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Ofer H. Gill
NYU Bioinformatics Group,
715 Broadway, Rm 1005
New York, NY 10012
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Office Phone: 212 998 3351
e-mail:gill [at] cs.nyu.edu
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Research Interest
I have a strong background in graph theory, algebra, algorithms,
programming, and other areas of computer science and
mathematics. Bioinformatics provides an excellent way to apply all of
these. My specific interests include sequence alignment and string
correlations for proteins and DNA sequences, as well as gene identification.
Background
- B.S., Rutgers Univeristy, Rutgers College, 1997-2001 in Computer
Science and Mathematics
- Ph. D. student, NYU, 2001 - present in Computer Science with
concentration on BioInformatics
Current Work
I am currently working on a few improvements in the area of sequence alignment:
- Improving the p-values generated by sequence alignments to better
match the appropriate coincidental probabilities
- Scaling PLAINS, a local alignment tool designed for sequences of
lengths up to 12Kb, to work over whole genomes.
- Extending sequence alignments over DNA to better account for secondary structure and RNA behavior.
Papers
Multiple Sequence Alignment Techniques
Ofer Gill, Alyssa Less, Aris Tsirigos in December 2002
(pdf) (ps)
Piecewise-Linear Gap Formula Alignment in Linear Space
Ofer Gill, Bud Mishra in May 2003.
(pdf) (tex)
Aligning Sequences with Non-Affine Gap Penalty: PLAINS Algorithm, a
Practical Implementation, and its Biological Applications in
Comparative Genomics (Unabridged Version)
Ofer Gill, Yi Zhou, and Bud Mishra in August 2004.
Note: A shortened version of this paper has been
published in Series in Mathematical Biology and Medicine, Vol. 8, 2005.
(pdf) (tex)
SEPA: Approximate Non-Subjective Empirical p-Value Estimation
for Nucleotide Sequence Alignment (Full Version)
Ofer Gill, Bud Mishra in December 2005.
(pdf) (tex)
Presentations
Piecewise-Linear Gap Formula Alignment in Linear Space
Ofer Gill in April 2003 to NYU Computer Science Student
Seminars.
(pdf) (ppt)
Piecewise-Linear Gap Formula Alignment in Linear Space, Version
2.0
Ofer Gill in Novermber 2003 as part of the Systems Biology
Series.
(pdf) (ppt)
Pre-PLAINS Slides
Ofer Gill in March 2004 to NYU Computer Science Student Seminars
Note that the lab results and tool-comparision
techniques in these slides are inaccurate, but the alignment algorithm
is correct.
(pdf) (ppt)
PLAINS Slides
Ofer Gill in December 2004 to ICBA 2004
(pdf) (ppt)
Links
For non-academic info, see my other webpage:
http://homepages.nyu.edu/~ohg200/
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