Note that I am not looking for a job right now,

and this resume is horribly out of date anyways

Home
Res
ear
ch
&
Tea
chi
ng
Res
um
e/C
V
Ess
ays
Pict
ure
s
Lin
ks

Michael Brudno
brudno@cs.stanford.edu

Address available
upon request

Interests: Computational Biology, Bioinformatics, Design and

Implementation of Algorithms
Education & Honors:
2000- Stanford University Ph.D. Program in Computer Science
2001 - Achieved Candidacy
1996-2000 UC Berkeley B.A. with High Distinction, in Computer
Science (with Honors) and History.
Stanford School of Engineering Fellowship 2000
UC Berkeley EECS Dept. Samuel Silver Memorial Scholarship Award
2000
Dept. of Energy Undergraduate Laboratory Fellowship 1999
Member of Upsilon Pi Epsilon (CS Honors Society) 1997
Significant Projects and Publications:

VISTA: VISualization Tool for Alignments:

Software tool allowing for effective visualization and statistical
analysis of large orthologous DNA regions customized for
location of potential regulatory elements.
Genome Research 2000 Sep;10(9):1304-6;
Bioinformatics(Accepted).
ASDB: Alternative Splicing Database:
a database heavily used by biologists. Participated in both design
and implementation of many aspects, including significant
improvements to the search capabilities, collection of data and
writing of documentation.
Nucleic Acids Research 2000 Jan; 28(1):296-7.
BiSyCLES: Biological System for Cross-Linked Entry Search:
a program which allows concurrent searches of multiple
databases based on links between them, thus allowing more
information to be accessed.
Presented at Objects in Bioinformatics 1999, San Jose CA.
Protection of Genomic Databases:
analysis of legal methods, including copyright, different forms of
licensing and some potential database protection statutes, and
which of them is best suited for the subject.

Relevant Experience:
6/00 to 8/00: Instructor, CS Dept. UC Berkeley Taught a lower division
Data Structures course (200 students, 6 teaching assistants, 6 graders),
including giving lectures, writing assignments and handling
administrative issues. The course explored basic data structures and
algorithms using Java.
1/99 to pres.: Student Researcher, Center for Bioinformatics and
Computational Genomics, LBNL
Developed VISTA, BiSyCLES, and ASDB (see above). Developed
statistical methods and computer programs for finding potential
regulatory words in alternatively spliced DNA sequences, including the
selection of the data set and interpretation of results (publication
forthcoming).
6/98 to 12/98, 8/99 to 12/99: Teaching Assistant, CS Dept. UC Berkeley
Taught discussion sections and labs in a Data Structures course. Was a
lab TA for an upper-division Digital Design class. Supervised and
assisted students on a significant project (~100 hours).
5/97 to 8/98: System Administrator & Programmer, UC Berkeley and
Smith-Kettlewell Institute
Administered various stand-alone and networked computers. Wrote
several CGI programs and standalone applications.
References available upon request

Home | CV/Resume | Research | Coursework | Pictures | Links | Personal Info

CV/Resume
Click here for printable (plain text) version
John Michael Brockman (Michael preferred)
Contact:

michael3@bu.edu

Objective:
No positions being sought, currently working toward PhD in
Bioinformatics.
Education:

Boston University, Boston, MA

Doctor of Philosophy (PhD) in Bioinformatics
Advisor: Joel Graber, PhD (The Jackson Laboratory)
September 2002 - Present GPA 3.85/4.0
Graduating (projected) May 2006
Boston University, Boston, MA
Master of Science (MS) in Bioinformatics
September 2002 - May 2004 GPA 3.85/4.0
Western Kentucky University (WKU), Bowling Green, KY
Bachelor of Science (BS) in Computer Science and Mathematics,
minor in Recombinant Genetics
Graduated August 2002 GPA 3.98/4.0

Languages:

C/C++, Perl, R/Splus, Java, PHP, ASP, HTML, XHTML/CSS, XML,

SQL, OpenGL, LISP

Software:

C++ Builder, Mathematica (and Wavelet Explorer), SAS

CVS, Oracle, MySQL, Stand Alone BLAST,
Linux, UNIX, Windows 95/98/NT/Me/2000/XP

Experience:

Graduate Research Assistant, January 2004 - Present

The Jackson Laboratory, Bar Harbor, ME
Biomolecular Engineering Research Center (BMERC), Boston, MA
Bioinformatics research assistant in the lab of Dr Joel Graber.
Current development on the PolyA Cleavage Site and 3' UTR
database (PACdb) as well as research into RNA localization
via non-tandem short repeats.
General Teaching Fellow, Fall 2003
Boston University Bioinformatics Program, Boston, MA
Responsible for homework sets, webpage, classroom laptops,
occasional lecture, and office hours for the graduate level
course, "Bioinformatics Applications." Also the grader for the
graduate level course, "DNA & Protein Sequence Analysis."
Scientific Research Visitor, Summer 2003

National Center for Biotechnology Information (NCBI), Bethesda, MD

NCBI is part of the National Library of Medicine (NLM) which is
part of the National Institutes of Health (NIH).
Research collaboration with Dr Steve Bryant and Dr Anya Panchenko
of NCBI. Learned Splus. Investigated the use of protein
structural information to cluster sequences in conserved domains
found in NCBI's Conserved Domain Database (CDD).
Bioinformatics Research Assistant, Fall 2001 to Summer 2002
WKU Department of Biology, Bowling Green, KY
Research collaboration with Dr Claire A. Rinehart.
Learned ASP. Setup local BLAST database and programmed ASP
web-interface. Wrote other ASP programs to complement Stand Alone
Blast. Setup distributed cluster and implemented algorithms and a
Perl/HTML front end for that cluster. Trained incoming students in
Perl and bioinformatics (graduate and undergraduate).
Teaching Assistant, Spring 2001
WKU Department of Biology, Bowling Green, KY
Assisted professor in teaching senior level course,
"Recombinant Genetics Techniques." Supervised and assisted student
research projects and taught sterile cell culture techniques.
Bioinformatics Programmer/Analyst, Summer 2000
Research Genetics, Huntsville, AL
Worked on a team of six developing gene expression analysis software
(Pathways) written in Java. Worked in Macintosh, Windows NT, and
Linux environments testing cross-platform performance. Researched and
recommended secure web-based software deployment system. Helped
develop microarray image import and alignment system for multiple
image types. Learned Java SWING.
Junior Programmer/Analyst, Summer 1999
Intergraph Corporation, Huntsville, AL
Worked in Corporate Information Systems group on the Reports Team
transferring financial data from legacy systems to PeopleSoft.
Learned Crystal Reports, SQA, PeopleSoft, MS Visual Source Safe,
trained another intern and a new employee.

Honors and Awards:

Appointment to NCBI Scientific Visitor's Program,
sponsored by the NLM and administered by
Oak Ridge Institute for Science and Education (ORISE) 2003
National Science Foundation IGERT Grant (for bioinformatics), BU 2002
Outstanding Junior Computer Science Major, WKU 1999
President & Dean's Honors List WKU 1997-2002
Golden Key National Honor Society
WKU Honors Program Participant
Second Place in Computer Science/Mathematics, Undergraduate Research Competition,
Kentucky Academy of Science/Tennessee Academy of Science
Joint Meeting, Fall 2001

Title: The Effects of Wavelet Transforms on the Entropy of a Signal (as

applied to DNA sequences)
Second Place (tie) in Cell/Molecular Biology, Undergraduate Research Competition,
Kentucky Academy of Science/Tennessee Academy of Science
Joint Meeting, Fall 2001
Title: Applying Wavelet Transforms to Predict Functional Motifs in Proteins
Activities and Professional Associations:
WKU Diversity Coalition, Member 1999-2002,
President 2001-2002,
Vice President 2000-2001
Association of Undergraduate Geneticists, Member 1999-2001,
Webmaster 2000-2001
Association for Computing Machinery (ACM), Member 1999-2000
WKU Linux Users' Group, 1999-2002
WKU Big Red Marching Band, 1997-1999
Volunteer for WKU's freshman orientation week, 2000
Beginning & advanced American Sign Language programs, 2000-2001
Founder and leader of WKU's "Diversity Rocks" 2001 & 2002

References:
Available upon request.

Last Modified -

10/31/2004 11:27:57

Unless you're going to spam or harass me, feel free to send me e-mail at michael3@bu.edu

Disclaimer