bioconductor: arrayQualityMetrics | Projects

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: over 15 years ago

MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data
Cited by: 11
Author(s): Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia L. Webb, Robert M. Greene, M. Michele Pisano
Software Mentions: 24
Published: over 11 years ago

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: over 13 years ago

10.3389/fimmu.2019.02887

Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo
Cited by: 29
Author(s): Hung Jen Chen, Andrew Y. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
Software Mentions: 13
Published: over 4 years ago

10.3389/fmolb.2021.681526

Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: almost 3 years ago

10.3389/fonc.2020.00691

Immunoscore Predicts Survival in Early-Stage Lung Adenocarcinoma Patients
Cited by: 12
Author(s): Zihuan Zhao, Dan Zhao, Jianguo Xia, Yichuan Wang, Buhai Wang
Software Mentions: 11
Published: about 4 years ago

10.1371/journal.pcbi.1002276

BeadArray Expression Analysis Using Bioconductor
Cited by: 50
Author(s): Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch
Software Mentions: 11
Published: over 12 years ago

10.3389/fonc.2014.00147

An Integrative Analysis of Meningioma Tumors Reveals the Determinant Genes and Pathways of Malignant Transformation
Cited by: 7
Author(s): José Carlos Iglesias Gómez, Adrián Mosquera Orgueira
Software Mentions: 11
Published: almost 10 years ago

10.1186/1471-2105-10-74

RGG: A general GUI Framework for R scripts
Cited by: 7
Author(s): Ilhami Visne, Erkan Dilaveroǧlu, Klemens Vierlinger, Martin Lauss, Ahmet Yıldız, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner
Software Mentions: 11
Published: about 15 years ago

10.1016/j.ebiom.2018.04.010

Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial
Cited by: 28
Author(s): Antonio J. Berlanga‐Taylor, Katharine Plant, Andrew Dahl, Evelyn Lau, Michael Hill, David Sims, Andreas Heger, Jonathan Emberson, Jane Armitage, Robert Clarke, Julian C. Knight
Software Mentions: 11
Published: about 6 years ago

10.1126/sciadv.1600760

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia
Cited by: 85
Author(s): S. Picaud, Katharina Leonards, Jean-Philippe Lambert, Oliver M. Dovey, Christopher Wells, Oleg Fedorov, Octovia Monteiro, Takao Fujisawa, Chenyi Wang, Hannah Lingard, C. Tallant, Nikzad Nikbin, Lucie Guetzoyan, Richard J. Ingham, Steven V. Ley, P.E. Brennan, Susanne Müller, Anastasia Samsonova, Anne‐Claude Gingras, Juerg Schwaller, George S. Vassiliou, Stefan Knapp, P. Filippakopoulos
Software Mentions: 10
Published: over 7 years ago

10.3389/fgene.2020.586602

Multi-Approach Bioinformatics Analysis of Curated Omics Data Provides a Gene Expression Panorama for Multiple Cancer Types
Cited by: 13
Author(s): Bruno César Feltes, Joice de Faria Poloni, Itamar José Guimarães Nunes, Sara Socorro Faria, Márcio Dorn
Software Mentions: 10
Published: over 3 years ago

10.3390/cancers13081768

Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumour-Associated Modules and Potential Therapeutic Targets in Hepatocellular Carcinoma
Cited by: 8
Author(s): Thomas Mohr, Sonja Katz, Verena Paulitschke, Nadim Aizarani, Alexander Tolios
Software Mentions: 9
Published: about 3 years ago

10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: about 4 years ago

10.1038/s41598-017-02685-1

Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora
Cited by: 73
Author(s): Rachel M. Wright, Carly D. Kenkel, Carly E. Dunn, Erin N. Shilling, Line K. Bay, Mikhail V. Matz
Software Mentions: 8
Published: almost 7 years ago

10.3390/ijms21072337

Differential Targeting of Gr-MDSCs, T Cells and Prostate Cancer Cells by Dactolisib and Dasatinib
Cited by: 10
Author(s): Guoqiang Lü, Zhijian Jin, Xin Lü
Software Mentions: 8
Published: about 4 years ago

10.3233/JAD-170011

Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data
Cited by: 17
Author(s): Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Software Mentions: 8
Published: almost 7 years ago

10.3390/ijms22179426

Gravitational Force—Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells
Cited by: 14
Author(s): Christian Vahlensieck, Cora S. Thiel, Ye Zhang, Andreas Huge, Oliver Ullrich
Software Mentions: 8
Published: over 2 years ago

10.1371/journal.pone.0143970

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome
Cited by: 37
Author(s): Katherine James, Shereen Al-Ali, Jessica Tarn, Simon Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin Pease, Paul Emery, Peter Lanyon, John Hunter, Monica Gupta, Michèle Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert J. Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, Anil Wipat, Julia L. Newton, David Jones, John D. Isaacs, Jennifer Hallinan, Wan‐Fai Ng
Software Mentions: 8
Published: over 8 years ago

10.1186/1471-2105-15-69

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data
Cited by: 15
Author(s): Gan Zhang, Jianwu Wang, Nathan Salomonis, Jennifer Stowe, Gabriel G. Haddad, Andrew D. McCulloch, Ilkay Altıntaş, Alexander C. Zambon
Software Mentions: 7
Published: about 10 years ago

10.1136/gutjnl-2019-318343

A blood-based prognostic biomarker in IBD
Cited by: 125
Author(s): Daniele Biasci, James C. Lee, Nurulamin M Noor, Diana R Pombal, Monica Hou, Nina Lewis, Tariq Ahmad, Ailsa Hart, Miles Parkes, Eoín McKinney, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 7
Published: about 5 years ago

10.3389/fmolb.2020.598583

SARS-CoV-2 Proteins Exploit Host’s Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways
Cited by: 29
Author(s): A. A. Khan, Abul B.M.M.K. Islam
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.11491

Localized JNK signaling regulates organ size during development
Cited by: 37
Author(s): Helen Rankin Willsey, Xiaoyan Zheng, José Carlos Pastor-Pareja, A. Jeremy Willsey, Philip A. Beachy, Tian Xu
Software Mentions: 6
Published: about 8 years ago

10.1186/s13073-016-0282-3

Identification of key regulators of pancreatic cancer progression through multidimensional systems-level analysis
Cited by: 45
Author(s): Deepa Rajamani, Manoj Bhasin
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0073938

A Toxicogenomic Approach for the Prediction of Murine Hepatocarcinogenesis Using Ensemble Feature Selection
Cited by: 16
Author(s): Johannes Eichner, Nadine Kossler, Clemens Wrzodek, Arno Kalkuhl, Dorthe Bach Toft, Nina Ostenfeldt, V. Espley Richard, Andreas Zell
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pgen.1005908

Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease
Cited by: 83
Author(s): James E. Peters, Paul Lyons, James C. Lee, Alison F. Richard, Mary D Fortune, Paul Newcombe, Sylvia Richardson, Kenneth G. C. Smith
Software Mentions: 6
Published: about 8 years ago

10.1186/1471-2105-9-493

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management
Cited by: 13
Author(s): Geraint Barton, James Abbott, Norie Chiba, Daniel Huang, Yanyan Huang, Marko Krznarić, J. Mack-Smith, Ammar Saleem, Brad T. Sherman, Brijesh K. Tiwari, Christopher Tomlinson, Timothy J. Aitman, John Darlington, Laurence Gamé, Michael J.E. Sternberg, Sarah Butcher
Software Mentions: 6
Published: over 15 years ago

10.1186/s12864-016-2718-y

Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin
Cited by: 11
Author(s): Karl G. Kugler, Zeljkica Jandric, Reinhard Beyer, Eva Klopf, Walter Glaser, Marc Lemmens, Mehrdad Shams, Klaus Mayer, Gerhard Adam, Christoph Schüller
Software Mentions: 6
Published: almost 8 years ago

10.3390/ijms20164037

Consistent Biomarkers and Related Pathogenesis Underlying Asthma Revealed by Systems Biology Approach
Cited by: 18
Author(s): Xiner Nie, Jinyi Wei, Youjin Hao, Jingxin Tao, Yinghong Li, Mingwei Liu, Bo-Ying Xu, Bo Li
Software Mentions: 6
Published: almost 5 years ago

10.3389/fcell.2021.648856

Comprehensive Characterization of Cachexia-Inducing Factors in Diffuse Large B-Cell Lymphoma Reveals a Molecular Subtype and a Prognosis-Related Signature
Cited by: 5
Author(s): Zhixing Kuang, Xun Li, Rongqiang Liu, Shaoxing Chen, Jiannan Tu
Software Mentions: 6
Published: about 3 years ago

10.1186/s13229-019-0287-z

A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood
Cited by: 12
Author(s): Charles E. Mordaunt, Bo Y. Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca Jean Schmidt, M. Daniele Fallin
Software Mentions: 6
Published: over 4 years ago

10.1128/mSphere.00167-17

Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans
Cited by: 25
Author(s): Tobias Weil, Rodrigo Santamaría, Wanseon Lee, Johan Rung, Noemi Tocci, Darren Abbey, Ana R. Bezerra, Laura Carreto, Gabriela Moura, Mònica Bayés, Marta Gut, Attila Csikász‐Nagy, Duccio Cavalieri, Judith Berman, Manuel A. S. Santos
Software Mentions: 6
Published: over 6 years ago

10.1128/mBio.02495-18

The Transcriptional Cycle Is Suited to Daytime N 2 Fixation in the Unicellular Cyanobacterium “ Candidatus Atelocyanobacterium thalassa” (UCYN-A)
Cited by: 28
Author(s): María del Carmen Muñoz-Marín, Irina N. Shilova, Tianshu Shi, Hanna Farnelid, Ana María Cabello, Jonathan P. Zehr
Software Mentions: 6
Published: about 5 years ago

10.1186/1471-2105-13-326

A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers
Cited by: 29
Author(s): Oliver P. Günther, Virginia Chen, Gabriela Cohen Freue, Robert Balshaw, Scott J. Tebbutt, Zsuzsanna Hollander, Mandeep Takhar, W. Robert McMaster, Bruce M. McManus, Paul Keown, Raymond T. Ng
Software Mentions: 5
Published: over 11 years ago

10.1186/s13072-015-0046-0

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia
Cited by: 16
Author(s): Jiansheng Wu, Luca Pinello, Elinor Yissachar, Jonathan W. Wischhusen, Guo‐Cheng Yuan, Charles W.M. Roberts
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-015-1540-2

Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus
Cited by: 185
Author(s): Rachel M. Wright, Galina V. Aglyamova, Eli Meyer, Mikhail V. Matz
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-018-37098-1

Comparison between dopaminergic and non-dopaminergic neurons in the VTA following chronic nicotine exposure during pregnancy
Cited by: 9
Author(s): Renee F. Keller, Tina Kazemi, Andrei Dragomir, Yasemin M. Akay, Metin Akay
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-14-725

Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence
Cited by: 113
Author(s): Yury O. Nunez, Jay Truitt, Giorgio Gorini, Olga N. Ponomareva, Yuri A. Blednov, R. Adron Harris
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0050253

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Cited by: 2
Author(s): Andrew R. Dalby, Ibrahim Emam, Raimo Franke
Software Mentions: 5
Published: over 11 years ago

10.1186/s12967-020-02695-0

Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2
Cited by: 39
Author(s): Abul B.M.M.K. Islam, A. A. Khan, Rasel Ahmed, Md. Sabbir Hossain, Shah Md. Tamim Kabir, Md Shahidul Islam, Amam Zonaed Siddiki
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-31882-9

Investigating the genetic profile of dopaminergic neurons in the VTA in response to perinatal nicotine exposure using mRNA-miRNA analyses
Cited by: 14
Author(s): Renee F. Keller, Andrei Dragomir, Yonggang Fan, Yasemin M. Akay, Metin Akay
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0070433

Genome-Wide Expression of Transcriptomes and Their Co-Expression Pattern in Subtropical Maize (Zea mays L.) under Waterlogging Stress
Cited by: 54
Author(s): Nepolean Thirunavukkarasu, Firoz Hossain, Sweta Mohan, Kaliyugam Shiriga, Swati Mittal, R.C. Sharma, Rita Singh, H. S. Gupta
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pgen.1006643

Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells
Cited by: 102
Author(s): Silva Kasela, Kai Kisand, Liina Tserel, Epp Kaleviste, Anu Remm, Krista Fischer, Tõnu Esko, Harm-Jan Westra, Benjamin P. Fairfax, Seiko Makino, Julian C. Knight, Lude Franke, Andres Metspalu, Pärt Peterson, Lili Milani
Software Mentions: 5
Published: about 7 years ago

10.1186/s12885-020-06922-1

Gene networks and expression quantitative trait loci associated with adjuvant chemotherapy response in high-grade serous ovarian cancer
Cited by: 5
Author(s): Jihoon Choi, Danai G. Topouza, Anastasiya Tarnouskaya, Sean Nesdoly, Madhuri Koti, Qing Duan
Software Mentions: 5
Published: about 4 years ago

10.1038/srep22932

Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse
Cited by: 44
Author(s): Núria Mach, Sandra Plancade, Alicja Pacholewska, Jérôme Lecardonnel, Julie Rivière, Marco Moroldo, Anne Vaiman, Caroline Morgenthaler, Marine Beinat, Alizée Nevot, Céline Robert, Éric Barrey
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pbio.2002940

The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity
Cited by: 46
Author(s): Rukeia El-Athman, Nikolaï Genov, J Mazùch, Kaiyang Zhang, Yong A. Yu, Luise Fuhr, Marconi Abreu, Yin Li, Thomas Wallach, Achim Kramer, Clemens A. Schmitt, Angela Relógio
Software Mentions: 5
Published: over 6 years ago

10.1016/j.molp.2020.07.010

The IBI1 Receptor of β-Aminobutyric Acid Interacts with VOZ Transcription Factors to Regulate Abscisic Acid Signaling and Callose-Associated Defense
Cited by: 25
Author(s): Roland E. Schwarzenbacher, Grace Wardell, Joost H. M. Stassen, Emily Guest, Peijun Zhang, Estrella Luna, Jurriaan Ton
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0204236

In silico analysis of the Mus musculus uterine gene expression landscape during pregnancy identifies putative upstream regulators for labour
Cited by: 1
Author(s): Febilla Fernando, Souad Boussata, Aldo Jongejan, Joris A. M. van der Post, Gijs B. Afink, Carrie Ris‐Stalpers
Software Mentions: 5
Published: over 5 years ago

10.1111/jcmm.15851

Prognostic and predictive value of a mRNA signature in peripheral T‐cell lymphomas: A mRNA expression analysis
Cited by: 6
Author(s): Jiannan Tu, Zhixing Kuang, Xiaoxiao Xie, Shizhen Wu, Ting Wu, Shengchi Chen
Software Mentions: 5
Published: over 3 years ago

10.1186/s13029-019-0071-7

eUTOPIA: solUTion for Omics data PreprocessIng and Analysis
Cited by: 34
Author(s): Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino, Dario Greco
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-76404-8

Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy
Cited by: 67
Author(s): Abul B.M.M.K. Islam, A. A. Khan
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2017.01071

Gene Expression Contributes to the Recent Evolution of Host Resistance in a Model Host Parasite System
Cited by: 33
Author(s): Brian K. Lohman, Natalie C. Steinel, Jesse N. Weber, Daniel I. Bolnick
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0178151

Analysis of early mesothelial cell responses to Staphylococcus epidermidis isolated from patients with peritoneal dialysis-associated peritonitis
Cited by: 5
Author(s): Amanda L. McGuire, Kieran T. Mulroney, Christine Carson, Ram Ramesh, Grant Morahan, Aron Chakera
Software Mentions: 4
Published: almost 7 years ago

10.1002/JLB.3A0617-261R

Effects of anti-inflammatory drugs on the expression of tryptophan-metabolism genes by human macrophages
Cited by: 22
Author(s): Tim Regan, Andrew C. Gill, Sara Clohisey, Mark W. Barnett, Carmine M. Pariante, Neil A. Harrison, David Hume, Edward T. Bullmore, Tom C. Freeman
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0068551

A Systems-Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa
Cited by: 17
Author(s): Stephen P. Ficklin, F. Alex Feltus
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-017-3745-z

The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model
Cited by: 20
Author(s): Martijn van Hagen, Diewertje G. E. Piebes, Wim C. de Leeuw, Ilona M. Vuist, Willeke M. C. van Roon‐Mom, Perry D. Moerland, Pernette J. Verschure
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0057886

Integrative Genome-Wide Gene Expression Profiling of Clear Cell Renal Cell Carcinoma in Czech Republic and in the United States
Cited by: 94
Author(s): Magdalena B. Wozniak, Florence Le Calvez-Kelm, Behnoush Abedi-Ardekani, Graham Byrnes, G. Durand, Christine Carreira, Jocelyne Michelon, Vladimír Janout, Ivana Holcátová, Lenka Foretová, A. Brisuda, Fabienne Lesueur, James McKay, Paul Brennan, Ghislaine Scélo
Software Mentions: 4
Published: about 11 years ago

10.1242/dmm.034850

Identification of brain metastasis genes and therapeutic evaluation of histone deacetylase inhibitors in a clinically relevant model of breast cancer brain metastasis
Cited by: 21
Author(s): Soo-Hyun Kim, Richard P. Redvers, Lap Hing, Xiawei Ling, Andrew J. Lucke, Robert C. Reid, David P. Fairlie, Ángel G. Martín, Robin L. Anderson, Delphine Denoyer, Normand Pouliot
Software Mentions: 4
Published: over 6 years ago

10.1186/s13054-020-2788-8

Dynamic LTR retrotransposon transcriptome landscape in septic shock patients
Cited by: 5
Author(s): Marine Mommert, Olivier Tabone, Audrey Guichard, Guy Oriol, Elisabeth Cerrato, Mélanie Denizot, Valérie Cheynet, Alexandre Pachot, Alain Lepape, Guillaume Monneret, Fabienne Venet, Karen Brengel‐Pesce, Julien Textoris, François Mallet
Software Mentions: 4
Published: about 4 years ago

10.1186/1868-7083-4-20

Genome-scale case-control analysis of CD4+ T-cell DNA methylation in juvenile idiopathic arthritis reveals potential targets involved in disease
Cited by: 41
Author(s): Justine A. Ellis, Jane Munro, Raul A Chavez, Lavinia Gordon, Jihoon E. Joo, Jonathan Akikusa, Roger C. Allen, Anne‐Louise Ponsonby, Jeffrey M Craig, Richard Saffery
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-020-6766-y

Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian
Cited by: 9
Author(s): Whitney B. Leach, Adam M. Reitzel
Software Mentions: 4
Published: about 4 years ago

10.1186/s13395-016-0115-5

Skeletal muscle characteristics are preserved in hTERT/cdk4 human myogenic cell lines
Cited by: 53
Author(s): Matthew Thorley, Stéphanie Duguez, Emilia Maria Cristina Mazza, Sara Valsoni, Anne Bigot, Kamel Mamchaoui, Brennan Harmon, Thomas Voït, Vincent Mouly, William Duddy
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-91907-8

Y disruption, autosomal hypomethylation and poor male lung cancer survival
Cited by: 13
Author(s): Saffron A.G. Willis‐Owen, C. Domingo-Sabugo, E. Starren, Liming Liang, Maxim B. Freidin, Madeleine Arseneault, Youming Zhang, Shir Kiong Lu, Sanjay Popat, Eric Lim, Andrew G. Nicholson, Yasser Riazalhosseini, Mark Lathrop, William Cookson, Miriam F. Moffatt
Software Mentions: 4
Published: almost 3 years ago

10.1186/1471-2164-15-763

Transcriptome of Saccharomyces cerevisiae during production of D-xylonate
Cited by: 5
Author(s): Dominik Mojžita, Merja Oja, Eija Rintala, Marilyn G. Wiebe, Merja Penttilä, Laura Ruohonen
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2164-13-42

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies
Cited by: 17
Author(s): Michiel E. Adriaens, Magali Jaillard, Lars Eijssen, Claus Mayer, Chris T. Evelo
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-020-74947-4

Pancreatic duct ligation reduces premalignant pancreatic lesions in a Kras model of pancreatic adenocarcinoma in mice
Cited by: 4
Author(s): Marta Cáceres, Rita Quesada, Mar Iglesias, Francisco X. Real, María Villamonte, Jaime Martínez de Villarreal, M.E. Ruíz Pérez, Anna Andaluz, Xavier Moll, Enrique Berjano, Dimitri Dorcaratto, Patricia Sánchez-Velázquez, Luís Grande, Fernando Burdı́o
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.63838

Inducible mechanisms of disease tolerance provide an alternative strategy of acquired immunity to malaria
Cited by: 39
Author(s): Wiebke Nahrendorf, Alasdair Ivens, Philip J. Spence
Software Mentions: 4
Published: about 3 years ago

10.1155/2013/848952

Integration of Data from Omic Studies with the Literature-Based Discovery towards Identification of Novel Treatments for Neovascularization in Diabetic Retinopathy
Cited by: 4
Author(s): Aleš Maver, Dimitar Hristovski, Thomas C. Rindflesch, Borut Peterlin
Software Mentions: 4
Published: over 11 years ago

10.1093/jas/skaa181

The effect of maternal antibiotic use in sows on intestinal development in offspring
Cited by: 10
Author(s): Astrid de Greeff, Dirkjan Schokker, Petra Roubos-van den Hil, P. Ramaekers, S.A. Vastenhouw, Frank Harders, Alex Bossers, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 4
Published: almost 4 years ago

10.1007/s12032-021-01464-3

Dual inhibition of TGFβ and AXL as a novel therapy for human colorectal adenocarcinoma with mesenchymal phenotype
Cited by: 6
Author(s): Davide Ciardiello, Bernadette Blauensteiner, Nunzia Matrone, Valentina Belli, Thomas Mohr, Pietro Paolo Vitiello, Giulia Martini, L. Poliero, Claudia Cardone, Stefania Napolitano, Vincenzo De Falco, Emilio Francesco Giunta, Vincenza Ciaramella, Carminia Della Corte, Giusi Barra, Francesco Selvaggi, Renato Franco, Federica Zito Marino, Antonio Cuomo, Teresa Troiani, Maria Sibilia, Fortunato Ciardiello, Erika Martinelli
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.120.401166

DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood inCaenorhabditis elegans
Cited by: 14
Author(s): Daniel R. McHugh, Elena Koumis, Paul Jacob, Jennifer Goldfarb, Michelle Schlaubitz-Garcia, Safae Bennani, Paul Regan, Prem Patel, Matthew J. Youngman
Software Mentions: 4
Published: about 4 years ago

10.15252/msb.20177998

The relative resistance of children to sepsis mortality: from pathways to drug candidates
Cited by: 10
Author(s): Rose Bernadette Joachim, Gabriel Altschuler, John N. Hutchinson, Hector R. Wong, Winston Hide, Lester Kobzik
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.3737

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
Cited by: 16
Author(s): M. Rocío Aguilar-Rangel, Ricardo A. Chávez Montes, Eric González‐Segovia, Jeffrey Ross‐Ibarra, June Simpson, Ruairidh J. H. Sawers
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.12766

Characterization of pancreatic glucagon-producing tumors and pituitary gland tumors in transgenic mice overexpressingMYCNinhGFAP-positive cells
Cited by: 20
Author(s): Kathrin Fielitz, Kristina Althoff, Katleen De Preter, Julie Nonnekens, Jasmin Ohli, Sandra Elges, Wolfgang Hartmann, Günter Klöppel, Thomas Knösel, Marc Schulte, Ludger Klein-Hitpaß, Daniela Beißer, Henning Reis, Annette Eyking, Elke Cario, Johannes H. Schulte, Alexander Schramm, Ulrich Schüller
Software Mentions: 4
Published: over 7 years ago

10.1534/g3.118.200585

Transcriptomic Plasticity in the Arthropod Generalist Tetranychus urticae Upon Long-Term Acclimation to Different Host Plants
Cited by: 36
Author(s): Simon Snoeck, Nicky Wybouw, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1003503

HDAC7 Is a Repressor of Myeloid Genes Whose Downregulation Is Required for Transdifferentiation of Pre-B Cells into Macrophages
Cited by: 55
Author(s): Bruna Barneda-Zahonero, Lidia Román-González, Olga Collazo, Hasan Rafati, Abul B.M.M.K. Islam, Lars H. Bussmann, Alessandro Di Tullio, Luisa I. De Andres, Thomas Graf, Núria López‐Bigas, Tokameh Mahmoudi, Maribel Parra
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0021681

An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction
Cited by: 8
Author(s): Herman M. J. Sontrop, Wim Verhaegh, Marcel J. T. Reinders, Perry D. Moerland
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0203266

Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress
Cited by: 54
Author(s): R.C. Sharma, Garima Singh, Sitangshu Bhattacharya, Ashutosh Singh
Software Mentions: 4
Published: over 5 years ago

10.1080/21623945.2021.1910154

Cleavage of the vaspin N-terminus releases cell-penetrating peptides that affect early stages of adipogenesis and inhibit lipolysis in mature adipocytes
Cited by: 4
Author(s): Catherine A Tindall, Estelle Erkner, Jan Stichel, Annette G. Beck‐Sickinger, Anne Hoffmann, Juliane Weiner, John T. Heiker
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2407-13-585

The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts
Cited by: 10
Author(s): Pratiti Bandopadhayay, Anissa Jabbour, Christopher D. Riffkin, Marika Salmanidis, Lavinia Gordon, Dean Popovski, Lin Rigby, David M. Ashley, D. Neil Watkins, David M. Thomas, Elizabeth Algar, Paul G. Ekert
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2407-14-64

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Cited by: 21
Author(s): Marion Fehlker, Matthew R. Huska, Thomas Jöns, Miguel A. Andrade‐Navarro, Wolfgang Kemmner
Software Mentions: 3
Published: over 10 years ago

10.1186/s12885-015-1994-2

Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells
Cited by: 28
Author(s): Ruud Weijer, Mans Broekgaarden, Rowan F. van Golen, Esther Bulle, E. E. S. Nieuwenhuis, Aldo Jongejan, Perry D. Moerland, Antoine H. C. van Kampen, Thomas M. van Gulik, Michal Heger
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2407-14-246

Gene expression profiling reveals activation of the FA/BRCA pathway in advanced squamous cervical cancer with intrinsic resistance and therapy failure
Cited by: 41
Author(s): Ovidiu Bălăcescu, Loredana Bălăcescu, Oana Tudoran, Nicolae Todor, Meda Rus, Rareș Buiga, Sergiu Şuşman, Bogdan Fetică, Laura Pop, Laura Iuliana Maja, Simona Vișan, Claudia Ordeanu, Ioana Berindan‐Neagoe, Viorica Nagy
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-15-595

Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors
Cited by: 34
Author(s): Mark Kidd, Irvin M. Modlin, Ignat Drozdov
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-019-5748-4

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Cited by: 1
Author(s): Dirkjan Schokker, Ina Hulsegge, H. Woelders, Johanna M.J. Rebel
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-015-1646-6

Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines
Cited by: 91
Author(s): Dirkjan Schokker, Gosse Veninga, S.A. Vastenhouw, Alex Bossers, F.M. de Bree, L.M.T.E. Kaal-Lansbergen, Johanna M.J. Rebel, M.A. Smits
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-019-5527-2

Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress
Cited by: 27
Author(s): Catalina Aguilar, Jean-Baptiste Raina, Sylvain Forêt, David C. Hayward, Bruno Lapeyre, David G. Bourne, David J. Miller
Software Mentions: 3
Published: about 5 years ago

10.1186/s12920-020-00761-6

Comparative transcriptome analysis of Parkinson’s disease and Hutchinson-Gilford progeria syndrome reveals shared susceptible cellular network processes
Cited by: 2
Author(s): Diana M. Hendrickx, Enrico Glaab
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2229-10-59

Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thalianareveal the involvement of hormone and defense signaling pathways
Cited by: 89
Author(s): David Weisman, Merianne Alkio, Adán Colón‐Carmona
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2229-13-147

Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine
Cited by: 79
Author(s): Sarah Jane Cookson, Nathalie Ollat
Software Mentions: 3
Published: over 11 years ago

10.1186/s12934-016-0470-2

Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Cited by: 68
Author(s): Véronique Beckers, Ignacio Poblete‐Castro, Jürgen Tomasch, Christoph Wittmann
Software Mentions: 3
Published: about 8 years ago

10.3390/plants9121812

Comparative Transcriptome Analysis of Iron and Zinc Deficiency in Maize (Zea mays L.)
Cited by: 23
Author(s): Mallana Gowdra Mallikarjuna, Nepolean Thirunavukkarasu, R.C. Sharma, Kaliyugam Shiriga, Firoz Hossain, Jayant S. Bhat, Amitha Cr Mithra, Soma S. Marla, K.M. Manjaiah, A. Ramachandra Rao, H. S. Gupta
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1008608

miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer
Cited by: 2
Author(s): Shay Ben-Elazar, Miriam Ragle Aure, Kristín Jónsdóttir, Suvi‐Katri Leivonen, Vessela N. Kristensen, E. A. M. Janssen, Kristine Kleivi Sahlberg, Ole Christian Lingjærde, Zohar Yakhini
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0137027

Gene Expression and MicroRNA Expression Analysis in Small Arteries of Spontaneously Hypertensive Rats. Evidence for ER Stress
Cited by: 21
Author(s): Teresa Palao, Karl Swärd, Aldo Jongejan, Perry D. Moerland, Judith de Vos, Angela van Weert, Silvia M. Arribas, Gergely Groma, Ed vanBavel, Erik N. T. P. Bakker
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0055871

Massive-Scale Gene Co-Expression Network Construction and Robustness Testing Using Random Matrix Theory
Cited by: 44
Author(s): Scott M. Gibson, Stephen P. Ficklin, Sven Isaacson, Feng Luo, Frank Alexander Feltus, Melinda Smith
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0019322

Generation of a Predictive Melphalan Resistance Index by Drug Screen of B-Cell Cancer Cell Lines
Cited by: 19
Author(s): Martin Boegsted, Johanne Marie Holst, Kirsten Fogd, Steffen Falgreen, Susanne Sørensen, Alexander Schmitz, Anne Bukh, Hans Erik Johnsen, Mette Nyegaard, Karen Dybkær
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0113660

Diffusion of Information throughout the Host Interactome Reveals Gene Expression Variations in Network Proximity to Target Proteins of Hepatitis C Virus
Cited by: 9
Author(s): Ettore Mosca, Roberta Alfieri, Luciano Milanesi
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0028402

Influence of 17β-Estradiol on Gene Expression of Paracoccidioides during Mycelia-to-Yeast Transition
Cited by: 40
Author(s): Jata Shankar, Thomas D. Wu, Karl V. Clemons, J. P. Monteiro, Laurence F. Mirels, David A. Stevens
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0164353

Induced Human Decidual NK-Like Cells Improve Utero-Placental Perfusion in Mice
Cited by: 20
Author(s): Ricardo de Carvalho Cavalli, Ana Sofia Cerdeira, Elizabeth Pernicone, Henri Augusto Korkes, Suzanne D. Burke, Augustine Rajakumar, Ravi Thadhani, Drucilla J. Roberts, Manoj Bhasin, S. Ananth Karumanchi, Hernan D. Kopcow
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0084634

Suppression of Molecular Inflammatory Pathways by Toll-Like Receptor 7, 8, and 9 Antagonists in a Model of IL-23-Induced Skin Inflammation
Cited by: 90
Author(s): Mayte Suárez‐Fariñas, Robert D. Arbeit, Weiwen Jiang, Francesca S. Ortenzio, Tim Sullivan, James G. Krueger
Software Mentions: 3
Published: over 10 years ago

Projects: bioconductor: arrayQualityMetrics

Papers Mentioning arrayQualityMetrics 190