Daniel Carlin

TitlePostdoctoral Scholar
InstitutionUniversity of California San Diego
Address9500 Gilman Drive #0681
La Jolla CA 92093
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    1. Ozturk K, Dow M, Carlin D, Bejar R, Carter H. The emerging potential for network analysis to inform precision cancer medicine. J Mol Biol. 2018 Jun 14. PMID: 29908887.
      View in: PubMed
    2. Huang JK, Jia T, Carlin D, Ideker T. pyNBS: A Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018 Mar 28. PMID: 29608663.
      View in: PubMed
    3. Huang JK, Carlin D, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst. 2018 Apr 25; 6(4):484-495.e5. PMID: 29605183.
      View in: PubMed
    4. Carlin D, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM. Prophetic Granger Causality to infer gene regulatory networks. PLoS One. 2017; 12(12):e0170340. PMID: 29211761.
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    5. Carlin D, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017 Oct; 13(10):e1005598. PMID: 29023449.
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    6. Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017; 6:784. PMID: 29487738.
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    7. Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin D, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell. 2016 Aug 11; 166(4):1041-1054. PMID: 27499020; PMCID: PMC4985183 [Available on 08/11/17].
    8. Sokolov A, Carlin D, Paull EO, Baertsch R, Stuart JM. Pathway-Based Genomics Prediction using Generalized Elastic Net. PLoS Comput Biol. 2016 Mar; 12(3):e1004790. PMID: 26960204; PMCID: PMC4784899.
    9. Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin D, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ. Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods. 2016 Apr; 13(4):310-8. PMID: 26901648; PMCID: PMC4854847.
    10. Paull EO, Carlin D, Niepel M, Sorger PK, Haussler D, Stuart JM. Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics. 2013 Nov 01; 29(21):2757-64. PMID: 23986566; PMCID: PMC3799471.
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