Curriculum Vitae
CV — Bernard Delacruz, PhD
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 RS, Ghahramani Z, Griffin JE, de la Cruz BJ, Wild DL. Discovering transcriptional modules by Bayesian data integration. Bioinformatics. 2010 Jun 15;26(12):i158-67.
* Rasmussen CE, de la Cruz BJ, Ghahramani Z, Wild DL. Modeling and visualizing uncertainty in gene expression clusters using dirichlet process mixtures. IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):615-28.
*Wriessnegger T, Gübitz G, Leitner E, Ingolic E, Cregg J, de la Cruz BJ, Daum G. Lipid composition of peroxisomes from the yeast Pichia pastoris grown on different carbon sources. Biochim Biophys Acta. 2007 Apr;1771(4):455-61.
* Lin-Cereghino GP, Godfrey L, de la Cruz BJ, Johnson S, Khuongsathiene S, Tolstorukov I, Yan M, Lin-Cereghino J, Veenhuis M, Subramani S, Cregg JM. Mxr1p, a key regulator of the methanol utilization pathway and peroxisomal genes in Pichia pastoris. Mol Cell Biol. 2006 Feb;26(3):883-97.
* de la Cruz BJ, Prieto S, Scheffler IE. The role of the 5′ untranslated region (UTR) in glucose-dependent mRNA decay. Yeast. 2002 Jul;19(10):887-902.
* Prieto S, de la Cruz BJ, Scheffler IE. Glucose-regulated turnover of mRNA and the influence of poly(A) tail length on half-life. J Biol Chem. 2000 May 12;275(19):14155-66.
* Scheffler IE, de la Cruz BJ, Prieto S. Control of mRNA turnover as a mechanism of glucose repression in Saccharomyces cerevisiae. Int J Biochem Cell Biol. 1998 Nov;30(11):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
* VP Education, Life Tech Toastmasters Carlsbad—July 2010-Apr 2011
* 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)