This list includes all publications that feature Bioinformatics Core members as co-authors, and most of the papers where we are acknowledged for providing assistance and/or software that was developed in the Core.














  • [Co-authors]Assemblathon 1: a competitive assessment of de novo short read assembly methods. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, et al.    Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. PMID:21926179 | PMCID:PMC3227110
  • [Co-authors] —Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TM, Lin D, Joshi NA, Martinez-Garcia PJ, Crisosto CH.   BMC Genomics. 2011 Nov 22;12:569. doi: 10.1186/1471-2164-12-569. PMID:22108025 | PMCID:PMC3253712
  • [Co-authors] — Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K.  G3 (Bethesda). 2011 Nov;1(6):515-22. doi: 10.1534/g3.111.000927. Epub 2011 Nov 1. PMID:22384362 | PMCID:PMC3276166
  • [Co-authors] — Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery. Ono NN, Britton MT, Fass JN, Nicolet CM, Lin D, Tian L.   J Integr Plant Biol. 2011 Sep 12. doi: 10.1111/j.1744-7909.2011.01073.x. [Epub ahead of print]  PMID:21910825
  • [Co-authors] — Discovery of rare mutations in populations: TILLING by sequencing. Tsai H, Howell T, Nitcher R, Missirian V, Watson B, Ngo KJ, Lieberman M, Fass J, Uauy C, Tran RK, Khan AA, Filkov V, Tai TH, Dubcovsky J, Comai L. Plant Physiol. 2011 Jul;156(3):1257-68. doi: 10.1104/pp.110.169748. Epub 2011 Apr 29. PMID:21531898 | PMCID:PMC3135940


  • [Co-authors] — A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development. Katz E, Fon M, Eigenheer RA, Phinney BS, Fass JN, Lin D, Sadka A, Blumwald E.   Proteome Sci. 2010 Dec 16;8:68. doi: 10.1186/1477-5956-8-68.  PMID:21162737 | PMCID:PMC3017515
  • [Co-authors] — Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing. Zaragoza MV, Fass J, Diegoli M, Lin D, Arbustini E.    PLoS One. 2010 Aug 20;5(8):e12295. doi: 10.1371/journal.pone.0012295.  PMID:20808834 | PMCID:PMC2924892
  • [Co-authors] — Analysis of early host responses for asymptomatic disease detection and management of specialty crops. Dandekar AM, Martinelli F, Davis CE, Bhushan A, Zhao W, Fiehn O, Skogerson K, Wohlgemuth G, D’Souza R, Roy S, Reagan RL, Lin D, Cary R, Pardington P, Gupta G. Crit Rev Immunol. 2010;30(3):277-89. Review. PMID:20370635


  • [Co-authors] — Functional consequences of overexpressing the gap junction Cx43 in the cardiogenic potential of pluripotent human embryonic stem cells. Moore JC, Tsang SY, Rushing SN, Lin D, Tse HF, Chan CW, Li RA. Biochem Biophys Res Commun. 2008 Dec 5;377(1):46-51. doi: 10.1016/j.bbrc.2008.09.076. Epub 2008 Sep 25. PMID: 18823947