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Michael Brudnobrudno@cs.stanford.edu

Address availableupon request

Interests: Computational Biology, Bioinformatics, Design and Implementation of Algorithms

Education & Honors:2000- Stanford University Ph.D. Program in Computer Science2001 - Achieved Candidacy1996-2000 UC Berkeley B.A. with High Distinction, in Computer Science (with Honors) and History.

Stanford School of Engineering Fellowship 2000UC Berkeley EECS Dept. Samuel Silver Memorial Scholarship Award 2000Dept. of Energy Undergraduate Laboratory Fellowship 1999Member 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, LBNLDeveloped 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

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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

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