Hamidreza
Chitsaz, PhD
Assistant Professor
Director of Algorithmic Biology Laboratory (ABL)
Department of Computer Science
Wayne State University
5057
Woodward Ave, 14001.3
Detroit, MI 48202
Tel: 313-577-6782
Email: chitsaz@wayne.edu
- B.Sc. in Computer
Engineering and Mathematics,
Sharif University of Technology,
2001
-
M.S. in Mathematics,
University of Illinois at
Urbana-Champaign, 2006
-
Ph.D. in Computer
Science, University of Illinois
at Urbana-Champaign, 2008
Teaching
Winter 2012: CSC
7991: Advanced Topics in Computer Science - Bioinformatics II
Fall 2011: CSC
7991: Advanced Topics in Computer Science - Bioinformatics
Research
Interests
Genome
and transcriptome assembly
RNA
folding and RNA-RNA interaction
Optimal
control and geodesics for mobile robots
Motion
planning for nonholonomic robots
CV
Software
Camel:
Maximum Likelihood error correction for single cell (MDA) Illumina reads. Usage of Camel before assembly with Velvet-SC improves the results.
Velvet-SC:
Bacterial genome assembler from single cell (MDA) Illumina reads
piRNA:
RNA-RNA interaction partition function, probability, equilibrium
concentration, and melting temperature
biRNA:
RNA-RNA binding sites prediction
Publications
2011
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
Hamidreza Chitsaz, Joyclyn L. Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L. Dupont, Jonathan H. Badger, Mark Novotny, Douglas B. Rusch, Louise J. Fraser, Niall A. Gormley, Ole Schulz-Trieglaff, Geoffrey P. Smith, Dirk J. Evers, Pavel A. Pevzner, Roger S. Lasken
Nature
Biotechnology, Vol. 29, No. 10, pp 915 - 921, October 2011
(doi:10.1038/nbt.1966)
Featured on the cover
2010
COMPUTATIONAL
STUDIES OF NON-CODING RNAS - Session Introduction
R.
Backofen, H. Chitsaz,
I. Hofacker, S. C. Sahinalp, and P. F. Stadler
Pacific
Symposium on Biocomputing (PSB), 2010
Tutorial
2009
biRNA:
Fast RNA-RNA Binding Sites Prediction
Hamidreza
Chitsaz, Rolf Backofen, S. Cenk
Sahinalp
Proceedings of the 9th Workshop on
Algorithms in Bioinformatics (WABI), 2009
Supplementary
material
A
Partition Function Algorithm for Interacting Nucleic Acid Strands
Hamidreza Chitsaz,
Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen
Bioinformatics
25(12): i365-i373; doi:10.1093/bioinformatics/btp212
Also,
17th Annual International Conference on Intelligent Systems for
Molecular Biology ISMB/ECCB 2009, Stockholm, Sweden
Supplementary
material
Minimum
Wheel-Rotation Paths for Differential-Drive Mobile Robots
Hamidreza
Chitsaz, Steven M. LaValle, Devin J. Balkcom,
Matthew T. Mason
International Journal of
Robotics Research 28(1): 66-80, 2009
2008
Exact
Pareto-Optimal Coordination of Two Translating Polygonal Robots on a
Cyclic Roadmap
Hamidreza
Chitsaz, Steven M. LaValle, Jason M.
O'Kane
Proceedings of 20th Canadian
Conference on Computational Geometry (CCCG), 2008
Generalizing
the Dubins and Reeds-Shepp cars: fastest paths for bounded-velocity
mobile robots
Andrei Furtuna, Devin
J. Balkcom, Hamidreza Chitsaz,
Paritosh Kavathekar
Proceedings of IEEE
Conference on Robotics and Automation (ICRA), 2008
Geodesic
Problems for Mobile Robots
Hamidreza
Chitsaz
PhD Thesis,
Department of Computer Science, University of Illinois at
Urbana-Champaign (UIUC), 2008
2007
Time-optimal
Paths for a Dubins Airplane
Hamidreza
Chitsaz and Steven M. LaValle
Proceedings
of IEEE Conference on Decision and Control (CDC), 2007
Minimum
Wheel-Rotation Paths for Differential-Drive Mobile Robots Among
Piecewise Smooth Obstacles
Hamidreza
Chitsaz and Steven M. LaValle
Proceedings
of IEEE Conference on Robotics and Automation (ICRA), 2007
2006
An
Explicit Characterization of Minimum Wheel-Rotation Paths for
Differential-Drives
Hamidreza
Chitsaz, Steven M. LaValle, Devin J. Balkcom,
Matthew T. Mason
Proceedings of 12th IEEE
International Conference on Methods and Models in Automation and
Robotics (MMAR), 2006
Minimum
Wheel-Rotation Paths for Differential-Drive Mobile Robots
Hamidreza
Chitsaz, Steven M. LaValle, Devin J. Balkcom,
Matthew T. Mason
Proceedings of IEEE
Conference on Robotics and Automation (ICRA), 2006
[Slides]
2004
Exact
Pareto-Optimal Coordination of Two Translating Polygonal Robots on an
Acyclic Roadmap
Hamidreza
Chitsaz, Jason M. O'Kane, Steven M.
LaValle
Proceedings of IEEE Conference on
Robotics and Automation (ICRA), 2004 [Slides]
2002
A
Fast Vision System for Middle Size Robots in RoboCup
M.
Jamzad, B. S. Sadjad, V. S. Mirrokni, M. Kazemi, H.
Chitsaz, A. Heydarnoori, M. T. Hajiaghai, E.
Chiniforooshan
Lecture Notes in Computer
Science Vol. 2377, pp 71-80, 2002
This
paper is awarded the best Engineering Challenge Award in RoboCup 2001
Basic
Requirements for a Teamwork in Middle Size RoboCup
Mansour
Jamzad, Hamid Reza Chitsaz,
Amirali Foroughnassirai, Reza Ghorbani, Moslem Kazemi, V. S.
Mirrokni, B. S. Sadjad
RoboCup 2001:
Lecture Notes in Computer Science Vol. 2377, pp 621-626,
2002
Sharif
CESR Small Size Robocup Team
Mohammad
Taghi Manzuri, Hamid Reza Chitsaz,
Reza Ghorbani, Pooya Karimian, Alireza Mirazi, Mehran Motamed,
Roozbeh Mottaghi, Payam Sabzmeydani
RoboCup
2001: Lecture Notes in Computer Science Vol. 2377, pp 595-598,
2002
RoboCup2001:
The Fifth Robotic Soccer World Championships
Manuela M.
Veloso, Tucker R. Balch, Peter Stone, Hiroaki Kitano, Fuminori
Yamasaki, Ken Endo, Minoru Asada, Mansour Jamzad, B. S. Sadjad, V. S.
Mirrokni, Moslem Kazemi, Hamid Reza Chitsaz, A. Heydarnoori,
Mohammad Taghi Hajiaghayi, Ehsan Chiniforooshan
AI Magazine
Vol. 23(1), American Association for Artificial Intelligence, pp
55-68, 2002
2001
Design
and Implementation of A Controller for Small Size Soccer Player Robot
(in Farsi)
Hamid
Reza Chitsaz
BS
Project, Computer Engineering Department, Sharif University of Tech,
2001
A
Goalkeeper for Middle Size RoboCup
M.
Jamzad, A. Foroughnassiraei, T.Hadjiaghai, V.S.Mirrokni, R. Ghorbani,
A. Heydar Noori, M. Kazemi, H. Chitsaz,
F. Mobasser, M. Ebraahimi Moghaddam, M. Gudarzi, N.
Ghaffarzadegan
RoboCup2000: Robot
Soccer World Cup IV. Lecture notes in Artificial Intelligence, Vol.
2019, pp 583-586, Springer, 2001
2000
ARVAND:
A Soccer Player Robot
M. Jamzad, A. Foroughnassiraei, E.
Chiniforooshan, R. Ghorbani, M. Kazemi, H. Chitsaz, F.
Mobasser, and S.B. Sadjad
AI Magazine, American Association for
Artificial Intelligence, pp 47-51, Fall 2000
Middle
Sized Soccer Robots: ARVAND
M.
Jamzad, A. Foroughnassiraei, E. Chiniforooshan, R. Ghorbani, M.
Kazemi, H. Chitsaz, F.
Mobasser, and S.B. Sadjad
RoboCup99:
Robot Soccer World Cup III. Lecture notes in Artificial Intelligence,
Vol. 1856, pp 61-73, Springer, 2000
Design
and Construction of a Soccer Player Robot ARVAND
M.
Jamzad, A. Foroughnassiraei, E. Chiniforooshan, R. Ghorbani, M.
Kazemi, H. Chitsaz, F.
Mobasser, and S.B. Sadjad
RoboCup99:
Robot Soccer World Cup III. Lecture notes in Artificial Intelligence,
Vol. 1856, pp 745-749, Springer, 2000