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John Harrison Platig, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Gaynor SM, Fagny M, Lin X, Platig J, Quackenbush J. Connectivity in eQTL networks dictates reproducibility and genomic properties. Cell Rep Methods. 2022 May 23; 2(5):100218. PMID: 35637906; PMCID: PMC9142682.
  2. Ben Guebila M, Weighill D, Lopes-Ramos CM, Burkholz R, Pop RT, Palepu K, Shapoval M, Fagny M, Schlauch D, Glass K, Altenbuchinger M, Kuijjer ML, Platig J, Quackenbush J. An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nat Methods. 2022 05; 19(5):511-513. PMID: 35459940; PMCID: PMC9239854.
    Citations:    Fields:    
  3. Weighill D, Ben Guebila M, Glass K, Quackenbush J, Platig J. Predicting genotype-specific gene regulatory networks. Genome Res. 2022 03; 32(3):524-533. PMID: 35193937; PMCID: PMC8896459.
    Citations: 3     Fields:    Translation:HumansCells
  4. Ben Guebila M, Lopes-Ramos CM, Weighill D, Sonawane AR, Burkholz R, Shamsaei B, Platig J, Glass K, Kuijjer ML, Quackenbush J. GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 2022 01 07; 50(D1):D610-D621. PMID: 34508353; PMCID: PMC8728257.
    Citations: 5     Fields:    Translation:Humans
  5. Lackey L, Coria A, Ghosh AJ, Grayeski P, Hatfield A, Shankar V, Platig J, Xu Z, Ramos SBV, Silverman EK, Ortega VE, Cho MH, Hersh CP, Hobbs BD, Castaldi P, Laederach A. Alternative poly-adenylation modulates a1-antitrypsin expression in chronic obstructive pulmonary disease. PLoS Genet. 2021 11; 17(11):e1009912. PMID: 34784346; PMCID: PMC8631626.
    Citations:    Fields:    Translation:HumansCells
  6. Xu Z, Platig J, Lee S, Boueiz A, Chase R, Jain D, Gregory A, Suryadevara R, Berman S, Bowler R, Hersh CP, Laederach A, Castaldi PJ. Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation. Genomics. 2021 11; 113(6):4184-4195. PMID: 34763026; PMCID: PMC8722433.
    Citations:    Fields:    Translation:Cells
  7. Weighill D, Guebila MB, Lopes-Ramos C, Glass K, Quackenbush J, Platig J, Burkholz R. Gene regulatory network inference as relaxed graph matching. Proc Conf AAAI Artif Intell. 2021 Feb; 35(11):10263-10272. PMID: 34707916; PMCID: PMC8546743.
    Citations: 1     
  8. Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J. Gene Targeting in Disease Networks. Front Genet. 2021; 12:649942. PMID: 33968133; PMCID: PMC8103030.
    Citations: 2     
  9. Young AT, Carette X, Helmel M, Steen H, Husson RN, Quackenbush J, Platig J. Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. NPJ Syst Biol Appl. 2021 01 29; 7(1):8. PMID: 33514755; PMCID: PMC7846781.
    Citations: 1     Fields:    Translation:Cells
  10. Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Rep. 2020 06 23; 31(12):107795. PMID: 32579922.
    Citations: 53     Fields:    Translation:HumansCells
  11. Zeng J, Platig J, Cheng TY, Ahmed S, Skaf Y, Potluri LP, Schwartz D, Steen H, Moody DB, Husson RN. Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility. PLoS Pathog. 2020 04; 16(4):e1008452. PMID: 32255801; PMCID: PMC7164672.
    Citations: 7     Fields:    Translation:HumansCells
  12. Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush J. Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. Br J Cancer. 2020 02; 122(4):569-577. PMID: 31806877; PMCID: PMC7028992.
    Citations: 14     Fields:    Translation:Humans
  13. Parker MM, Hao Y, Guo F, Pham B, Chase R, Platig J, Cho MH, Hersh CP, Thannickal VJ, Crapo J, Washko G, Randell SH, Silverman EK, San José Estépar R, Zhou X, Castaldi PJ. Identification of an emphysema-associated genetic variant near TGFB2 with regulatory effects in lung fibroblasts. Elife. 2019 07 25; 8. PMID: 31343404.
    Citations: 13     Fields:    Translation:HumansCells
  14. Barry JD, Fagny M, Paulson JN, Aerts HJWL, Platig J, Quackenbush J. Histopathological Image QTL Discovery of Immune Infiltration Variants. iScience. 2018 Jul 27; 5:80-89. PMID: 30240647.
    Citations: 7     
  15. Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN. Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. mBio. 2018 03 06; 9(2). PMID: 29511081; PMCID: PMC5845002.
    Citations: 20     Fields:    Translation:Cells
  16. Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics. 2018 01 15; 12(1):1. PMID: 29335020; PMCID: PMC5769240.
    Citations: 10     Fields:    Translation:Humans
  17. Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML. Understanding Tissue-Specific Gene Regulation. Cell Rep. 2017 Oct 24; 21(4):1077-1088. PMID: 29069589.
    Citations: 120     Fields:    Translation:HumansCells
  18. Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics. 2017 Oct 03; 18(1):437. PMID: 28974199; PMCID: PMC5627434.
    Citations: 18     Fields:    Translation:Humans
  19. Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics. 2017 Sep 12; 18(1):723. PMID: 28899340; PMCID: PMC5596945.
    Citations: 20     Fields:    Translation:HumansCells
  20. Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proc Natl Acad Sci U S A. 2017 09 12; 114(37):E7841-E7850. PMID: 28851834; PMCID: PMC5604022.
    Citations: 46     Fields:    Translation:HumansCells
  21. Platig J, Castaldi PJ, DeMeo D, Quackenbush J. Bipartite Community Structure of eQTLs. PLoS Comput Biol. 2016 09; 12(9):e1005033. PMID: 27618581.
    Citations: 19     Fields:    Translation:Humans
  22. Rietman EA, Platig J, Tuszynski JA, Lakka Klement G. Thermodynamic measures of cancer: Gibbs free energy and entropy of protein-protein interactions. J Biol Phys. 2016 06; 42(3):339-50. PMID: 27012959.
    Citations: 10     Fields:    
  23. Platig J, Ott E, Girvan M. Robustness of network measures to link errors. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec; 88(6):062812. PMID: 24483516.
    Citations: 6     Fields:    
  24. Yang Y, Shaffer AL, Emre NC, Ceribelli M, Zhang M, Wright G, Xiao W, Powell J, Platig J, Kohlhammer H, Young RM, Zhao H, Yang Y, Xu W, Buggy JJ, Balasubramanian S, Mathews LA, Shinn P, Guha R, Ferrer M, Thomas C, Waldmann TA, Staudt LM. Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma. Cancer Cell. 2012 Jun 12; 21(6):723-37. PMID: 22698399; PMCID: PMC4059833.
    Citations: 213     Fields:    Translation:HumansAnimalsCells
  25. Ott E, Platig JH, Antonsen TM, Girvan M. Echo phenomena in large systems of coupled oscillators. Chaos. 2008 Sep; 18(3):037115. PMID: 19045489.
    Citations:    Fields:    
  26. Antonsen TM, Faghih RT, Girvan M, Ott E, Platig J. External periodic driving of large systems of globally coupled phase oscillators. Chaos. 2008 Sep; 18(3):037112. PMID: 19045486.
    Citations: 9     Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.