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SWIFT clustering analysis of intracellular cytokine staining flow cytometry data of the HVTN 105 vaccine trial reveals high frequencies of HIV-specific CD4+ T cell responses and associations with humoral responses.
- Published in:
- Frontiers in Immunology, 2024, p. 01, doi. 10.3389/fimmu.2024.1347926
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- Article
Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons.
- Published in:
- eLife, 2023, p. 1, doi. 10.7554/eLife.85792
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- Publication type:
- Article
IgE Sensitization Drives the Atopic March.
- Published in:
- 2023
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- Publication type:
- Letter to the Editor
Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells.
- Published in:
- PLoS ONE, 2023, v. 17, n. 2, p. 1, doi. 10.1371/journal.pone.0281898
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- Article
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting.
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- Bioinformatics, 2022, v. 38, n. 21, p. 4990, doi. 10.1093/bioinformatics/btac609
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- Publication type:
- Article
Executable models of immune signaling pathways in HIV-associated atherosclerosis.
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- NPJ Systems Biology & Applications, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41540-022-00246-5
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- Publication type:
- Article
Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O 2 Levels.
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- Life (2075-1729), 2022, v. 12, n. 8, p. 1284, doi. 10.3390/life12081284
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- Publication type:
- Article
The Replica Set Method is a Robust, Accurate, and High-Throughput Approach for Assessing and Comparing Lifespan in C. elegans Experiments.
- Published in:
- Frontiers in Aging, 2022, p. 1, doi. 10.3389/fragi.2022.861701
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- Publication type:
- Article
WikiNetworks: translating manually created biological pathways for topological analysis.
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- Bioinformatics, 2022, v. 38, n. 3, p. 869, doi. 10.1093/bioinformatics/btab699
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- Publication type:
- Article
A systems genomics approach uncovers molecular associates of RSV severity.
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- PLoS Computational Biology, 2021, v. 17, n. 12, p. 1, doi. 10.1371/journal.pcbi.1009617
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- Publication type:
- Article
Infant gut microbiome is enriched with Bifidobacterium longumssp. infantis in Old Order Mennonites with traditional farming lifestyle.
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- Allergy, 2021, v. 76, n. 11, p. 3489, doi. 10.1111/all.14877
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- Publication type:
- Article
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.
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- Bioinformatics, 2021, v. 37, n. 21, p. 3702, doi. 10.1093/bioinformatics/btab229
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- Publication type:
- Article
Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition.
- Published in:
- Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.741513
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- Publication type:
- Article
Molecular characterization of atherosclerosis in HIV positive persons.
- Published in:
- Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-82429-4
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- Publication type:
- Article
Editorial: User-Friendly Tools Applied to Genetics or Systems Biology.
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- 2020
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- Publication type:
- Editorial
Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature.
- Published in:
- Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-69007-w
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- Publication type:
- Article
Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch.
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- BMC Immunology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12865-020-0342-8
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- Publication type:
- Article
IL-1β-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia.
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- 2019
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- Publication type:
- journal article
Executable pathway analysis using ensemble discrete-state modeling for large-scale data.
- Published in:
- PLoS Computational Biology, 2019, v. 15, n. 9, p. 1, doi. 10.1371/journal.pcbi.1007317
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- Publication type:
- Article
SOME EQUIVALENCE RELATIONSHIPS OF REGULARIZED REGRESSIONS.
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- Mathematics for Application, 2018, v. 7, n. 1, p. 3, doi. 10.13164/ma.2018.01
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- Publication type:
- Article
Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants.
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- 2017
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- Publication type:
- journal article
Frontline Science: c‐Myc regulates P‐selectin glycoprotein ligand‐1 expression in monocytes during HIV‐1 infection.
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- Journal of Leukocyte Biology, 2017, v. 102, n. 4, p. 953, doi. 10.1189/jlb.6HI0217-043R
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- Publication type:
- Article
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.
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- Bioinformatics, 2017, v. 33, n. 13, p. 1944, doi. 10.1093/bioinformatics/btx104
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- Publication type:
- Article
Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes.
- Published in:
- BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1669-x
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- Publication type:
- Article
Optimized logic rules reveal interferon- γ-induced modes regulated by histone deacetylases and protein tyrosine phosphatases.
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- Immunology, 2017, v. 151, n. 1, p. 71, doi. 10.1111/imm.12707
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- Publication type:
- Article
Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates.
- Published in:
- PLoS ONE, 2016, v. 11, n. 8, p. 1, doi. 10.1371/journal.pone.0160510
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- Publication type:
- Article
Humoral Dysregulation Associated with Increased Systemic Inflammation among Injection Heroin Users.
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- PLoS ONE, 2016, v. 11, n. 7, p. 1, doi. 10.1371/journal.pone.0158641
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- Publication type:
- Article
Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis.
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- Bioengineering & Translational Medicine, 2016, v. 1, n. 2, p. 193, doi. 10.1002/btm2.10035
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- Publication type:
- Article
Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection.
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- Computational & Mathematical Methods in Medicine, 2016, p. 1, doi. 10.1155/2016/7686081
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- Publication type:
- Article
Competitive SWIFT cluster templates enhance detection of aging changes.
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- Cytometry. Part A, 2016, v. 89, n. 1, p. 59, doi. 10.1002/cyto.a.22740
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- Publication type:
- Article
Introduction of a framework for dynamic knowledge representation of the control structure of transplant immunology: employing the power of abstraction with a solid organ transplant agent-based model.
- Published in:
- Frontiers in Immunology, 2015, v. 6, p. 1, doi. 10.3389/fimmu.2015.00561
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- Publication type:
- Article
Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice.
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- PLoS ONE, 2015, v. 10, n. 9, p. 1, doi. 10.1371/journal.pone.0138110
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- Publication type:
- Article
Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism.
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- BMC Immunology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12865-015-0107-y
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- Publication type:
- Article
GESPA: classifying nsSNPs to predict disease association.
- Published in:
- BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0673-2
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- Publication type:
- Article
Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism.
- Published in:
- BMC Immunology, 2015, v. 16, n. 1, p. 46, doi. 10.1186/s12865-015-0107-y
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- Publication type:
- Article
GESPA: classifying nsSNPs to predict disease association
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- BMC Bioinformatics, 2015, v. 16, n. 1, p. 228, doi. 10.1186/s12859-015-0673-2
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- Publication type:
- Article
Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.
- Published in:
- Nucleic Acids Research, 2013, v. 41, n. 18, p. e170, doi. 10.1093/nar/gkt660
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- Publication type:
- Article
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection.
- Published in:
- BMC Bioinformatics, 2013, v. 14, n. Suppl 6, p. 1, doi. 10.1186/1471-2105-14-S6-S1
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- Publication type:
- Article
Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth.
- Published in:
- PLoS Computational Biology, 2012, v. 8, n. 1, p. 1, doi. 10.1371/journal.pcbi.1002345
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- Publication type:
- Article
Dynamic models of immune responses: what is the ideal level of detail?
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- Theoretical Biology & Medical Modelling, 2010, v. 7, p. 35, doi. 10.1186/1742-4682-7-35
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- Publication type:
- Article
Modeling Systems-Level Regulation of Host Immune Responses.
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- PLoS Computational Biology, 2007, v. 3, n. 6, p. e109, doi. 10.1371/journal.pcbi.0030109
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- Publication type:
- Article
RIP death domain structural interactions implicated in TNF-mediated proliferation and survival.
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- Proteins, 2006, v. 63, n. 3, p. 413, doi. 10.1002/prot.20895
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- Publication type:
- Article
Nectarless flowers: ecological correlates and evolutionary stability.
- Published in:
- Oecologia, 2003, v. 136, n. 4, p. 565, doi. 10.1007/s00442-003-1304-6
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- Publication type:
- Article