Below is a sampling of our projects:

Assemblathon 1 and 2: The field of genome assembly has exploded since the advent of next generation sequencing, and benchmarking is sorely needed. The Assemblathon competitions are one of the efforts to provide comparison and evaluation of different genome assembly tools and pipelines. The Assemblathon 2 manuscript was recently published in GigaScience.

Peach Genome Assembly & SNP Discovery: The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft ‘Lovell’ peach sequence as well as sufficient depth of coverage for ‘in silico’ SNP discovery.

PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism: PhaseolusGenes is a web tool that was developed for Marker Assisted Selection (MAS) in Phaseolus bean breeding.  The platform provides a user-friendly Web interface to navigate through interconnected resources including genomic sequences, genetic markers, cDNAs, ESTs, BAC sequences and marker annotations. PhaseolusGenes not only provides a comprehensive view of the region of focus, but more importantly it allows discovery of new sequence specific markers based on the flanking sequences brought together by the comparative genome comparisons, which was not possible before.

Tetrahymena thermophila micronucleus (MIC) sequence assembly: We found and assembled the internally eliminated sequences (IES) in T. thermophila that are spliced out of the chromosomal DNA when the macronucleus (MAC) is generated.  We used BWA (short read aligner) and Velvet (genome assembler) for this work (see publication below).

Comai lab advanced TILLING LIMS system: Dr. Luca Comai’s TILLING Core provides access to a library of mutations in several species, which can be ordered based on gene and mutation of interest. The Bioinformatics Core designed a clean user interface complete with order submission and reporting, status updates, and discussions.

Bioshare: A web application designed for sharing the big data produced by today’s technologies, such as that produced by gene sequencers.

Full Publication List:

  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, İnanç Birol, Sébastien Boisvert10, Jarrod A. Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T. Roderick Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A. Fonseca, Ganeshkumar Ganapathy, Richard A. Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B. Hiatt, Isaac Y. Ho, Jason Howard, Martin Hunt, Shaun D. Jackman, David B Jaffe, Erich Jarvis, Huaiyang Jiang, et al. arXiv:1301.5406 [q-bio.GN]
  • Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. Kanthaswamy S, Ng J, Ross CT, Trask JS, Smith DG, Buffalo VS, Fass JN, Lin D. Genomics. 2013 Jan;101(1):30-7. doi: 10.1016/j.ygeno.2012.09.001. Epub 2012 Sep 12. PMID:22982528 | PMCID:PMC3534948
  • Multiple clonal MLL fusions in a patient receiving CHOP-based chemotherapy. Shih SJ, Fass J, Buffalo V, Lin D, Singh SP, Diaz MO, Vaughan AT.  Br J Haematol. 2012 Oct;159(1):50-7. doi: 10.1111/j.1365-2141.2012.09248.x. Epub 2012 Jul 30.  PMID:22845170 | PMCID:PMC3444640
  • Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms. You FM, Deal KR, Wang J, Britton MT, Fass JN, Lin D, Dandekar AM, Leslie CA, Aradhya M, Luo MC, Dvorak J. BMC Genomics. 2012 Jul 31;13:354. doi: 10.1186/1471-2164-13-354. PMID:22849334 | PMCID:PMC3527177
  • Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. Monson-Miller J, Sanchez-Mendez DC, Fass J, Henry IM, Tai TH, Comai L.   BMC Genomics. 2012 Feb 14;13:72. doi: 10.1186/1471-2164-13-72.  PMID:22333298 | PMCID:PMC3305632
  • Transcriptome profiling of citrus fruit response to huanglongbing disease. Martinelli F, Uratsu SL, Albrecht U, Reagan RL, Phu ML, Britton M, Buffalo V, Fass J, Leicht E, Zhao W, Lin D, D’Souza R, Davis CE, Bowman KD, Dandekar AM.    PLoS One. 2012;7(5):e38039. doi: 10.1371/journal.pone.0038039. Epub 2012 May 31. PMID:22675433 | PMCID:PMC3364978
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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