bioconductor: ArrayExpress | Projects

10.3390/cancers12102738

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

10.1186/1471-2105-10-151

MIMAS 3.0 is a Multiomics Information Management and Annotation System
Cited by: 16
Author(s): Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig
Software Mentions: 1
Published: over 16 years ago

10.1186/s12859-019-2651-6

Identification of trans-eQTLs using mediation analysis with multiple mediators
Cited by: 31
Author(s): Nayang Shan, Zuoheng Wang, Lin Hou
Software Mentions: 1
Published: almost 7 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: about 18 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 12 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: almost 12 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: almost 17 years ago

10.1038/cddis.2017.109

Convergence and divergence between the transcriptional responses to Zika virus infection and prenatal irradiation
Cited by: 5
Author(s): Roel Quintens
Software Mentions: 1
Published: almost 9 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: about 20 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: almost 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: over 7 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: almost 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: over 7 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: about 13 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: about 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: almost 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: almost 5 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: about 18 years ago

10.1016/j.celrep.2016.03.007

G9a/GLP Complex Maintains Imprinted DNA Methylation in Embryonic Stem Cells
Cited by: 90
Author(s): Tuo Zhang, Ausma Termanis, Burak Özkan, Xun X. Bao, Jayne Culley, Flávia de Lima Alves, Juri Rappsilber, Bernard Ramsahoye, Irina Stancheva
Software Mentions: 1
Published: almost 10 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: about 15 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: over 14 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 4 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: over 13 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: over 11 years ago

10.18632/oncotarget.26330

Whole genome duplication is an early event leading to aneuploidy in <i>IDH</i>-wild type glioblastoma
Cited by: 15
Author(s): Blandine Boisselier, Frédéric Dugay, Marc‐Antoine Belaud‐Rotureau, Anne Coutolleau, Emmanuel Garcion, Philippe Meneï, Philippe Guardiola, Audrey Rousseau
Software Mentions: 1
Published: about 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: about 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: over 15 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 4 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: about 15 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: almost 19 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 4 years ago

10.1186/1471-2105-7-489

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Cited by: 197
Author(s): Tim Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert, Joseph A. White, Patricia L. Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brāzma
Software Mentions: 1
Published: over 19 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: about 18 years ago

10.1172/jci.insight.143643

CMTM6 drives cisplatin resistance by regulating Wnt signaling through ENO-1/AKT/GSK3β axis
Cited by: 21
Author(s): Pallavi Mohapatra, Omprakash Shriwas, Sibasish Mohanty, Arup Ghosh, Shuchi Smita, Sandeep Rai Kaushik, Rakesh Arya, Rachna Rath, Saroj Kumar Das Majumdar, Dillip Kumar Muduly, Sunil K. Raghav, Ranjan Kumar Nanda, Rupesh Dash
Software Mentions: 1
Published: about 5 years ago

10.1002/path.5335

Overactivity or blockade of transforming growth factor‐β each generate a specific ureter malformation
Cited by: 11
Author(s): Filipa Lopes, Neil Roberts, Leo Zeef, Natalie J. Gardiner, Adrian S. Woolf
Software Mentions: 1
Published: over 6 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: about 17 years ago

10.1186/1471-2105-11-150

Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes
Cited by: 41
Author(s): Sigrid Rouam, Thierry Moreau, Philippe Broët
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-9-183

Data capture in bioinformatics: requirements and experiences with Pedro
Cited by: 16
Author(s): Daniel Jameson, Kevin Garwood, Christopher Garwood, Tim Booth, Pinar Alper, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: almost 18 years ago

10.1128/JB.00473-13

The <i>agr</i> Locus Regulates Virulence and Colonization Genes in Clostridium difficile 027
Cited by: 95
Author(s): Melissa J. Martin, Simon Clare, David Goulding, Alexandra Faulds-Pain, Lars Barquist, Hilary P. Browne, Laura J. Pettit, Gordon Dougan, Trevor D. Lawley, Brendan W. Wren
Software Mentions: 1
Published: over 12 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: almost 18 years ago

10.1186/1471-2105-10-S12-S10

Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
Cited by: 4
Author(s): Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer
Software Mentions: 1
Published: over 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: over 19 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: almost 11 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: about 11 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: over 6 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: about 13 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: over 12 years ago

10.1186/jbiol54

Growth control of the eukaryote cell: a systems biology study in yeast
Cited by: 244
Author(s): Juan I. Castrillo, Leo Zeef, David C. Hoyle, Nianshu Zhang, Andrew Hayes, David C. Gardner, Michael Cornell, June Petty, Luke Hakes, Leanne Wardleworth, Bharat Rash, Marie Brown, Warwick B. Dunn, David Broadhurst, Kerry O'Donoghue, Svenja Hester, Tom Dunkley, Sarah R. Hart, Neil Swainston, Peter Li, Simon J. Gaskell, Norman W. Paton, Kathryn S. Lilley, Douglas B. Kell, Stephen G. Oliver
Software Mentions: 1
Published: about 19 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: about 11 years ago

10.1186/s12864-016-2537-1

On the genome base composition of teleosts: the effect of environment and lifestyle
Cited by: 14
Author(s): Andrea Tarallo, Claudia Angelini, Remo Sanges, Mitsuharu Yagi, Claudio Agnisola, Giuseppe D’Onofrio
Software Mentions: 1
Published: almost 10 years ago

10.1074/jbc.M114.598300

Cross-talk between Two Nucleotide-signaling Pathways in Staphylococcus aureus
Cited by: 103
Author(s): Rebecca M. Corrigan, Lisa Bowman, Alexandra R. Willis, Volkhard Kaever, Angelika Gründling
Software Mentions: 1
Published: about 11 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 11 years ago

10.1186/1471-2164-15-315

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach
Cited by: 66
Author(s): Tommy Bengtsson, Deborah Weighill, Estelle Proux‐Wéra, Fredrik Levander, Svante Resjö, Dharani Dhar Burra, Laith Ibrahim Moushib, Pete E. Hedley, Erland Liljeroth, Dan Jacobson, Erik Alexandersson, Erik Andréasson
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-14-8

XperimentR: painless annotation of a biological experiment for the laboratory scientist
Cited by: 7
Author(s): Christopher Tomlinson, Geraint Barton, Mark Woodbridge, Sarah Butcher
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2105-8-360

Linking microarray reporters with protein functions
Cited by: 12
Author(s): Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. Evelo
Software Mentions: 1
Published: over 18 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: almost 8 years ago

10.1002/cjp2.138

High immune cytolytic activity in tumor‐free tongue tissue confers better prognosis in patients with squamous cell carcinoma of the oral tongue
Cited by: 13
Author(s): Xiaolian Gu, Linda Boldrup, Philip J. Coates, Robin Fåhræus, Lixiao Wang, Torben Wilms, Lena Norberg‐Spaak, Nicola Sgaramella, Karin Nylander
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-8-208

Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits
Cited by: 22
Author(s): Carl-Johan Rubin, Johan Lindberg, Carolyn Fitzsimmons, Peter Savolainen, Per Jensen, Joakim Lundeberg, Leif C. Andersson, Andreas Kindmark
Software Mentions: 1
Published: over 18 years ago

10.1186/s12864-016-2814-z

A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease
Cited by: 20
Author(s): Helgi B. Schiöth, Adrian Boström, Susan K. Murphy, Wiebke Erhart, Jochen Hampe, Cynthia A. Moylan, Jessica Mwinyi
Software Mentions: 1
Published: over 9 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: about 20 years ago

10.1186/2041-1480-1-S1-S1

Building a biomedical ontology recommender web service
Cited by: 68
Author(s): Clément Jonquet, Mark A. Musen, Nigam H. Shah
Software Mentions: 1
Published: about 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 11 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: about 13 years ago

10.1186/1471-2164-8-210

Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state
Cited by: 1
Author(s): Daniel Y L Yap, David K. Smith, Xue W Zhang, Jeffrey Hill
Software Mentions: 1
Published: about 19 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 4 years ago

10.1186/1471-2164-7-78

Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity
Cited by: 34
Author(s): Vattipally B Sreenu, Pankaj Kumar, Javaregowda Nagaraju, Hampapathalu A. Nagarajaram
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-10-560

ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles
Cited by: 1
Author(s): Weizhong Li, Andrew Y. Gracey, Luciane V. Mello, Andy Brass, Andrew R. Cossins
Software Mentions: 1
Published: about 16 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: about 5 years ago

10.1186/1471-2164-10-153

Learning from microarray interlaboratory studies: measures of precision for gene expression
Cited by: 9
Author(s): David L. Duewer, Wendell Jones, Laura Reid, Marc Salit
Software Mentions: 1
Published: about 17 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 7 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 9 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: about 8 years ago

10.1186/ar2294

Expression and regulation of CCL18 in synovial fluid neutrophils of patients with rheumatoid arthritis
Cited by: 49
Author(s): Judith Auer, Bläss Markus, Hendrik Schulze‐Koops, Stefan Rußwurm, Thomas Nagel, Joachim R. Kalden, Martin Röllinghoff, H U Beuscher
Software Mentions: 1
Published: about 19 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: almost 9 years ago

10.1186/1471-2164-10-306

Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Cited by: 30
Author(s): Jin Hwan, Rui Yamaguchi, Satoru Miyano
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-8-401

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
Cited by: 12
Author(s): Santiago P. Aubourg, Marie‐Laure Martin‐Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E. Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, Jean-Pierre Renou
Software Mentions: 1
Published: about 19 years ago

10.1186/2041-1480-5-25

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
Cited by: 60
Author(s): James Malone, Andy Brown, Allyson L. Lister, Jon C. Ison, Duncan Hull, Helen Parkinson, Robert Stevens
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-10-42

Positive correlation between gene coexpression and positional clustering in the zebrafish genome
Cited by: 28
Author(s): Yen Kaow Ng, Wei Wu, Louxin Zhang
Software Mentions: 1
Published: about 17 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 12 years ago

10.3389/fimmu.2020.585414

Oral Microbiome and Gingival Tissue Apoptosis and Autophagy Transcriptomics
Cited by: 10
Author(s): Jeffrey L. Ebersole, Sreenatha Kirakodu, Elliot Neumann, Luis Orraca, Janis Gonzalez Martinez, Octavio A. González
Software Mentions: 1
Published: over 5 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: 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: over 9 years ago

10.1186/1471-2164-12-620

An expression map for Anopheles gambiae
Cited by: 27
Author(s): Robert M. MacCallum, Seth Redmond, George K. Christophides
Software Mentions: 1
Published: about 14 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: almost 6 years ago

10.1186/2041-1480-5-37

CLO: The cell line ontology
Cited by: 84
Author(s): Sirarat Sarntivijai, Yuling Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew Brush, Melissa Haendel, Jie Zheng, Christian J. Stoeckert, Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-9-340

Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
Cited by: 87
Author(s): Marcel Scheideler, Christian Elabd, Laure‐Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fátima Sánchez‐Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gérard Ailhaud, Christian Dani, Ez-Zoubir Amri, Zlatko Trajanoski
Software Mentions: 1
Published: over 17 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: over 5 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 6 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: over 8 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 9 years ago

10.1186/1471-2164-6-178

GPX-Macrophage Expression Atlas: A database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
Cited by: 16
Author(s): Graeme R. Grimes, Stuart Moodie, John S. Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D. Livingston, Muriel Mewissen, Kevin A. Robertson, Alan J. Ross, Garwin K. Sing, Peter Ghazal
Software Mentions: 1
Published: about 20 years ago

10.1098/rsob.120091

Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations
Cited by: 27
Author(s): Matthew D. Rolfe, Andrea Ocone, Melanie R. Stapleton, Simon T.E. Hall, Eleanor W. Trotter, Robert K. Poole, Guido Sanguinetti, Jeffrey Green
Software Mentions: 1
Published: over 13 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 7 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: about 20 years ago

10.7150/jca.29293

Clinical Significance of microRNA-196b-5p in Hepatocellular Carcinoma and its Potential Molecular Mechanism
Cited by: 11
Author(s): Lu Zhang, Bin Luo, Yi‐Wu Dang, Rong‐Quan He, Zhigang Peng, Gang Chen, Zhaoyong Feng
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-9-221

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA
Cited by: 5
Author(s): Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A. Setterquist, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 17 years ago

10.7150/jca.34693

Distinct Roles of VEGFA and ANGPT2 in Lung Adenocarcinoma and Squamous Cell Carcinoma
Cited by: 20
Author(s): Shuang Qin, Ming Yi, Dechao Jiao, An‐Ping Li, Zeyu Wu
Software Mentions: 1
Published: about 6 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: almost 8 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: about 20 years ago

10.1186/1471-2164-13-33

Transcriptional ontogeny of the developing liver
Cited by: 41
Author(s): Janice S. Lee, William O. Ward, Geremy W. Knapp, Hongzu Ren, Beena Vallanat, Barbara D. Abbott, Karen J. Ho, Seth J. Karp, J. Christopher Corton
Software Mentions: 1
Published: about 14 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962