bioconductor: ArrayExpress | Projects

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: almost 14 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

10.3389/fnbeh.2019.00103

Autonomic and Redox Imbalance Correlates With T-Lymphocyte Inflammation in a Model of Chronic Social Defeat Stress
Cited by: 23
Author(s): Cassandra Moshfegh, Safwan Elkhatib, Christopher W. Collins, Allison J. Kohl, Adam J. Case
Software Mentions: 1
Published: over 7 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: over 16 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: about 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: almost 13 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: 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: over 15 years ago

10.3389/fbioe.2015.00058

SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human
Cited by: 13
Author(s): Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Software Mentions: 1
Published: over 11 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/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: over 7 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

10.1186/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: over 20 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: about 12 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: over 19 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: over 20 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: over 19 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

10.1186/1471-2164-9-3

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: over 18 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

10.1186/1471-2164-8-202

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: over 19 years ago

10.1186/ar2090

Cited by: 71
Author(s): Johan Lindberg, Erik af Klint, Anca I. Catrina, Peter Nilsson, Lars Klareskog, Ann‐Kristin Ulfgren, Joakim Lundeberg
Software Mentions: 1
Published: over 20 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: over 13 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: over 19 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: almost 19 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 10 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: about 8 years ago

10.3390/ijms21103480

The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds
Cited by: 33
Author(s): Juliette Legler, Daniel Zalko, Fabien Jourdan, Miriam N. Jacobs, Bernard Fromenty, Patrick Balaguer, William Bourguet, Vesna Munić Kos, Ángel Nadal, Claire Beausoleil, Susana Cristóbal, Sylvie Remy, Sibylle Ermler, Luigi Margiotta-Casaluci, Julian L. Griffin, Bruce Blumberg, Christophe Chesné, Sebastian Hoffmann, Patrik L. Andersson, Jorke H. Kamstra
Software Mentions: 1
Published: over 6 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

10.1186/1471-2164-7-113

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 20 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

10.1186/1471-2164-14-301

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 13 years ago

10.3390/ijms21113749

17-Aminogeldanamycin Inhibits Constitutive Nuclear Factor-Kappa B (NF-κB) Activity in Patient-Derived Melanoma Cell Lines
Cited by: 7
Author(s): Mariusz L. Hartman, Magdalena Rogut, Aleksandra Mielczarek-Lewandowska, Michal Wozniak, Małgorzata Czyż
Software Mentions: 1
Published: about 6 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: over 18 years ago

10.1186/ar2311

SOX9 transduction of a human chondrocytic cell line identifies novel genes regulated in primary human chondrocytes and in osteoarthritis
Cited by: 61
Author(s): Simon R. Tew, Peter Clegg, Christopher J Brew, C. Redmond, Timothy E. Hardingham
Software Mentions: 1
Published: over 19 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: over 13 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 6 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: almost 9 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: about 6 years ago

10.3390/ijms21124442

Functional Heterogeneity of Protein Kinase A Activation in Multipotent Stromal Cells
Cited by: 11
Author(s): Pyotr A. Tyurin‐Kuzmin, Maxim Karagyaur, Konstantin Kulebyakin, Daniyar T. Dyikanov, Vadim Chechekhin, Anastasiya M Ivanova, Mariya Skryabina, Mikhail Arbatskiy, Veronika Sysoeva, Kalinina Ni, В. А. Ткачук
Software Mentions: 1
Published: about 6 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

10.1186/s13023-014-0160-2

Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes
Cited by: 15
Author(s): Pilvi Maliniemi, Sonja Hahtola, Kristian Ovaska, Leila Jeskanen, Liisa Väkevä, Kirsi Jäntti, Rudolf Stadler, David Michonneau, Sylvie Fraïtag, Sampsa Hautaniemi, Annamari Ranki
Software Mentions: 1
Published: almost 12 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: over 6 years ago

10.3390/ijms21207437

Targeting SRC Kinase Signaling in Pancreatic Cancer Stem Cells
Cited by: 17
Author(s): Sonia Alcalá, Víctor Mayoral-Varo, Laura Ruiz-Cañas, Juan Carlos López-Gil, Christopher Heeschen, Jorge Martı́n-Pérez, Bruno Sáinz
Software Mentions: 1
Published: almost 6 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: almost 6 years ago

10.3390/ijms21218069

Intra-Individual Behavioural Variability: A Trait under Genetic Control
Cited by: 12
Author(s): Rie Henriksen, Andrey Höglund, Jesper Fogelholm, Robin N. Abbey-Lee, Martin Johnsson, Niels Jeroen Dingemanse, Dominic Wright
Software Mentions: 1
Published: almost 6 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: almost 10 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: over 15 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: about 13 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: about 10 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: about 16 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

10.1186/1471-2164-11-93

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: 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: over 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: over 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

10.1186/1471-2164-8-377

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards
Cited by: 4
Author(s): Torunn Bruland, Endre Anderssen, Berit Doseth, Hallgeir Bergum, Vidar Beisvåg, Astrid Lægreid
Software Mentions: 1
Published: over 19 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: over 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

10.1186/1471-2164-11-389

Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile
Cited by: 24
Author(s): Gemma Marsden, Ian J. Davis, Victoria Wright, Mohammed Sebaihia, Ed J. Kuijper, Nigel P. Minton
Software Mentions: 1
Published: about 16 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: over 10 years ago

10.1186/1471-2164-7-224

Development and validation of a bovine macrophage specific cDNA microarray
Cited by: 38
Author(s): Kirsty Jensen, Richard Talbot, Edith Paxton, David Waddington, Elizabeth J. Glass
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2148-9-59

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation
Cited by: 53
Author(s): Arne W. Nolte, Sébastien Renaut, Louis Bernatchez
Software Mentions: 1
Published: over 17 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: about 5 years ago

10.1186/1471-213X-7-129

Gene array identification of Ipf1/Pdx1-/-regulated genes in pancreatic progenitor cells
Cited by: 26
Author(s): Per H. Svensson, Cecilia Williams, Joakim Lundeberg, Patrik Rydén, Ingela Bergqvist, Helena Edlund
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-213X-10-54

Analysis of the asymmetrically expressed Ablim1 locus reveals existence of a lateral plate Nodal-independent left sided signal and an early, left-right independent role for nodal flow
Cited by: 11
Author(s): Jonathan L. Stevens, А. Н. Ермаков, José Bragança, Helen Hilton, Peter A. Underhill, Shoumo Bhattacharya, Nigel A. Brown, Dominic P. Norris
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2407-12-260

Colon cancer molecular subtypes identified by expression profiling and associatedto stroma, mucinous type and different clinical behavior
Cited by: 112
Author(s): Beatriz Pérez-Villamil, Alejandro Romera Lopez, Susana Prieto, Guillermo López–Campos, Antonio Calles, J. A. Asenjo, Julián Sanz-Ortega, Cristina Fernández Pérez, Javier Sastre, Rosario Alfonso, Trinidad Caldés, Fernando Martín-Sánchez, Eduardo Díaz-Rubio
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2407-13-184

Expressional alterations in functional ultra-conserved non-coding rnas in response to all-transretinoic acid - induced differentiation in neuroblastoma cells
Cited by: 34
Author(s): Karen M. Watters, Kenneth Bryan, Niamh H. Foley, Maria Meehan, Raymond L. Stallings
Software Mentions: 1
Published: over 13 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

10.1186/ar3062

New insights into the pathogenesis of glucocorticoid-induced avascular necrosis: microarray analysis of gene expression in a rat model
Cited by: 47
Author(s): Mohammad Amin Kerachian, Denis Cournoyer, Edward J. Harvey, Terry Y.-K. Chow, Louis R. Bégin, Ayoub Nahal, Chantal Séguin
Software Mentions: 1
Published: over 16 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: over 5 years ago

10.1186/1471-2407-14-871

Estrogen independent gene expression defines clinically relevant subgroups of estrogen receptor positive breast cancer
Cited by: 4
Author(s): Robin Hallett, John A. Hassell
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2407-10-176

Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells
Cited by: 12
Author(s): Michael St.Pierre, Benoît DeHertogh, Anthoula Gaigneaux, Bertrand DeMeulder, Fabrice Berger, Eric Bareke, Carine Michiels, Eric Depiereux
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2407-10-482

Differential detection of alternatively spliced variants of Ciz1 in normal and cancer cells using a custom exon-junction microarray
Cited by: 22
Author(s): Faisal Rahman, Naveed Aziz, Dawn Coverley
Software Mentions: 1
Published: almost 16 years ago

10.3390/ijms22126505

Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods
Cited by: 2
Author(s): Jishizhan Chen, Jia Hua, Wenhui Song
Software Mentions: 1
Published: about 5 years ago

10.1186/1479-5876-9-72

SULFs in human neoplasia: implication as progression and prognosis factors
Cited by: 68
Author(s): Caroline Bret, Jérôme Moreaux, Jean‐François Schved, Dirk Hose, Bernard Klein
Software Mentions: 1
Published: about 15 years ago

10.1155/2019/1697913

Plasticity of Drug-Naïve and Vemurafenib- or Trametinib-Resistant Melanoma Cells in Execution of Differentiation/Pigmentation Program
Cited by: 24
Author(s): Małgorzata Czyż, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Marta Osrodek, Mariusz L. Hartman
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2407-12-608

Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon
Cited by: 16
Author(s): Rosalia Maglietta, Vania C. Liuzzi, Elisa Cattaneo, Endre Laczkó, Ada Piepoli, Anna Panza, Massimo Carella, Orazio Palumbo, Teresa Staiano, Federico Buffoli, Angelo Andriulli, Giancarlo Marra, Nicola Ancona
Software Mentions: 1
Published: over 13 years ago

10.3390/md17100576

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
Cited by: 21
Author(s): Luca Ambrosino, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone, Maria Luisa Chiusano
Software Mentions: 1
Published: almost 7 years ago

10.1155/2010/784343

Leptin Administration Downregulates the Increased Expression Levels of Genes Related to Oxidative Stress and Inflammation in the Skeletal Muscle of<i>ob/ob</i>Mice
Cited by: 32
Author(s): Neira Sáinz, Amaia Rodríguez, Victoria Catalán, Sara Becerril, Beatriz Ramírez, Javier Gómez-Ambrosi, Gema Frühbeck
Software Mentions: 1
Published: over 16 years ago

10.1097/MD.0000000000004085

Expression profile of SIX family members correlates with clinic-pathological features and prognosis of breast cancer
Cited by: 32
Author(s): Xu Han, Kong Ju Wu, Yi Jun Tian, Qian Liu, Na Han, Xue Lian He, Xun Yuan, Gen Sheng Wu, Kai Wu
Software Mentions: 1
Published: about 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

10.26508/lsa.201900371

Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS
Cited by: 9
Author(s): Shaked Afik, Gabriel Raulet, Nir Yosef
Software Mentions: 1
Published: about 7 years ago

10.3390/metabo2040983

Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore
Cited by: 3
Author(s): Andreas Hoppe, Iryna Ilkavets, Steven Dooley, Hermann−Georg Holzhütter
Software Mentions: 1
Published: over 13 years ago

10.26508/lsa.201900494

The CCR4–NOT complex maintains liver homeostasis through mRNA deadenylation
Cited by: 15
Author(s): Akinori Takahashi, Toru Suzuki, Shou Soeda, Shohei Takaoka, Shungo Kobori, Tomokazu Yamaguchi, Haytham Mohamed Aly Mohamed, Akiko Yanagiya, Takaya Abe, Mayo Shigeta, Yasuhide Furuta, Keiji Kuba, Tadashi Yamamoto
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2407-8-18

Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation
Cited by: 11
Author(s): Olivier Gevaert, Frank De Smet, Toon Van Gorp, Nathalie Pochet, Kristof Engelen, Frédéric Amant, Bart De Moor, Dirk Timmerman, Ignace Vergote
Software Mentions: 1
Published: over 18 years ago

10.3390/microarrays3040322

Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data
Cited by: 10
Author(s): Mario Fasold, Hans Binder
Software Mentions: 1
Published: over 11 years ago

10.3390/microarrays4040454

Genomic-Wide Analysis with Microarrays in Human Oncology
Cited by: 10
Author(s): Kenichi Inaoka, Yoshikuni Inokawa, Shuji Nomoto
Software Mentions: 1
Published: almost 11 years ago

10.3390/life6040042

Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects
Cited by: 60
Author(s): Lamya Al‐Haj, Yuen Tin Lui, Raeid M. M. Abed, Mohamed Gomaa, Saul Purton
Software Mentions: 1
Published: over 9 years ago

10.1016/S2213-2600(19)30282-6

Concise whole blood transcriptional signatures for incipient tuberculosis: a systematic review and patient-level pooled meta-analysis
Cited by: 112
Author(s): Gupta Rk, Chris Turner, Cristina Venturini, Hanif Esmail, Molebogeng X Rangaka, Andrew Copas, Marc Lipman, Ibrahim Abubakar, Mahdad Noursadeghi
Software Mentions: 1
Published: over 6 years ago

10.1186/s41199-020-0047-y

Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures
Cited by: 21
Author(s): Mara Serena Serafini, Laura Lopez-Perez, Giuseppe Fico, Lisa Licitra, Loris De Cecco, Carlo Resteghini
Software Mentions: 1
Published: over 6 years ago

10.1186/1475-2859-6-4

A perspective on microarrays: current applications, pitfalls, and potential uses
Cited by: 90
Author(s): Pratik Jaluria, Κωνσταντίνος Κωνσταντόπουλος, Michael J. Betenbaugh, Joseph Shiloach
Software Mentions: 1
Published: over 19 years ago

10.1099/mic.0.000423

Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon
Cited by: 19
Author(s): Thomas D Curran, Fatima Abacha, Stephen P Hibberd, Matthew D. Rolfe, Melissa M. Lacey, Jeffrey Green
Software Mentions: 1
Published: over 9 years ago

10.1099/mic.0.028282-0

The pneumococcal response to oxidative stress includes a role for Rgg
Cited by: 45
Author(s): Magda E. Bortoni, Vanessa S. Terra, Jason Hinds, Peter W. Andrew, Hasan Yeşilkaya
Software Mentions: 1
Published: over 16 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962