Publications
2024
Repositioning the Early Pathology of Type 1 Diabetes to the Extraislet Vasculature
The Journal of Immunology
·
01 Mar 2024
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doi:10.4049/jimmunol.2300769
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PMID: 38426888
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PMCID: PMC10944819
Perspectives on tracking data reuse across biodata resources
Bioinformatics Advances
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01 Jan 2024
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doi:10.1093/bioadv/vbae057
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PMID: 38721398
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PMCID: PMC11076920
2023
DrugMechDB: A Curated Database of Drug Mechanisms
Scientific Data
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16 Sep 2023
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doi:10.1038/s41597-023-02534-z
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PMID: 37717042
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PMCID: PMC10505144
BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs
Bioinformatics
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01 Sep 2023
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doi:10.1093/bioinformatics/btad570
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PMID: 37707514
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PMCID: PMC11015316
Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database
Alzheimer's Research & Therapy
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24 Jun 2023
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doi:10.1186/s13195-023-01255-0
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PMID: 37355615
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PMCID: PMC10290352
Drug Repositioning using Consilience of Knowledge Graph Completion Methods
Cold Spring Harbor Laboratory
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14 May 2023
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doi:10.1101/2023.05.12.540594
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
BMC Bioinformatics
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20 Apr 2023
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doi:10.1186/s12859-023-05258-4
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PMID: 37081398
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PMCID: PMC10116472
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
Journal of Clinical and Translational Science
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01 Jan 2023
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doi:10.1017/cts.2023.619
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PMID: 37900350
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PMCID: PMC10603356
2022
Progress toward a universal biomedical data translator
Clinical and Translational Science
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06 Jun 2022
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doi:10.1111/cts.13301
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PMID: 35611543
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PMCID: PMC9372428
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Clinical and Translational Science
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06 Jun 2022
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doi:10.1111/cts.13302
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PMID: 36125173
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PMCID: PMC9372416
Design and application of a knowledge network for automatic prioritization of drug mechanisms
Bioinformatics
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06 Apr 2022
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doi:10.1093/bioinformatics/btac205
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PMID: 35561182
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PMCID: PMC9113361
Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis
Molecular & Cellular Proteomics
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01 Mar 2022
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doi:10.1016/j.mcpro.2022.100197
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PMID: 35033677
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PMCID: PMC8941213
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research
Bioinformatics
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10 Jan 2022
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doi:10.1093/bioinformatics/btac017
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PMID: 35020801
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PMCID: PMC8963279
2021
2020
Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity
Science Translational Medicine
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28 Oct 2020
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doi:10.1126/scitranslmed.aan7967
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PMID: 33115953
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PMCID: PMC7955769
Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas
Frontiers in Genetics
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14 Feb 2020
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doi:10.3389/fgene.2019.01355
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PMID: 32117413
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PMCID: PMC7034361
2019
Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network
BMC Bioinformatics
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01 Dec 2019
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doi:10.1186/s12859-019-3297-0
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PMID: 31829175
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PMCID: PMC6907279
Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts
Bioinformatics
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03 Sep 2019
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doi:10.1093/bioinformatics/btz678
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PMID: 31504205
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PMCID: PMC8104067
Position β57 of I-A
g7
controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset
Science Immunology
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02 Aug 2019
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doi:10.1126/sciimmunol.aaw6329
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PMID: 31471352
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PMCID: PMC6816460
Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements.
Human Computation
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02 Jun 2019
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doi:10.15346/hc.v6i1.4
2018
Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges
Molecular Immunology
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01 Nov 2018
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doi:10.1016/j.molimm.2018.09.020
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PMID: 30300798
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PMCID: PMC6258053
Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis
Osteoarthritis and Cartilage
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01 Nov 2018
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doi:10.1016/j.joca.2018.07.012
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PMID: 30081074
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PMCID: PMC6245598
Association study of long-term kidney transplant rejection using whole-exome sequencing
Cold Spring Harbor Laboratory
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16 Oct 2018
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doi:10.1101/444497
The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis
Proceedings of the National Academy of Sciences
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03 Oct 2018
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doi:10.1073/pnas.1810137115
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PMID: 30282735
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PMCID: PMC6196526
The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app
npj Digital Medicine
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05 Sep 2018
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doi:10.1038/s41746-018-0052-2
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PMID: 31304325
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PMCID: PMC6550256
Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3–mediated translation initiation
Journal of Biological Chemistry
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01 Aug 2018
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doi:10.1074/jbc.RA118.003192
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PMID: 30006345
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PMCID: PMC6120211
Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass
Cold Spring Harbor Laboratory
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11 Jul 2018
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doi:10.1101/367599
Exploring applications of crowdsourcing to cryo-EM
Journal of Structural Biology
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01 Jul 2018
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doi:10.1016/j.jsb.2018.02.006
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PMID: 29486249
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PMCID: PMC6086358
FoxO transcription factors modulate autophagy and proteoglycan 4 in cartilage homeostasis and osteoarthritis
Science Translational Medicine
·
14 Feb 2018
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doi:10.1126/scitranslmed.aan0746
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PMID: 29444976
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PMCID: PMC6204214
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
BMC Bioinformatics
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01 Feb 2018
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doi:10.1186/s12859-018-2041-5
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PMID: 29390967
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PMCID: PMC5796402
2017
Science Game Lab: tool for the unification of biomedical games with a purpose
Cold Spring Harbor Laboratory
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10 Jul 2017
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doi:10.1101/156141
Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes
Osteoarthritis and Cartilage
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01 Jun 2017
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doi:10.1016/j.joca.2016.11.007
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PMID: 27884645
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PMCID: PMC5438901
EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices
Cold Spring Harbor Laboratory
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29 Mar 2017
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doi:10.1101/121178
Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease
Journal of Proteome Research
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23 Jan 2017
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doi:10.1021/acs.jproteome.6b00938
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PMID: 28052195
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PMCID: PMC5441882
2016
Citizen Science for Mining the Biomedical Literature
Citizen Science: Theory and Practice
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31 Dec 2016
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doi:10.5334/cstp.56
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PMID: 30416754
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PMCID: PMC6226017
Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy
Osteoarthritis and Cartilage
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01 Sep 2016
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doi:10.1016/j.joca.2016.04.015
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PMID: 27118398
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PMCID: PMC4992644
Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems
Journal of Proteome Research
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19 Jul 2016
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doi:10.1021/acs.jproteome.6b00095
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PMID: 27356587
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PMCID: PMC5120959
Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long‐Term Outcomes
American Journal of Transplantation
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01 Jul 2016
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doi:10.1111/ajt.13728
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PMID: 26990570
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PMCID: PMC5501990
YY1 plays an essential role at all stages of B-cell differentiation
Proceedings of the National Academy of Sciences
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22 Jun 2016
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doi:10.1073/pnas.1606297113
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PMID: 27335461
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PMCID: PMC4941496
Extending gene ontology in the context of extracellular RNA and vesicle communication
Journal of Biomedical Semantics
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12 Apr 2016
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doi:10.1186/s13326-016-0061-5
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PMID: 27076901
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PMCID: PMC4830068
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models
Bioinformatics
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07 Mar 2016
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doi:10.1093/bioinformatics/btw117
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PMID: 27153723
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PMCID: PMC4920125
2015
Prioritizing Proteomics Assay Development for Clinical Translation
Journal of the American College of Cardiology
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01 Jul 2015
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doi:10.1016/j.jacc.2015.04.072
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PMID: 26160638
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
BMC Medical Genomics
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21 May 2015
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doi:10.1186/s12920-015-0095-z
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PMID: 25989980
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PMCID: PMC4494802
The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors
Science Translational Medicine
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13 May 2015
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doi:10.1126/scitranslmed.3009986
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PMID: 25972004
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PMCID: PMC5018401
Crowdsourcing in biomedicine: challenges and opportunities
Briefings in Bioinformatics
·
17 Apr 2015
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doi:10.1093/bib/bbv021
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PMID: 25888696
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PMCID: PMC4719068
Harnessing the Heart of Big Data
Circulation Research
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27 Mar 2015
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doi:10.1161/CIRCRESAHA.115.306013
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PMID: 25814682
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PMCID: PMC4721634
Omics Pipe: a community-based framework for reproducible multi-omics data analysis
Bioinformatics
·
30 Jan 2015
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doi:10.1093/bioinformatics/btv061
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PMID: 25637560
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PMCID: PMC4443682
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies
Journal of Extracellular Vesicles
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01 Jan 2015
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doi:10.3402/jev.v4.27497
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PMID: 26320941
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PMCID: PMC4553261
2014
MICROTASK CROWDSOURCING FOR DISEASE MENTION ANNOTATION IN PUBMED ABSTRACTS
Biocomputing 2015
·
01 Nov 2014
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doi:10.1142/9789814644730_0028
CROWDSOURCING AND MINING CROWD DATA
Biocomputing 2015
·
01 Nov 2014
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doi:10.1142/9789814644730_0026
Oxidative Stress Diverts tRNA Synthetase to Nucleus for Protection against DNA Damage
Molecular Cell
·
01 Oct 2014
·
doi:10.1016/j.molcel.2014.09.006
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PMID: 25284223
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PMCID: PMC4224670
MyGene.info: gene annotation query as a service
Cold Spring Harbor Laboratory
·
18 Sep 2014
·
doi:10.1101/009332
Functional expression of dental plaque microbiota
Frontiers in Cellular and Infection Microbiology
·
14 Aug 2014
·
doi:10.3389/fcimb.2014.00108
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PMID: 25177549
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PMCID: PMC4132376
2013
Ten Simple Rules for Cultivating Open Science and Collaborative R&D
PLoS Computational Biology
·
26 Sep 2013
·
doi:10.1371/journal.pcbi.1003244
·
PMID: 24086123
·
PMCID: PMC3784487
Deep Sequencing of the Murine Igh Repertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies
The Journal of Immunology
·
01 Sep 2013
·
doi:10.4049/jimmunol.1301279
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PMID: 23898036
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PMCID: PMC3778908
Unifying model for molecular determinants of the preselection Vβ repertoire
Proceedings of the National Academy of Sciences
·
05 Aug 2013
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doi:10.1073/pnas.1304048110
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PMID: 23918392
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PMCID: PMC3752219
Crowdsourcing for bioinformatics
Bioinformatics
·
19 Jun 2013
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doi:10.1093/bioinformatics/btt333
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PMID: 23782614
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PMCID: PMC3722523
A task-based approach for Gene Ontology evaluation
Journal of Biomedical Semantics
·
01 Apr 2013
·
doi:10.1186/2041-1480-4-S1-S4
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PMID: 23734599
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PMCID: PMC3633003
2012
genegames.org: High-Throughput Access to Biological Knowledge and Reasoning through Online Games
2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology
·
01 Sep 2012
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doi:10.1109/HISB.2012.70
Linking genes to diseases with a SNPedia-Gene Wiki mashup
Journal of Biomedical Semantics
·
24 Apr 2012
·
doi:10.1186/2041-1480-3-S1-S6
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PMID: 22541597
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PMCID: PMC3337266
2011
TCLUST: A Fast Method for Clustering Genome-Scale Expression Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics
·
01 May 2011
·
doi:10.1109/TCBB.2010.34
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PMID: 20479508
2010
Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency
Proceedings of the National Academy of Sciences
·
23 Feb 2010
·
doi:10.1073/pnas.0914019107
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PMID: 20133595
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PMCID: PMC2840467
2009
2008
2007
2006
Reply to “Normalization procedures and detection of linkage signal in genetical-genomics experiments”
Nature Genetics
·
01 Aug 2006
·
doi:10.1038/ng0806-856
An efficient rapid system for profiling the cellular activities of molecular libraries
Proceedings of the National Academy of Sciences
·
21 Feb 2006
·
doi:10.1073/pnas.0511292103
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PMID: 16492761
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PMCID: PMC1413928
2005
Large-Scale Profiling of Rab GTPase Trafficking Networks: The Membrome
Molecular Biology of the Cell
·
01 Aug 2005
·
doi:10.1091/mbc.E05-01-0062
·
PMID: 15944222
·
PMCID: PMC1182321
2004
2003
Genome-Wide Analysis of CREB Target Genes Reveals A Core Promoter Requirement for cAMP Responsiveness
Molecular Cell
·
01 May 2003
·
doi:10.1016/S1097-2765(03)00199-0
2002
Large Scale Molecular Analysis Identifies Genes with Altered Expression in Salivary Adenoid Cystic Carcinoma
The American Journal of Pathology
·
01 Oct 2002
·
doi:10.1016/S0002-9440(10)64408-2
·
PMID: 12368205
·
PMCID: PMC1867312
2001
2000
Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation
Proteins: Structure, Function, and Genetics
·
01 Jan 2000
·
doi:10.1002/1097-0134(20010201)42:2<279::AID-PROT150>3.0.CO;2-U
·
PMID: 11119652