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Marco Antoniotti
NYU Courant Bioinformatics Group,
715 Broadway, Rm 1013
New York, NY 10003
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Phone: +1 - 212 998 3488
Fax: +1 - 212 998 3484
E-mail: marcoxa [at] cs.nyu.edu
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My current work is at the intersection of Computer Science, Biology
and Engineering. The topics I have been interested in recently have
dealt with the validation of sequence data , the simulation of
biological processes (most notably "pathway" and related problems) and
the application of inference schemes based on a mix of Temporal Logic
and Numerical Analysis to the model reconstruction problem for
biological systems. I have been working on the construction of tools
based on a variety of advanced theoretical foundations. All these
tools have always been driven by concrete examples and problems from
Biology and Genomics, Robotics, Automotive and Highway Systems, and
Embedded Systems. The foundations upon which I laid my work are
Mathematical Statistics, Temporal Logic, Control of Discrete Systems
and Formal Specification of Reactive and Hybrid Systems. My current
interests in System Biology require an interaction with researchers in
fields where I cannot claim a deep knowledge, therefore I devote
particular attention to understanding the specific problems at hand,
while trying to contribute statistical and algorithmic solutions based
on a continuous dialogue.
I am currently involved with several projects at the NYU
bioinformatics group.
- GOALIE (Group Leader): a system capable of
reconstructing temporal phenomenological descriptions of the
behavior of a biological system from meausured experimental
(microarray) data. The system can reconstruct a description of the
system behavior using a controlled vocabulary or an ontology (in
particular, the Gene Ontology.)
- Simpathica (Group Leader): an integrated system
whose aim is to empower a biologist looking for systemic properties
of an organism or a pathway, with a set of tools ranging from
simulation algorithms, temporal logic analysis and multiresolution
time-frequency analysis.
Simpathica is part of the
BioSpice
DARPA project.
See the
Simpathica
project section of our site for more information.
- NYUMAD (Group Leader): our integrated microarray
clustering, analysis, and database tool, currently supported by an
NSF grant.
See the
NYUMAD
project section of our site for more information.
International Journals and Book Chapters
- M. Antoniotti, P. E. Barbano, W. Casey, J. Feng, N. Ugel, B. Mishra
Multiple Biological Model Classification: From System Biology to
Synthetic Biology, BioCONCUR-04, The Royal Society, London,
Transactions on Computational Biology, 2006, to appear
(PDF)
-
P. Barbano, M. Antoniotti, J. Feng, M. Spivak, B. Mishra
A Coherent Framework for Multi-resolution Analysis of Biological
Networks with Memory: RAS pathwway, Cell Cycle and Immune System,
PNAS, 102(18):6245-6250, 2005.
- M. Antoniotti, S. Paxia, N. Ugel, B. Mishra
Simpathica: A Computational System Biology Tool within the VALIS
Bioinformatics Environment
, in Computational Systems Biology, E. Eiles and
A. Ktiete eds., Elsevier, 2005 in press.
- M. Antoniotti, B. Mishra, C. Piazza, A. Policriti, M. Simeoni
Taming the Complexity of Biochemical Models through Bisimulation
and Collapsing: Theory and Practice, Theoretical Computer
Science 325(1):45-67, 2004
(PDF)
- B. Mishra, M. Antoniotti et al., A Sense of Life:
Computational & Experimental Investigations with Models of Biochemical
& Evolutionary Processes, OMICS - A Journal of Integrative
Biology, (Special Issue on BioCOMP, S. Kumar, ed.), 7(3), 2003
- M. Antoniotti, A. Policriti, N. Ugel, B. Mishra
Model Building and Model Checking for Biochemical Processes,
Cell Biochemistry and Biophysics, 38:271-286, 2003
(PDF)
- M. Antoniotti, A. Ferrari, A. Flesca, A. L. Sangiovanni-Vincentelli,
JESTER: An Esterel-based Reactive Java Extension for Reactive
Embedded Systems Co-Design, in System on Chip Methodologies and
Design Languages, Kluwer, 2001
(PDF)
International Conferences
- C. Piazza, M. Antoniotti, V. Mysore, A. Policriti, F. Winkler, and
B. Mishra, Algorithmic Algebraic Model Checking I: Challenges form
Systems Biology, 17th International Conference on Computer Aided
Verification (CAV05), Edimburgh, Scotland, UK, July 2005 (PDF).
- N. Ramakrishnan, M. Antoniotti, and B. Mishra, Reconstructing
Formal Temporal Models of Cellular Events using the GO Process
Ontology, Bio-Ontologies SIG Meeting, ISMB 2005, Detroit, USA,
2005.
- M. Antoniotti, N. Ramakrishnan, B. Mishra,
GOALIE, A Common Lisp Application to Discover "Kripke Models:"
Redescribing Biological Processes from Time-Course Data.,
International Lisp Conference, Stanford, CA, U.S.A., June 19-22, 2005 (PDF).
- M. Antoniotti, I. T. Lau, B. Mishra,
Naturally Speaking: A System Biology Tool with Natural Language
Based Interfaces, Biological Language Conference (BLC04),
Pittsburgh, PA, USA, November 2004 (PDF)
- M. Antoniotti, B. Mishra, C. Piazza, A. Policriti, M. Simeoni
Modeling Cellular Behavior with Hybrid Automata: Collapsing and
Bisimulation, Computational Methods in System Biology (CMSB
2003), C. Priami ed., LNCS 2602, Springer 2003
(PDF)
- M. Antoniotti, F. Park, A. Policriti, N. Ugel, B. Mishra
Foundations of a Query and Simulation System for the Modeling of
Biochemical and Biological Processes, PSB 2003, Lihu'e, HW,
U.S.A., January 2003
(PDF)
- M. Antoniotti, A. Policriti, N. Ugel, B. Mishra
XS-systems: eXtended S-systems and Algebraic Differential Automata
for Modeling Cell Behavior, High Performance Computing (HiPC
2002), S. Sahni, V. K. Prasanna e U. Shukla eds., LNCS 2552, Springer
2002
(PDF)
- M. Antoniotti
Two Bioinformatics Applications of Common Lisp, ILC 2002,
San Francisco, U.S.A., 2002
(PDF)
- M. Antoniotti, A. Ferrari, A. L. Sangiovanni-Vincentelli, E. Sentovich
Embedded System Design Specification: Merging Reactive Control and
Data Computation, 40th IEEE Conference on Decision and Control
(CDC 2001), Orlando, U.S.A., 2001
(PDF)
- M. Antoniotti, A. Ferrari, A. Flesca A. L. Sangiovanni-Vincentelli,
JESTER: An Esterel-based Reactive Java Extension for Reactive
Embedded Systems Co-Design, Forum on Design Languages 2000,
Tübingen, Germany, September 2000
- M. Antoniotti, A. Balluchi, L. Benvenuti, A. Ferrari, R. Flora, W. Nesci, C. Pinello, C. Rossi, A. L. Sangiovanni-Vincentelli, G. Serra, M. Tabaro,
A Top-Down Constraints-Driven Design Methodology for Powertrain
Control Systems, Proceedings of the Global Powertrain Congress,
Detroit, MI, U.S.A., October 1998
- M. Antoniotti, A. Deshpande, A. Girault,
Microsimulation Analysis of Multiple Merge Junctions under
Autonomous AHS Operations, Proceedings of the IEEE Conference on
Intelligent Transportation Systems, Boston, MA, U.S.A. November
1997
(PDF)
- M. Antoniotti, A. Deshpande, A. Girault,
Microsimulation Analysis of a Hybrid System Model of Multiple
Merge Junction Highways and Semi-Automated Vehicles, Proceedings
of the IEEE Conference on Systems, Man and Cybernetics, Orlando, FL,
U.S.A. October 1997
- M. Antoniotti, A. Göllü,
SHIFT and SMART-AHS: A Language for Hybrid System Engineering,
Modeling and Simulation, USENIX Conference on Domain Specific
Languages, Santa Barbara, CA, U.S.A., October 1997
(PDF)
- M. Antoniotti, B. Mishra,
NP-completeness of the Supervisor Synthesis Problem for
Unrestricted CTL Specifications, Workshop on Discrete Event
Systems, Edinburgh, Scotland, U.K., 1996
(PDF)
- M. Antoniotti, M. Jafari, B. Mishra,
Applying Temporal Logic Verification and Synthesis to
Manufacturing Systems, Proceedings of the IEEE Conference on Man,
Systems and Cybernetics, Vancouver, Canada, 1995
- M. Antoniotti, B. Mishra,
Discrete Event Models + Temporal Logic = Supervisory Controller:
Automatic Synthesis of Locomotion Controllers, Proceedings of the
IEEE International Conference on Robotics and Automation (ICRA 95),
Nagoya, Japan, 1995
(PDF)
- M. Antoniotti, B. Mishra,
Automatic Synthesis Algorithms for Supervisory Controllers,
Proceedings of the IEEE Conference on Computer Integrated
Manufacturing and Automation Technology (CIMAT 94), Troy, NY, U.S.A.,
1994
Presentations at International Conferences
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M. Antoniotti, N. Ramakrishnan, B. Mishra,
Reconstructing Formal Temporal Logic Models of Cellular Events
using the GO Process Ontology, Eight Annual Bio-Ontologies
Meeting, ISMB 2005, Detroit, Michigan, June 24th 2005.
- M. Antoniotti, F. Park, A. Policriti, N. Ugel, B. Mishra
Simulating Large Biochemical and Biological Processes and
Reasoning about their Behavior, Poster at ICSB 2002, Stokholm,
Sweden, December 2002
- M. Antoniotti, M. Isopi, V. Mittal, N. Ugel, B. Mishra
Mathematically Modeling Stem Cells Populations, Poster at
2002 Meeting on Genome Sequencing and Biology, CSHL, Cold Spring
Harbor, NY, U.S.A., May 2002
- M. Rejali, M. Antoniotti, V. Cherepinsky, C. Leventhal, S. Paxia, A. Rudra, J. West, B. Mishra
Goals, Design and Implementation of a Versatile MicroArray Data
Base, Poster at CGC 2001, Baltimore, U.S.A., November 2001
- M. Antoniotti, T. Anantharaman, C.-W. Chang, D. C. Schwartz, B. Mishra
Algorithms for combining Sequences and Maps: Examples from
P. falciparum and E. coli, Poster at GSAC 2001, San Diego,
U.S.A., October 2001
- M. Antoniotti, T. Anantharaman, C.-W. Chang, J. Colinas, D. C. Schwartz, B. Mishra
Algorithms and Analysis for combining Sequences and Maps:
Applications to the Malaria Parasite P. falciparum, Poster at
WABI 2001, Aarhus, Denmark, August 2001
- M. Antoniotti, A. Ferrari, L. Lavagno, A. L. Sangiovanni-Vincentelli,
JESTER = Java || Esterel, Presentation at the 1999 Synchronous
Workshop, Hyeres, France, November 1999
- M. Antoniotti, A. Ferrari, L. Lavagno, A. L. Sangiovanni-Vincentelli,
Object-Oriented System Level Design for Embedded Reactive
Systems, Presentation at Forum on Design Languages, EPFL,
Lousanne, CH, September 1998
Technical Reports
- M. Antoniotti, I. T. Lau, B. Mishra,
Naturally Speaking: A System Biology Tool with Natural Language
Based Interfaces, CIMS TR2004-853, June 2004
(PDF)
- M. Antoniotti, T. Anantharaman, S. Paxia, B. Mishra
Genomics via Optical Mapping IV: Sequence Validation via Optical
Map Matching, CIMS TR-811, Courant Institute of Mathematical
Sciences, NYU, March 2001
- M. Antoniotti, B. Mishra
Automatic Synthesis Algorithms for Supervisory Controllers
(Preliminary Report), CIMS TR-664, Courant Institute of
Mathematical Sciences, NYU, November 1994
- B. Mishra, M. Antoniotti, F. Hansen, R. Wallace,
NYU Educational Robotics Project: A Pedagogic Overview, CIMS
TR-653, Courant Institute of Mathematical Sciences, NYU, November
1993
- B. Mishra, M. Antoniotti,
ED I: NYU Educational Robot Design and Evaluation, CIMS-TR
643, Courant Institute of Mathematical Sciences, NYU, Aug. 1993
- M. Antoniotti,
Conceptual and Pragmatic Tools for Design and Control of
Manufacturing Systems (Petri Nets and Ramadge-Wonham Discrete Event
Systems), CIMS-TR 664, Courant Institute of Mathematical
Sciences, NYU, Jul. 1993
Submitted
- M. Antoniotti, N. Ramakrishnan, D. Kumar, M. Spivak, B. Mishra
Remembrance of Experiments Past: Analyzing Time Course Datasets to
Discover Complex Temporal Invariants, under review 2006
- M. Antoniotti, P. E. Barbano, W. Casey, J. Feng, M. Rejali,
M. Spivak, N. Ugel, B. Mishra
NYU BioWave & NYU BioSim: Tools for Classifying Trajectories
of Biochemical Pathways, under review 2006
- J. P. Mathew, A. Chinnaiyan, G. Bader, S. Pyarajan, B. Taylor,
R. Daruwala, M. Antoniotti, C. Sander, S. J. Burakoff, B. Mishra,
From Bytes to Bedside: Computational Biology for Biomedical
Tranlsational Research, under review 2006
Patents
- U.S. Patent application #60/236,296, System and Method for a Sequence
Validation via Optical Map Matching, filed 2000-09-28
- U.S. Patent application #60/293,254, Automatic Validation,
Alignment, and Reordering of Sequences via Optical Mapping, filed
2001-05-24
My old Courant home page.
Some more personal stuff can be found here.
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