Projects

Below is a sampling of our projects:

PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism: PhaseolusGenes is a web tool that has been developed for Marker Assisted Selection (MAS) in Phaseolus bean breeding, an important source of dietary protein in human nutrition. PhaseolusGenes takes advantage of the close relationship of soybean (Glycine max, Glyma1 release, 2008, JGI) to anchor a variety of Phaseolus sequences through syntenic mapping and other bioinformatics means into an integrated platform. The platform provides a user-friendly Web interface to help users navigate through a web of interconnected resources including genomic sequences, genetic markers, cDNAs, ESTs, BAC sequences and marker annotations. Breeders can use either keywords or DNA sequences to search traits, markers or genes of interest. The results are conveniently presented in the respective genomic contexts using gBrowse, cMAP, a relational database back-end, and AJAX-based Web forms to enhance the interactive experience. 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. PhaseolusGenes demonstrates a novel way for complex genomics information management and new marker discovery.

RediscoveryDB: Many plant diseases and health traits are connected through shared molecular functions in which multiple genes participate. Hence, a global consideration of cell biology is needed to understand the mechanism of diseases and to conduct an effective drug development. How to integrate system level data from various large biological databases and be able to ask biological meaningful questions are both a challenge and an opportunity. RediscoveryDB addresses the issue by compiling and integrating a large array of information including genes and their annotations, pathways, compounds, reactions, protein-protein interactions, disease/gene associations, and publications into a coherent form that greatly facilitate cross queries among the aforementioned resources. The commonly shared pathways among large number of genes or metabolites are presented in a table that can be sorted and filtered through a clean and informative interface using a Web Browser. It can present complex relationships into a network that can be visualized via Cytoscape and queried across molecular resources through Gaggle (http://gaggle.systemsbiology.org/docs/). RedicoveryDB uses a unique layered approach to separate the original data source from data tables used for queries. This makes it easy to import and standardize data, as well as updating information. RediscoveryDB’s schema and database backend is optimized for responsiveness necessary for Web-based interactions. RediscoveryDB is the perfect tool for automatically annotating large data set from proteomics and metabolmics experiments. The RediscoveryDB is currently available at http://rediscovery.bioinformatics.ucdavis.edu

Tetrahymena thermophila micronucleus (MIC) sequence assembly: Dr. Kathleen Collins coordinated with us in the assembly of internally eliminated sequences (IES) 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 and his lab technicians work on deconvolving a series of gene sequences in order to find mutations within the genome. Once mutation candidates are found, Dr. Comai’s lab can process chosen candidates and provide resources for obtaining source material for further experiments. This advanced technique provides full mutation pursual in a professional and cost-effective manner. The Bioinformatics Core was tapped to help the lab handle its workflow as well as provide a clean front-facing user interface complete with order reporting, status updates, and discussions.

We presented the project at the TILLING Workshop at the University of California, Davis Genome Center on August 25th. We have the slides online here.

Highlights

• The Bioinformatcs Core maintains an active Training Program comprised of single-day Boot Camps and a week-long Short Course, covering next generation sequencing technology fundamentals, applications such as sequence read quality assessment and improvement, genome assembly, expression profiling (RNA-Seq), and the open source, extensible, general purpose bioinformatics GUI and workflow tool Galaxy. We have multiple offerings throughout the year; check the training site for current offerings and registration information.
• The analysis of the first Solexa sequencing run has been done at Bioinformatics core, Sept 1, 2007
• We used Plone to build easy user editable customized Web site for Pam Ronald’s lab. The site is at http://indica.ucdavis.edu August 28, 2007
• Some (old) example projects: SNP Pipeline and Circular Microarray

Publications

• 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