Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Ping Hu's Professional Experience

Principle Scientific Engineering Associate

Lawrence Berkeley National Laboratory  -  2008-present

  • Managed SNP validation project, including designing high density genotyping microarray, modifying and validating assay and quality control protocols, managing project operation and reporting and developing algorithms for data analysis.
  • Completed over twenty gene syntheses for studies of cell division in Caulobacter crescentus and system biology of Zymomonas bobilis.
  • Supplied Clostridia culture for micro fluidics-IR spectroscopic study of lignocellulose degradation.
  • Organized and supplied cross hybridization information for analyzing Dehalococcoides community expression microarrays.

Staff Research Associate

Lawrence Berkeley National Laboratory  -  Feb. 2004-2008

  • Responsible for setting up and operating microbiology laboratory and various types of custom Affymetrix microarrays (expression, SNP and resequencing). The projects range from model organism, bacteria important in ecosystem and bioremediation to antibiotic resistance with clinical samples.
  • Responsible for resource application, data presentation and scientific collaboration.
  • Developed database/scripts to data mining the custom chip, which requires analyze at the probe level and dynamically setting probeset boundaries.
  • Discovered and proved that Caulobacter crescentus is more resistant to uranium toxicity than reference species by physiology, expression and imaging analysis
  • Investigating two-component systems which were implicated under uranium stress and possible of uranium mechanisms through collaborative efforts.
  • Organize and assist in grant/facility applications. Proposal for studying metal resistance using advanced image techniques has been funded through GenomeToLife program. Beamtime was awarded for proposal to investigating mechanism of uranium resistance.

Computational Biologist

Metabolex, Inc  -  2000-Dec.2003

  • Responsible for developing database/scripts to provide an integrated environment to access proprietary/public gene annotation and pathway analysis (NCBI, KEGG, GeneOntology, SWISSPRO, GenMapp).
  • Analyze proprietary novel ESTs: use multiple species genomic information to extend gene in silico – predict full-length gene; identify protein domains, splice variants, SNPs, pathways, orthologues, possible regulatory elements, and help to prioritize target selection and validation.
  • Successfully developed easy to use/maintain web application to access data and bioinformatics programs.
  • Provided bioinformatics support for patent filing.
  • Participate in development of LIMS to integrate data from target discovery and validation (sequences, annotation, gene expression, protein analysis, siRNA, etc).

Bioinformatics Scientist II

diaDexus, Inc  -  1998-2000

  • Designed and implemented LIMS to provide and to manage access to sequences, R&D experimental data, user annotation, bioinformatic analysis (blast alignment, chromosomal mapping, motif analysis, protein function) public annotation and patent information.
  • Completed studies on microbial identification projects. Designed degenerate primers and low density chip for identification of blood pathogens. The results demonstrated that it is possible in sillico to distinguish blood pathogens by using diaDexus chip model. Developed multi-threaded program (ePCR) in C to simulate PCR reaction in sillico. This software has been successfully applied in primers screening against microbial and human sequence databases.
  • Identified SNP markers in drug metabolizing enzyme genes by sequence analysis.
  • Developed a mixture of PERL scripts and JAVA applets that enable users to query experimental data with bioinformatic analysis (BLAST, HMM profiles, protein analysis tools, expression profiling, physical and genetic mapping to chromosome, SNP, disease information, statistic analysis of libraries) and patent information on web. Users can enter and update their data. The system provides automatic error checking (at database and sequence level) to minimize human errors.
  • Developed tools to extract sequences and utility information from published patents and provide relevant information. This project provide business development with licensing opportunities; R&D with technology recommendations; data mining algorithms with potential targets for improvement; and management with patent filing strategy and data for R&D strategy. Users are able to search nucleotide or protein sequences against GENESEQ patent database and provide relevant information.
  • Developed program for automatic analysis of protein secretory signal and transmembrane domain. Such program will run several different analyses, reach an interpretation using its unique algorithms and present the recommendation.

Biomedical Scientist

Lawrence Livermore National Lab  -  1997-1998

  • Analyzed and annotated sequences of three naturally occurring plasmids (10-100kb each) and other chromosomal regions in Yersinia pestis. Predicted genes and their structural motifs and functions by advanced sequence analysis tools.
  • From data mining of available Yersinia pestis insertion sequences, developed primer sets for DNA-based biotyping of Yersinia pestis. Such tool can be used to identify geographically diverse strains and survey strain evolution.

Postdoctoral Research Associate                                                                             

University of California at Berkeley  -  1995-1997

  • Elucidated cellular response to nitrogen starvation and possible metabolite flux control mechanism in Bacillus subtilis.

Postdoctoral Research Associate

University of Illinois at Urbana-Champaign  -  1992-1994                                                                                

  • Determined mechanism of the regulation of glutamine-PRPP amidotransferase and degradation of aspartate transcarbamylase in Bacillus subtilis.