bioconductor: ArrayExpress | Projects

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

10.1186/1471-2199-8-119

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

10.1186/1471-2164-14-799

Chronic parasitization by Nosema microsporidia causes global expression changes in core nutritional, metabolic and behavioral pathways in honey bee workers (Apis mellifera)
Cited by: 85
Author(s): Holly L. Holt, Katherine A. Aronstein, Christina M. Grozinger
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pmed.1002786

Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures
Cited by: 115
Author(s): Hayley Warsinske, Rohit Vashisht, Purvesh Khatri
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-9-628

Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality
Cited by: 13
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pmed.1000046

A Compendium of Potential Biomarkers of Pancreatic Cancer
Cited by: 256
Author(s): H. C. Harsha, Kumaran Kandasamy, Prathibha Ranganathan, Sandhya Rani, Subhashri Ramabadran, Sashikanth Gollapudi, Lavanya Balakrishnan, Sutopa B. Dwivedi, Deepthi Telikicherla, Lakshmi Dhevi N. Selvan, Renu Goel, Suresh Mathivanan, Arivusudar Marimuthu, Manoj Kumar Kashyap, Robert F. Vizza, Robert J. Mayer, James A. DeCaprio, Sudhir Srivastava, Samir Hanash, Ralph H. Hruban, Akhilesh Pandey
Software Mentions: 1
Published: over 17 years ago

10.1534/g3.117.300225

A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes
Cited by: 30
Author(s): Jean-Clément Mars, Marianne Sabourin-Felix, Michel G. Tremblay, Tom Moss
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pntd.0005972

Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes
Cited by: 28
Author(s): Juan Mucci, Santiago J. Carmona, Romina Volcovich, Jaime Altcheh, Estefanisa Bracamonte, Jorge Diego Marco, Morten Nielsen, Carlos A. Buscaglia, Fernán Agüero
Software Mentions: 1
Published: almost 9 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

10.7554/eLife.69160

GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility
Cited by: 5
Author(s): Sequoyah Reynoso, Vanessa Castillo, Gajanan D. Katkar, Inmaculada López-Sánchez, Sahar Taheri, Celia R. Espinoza, Cristina C. Rohena, Debashis Sahoo, Pascal Gagneux, Pradipta Ghosh
Software Mentions: 1
Published: almost 5 years ago

10.3390/genes5030726

Enterococcus faecalis Infection and Reactive Oxygen Species Down-Regulates the miR-17-92 Cluster in Gastric Adenocarcinoma Cell Culture
Cited by: 22
Author(s): Jesper A.B. Strickertsson, Lene Juel Rasmussen, Lennart Friis‐Hansen
Software Mentions: 1
Published: almost 12 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: about 14 years ago

10.1186/1471-2164-11-714

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources
Cited by: 22
Author(s): Camille Rustenholz, Pete E. Hedley, Jenny Morris, Frédéric Choulet, Catherine Feuillet, Robbie Waugh, Etienne Paux
Software Mentions: 1
Published: over 15 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.pntd.0001692

Gene Amplification, ABC Transporters and Cytochrome P450s: Unraveling the Molecular Basis of Pyrethroid Resistance in the Dengue Vector, Aedes aegypti
Cited by: 156
Author(s): Vassiliki Bariami, Christopher M. Jones, Rodolphe Poupardin, John Vontas, Hilary Ranson
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pntd.0005069

Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection
Cited by: 67
Author(s): Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pntd.0002607

Bioassay-Guided Fractionation of Extracts from Codiaeum variegatum against Entamoeba histolytica Discovers Compounds That Modify Expression of Ceramide Biosynthesis Related Genes
Cited by: 14
Author(s): Emmanuel Mfotie Njoya, Christian Weber, Nora Adriana Hernández‐Cuevas, Chung-Chau Hon, Yves L. Janin, Melanie F. G. Kamini, Paul Fewou Moundipa, Nancy Guillén
Software Mentions: 1
Published: over 12 years ago

10.3390/genes9060275

Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson’s Disease Data
Cited by: 16
Author(s): Elisa Mariani, Lorenza Lombardini, Federica Facchin, Fabrizio Pizzetti, Flavia Frabetti, Andrea Tarozzi, Raffaella Casadei
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pntd.0002438

Temephos Resistance in Aedes aegypti in Colombia Compromises Dengue Vector Control
Cited by: 106
Author(s): Nelson Grisales, Rodolphe Poupardin, Santiago Gómez, Idalyd Fonseca-González, Hilary Ranson, Audrey Lenhart
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-12-452

Histological and global gene expression analysis of the 'lactating' pigeon crop
Cited by: 43
Author(s): Meagan J Gillespie, Volker Häring, Kenneth A. McColl, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-13-407

Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins
Cited by: 75
Author(s): David Peris, Christian A. Lopes, Carmela Belloch, Amparo Querol, Eladio Barrio
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-15-649

Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation
Cited by: 28
Author(s): Alison F. Richard, Paul Lyons, James E. Peters, Daniele Biasci, Shaun Flint, James C. Lee, Eoín McKinney, Richard M. Siegel, Kenneth G. C. Smith
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0052321

Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
Cited by: 37
Author(s): Candy Kumps, Annelies Fieuw, Pieter Mestdagh, Björn Menten, Steve Lefever, Filip Pattyn, Sara De Brouwer, Tom Sante, Johannes H. Schulte, Alexander Schramm, Nadine Van Roy, Tom Van Maerken, Rosa Noguera, Valérie Combaret, Christine Devalck, Frank Westermann, Geneviève Laureys, Angelika Eggert, Jo Vandesompele, Katleen De Preter, Franki Speleman
Software Mentions: 1
Published: over 13 years ago

10.3390/genes10050341

Genetical Genomics of Tonic Immobility in the Chicken
Cited by: 19
Author(s): Jesper Fogelholm, Samuel Eguasi Inkabi, Andrey Höglund, Robin N. Abbey-Lee, Martin Johnsson, Per Jensen, Rie Henriksen, I. A. Wright
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-11-142

TobEA: an atlas of tobacco gene expression from seed to senescence
Cited by: 61
Author(s): Kieron D. Edwards, Aureliano Bombarely, Geraint W. Story, F H Allen, Lukas A. Mueller, Steve Coates, Louise Jones
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0043249

Induction of Endoplasmic Reticulum Stress Response by the Indole-3-Carbinol Cyclic Tetrameric Derivative CTet in Human Breast Cancer Cell Lines
Cited by: 43
Author(s): Luca Galluzzi, Mauro De Santi, Rita Crinelli, Cinzia De Marco, Nadia Zaffaroni, Andrea Duranti, Giorgio Brandi, Mauro Magnani
Software Mentions: 1
Published: about 14 years ago

10.1186/1756-0381-1-9

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

10.1371/journal.pone.0141710

Expression of CCL20 and Its Corresponding Receptor CCR6 Is Enhanced in Active Inflammatory Bowel Disease, and TLR3 Mediates CCL20 Expression in Colonic Epithelial Cells
Cited by: 51
Author(s): Helene Kolstad Skovdahl, Atle van Beelen Granlund, Ann Elisabet Østvik, Ingrid Bakke, Sverre Helge Torp, Jan Kristian Damås, Arne K. Sandvik
Software Mentions: 1
Published: almost 11 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

10.1186/1471-2164-11-343

Regulation of the cardiomyocyte transcriptome vs translatome by endothelin-1 and insulin: translational regulation of 5' terminal oligopyrimidine tract (TOP) mRNAs by insulin
Cited by: 15
Author(s): Thomais Markou, Andrew Keith Marshall, Timothy E. Cullingford, El Li Tham, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0009867

Oral Activated Charcoal Prevents Experimental Cerebral Malaria in Mice and in a Randomized Controlled Clinical Trial in Man Did Not Interfere with the Pharmacokinetics of Parenteral Artesunate
Cited by: 10
Author(s): J. Brian de Souza, Uduak Okomo, Alexander Nast, Naveed Aziz, Benjamin M. J. Owens, Harsimran Kaur, Momodou Jasseh, Sant Muangnoicharoen, Percy F. Sumariwalla, David C. Warhurst, Stephen A. Ward, David J. Conway, Luis Ulloa, Kevin J. Tracey, Brian M. J. Foxwell, Paul M. Kaye, Michael Walther
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-11-709

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans
Cited by: 62
Author(s): Jessica Cleiss-Arnold, Sandrine Koechler, Caroline Proux, Marie‐Laure Fardeau, Marie‐Agnès Dillies, Jean‐Yves Coppée, Florence Arsène-Ploetze, Philippe Bertin
Software Mentions: 1
Published: over 15 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: over 21 years ago

10.1371/journal.pone.0183410

snoRNA and piRNA expression levels modified by tobacco use in women with lung adenocarcinoma
Cited by: 25
Author(s): Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton Carvalho, Fábio Passetti
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0013658

Whole Blood Transcriptomics in Cardiac Surgery Identifies a Gene Regulatory Network Connecting Ischemia Reperfusion with Systemic Inflammation
Cited by: 34
Author(s): Orfeas Liangos, Sophie Domhan, Christian Schwager, Martin Zeier, Peter E. Huber, Francesco Addabbo, Michael S. Goligorsky, Lynn Hlatky, Bertrand L. Jaber, Amir Abdollahi
Software Mentions: 1
Published: almost 16 years ago

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: over 7 years ago

10.1186/1471-2105-7-311

Web-based analysis of the mouse transcriptome using Genevestigator
Cited by: 25
Author(s): Oliver Laule, Matthias Hirsch‐Hoffmann, Tomás Hrúz, Wilhelm Gruissem, Philip Zimmermann
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pone.0013079

QKI-7 Regulates Expression of Interferon-Related Genes in Human Astrocyte Glioma Cells
Cited by: 8
Author(s): Lin Jiang, Peter Saetre, Katarzyna J. Radomska, Elena Jazin, Eva Carlström
Software Mentions: 1
Published: almost 16 years ago

10.7150/thno.42480

Esophageal, gastric and colorectal cancers: Looking beyond classical serological biomarkers towards glycoproteomics-assisted precision oncology
Cited by: 34
Author(s): Elisabete Fernandes, Janine Sores, Sofia Cotton, Andreia Peixoto, Dylan Ferreira, Rui Freitas, Celso A. Reis, Lúcio Lara Santos, José Alexandre Ferreira
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0049077

Gadd45α: A Novel Diabetes-Associated Gene Potentially Linking Diabetic Cardiomyopathy and Baroreflex Dysfunction
Cited by: 13
Author(s): Ning Wang, Chao Yang, Fang Xie, Lichao Sun, Xiaolin Su, Ying Wang, Ran Wei, Rong Zhang, Xia Li, Baofeng Yang, Jing Ai
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0118511

MicroRNA-572 Improves Early Post-Operative Cognitive Dysfunction by Down-Regulating Neural Cell Adhesion Molecule 1
Cited by: 31
Author(s): Xiuchong Yu, Shupeng Liu, Jinbao Li, Xiaoping Fan, Yuanjie Chen, Xiaoying Bi, Shanrong Liu, Xiaoming Deng
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0055506

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
Cited by: 34
Author(s): David Cohen, Marie‐Béatrice Bogeat‐Triboulot, Silvère Vialet-Chabrand, Rémy Merret, Pierre‐Emmanuel Courty, Sébastien Moretti, François Bizet, Agnès Guilliot, Irène Hummel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0199991

PASI: A novel pathway method to identify delicate group effects
Cited by: 4
Author(s): Maria K. Jaakkola, Aidan McGlinchey, Рику Клен, Laura L. Elo
Software Mentions: 1
Published: about 8 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: almost 17 years ago

10.1186/s13195-014-0070-5

PLD3 is accumulated on neuritic plaques in Alzheimer’s disease brains
Cited by: 35
Author(s): Jun‐ichi Satoh, Yoshihiro Kino, Yoji Yamamoto, Natsuki Kawana, Tsuyoshi Ishida, Yuko Saito, Kunimasa Arima
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-8-70

Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation
Cited by: 338
Author(s): Birgit Kulterer, Gerald Friedl, Anita Jandrositz, Fátima Sánchez‐Cabo, Andreas Prokesch, Christine Paar, Marcel Scheideler, Reinhard Windhager, Karl‐Heinz Preisegger, Zlatko Trajanoski
Software Mentions: 1
Published: over 19 years ago

10.1186/2050-6511-15-5

Skin sensitizers differentially regulate signaling pathways in MUTZ-3 cells in relation to their individual potency
Cited by: 34
Author(s): Ann-Sofie Albrekt, Henrik Johansson, Anna Börje, Carl Borrebaeck, Malin Lindstedt
Software Mentions: 1
Published: over 12 years ago

10.1038/s41436-018-0015-7

A homozygous FANCM frameshift pathogenic variant causes male infertility
Cited by: 61
Author(s): Hong Yin, Hui Ma, Sajjad Hussain, Huan Zhang, Xuefeng Xie, Long Jiang, Xiaohua Jiang, Furhan Iqbal, Ihtisham Bukhari, Hanwei Jiang, Asim Ali, Liangwen Zhong, Tao Li, Suixing Fan, Beibei Zhang, Jianing Gao, Yang Li, Nazish Jabeen, Teka Khan, Manan Khan, Muhammad Zubair, Qiaomei Hao, Hui Fang, Jun Huang, Mahmoud Huleihel, Jiahao Sha, Tej K. Pandita, Yuanwei Zhang, Qinghua Shi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12711-020-00587-x

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)
Cited by: 8
Author(s): Hanne Dvergedal, Thomas Nelson Harvey, Yang Jin, Jørgen Ødegård, Lars Grønvold, Simen Rød Sandve, Dag Inge Våge, Thomas Moen, G. Klemetsdal
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-9-375

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability
Cited by: 76
Author(s): Martin H. van Vliet, Fabien Reyal, Hugo M. Horlings, Marc J. van de Vijver, Marcel J. T. Reinders, Lodewyk Wessels
Software Mentions: 1
Published: over 18 years ago

10.1534/genetics.116.197376

Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function
Cited by: 11
Author(s): Tai‐Di Chen, Maxime Rotival, Ling-Yin Chiu, Marta Bagnati, Jeong‐Hun Ko, Prashant K. Srivastava, Enrico Petretto, Charles D. Pusey, Ping-Chin Lai, Timothy J. Aitman, H. Terence Cook, Jacques Behmoaras
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0123342

Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain
Cited by: 39
Author(s): Ann-Kristin Reinhold, Laura Batti, Daniel Bilbao, Andreas Buneß, Heike L. Rittner, Paul A. Heppenstall
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0045200

Transcriptomic Assay of CD8+ T Cells in Treatment-Naïve HIV, HCV-Mono-Infected and HIV/HCV-Co-Infected Chinese
Cited by: 7
Author(s): Jin Zhao, Yi Liu, Jing Lu, Zheng Yang, Ying Chen, Chenli Zheng, Dan Huang, Yufeng Li, Lin Chen, Jinquan Cheng, Hsiang‐Fu Kung, Ming‐Liang He
Software Mentions: 1
Published: almost 14 years ago

10.1534/genetics.119.302493

Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of <i>Heliconius</i> Butterflies
Cited by: 28
Author(s): Ana Catalán, Adriana D. Briscoe, Sebastian Höhna
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.gdata.2014.10.016

Transcriptional ontogeny of first trimester human fetal and placental mesenchymal stem cells: Gestational age versus niche
Cited by: 5
Author(s): Jennifer Ryan, Nicholas Matigian, Rebecca A. Pelekanos, Samuel Jesuadian, Christine A. Wells, Nicholas M. Fisk
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-10-324

Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues
Cited by: 28
Author(s): Anita Grigoriadis, Gavin R. Oliver, Austin Tanney, Howard Kendrick, Matthew J. Smalley, Parmjit Jat, A. Munro Neville
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0073072

Transmembrane Prostatic Acid Phosphatase (TMPAP) Interacts with Snapin and Deficient Mice Develop Prostate Adenocarcinoma
Cited by: 27
Author(s): Ileana B. Quintero, Annakaisa Herrala, César L. Araujo, Anitta E. Pulkka, Sampsa Hautaniemi, Kristian Ovaska, Evgeny Pryazhnikov, Evgeny Kulesskiy, Maija Ruuth, Ylermi Soini, Raija Sormunen, Leonard Khirug, Pirkko Vihko
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0007158

miR-155 Inhibition Sensitizes CD4+ Th Cells for TREG Mediated Suppression
Cited by: 81
Author(s): Heiko Stahl, Tanja Fauti, Nina D. Ullrich, Tobias Bopp, Jan Kubach, Werner Rust, Paul Labhart, Vassili Alexiadis, Christian Becker, Mathias Hafner, Andreas Weith, Martin Lenter, Helmut Jonuleit, Edgar Schmitt, Detlev Mennerich
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2229-9-28

Differential patterns of reactive oxygen species and antioxidative mechanisms during atrazine injury and sucrose-induced tolerance in Arabidopsis thaliana plantlets
Cited by: 264
Author(s): Fanny Ramel, Cécile Sulmon, Matthieu Bogard, Ivan Couée, Gwenola Gouesbet
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0152786

Adipocytes as a Link Between Gut Microbiota-Derived Flagellin and Hepatocyte Fat Accumulation
Cited by: 13
Author(s): Eveliina Munukka, Petri Wiklund, Tiina Partanen, Sakari Välimäki, Eija K. Laakkonen, Maarit Lehti, Pamela Fischer-Posovzsky, Martin Wabitsch, Sulin Cheng, Pentti Huovinen, Satu Pekkala
Software Mentions: 1
Published: over 10 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/s40246-020-00269-1

Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals
Cited by: 4
Author(s): Andreanna Burman, Rolando García-Milián, Shannon Whirledge
Software Mentions: 1
Published: about 6 years ago

10.1186/gb-2005-6-11-r94

Cited by: 155
Author(s): Bregje Wertheim, Alex R. Kraaijeveld, Eugene F. Schuster, Eric Blanc, Meirion Hopkins, Scott D. Pletcher, Michael R. Strand, Linda Partridge, H. C. J. Godfray
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2164-9-121

Transcriptome analysis of grain development in hexaploid wheat
Cited by: 183
Author(s): Yongfang Wan, Rebecca L Poole, Alison K. Huttly, C. Toscano-Underwood, Kevin A. Feeney, S. J. Welham, M. J. Gooding, Clare Mills, Keith J. Edwards, Peter R. Shewry, R. A. C. Mitchell
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0048896

Survival of Staphylococcus aureus ST398 in the Human Nose after Artificial Inoculation
Cited by: 23
Author(s): Bibi C. G. C. Slingerland, Mehri Tavakol, Alex J. McCarthy, Jodi A. Lindsay, Susan V. Snijders, Jaap A. Wagenaar, Alex van Belkum, Margreet C. Vos, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: almost 14 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

10.1186/1471-2164-7-266

Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™
Cited by: 14
Author(s): Carole L. Yauk, Andrew Williams, Sherri E. Boucher, Lynn Berndt, Gu Zhou, Jiangxia Zheng, Andrea Rowan-Carroll, Hongyan Dong, Iain B. Lambert, George R. Douglas, Craig L.J. Parfett
Software Mentions: 1
Published: almost 20 years ago

10.1371/journal.pone.0070294

Prediction Errors in Learning Drug Response from Gene Expression Data – Influence of Labeling, Sample Size, and Machine Learning Algorithm
Cited by: 15
Author(s): Immanuel Bayer, Philip Groth, Sebastian Schneckener
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0131336

MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing
Cited by: 29
Author(s): Li Zhang, Pengfei Wei, Xudong Shen, Yuanwei Zhang, Bo Xu, Jun Zhou, Song Fan, Zongyao Hao, Hao Shi, Xiansheng Zhang, Rui Kong, Lingfan Xu, Duohong Zou, Chaozhao Liang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0002798

Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors
Cited by: 63
Author(s): Paolo Facella, Loredana Lopez, Fabrizio Carbone, David W. Galbraith, Giovanni Giuliano, Gaetano Perrotta
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0008018

Sulfur Metabolism Actively Promotes Initiation of Cell Division in Yeast
Cited by: 17
Author(s): Heidi M. Blank, Shefali Rajendra Gajjar, Andrey Belyanin, Michael Polymenis
Software Mentions: 1
Published: over 16 years ago

10.1186/gb-2005-6-7-r56

Cited by: 41
Author(s): Shiri Freilich, Tim Massingham, Sumit Bhattacharyya, Hannes Ponstingl, Paul Lyons, Tom C. Freeman, Janet M. Thornton
Software Mentions: 1
Published: over 21 years ago

10.1371/journal.pone.0161993

PKC-ALDH2 Pathway Plays a Novel Role in Adipocyte Differentiation
Cited by: 20
Author(s): Yu-Hsiang Yu, Pei Ru Liao, Chien Jung Guo, Che Hong Chen, Daria Mochly‐Rosen, Lee‐Ming Chuang
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0079627

Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts
Cited by: 1
Author(s): Thong Tien Nguyen, Cathal Seoighe
Software Mentions: 1
Published: over 12 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

10.1371/journal.pone.0001546

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays
Cited by: 13
Author(s): Michael A. Cook, Chi Kin Chan, Paul Jorgensen, Troy Ketela, Daniel K. C. So, Mike Tyers, Chi Yip Ho
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2006-7-3-r26

Cited by: 40
Author(s): Colin C. Pritchard, David A. Coil, Sarah Hawley, Li Hsu, Peter S. Nelson
Software Mentions: 1
Published: over 20 years ago

10.1186/s12864-015-1342-6

The recent escalation in strength of pyrethroid resistance in Anopheles coluzzi in West Africa is linked to increased expression of multiple gene families
Cited by: 80
Author(s): Hyacinthe K. Toé, N’Falé Sagnon, Roch K. Dabiré, Hilary Ranson, Christopher M. Jones
Software Mentions: 1
Published: over 11 years ago

10.1186/gb-2006-7-6-r46

Cited by: 39
Author(s): Emma Laing, Vassilis Mersinias, Colin P. Smith, Simon J. Hubbard
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0048363

Functional Similarities between Pigeon ‘Milk’ and Mammalian Milk: Induction of Immune Gene Expression and Modification of the Microbiota
Cited by: 28
Author(s): Meagan J Gillespie, Dragana Stanley, Honglei Chen, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-14-376

Time-dependent changes in gene expression induced by secreted amyloid precursor protein-alpha in the rat hippocampus
Cited by: 35
Author(s): Margaret M. Ryan, Gary P. Morris, Bruce G. Mockett, Katie Bourne, Wickliffe C. Abraham, Warren P. Tate, Joanna M. Williams
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0080747

PaGenBase: A Pattern Gene Database for the Global and Dynamic Understanding of Gene Function
Cited by: 100
Author(s): Jianbo Pan, Shichang Hu, Dan Shi, Mei-Chun Cai, Yin-Bo Li, Quan Zou, Zhi-Liang Ji
Software Mentions: 1
Published: over 12 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/gb-2006-7-12-r114

Cited by: 56
Author(s): Hanni Willenbrock, Carsten Friis, Agnieszka Sierakowska Juncker, David W. Ussery
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0026023

Hormone Receptor and ERBB2 Status in Gene Expression Profiles of Human Breast Tumor Samples
Cited by: 6
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 1
Published: almost 15 years ago

10.1186/gb-2006-7-9-r84

Cited by: 140
Author(s): Katleen De Preter, Jo Vandesompele, Pierre Heimann, Nurten Yigit, Siv Beckman, Alexander Schramm, Angelika Eggert, Raymond L. Stallings, Yves Benoît, Marleen Renard, Anne De Paepe, Geneviève Laureys, Sven Påhlman, Franki Speleman
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0250747

Glycans unique to the relapse-prone subset within triple-negative breast cancer as revealed by lectin array-based analysis of surgical specimens
Cited by: 3
Author(s): Madoka Sakata-Matsuzawa, Kaori Denda-Nagai, Haruhiko Fujihira, Miki Noji, Katrin Ishii-Schrade, Atsushi Matsuda, Atsushi Kuno, Misato Okazaki, Keiichi Nakai, Yoshiya Horimoto, Mitsue Saito, Tatsuro Irimura
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-14-336

A simple and reproducible breast cancer prognostic test
Cited by: 47
Author(s): Luigi Marchionni, Bahman Afsari, Donald Geman, Jeffrey T. Leek
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-16-S1-S11

Transcriptomics profiling study of breast cancer from Kingdom of Saudi Arabia revealed altered expression of Adiponectin and Fatty Acid Binding Protein4: Is lipid metabolism associated with breast cancer?
Cited by: 25
Author(s): Adnan Merdad, Sajjad Karim, Hans-Juergen Schulten, Jayapal Manikandan, Ashraf Dallol, Abdelbaset Buhmeida, Fatima Al-Thubaity, Mamdooh A GariI, Adeel Chaudhary, Adel M. Abuzenadah, Mohammed Al‐Qahtani
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0113053

Toward Computational Cumulative Biology by Combining Models of Biological Datasets
Cited by: 8
Author(s): Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, Samuel Kaski
Software Mentions: 1
Published: over 11 years ago

10.1186/gb-2006-7-10-r99

Cited by: 78
Author(s): Anders F. Andersson, Magnus Lundgren, Stefan Eriksson, Magnus Rosenlund, Rolf Bernander, Peter Nilsson
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0080047

A Small RNA Encoded in the Rv2660c Locus of Mycobacterium tuberculosis Is Induced during Starvation and Infection
Cited by: 32
Author(s): Joanna Houghton, Teresa Cortes, Olga T. Schubert, Graham Rose, Angela Rodgers, Megan De Ste Croix, Rudolf Aebersold, Douglas B. Young, Kristine B. Arnvig
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0139446

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions
Cited by: 32
Author(s): Francesco Iorio, Roshan L. Shrestha, Nicolas Levin, Viviane Boilot, Mathew J. Garnett, Julio Sáez-Rodríguez, Viji M. Draviam
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0001403

Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages
Cited by: 185
Author(s): Ludovic Tailleux, Simon J. Waddell, Mattia Pelizzola, Alessandra Mortellaro, Michael Withers, Antoine Tanne, Paola Ricciardi Castagnoli, Brigitte Gicquel, Neil G. Stoker, Philip D. Butcher, Maria Foti, Olivier Neyrolles
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2006-7-10-r89

Cited by: 25
Author(s): Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M. Thornton
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0082684

Genetic Interaction between Mutations in c-Myb and the KIX Domains of CBP and p300 Affects Multiple Blood Cell Lineages and Influences Both Gene Activation and Repression
Cited by: 27
Author(s): Lawryn H. Kasper, Tsutomu Fükuyama, Stephanie Lerach, Yunchao Chang, Wu Xu, Song Wu, Kelli L. Boyd, Paul K. Brindle
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0106278

SDF-1 Chemokine Signalling Modulates the Apoptotic Responses to Iron Deprivation of Clathrin-Depleted DT40 Cells
Cited by: 2
Author(s): Alena Pance, Frank Ralf Morrissey-Wettey, Helen Craig, Alison Downing, Richard Talbot, Antony P. Jackson
Software Mentions: 1
Published: almost 12 years ago

10.1186/gb-2006-7-11-r107

Cited by: 211
Author(s): Birgitte Regenberg, Thomas Grotkjær, Ole Winther, Anders Fausbøll, Mats Åkesson, Christoffer Bro, Lars Kai Hansen, Søren Brunak, Jens Nielsen
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0030781

Circadian Rhythms of Fetal Liver Transcription Persist in the Absence of Canonical Circadian Clock Gene Expression Rhythms In Vivo
Cited by: 8
Author(s): Chengwei Li, Shuang Yu, Xiaoling Zhong, Jianguo Wu, Xiaodong Li
Software Mentions: 1
Published: over 14 years ago

10.1186/gb-2007-8-5-r74

Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies
Cited by: 23
Author(s): Björn Nilsson, Petra Håkansson, Mikael Johansson, Sven Nelander, Thoas Fioretos
Software Mentions: 1
Published: over 19 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962