bioconductor: ArrayExpress | Projects

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

10.3390/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: about 4 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: about 15 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: over 14 years ago

10.1186/1755-8794-2-18

PrognoScan: a new database for meta-analysis of the prognostic value of genes
Cited by: 698
Author(s): Hideaki Mizuno, Koji Kitada, Katsunori Nakai, Akinori Sarai
Software Mentions: 1
Published: 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: over 11 years ago

10.1186/1755-8794-2-41

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus
Cited by: 12
Author(s): Yaomin Hu, Pamela J. Kaisaki, Karène Argoud, Steven P. Wilder, Karin J. Wallace, Peng Yeong Woon, Christine Blancher, Lise Tarnow, Per‐Henrik Groop, Samy Hadjadj, Michel Marre, Hans‐Henrik Parving, Martin Farrall, Roger D. Cox, Mark Lathrop, Nathalie Vionnet, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 1
Published: over 15 years ago

10.1186/1755-8794-3-5

Insight in modulation of inflammation in response to diclofenac intervention: a human intervention study
Cited by: 34
Author(s): Marjan J. van Erk, Suzan Wopereis, Carina M. Rubingh, T. van Vliet, Elwin Verheij, N.H.P. Cnubben, Theresa L. Pedersen, John W. Newman, Age K. Smilde, J. van der Greef, H. Hendriks, Ben van Ommen
Software Mentions: 1
Published: over 14 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 7 years ago

10.1186/1755-8794-2-12

Impaired immune function in Gulf War Illness
Cited by: 71
Author(s): Toni Whistler, Mary A Fletcher, William Lonergan, Xiao Rong Zeng, Jin Mann S. Lin, A. LaPerriere, Suzanne D. Vernon, Nancy G. Klimas
Software Mentions: 1
Published: over 15 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 5 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: over 6 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 4 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: about 6 years ago

10.1186/1755-8794-1-33

An approach to analyse the specific impact of rapamycin on mRNA-ribosome association
Cited by: 16
Author(s): Raphaël Genolet, Tanguy Araud, Laetitia Maillard, Pascale Jaquier-Gubler, Joseph Curran
Software Mentions: 1
Published: over 16 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: almost 4 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 16 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 3 years ago

10.1186/1755-8794-2-11

Promoter methylation correlates with reduced NDRG2expression in advanced colon tumour
Cited by: 36
Author(s): Ada Piepoli, Rosa Cotugno, Giuseppe Merla, Annamaria Gentile, Bartolomeo Augello, M. Quitadamo, Antonio Merla, Anna Panza, Massimo Carella, Rosalia Maglietta, A. D’Addabbo, Nicola Ancona, Saverio Fusilli, Francesco Perri, Angelo Andriulli
Software Mentions: 1
Published: over 15 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 8 years ago

10.1186/s12920-016-0227-0

A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without
Cited by: 10
Author(s): Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner, Nicki Tiffin
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2350-8-36

Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets
Cited by: 110
Author(s): ChaRandle Jordan, Hong Hua Li, Helen H. Kwan, Uta Francke
Software Mentions: 1
Published: 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: over 3 years ago

10.1186/s12916-017-0929-y

A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes
Cited by: 40
Author(s): Jean‐Philippe Foy, Louis Bazire, Sandra Ortiz-Cuàran, Sophie Deneuve, Janice Kielbassa, Emilie Thomas, Alain Viari, Alain Puisieux, P. Goudot, Chloé Bertolus, Nicolas Foray, Youlia Kirova, Pierre Verrelle, Pierre Saintigny
Software Mentions: 1
Published: about 7 years ago

10.1186/s12916-016-0609-3

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy
Cited by: 45
Author(s): Isobella Honeyborne, Timothy D. McHugh, Iitu Kuittinen, Anna Cichońska, Dimitrios Evangelopoulos, Katharina Ronacher, Paul D. van Helden, Stephen H. Gillespie, Delmiro Fernández-Reyes, Gerhard Walzl, Juho Rousu, Philip D. Butcher, Simon J. Waddell
Software Mentions: 1
Published: over 8 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

10.1186/s12879-016-1533-z

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
Cited by: 13
Author(s): Steven T. Pullan, Jon C. Allnutt, Rebecca Devine, Kim A. Hatch, Rose E. Jeeves, Charlotte L. Hendon-Dunn, Philip Marsh, Joanna Bacon
Software Mentions: 1
Published: over 8 years ago

10.1186/s12865-017-0238-4

Cattle infection response network and its functional modules
Cited by: 5
Author(s): Hamid Beiki, A. Pakdel, A Nejati Javaremi, Ali Masoudi‐Nejad, James M. Reecy
Software Mentions: 1
Published: almost 7 years ago

10.3389/fcell.2021.673073

MeiosisOnline: A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis
Cited by: 4
Author(s): Xiaohua Jiang, Dingtao Zhao, Asim Ali, Bo Xu, Wei Liu, Jie Wen, Huan Zhang, Qinghua Shi, Yuanwei Zhang
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-13-49

Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice
Cited by: 29
Author(s): Rumdeep K Grewal, S. K. Gupta, Sampa Das
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-15-438

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Cited by: 26
Author(s): Marta Vergara-Irigaray, María Fookes, Nicholas R. Thomson, Christoph M. Tang
Software Mentions: 1
Published: over 10 years ago

10.3389/fcell.2021.716501

GADD45B Is a Potential Diagnostic and Therapeutic Target Gene in Chemotherapy-Resistant Prostate Cancer
Cited by: 4
Author(s): Qiong Wang, Wanhua Wu, Zhe Gao, Kaiwen Li, Shirong Peng, Huiyang Fan, Zhongqiu Xie, Zhanfang Guo, Hai Huang
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.00109-21

Metabolomics Reveal Potential Natural Substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium
Cited by: 14
Author(s): Xuan Wang-Kan, Giovanny Rodrı́guez-Blanco, Andrew D. Southam, Catherine Winder, Warwick B. Dunn, Alasdair Ivens, Laura J. V. Piddock
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-016-2771-6

Transcriptomic response of yeast cells to ATX1 deletion under different copper levels
Cited by: 12
Author(s): Ayca Cankorur-Cetinkaya, Serpil Eraslan, Betül Kırdar
Software Mentions: 1
Published: over 8 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: about 17 years ago

10.1186/s12859-015-0854-z

Evaluation of O2PLS in Omics data integration
Cited by: 91
Author(s): Said el Bouhaddani, Jeanine J. Houwing-Duistermaat, Perttu Salo, Markus Perola, Geurt Jongbloed, Hae‐Won Uh
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-10-215

Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays
Cited by: 29
Author(s): Minjie Wang, Xiaoli Qi, Shutang Zhao, Shougong Zhang, Mengzhu Lu
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2105-8-343

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model
Cited by: 12
Author(s): Ryoko Morioka, Shigehiko Kanaya, Masami Yokota Hirai, Mitsuru Yano, Nagahisa Ogasawara, Kazuki Saito
Software Mentions: 1
Published: about 17 years ago

10.7554/eLife.03743

The transcription factor Pitx2 positions the embryonic axis and regulates twinning
Cited by: 33
Author(s): Angela Torlopp, Mohsin A.F. Khan, Nidia M M Oliveira, Ingrid Lekk, Luz Mayela Soto‐Jiménez, Alona Sosinsky, Claudio D. Stern
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2105-12-S10-S2

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
Cited by: 14
Author(s): Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-11-682

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Cited by: 40
Author(s): Richard A. Lewis, Emma Laing, Nicholas E. E. Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M. Kierzek, Colin P. Smith
Software Mentions: 1
Published: almost 14 years ago

10.7554/eLife.09886

Protein kinase C coordinates histone H3 phosphorylation and acetylation
Cited by: 13
Author(s): Zoulfia Darieva, Aaron Webber, Stacey Warwood, Andrew D. Sharrocks
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-9-208

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina
Cited by: 14
Author(s): Ravi Kiran Reddy Kalathur, Nicolas Gagnière, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, Olivier Poch
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-10-575

Using transcriptome profiling to characterize QTL regions on chicken chromosome 5
Cited by: 13
Author(s): Guillaume Le Mignon, Colette Désert, Frédérique Pitel, Sophie Leroux, Olivier Demeure, Grégory Guernec, Behnam Abasht, Madeleine Douaire, Pascale Le Roy, Sandrine Lagarrigue
Software Mentions: 1
Published: almost 15 years ago

10.3389/fgene.2014.00470

A gene mapping bottleneck in the translational route from zebrafish to human
Cited by: 2
Author(s): Nigel Klein, Mark Ibberson, Isaac Crespo, Sophie Rodius, Francisco Azuaje
Software Mentions: 1
Published: almost 10 years ago

10.3389/fgene.2019.00769

Inferring Latent Disease-lncRNA Associations by Faster Matrix Completion on a Heterogeneous Network
Cited by: 14
Author(s): Li Wen, Shulin Wang, Junlin Xu, Guo Mao, Geng Tian, Jialiang Yang
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-5-68

PEDRo: A database for storing, searching and disseminating experimental proteomics data
Cited by: 66
Author(s): Kevin Garwood, Thomas J. McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen M. Carroll, Caroline A. Evans, Anthony D. Whetton, Sarah R. Hart, David Stead, Zhikang Yin, Alistair J. P. Brown, Andrew Hesketh, Keith F. Chater, Lena Hansson, Muriel Mewissen, Peter Ghazal, Julie A. Howard, Kathryn S. Lilley, Simon J. Gaskell, Andy Brass, Simon J. Hubbard, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2164-16-S1-S2

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data
Cited by: 41
Author(s): Anna L Swan, Dov J. Stekel, Charlie Hodgman, David Allaway, Mohammed Hussein Al-Qahtani, Ali Mobasheri, Jaume Bacardit
Software Mentions: 1
Published: almost 10 years ago

10.18632/aging.101078

Human exceptional longevity: transcriptome from centenarians is distinct from septuagenarians and reveals a role of Bcl-xL in successful aging
Cited by: 37
Author(s): Consuelo Borrás, Kheira M. Abdelaziz, Juan Gambini, Eva Serna, Marta Inglés, Mónica De la Fuente, Idoia García, Ander Matheu, Paula Sanchís, Ángel Belenguer, Alessandra Errigo, Juan A. Avellana, Ana Barettino, Carla Lloret-Fernández, Nuria Flames, Giovanni Mario Pes, Leocadio Rodríguez‐Mañas, José Viña
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-11-S1-S6

Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha
Cited by: 116
Author(s): Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir A. Kuznetsov, Lim Sai Kiang, Vivek Tanavde
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-9-291

Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium
Cited by: 66
Author(s): Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, Salvatore Bozzaro
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-12-137

Assessing affymetrix GeneChip microarray quality
Cited by: 70
Author(s): Matthew N. McCall, Peter Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry
Software Mentions: 1
Published: over 13 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

10.1186/1471-2164-11-478

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes
Cited by: 11
Author(s): Michael Klutstein, Zahava Siegfried, Ariel Gispan, Shlomit Farkash-Amar, Guy Zinman, Ziv Bar‐Joseph, Giora Simchen, Itamar Simon
Software Mentions: 1
Published: over 14 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: over 4 years ago

10.1186/1471-2105-13-323

Flexible and efficient genome tiling design with penalized uniqueness score
Cited by: 3
Author(s): Yang Du, Eduard Muráni, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 1
Published: almost 12 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

10.3390/ijms10083658

Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome
Cited by: 15
Author(s): Huai-Kuang Tsai, Peiying Huang, Cheng−Yan Kao, Daryi Wang
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-9-285

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
Cited by: 78
Author(s): Michael Boedigheimer, Russell D. Wolfinger, Michael Bass, Pierre R. Bushel, Jeff W. Chou, Matthew N. Cooper, J. Christopher Corton, Jennifer Fostel, Susan Hester, Janice S. Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, Karol L. Thompson
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-9-171

Transcriptional regulation by Poly(ADP-ribose) polymerase-1 during T cell activation
Cited by: 41
Author(s): Luis Sáenz, Juan José Lozano, Rut Valdor, Alberto Baroja‐Mazo, Pablo Ramı́rez, Pascual Parrilla, Pedro Aparicio, Lauro Sumoy, José Yélamos
Software Mentions: 1
Published: over 16 years ago

10.1093/hmg/ddw417

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus
Cited by: 25
Author(s): Christopher A. Odhams, Andrea Cortini, Lingyan Chen, Amy L. Roberts, Ana Viñuela, Alfonso Buil, Kerrin S. Small, Emmanouil T. Dermitzakis, David L. Morris, Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-10-S1-S54

Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data
Cited by: 3
Author(s): Dongxiao Zhu
Software Mentions: 1
Published: almost 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

10.1186/1471-2164-10-350

Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo
Cited by: 17
Author(s): Matthijs Raaben, Marian J. A. Groot Koerkamp, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 15 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

10.1186/1471-2164-15-S10-S4

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation
Cited by: 2
Author(s): Alexis Vandenbon, Shunsuke Teraguchi, Osamu Takeuchi, Yutaka Suzuki, Daron M. Standley
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-12-113

Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns
Cited by: 21
Author(s): Daniel Báron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péreón, Reiner A. Veitia, Frédérique Savagner, Gérard Ramstein, Rémi Houlgatte
Software Mentions: 1
Published: almost 14 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

10.1186/1471-2164-8-22

Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population
Cited by: 73
Author(s): Chun Shi, Anna Użarowska, Milena Ouzunova, Matthias Landbeck, G. Wenzel, Thomas Lübberstedt
Software Mentions: 1
Published: almost 18 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

10.1186/1471-2105-8-52

PASSIM – an open source software system for managing information in biomedical studies
Cited by: 23
Author(s): Juris Vīksna, Edgars Celms, Mārtiņš Opmanis, Kārlis Podnieks, Pēteris Ručevskis, Andris Zarins, Amy Barrett, Sudeshna Guha Neogi, Maria Krestyaninova, Mark I. McCarthy, Alvis Brāzma, Ugis Sarkans
Software Mentions: 1
Published: almost 18 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

10.1186/1471-2164-13-146

Meta-analysis of Chicken – Salmonella infection experiments
Cited by: 11
Author(s): M.F.W. te Pas, Ina Hulsegge, Dirkjan Schokker, M.A. Smits, Mark Fife, Rima Zoorob, Marie-Laure Endale, Johanna M.J. Rebel
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-9-324

Topoisomerase II inhibition involves characteristic chromosomal expression patterns
Cited by: 7
Author(s): Susanne Reymann, Jürgen Borlak
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2105-9-S6-S18

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses
Cited by: 29
Author(s): Todd H. Stokes, J.T. Torrance, Henry Li, May D. Wang
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-15-333

MicroRNA profiling of rats with ochratoxin A nephrotoxicity
Cited by: 47
Author(s): Dai Qiu, Jingbo Zhao, Xiaozhe Qi, Wentao Xu, Xiaoyun He, Mingzhang Guo, Harsh Dweep, Wen‐Hsing Cheng, Yunbo Luo, Kai Xia, Norbert Gretz, Kunlun Huang
Software Mentions: 1
Published: over 10 years ago

10.1186/s13046-016-0403-2

Microarray-based identification of genes associated with cancer progression and prognosis in hepatocellular carcinoma
Cited by: 33
Author(s): Fuqiang Yin, Liuyang Shu, Xia Liu, Ting Li, Tao Peng, Yueli Nan, Shu Li, Xianmin Zeng, Xiaoqiang Qiu
Software Mentions: 1
Published: about 8 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

10.1186/s13046-016-0477-x

Nomogram integrating gene expression signatures with clinicopathological features to predict survival in operable NSCLC: a pooled analysis of 2164 patients
Cited by: 18
Author(s): Jianhui Wu, Lizhi Zhou, Lixia Huang, Jincui Gu, Shaoli Li, Baomo Liu, Jinlun Feng, Yunyun Zhou
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-10-119

Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes
Cited by: 58
Author(s): José Osorio y Fortéa, Emilie de La Llave, Béatrice Regnault, Jean‐Yves Coppée, Geneviève Milon, Thierry Lang, Éric Prina
Software Mentions: 1
Published: over 15 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

10.1186/s13046-017-0568-3

miR-500a-3p promotes cancer stem cells properties via STAT3 pathway in human hepatocellular carcinoma
Cited by: 60
Author(s): Chonghe Jiang, Jianting Long, Baoxian Liu, Ming Xu, Wei Wang, Xian-Jin Xie, Xiaolin Wang, Ming Kuang
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-6-174

Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species of different survival strategies
Cited by: 137
Author(s): Heenam Stanley Kim, Mark A. Schell, Yan Yu, Ricky L. Ulrich, Saul Sarria, William C. Nierman, David DeShazer
Software Mentions: 1
Published: almost 19 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

10.1186/1471-2164-14-799

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: almost 12 years ago

10.1186/s13046-017-0642-x

Drug repurposing for the treatment of glioblastoma multiforme
Cited by: 56
Author(s): Claudia Abbruzzese, Silvia Matteoni, Michele Signore, Luca Cardone, Kavindra Nath, Jerry D. Glickson, Marco G. Paggi
Software Mentions: 1
Published: almost 7 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/s13046-019-1147-6

Anti-CD166/4-1BB chimeric antigen receptor T cell therapy for the treatment of osteosarcoma
Cited by: 42
Author(s): Yitian Wang, Wei Yu, Jian Zhu, Junjie Wang, Kaishun Xia, Chengzhen Liang, Huimin Tao
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-10-441

The Medicago truncatula gene expression atlas web server
Cited by: 172
Author(s): Ji He, Vagner A. Benedito, Mingyi Wang, J. D. Murray, Patrick Xuechun Zhao, Yuhong Tang, Michael K. Udvardi
Software Mentions: 1
Published: almost 15 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: almost 17 years ago

10.1186/1471-2105-11-610

BiologicalNetworks 2.0 - an integrative view of genome biology data
Cited by: 21
Author(s): Sergey Kozhenkov, Yulia Dubinina, Mayya Sedova, Amarnath Gupta, Julia Ponomarenko, Michael Baitaluk
Software Mentions: 1
Published: almost 14 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

10.1002/ijc.25688

Zinc deficiency activates S100A8 inflammation in the absence of COX‐2 and promotes murine oral‐esophageal tumor progression
Cited by: 37
Author(s): Shao Gui Wan, Cristian Taccioli, Yubao Jiang, Hongping Chen, Karl J. Smalley, Kun Huang, Xiu Ping Liu, John L. Farber, Carlo M. Croce, Louise Y.Y. Fong
Software Mentions: 1
Published: about 14 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962