cited by: 394
Author(s): Benoît Guillemette, Alain R. Bataille, Nicolas Gévry, Maryse Adam, Mathieu Blanchette, François Robert, Luc Gaudreau
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pbio.0020317

Submission of Microarray Data to Public Repositories
Cited by: 113
Author(s): Catherine A. Ball, Alvis Brāzma, Helen C. Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna Assunta Sansone, Gavin Sherlock, Paul T. Spellman, C. J. Stoeckert, Yoshio Tateno, Ron Taylor, Joseph A. White, Neil Winegarden
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pgen.1000479

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference
Cited by: 117
Author(s): Eric A. Stone, Julien F. Ayroles
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pgen.1000470

SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing
Cited by: 75
Author(s): Anu Tyagi, Jessica Ryme, David Brodin, A K Ostlund Farrants, Neus Visa
Software Mentions: 1
Published: over 15 years ago

10.1186/s13007-016-0144-4

Measures for interoperability of phenotypic data: minimum information requirements and formatting
Cited by: 98
Author(s): Hanna Ćwiek‐Kupczyńska, Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun Chen, Guillaume Cornut, Fabio Fiorani, Wojciech Frohmberg, Astrid Junker, Christian Klukas, Matthias Lange, Cezary Mazurek, Anahita Nafissi, Pascal Neveu, Jan van Oeveren, Cyril Pommier, Hendrik Poorter, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Marco van Schriek, Ümit Seren, Björn Usadel, Stéphan Weise, Paul J. Kersey, Paweł Krajewski
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1003734

Comparative Oncogenomic Analysis of Copy Number Alterations in Human and Zebrafish Tumors Enables Cancer Driver Discovery
Cited by: 31
Author(s): Guangjun Zhang, Sebastian Hoersch, Adam Amsterdam, Charles A. Whittaker, Eline Beert, Julian M. Catchen, Sarah Farrington, John H. Postlethwait, Eric Legius, Nancy Hopkins, Jacqueline A. Lees
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pgen.1006000

Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
Cited by: 50
Author(s): Katarina Truvé, Peter J. Dickinson, Anqi Xiong, Daniel York, Kartika Jayashankar, Gerli Pielberg, Michele Koltookian, Eva Murén, Hans Henrik Fuxelius, Holger Weishaupt, Fredrik J. Swartling, Gerhard Andersson, Åke Hedhammar, Erik Bongcam‐Rudloff, Karin Forsberg-Nilsson, Danika L. Bannasch, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962