EDUCATION
Ph.D., Biology — University of California, San Diego — 2000
B.A., Biology — University of California, Santa Cruz — 1992
HONORS/AWARDS/FELLOWSHIPS
* CMG Training Grant, UC San Diego — 1996-1999
* San Diego Graduate Fellowship, UC San Diego — 1994-1996
* Honors on Senior Thesis, UC Santa Cruz — 1992
* Honors on Senior Exam, UC Santa Cruz — 1992
* HHMI Summer Research Fellowship, UC Santa Cruz — 1992
* NIGMS MARC Undergraduate Fellowship, UC Santa Cruz — 1990-1992
RESEARCH EXPERIENCE
RESEARCH FELLOW
Keck Graduate Insitute
May-June 2006
* Principal Investigator: Dr. Alpan Raval
* Short-term contract to established project to analyze gene expression networks using networking software Pajek.
* Analysis of gene expression networks using Gene Ontology.
POSTDOCTORAL FELLOW
Keck Graduate Institute
Sep 2000 – Mar 2006
* Principal Investigator: Dr. James M. Cregg
* Co-wrote and participated on SBIR grant to sequence genome of industrial yeast Pichia pastoris. Assisted Masters student project to develop annotation pipeline for genome. Identified genes for collaborators (published).
* Coordinated development of oligonucleotide-based spotted microarrays for Pichia pastoris.
* Designed custom Affymetrix gene chip for Pichia pastoris.
* Applied molecular and cell biology techniques to study of peroxisome proliferation and methanol-regulated gene expression in Pichia pastoris (published).
* Collaborated with systems biology group on application of gene ontology to gene expression microarray data analyzed by Bayesian statistics (published).
* Collaborated with systems biology group on analysis of yeast genetic networks constructed from gene expression data.
* Managed Masters students and summer undergraduate students in laboratory.
GRADUATE STUDENT
UC San Diego
May 1995-Sep 2000
* Principal Investigator: Dr. Immo E. Scheffler
* Dissertation, “Selective translation and regulated decay of yeast mRNAs in response to carbon source: cis elements and trans factors.”
* Research in work on mRNA degradation, translation initiation, mitochondrial function, regulation of metabolic genes.
* Extensive experience with RNA including isolation from yeast and mammalian cells; reverse-transcription PCR and cloning; Northern analysis; polysome analysis.
* Mentored Masters student through thesis completion.
ROTATION PROJECT
UC San Diego
Feb-May 1995
* Principal Investigator: Dr. Douglas Smith
* Porting of ORF finding software from Cray to Paragon supercomputing platform.
* Modification and implementation of parallel processing code in C source.
ROTATION PROJECT
UC San Diego
Jan-Feb 1995
* Principal Investigator: Dr. Immo E. Scheffler
* Cloning of the SDHC gene from CHO cells by reverse transcription PCR.
* General molecular biology and mammalian tissue culture techniques.
ROTATION PROJECT
UC San Diego
Nov-Dec 1994
* Principal Investigator: Dr. Maarten Chrispeels
* Site-directed mutagenesis of protein targeting sequences in Arabidopsis thaliana.
* General molecular biology and plant transformation techniques.
ROTATION PROJECT
UC San Diego
Oct-Nov 1994
* Principal Investigator: Dr. Martin Yanofsky
* Cloning of novel MADS box genes from Arabidopsis thaliana by degenerate PCR.
* General molecular biology techniques, DNA sequencing, and sequence analysis.
NIGMS MARC UNDERGRADUATE FELLOW
UC Santa Cruz
1990-1992
* Principal Investigator: Dr. Barry Bowman
* Honors Thesis, “A Molecular Phylogeny of Neurospora crassa, Saccharomyces cerevisiae, and Schizosaccharomyces pombe based on the F-type and V-type ATPases.”
* Self-taught PHYLIP and Intelligenetics/GCG software packages on Solaris UNIX platform.
* Miscellaneous fungal cultural techniques.
TEACHING EXPERIENCE
TEACHING ASSISTANT
Molecular Evolution – UC San Diego, Dept. of Biology, Dr. Christopher Wills
Spring 1998
Ran discussion sections of ~10 students. Wrote exam questions. Ran exam review sessions. Graded exams.
TEACHING ASSISTANT
Introduction to Bioinformatics – UC San Diego, Dept. of Biology, Dr. Michael Gribskov
Winter 1997
Ran study sections of ~20 students. Ran group and one-on-one computer tutorials. Graded exams.
TEACHING ASSISTANT
Biochemical Techniques Laboratory – UC San Diego, Dept. of Biology, Dr. Gabriele Wienhausen
Spring 1996
Ran intensive laboratory sessions with 14-18 students in basic molecular biology techniques (bacterial DNA isolation, mRNA purification, gel electrophoresis, bacterial transformation). Graded lab reports.
CHEMISTRY INSTRUCTOR
Summer Bridge Program – UC Santa Cruz, SAA/EOP
May-Aug 1993
Co-designed and co-taught intensive 6-week chemistry course for entering SAA/EOP students. Course consisted of 10 lectures, 5 laboratory sections, 1 midterm, and 1 final exam. Prepared and graded homework and lab reports. Graded exams. Provided office hours.
SECTION LEADER
General Chemistry – UC Santa Cruz, Academic Excellence Honors Program [http://ace.ucsc.edu]
1992-1993
Ran intensive study sections for target students in a small group, collaborative learning environment. Met for two 2-hr sessions per week (4 hours total). Provided group and one-on-one tutorials. Prepared supplementary study materials. Graded homework. Prepared and ran practice exam sessions. Graded exams. Managed undergraduate section co-leaders and tutors.
UNDERGRADUATE SECTION CO-LEADER
General Chemistry – UC Santa Cruz, Academic Excellence Honors Program [http://ace.ucsc.edu]
1989-1992
Assisted section leader in running study sections. Provided group and one-on-one tutorials. Graded homework. Assisted in practice exams. Graded exams.
PUBLICATIONS
* Savage, R.S., Ghahramani, Z. Griffin, J.E., de la Cruz B.J., and Wild, D.L. Discovering Transcriptional Modules by Bayesian Data Integration. Bioinformatics. (ISMB 2010, accepted).
* Ghahramani, Z., Rasmussen C.E, de la Cruz, B.J., and Wild, D.L. (2007) A Bayesian Approach to Modeling Uncertainty in Gene Expression Clusters. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
* Wriessneggera, T., Gübitzb, G., Leitnerc, E., Ingolicd, E., Cregg, J.C., de la Cruz, B.J., and Daum, G. (2007) Isolation and biochemical characterization of peroxisomes from Pichia pastoris. Biochim Biophys Acta. 1771:455-461.
* Lin-Cereghino, G.P., Godfrey, L., de la Cruz, B.J., Johnson, S., Khuongsathiene, S., Tolstorukov, I., Yan, M., Lin-Cereghino, C., Veenhuis, M., Subramani, S., and Cregg, J.M. (2006) Mxr1p: a global regulator of the methanol-utilization pathway and peroxisomal genes in Pichia pastoris. Mol Cell Biol. 26:883-97.
* de la Cruz, B.J., Prieto, S., and Scheffler, I.E. (2002) The role of the 5′UTR on regulated decay of mRNA in response to carbon source. Yeast. 19:887-902.
* Prieto, S., de la Cruz, B.J., and Scheffler, I.E. (2000) Glucose-regulated turnover of mRNA and the influence of poly(A) tail length on half life. J Biol Chem. 275:14155-66.
* Scheffler, I. E., de la Cruz, B. J. , and Prieto, S. (1998) Control of mRNA turnover as a mechanism of glucose repression in Saccharomyces cerevisiae. Int J Biochem Cell Biol. 30:1175-93.
ADDITIONAL COURSEWORK
* Java for Bioinformatics I, UC San Diego Extension — Fall 2009
* Intermediate Biostatistics, UC San Diego Extension — Spring 2009
* Introduction to Data Mining, UC San Diego Extension — Winter 2009
* UCSC Genome Browser Workshop, City of Hope — December 2007
* NCBI GEO/Bioconductor Workshop, City of Hope — October 2007
* Ingenuity IPA 5.5 Workshop, City of Hope — October 2007
* Introductory Biostatistics, UC San Diego Extension — Winter 2007
* Medical Writing for IND Preparation, UC San Diego Extension — Fall 2006
* Proteomics Workshop, UC San Diego Extension — Mar 2006
* R/Bioconductor Workshop, CEPEB, UC Riverside — Nov 2005
* Agricultural Biotechnology, Keck Graduate Institute — Spring 2005
* Gene Expression Data Workshop, BTCI/Promega — May 2002
* Beginning Perl for Bioinformatics, Keck Graduate Institute — Spring 2001
* “Origins of Life” Graduate Seminar, UC San Diego — Spring 1999
* “Wisdom of the Genes” (Molecular Evolution), Graduate Seminar, UC San Diego — Winter 1998
CERTIFICATES
* Database Administration Certificate, Cal Poly Pomona — Oct 2004-Feb 2005
MEETINGS/TALKS
* INVITED TALK, 2001. “Selective stability and degradation of mRNA in response to carbon source: cis elements and trans factors.” Loyola Marymount University, Los Angeles, California.
* STUDENT VOLUNTEER, 2000. Intelligent Systems for Molecular Biology Conference, UC San Diego.
* STUDENT VOLUNTEER, 1999. International Conference on the Origins of Life, UC San Diego.
* POSTER, 1998. “Regulated degradation of the SDH2 mRNA in response to carbon source.” San Diego Cell Biology Meeting, La Jolla, California.
* SEMINAR, 1997. “Regulated decay of the yeast SDH2 mRNA: cis elements and trans factors.” CMG Student Symposium, UC San Diego.
* POSTER, 1997. “Glucose-induced rapid decay of SDH Ip mRNA: a case for competition between translation initiation and degradation.” RNA’97, San Francisco, California.
VOLUNTEER EXPERIENCE
* Meeting Volunteer, San Diego Biotechnology Network — 2009-Present
* Vice President Public Relations/Webmaster, BioToasters — Jan 2010-Present
* Vice President Public Relations/Webmaster, Expresso Toastmasters — Jun-Oct 2008
* Grant Reviewer, Systems Biology of Microorganisms Initiative, European Union — Apr 2006
* Socrates Café Discussion Facilitator, Society for Philosophical Inquiry (SPI) — 2005-Present
* Organizer, Researcher Roundtable, Keck Graduate Institute — Jan 2001-Mar 2002
* Safety Committee, Keck Graduate Institute — 2000-2001
* Graduate Student Admissions Committee, UC San Diego Dept of Biology — Winter 1997
PROFESSIONAL MEMBERSHIPS
* American Association for the Advancement of Science (AAAS)
* American Society of Microbiology (ASM)
* American Medical Writers Association (AMWA)
* Bioinformatics.org (past member)
* National Postdoctoral Association (past member)