Tomas Vinar's homepage

Name: Tomas Vinar (Tom\'a\v{s} Vina\v{r}) Nickname: Vinko Phone: 1(607)273-3076 Affiliation: Postdoctoral Researcher, Siepel Computational Genomics Lab, Dept. of Biological Statistics and Computational Biology, Cornell University Address: 1198 Comstock Hall, Ithaca, NY 14853 Office: 169 Biotechnology Building Phone: 1(607)255-7430 Professional interests: bioinformatics, algorithms, probabilistic modeling E-mail: Important: Brona

education:

• 2005: "PhD." at University of Waterloo
• 1999: "Magister" (diploma degree) of computer science at Comenius University in Bratislava (majors: theory, artificial intelligence)

plans for near future:

• Mon: 1-2 Computational genomics journal club
• Tue: 7-9:30 Chamber Singers
• Thu: 1-2 Lab meetings 4:15-5:30 CS colloquium
• Fri: 12-1:15 AI seminar 1:30-2:30 Sequence analysis journal club
• March 8-19, 2008: Europe (Spain and Switzerland)
• May 6-10, 2008: The Biology of Genomes, Cold Spring Harbor Laboratory
• July 19-23, 2008: ISMB 2008, Toronto

teaching:

• Fall 2005: UW CS240: Data Structure and Data Management (instructor)
• Winter 2003: UW CS341: Algorithms (instructor)
• Fall 2002: UW CS466: Advanced Algorithms (TA)
• Spring 2002: UW CS466: Advanced Algorithms (TA)
• Winter 2002: UNIX consultant
• Fall 2001: UNIX consultant
• Spring 2001: UNIX consultant
• Winter 2001: UW CS341: Algorithms (TA)
• Fall 2000: UW CS341: Algorithms (TA)
• Spring 2000: UW CS360: Theory of Computation
• Winter 2000: UW CS341: Algorithms (TA)
• Fall 1999: UW CS134: Principles of Computer Science (TA)
• Summer 1999: Comenius University: Introduction to programming theory (tutorial instructor)
• Winter 1998: Comenius University: Design of efficient algorithms (tutorial instructor)
• Winter 1998: Comenius University: Introduction to distributed algorithms (tutorial instructor)

software:

• ExonHunter: A comprehensive gene finding program that allows incorporation of ESTs, proteins matches, genome-genome similarities, and more. You can download a version compiled for Linux, or you can contact me if you need a version for other platforms, or parameters for organisms other than ones available there.
• Mikroskop: A simple, yet feature-rich viewer of gene finding and sequence annotation results. It is written in Perl, and you can download it here.
• TreeArrange and Treeps: A post-processing tool for analysis of expression arrays. Enhances output of hierarchical clustering programs such as Cluster or XCluster. Increases visibility of clusters by reordering the data and creates (potentially labeled) output in encapsulated postscript. Available for download.
• med2bib.pl: Downloads PubMed records and turns them into BibTeX for easy inclusion in LaTeX articles. Available as a web server and for download.
• Mendel: A simulation/educational program for instruction of mendelian genetics, written ages ago. You can still download MS-DOS executable. It was actually used in instruction for both high-school and university students.

former activities:

• 1994-1999 co-organizer Correspondence Seminar in Programming (CSP), Slovak Olympiad in Informatics and other activities around in the CSP group.
  • The Correspondence Seminar in Programming
  • Slovak Olympiad in Informatics
  • The Internet Problem Solving Competition
  • Other contests and activities in the CSP group
• 2002, 2003, 2004: TAM (Tyzden Absolventov Matfyzu) - annual alumni miniconference at Comenius University, Faculty of Mathematics, Physics, and Informatics, Bratislava, Slovakia. [TAM www page]
• 1997-1999 singing in Mixed choir Apollo, Bratislava
• 1999(F)-2000(F),2001(S) University of Waterloo choir [music ensembles]
• 2001(W,F),2002(F),2003(W,F),2004(W) University of Waterloo chamber choir [music ensembles]
• 1999-2001 board member of the TROJSTEN foundation (funds for correspondence seminars organized at Comenius University Bratislava) [foundation www page]

resources, downloads, publications:

• my (un)publications
• my wiki page - various notes and links
• my amazon.com wishlist
• my photographs: public photographs (conferences, trips, ...)
  rodinne fotografie (na heslo)
• sci-fi poviedky

Last update: 02/22/2008