Fall 2005
Selected Publications
NYU Technical Report
Under Review

"Genomics via Optical Mapping I: 01 Laws for Single Molecules,"
(with T.S. Anantharaman),
(Ed. S. Yancopoulos), Oxford University Press, 2007.

"Algorithms for Normalization and Segmentation of arrayCGH Data,"
(with T.S. Ananthraman, S. Paxia and R.S. Daruwala),
2007.

"Extensions to Segmentation Algorithms for ArrayCGH,"
(with T.S. Anantharaman and M. Sobel), 2007.

"CAPO: Comparative Analysis and Phylogeny using OpticalMaps,"
(with B. Sun, A. Briska and J.T. Schwartz), 2006.

"Optical Haplotype Mapping,"
(with T.S. Anantharaman et al.), 2007.

"A Computational Dissection of the Dynamics and Regulation of
Molecular Processes in Mammary Acinar Morphogenesis,"
(with F. Cheng et al.), 2007.

"On a Mathematical Method for Extracting Dynamic Models from Gene
Expression Data: The Case of Yeast Metabolic Cycle,"
(with S. Tadepalli, N. Ramakrishnan, and M. Antoniotti),
2007.

"Application Note  GOALIE: Reconstructing Temporal Models from Time
Course Datasets,"
(with M. Antoniotti et al.), 2007.

"Intelligently Deciphering Unintelligible Designs:
Algorithmic Algebraic Model Checking in Systems Biology"
, 2007.

"Inclusion Dynamics Hybrid Automata,"
(with A. Casagrande, C. Piazza, and A. Policriti), 2007.

"Discovering Relations among GOannotated Clusters by Graph Kernel
Methods,"
(with I. Zoppis, D. Merico, M. Antoniotti, G. Mauri), 2007.

"On Building and Checking a Systems Biology Model of Caspase9 and
Using it to Understand Intrinsic Apoptosis,"
(with S. Ryu et al.), 2007.

"Mapping Oncogenes using Multipoint Statistics from CopyNumber
Variation Data,"
(with I. IonitaLaza), 2007.

"On Evolution of the IntergenicSpacers in rDNA Analyzed by
DropoutAlignment of DNA sequences,"
(with S. Ryu et al.), 2007.

"Comparative analysis of prostate cancer array CGH data across
multiple platforms and algorithms,"
(with A. Pearlman, T.S. Anantharaman and H. Ostrer), 2007.

"Multiscale Curve and Strip Constructions,"
(with G. Lerman and J. McQuown),
2007.

"Translating Timecourse Gene Expression Profiles into SemiAlgebraic
Hybrid Automata via Dimensionality Reduction,"
(with A. Casagrande, K. Casey, R. Falchi, C. Piazza,
B. Ruperti, and G. Vizzotto), 2007.

"Algorithmic Algebraic Model Checking IV: Metabolic Networks,"
(with V. Mysore), 2007.
2007

"Successive Abstractions of Hybrid Automata for
Monotonic CTL Model Checking,"
(with R. Gentilini and K. Schneider),
Symposium on Logical Foundations of Computer Science:
LFCS '07, 2007.

"From Bytes to Bedside: Computational Biology for Biomedical
Translational Research,"
(with J.P. Mathew, A. Chinnaiyan, G. Bader, S. Pyarajan,
B. Taylor, M. Antoniotti, C. Sander and
S.J. Burakoff),
PLoS Computational Biology, (In press),
2007.

"Synchronized Product of SemiAlgebraic OMinimal Hybrid Automata,"
(with A. Casagrande, P. Corvaja, and C. Piazza),
HSCC '07, 2007.

"Single Molecule Transcription Profiling with AFM,"
(with J. Reed, B. Pittenger, S. Magonov, J. Troke,
M.A. Teitell, and J.K. Gimzewski),
Nanotechnology, 18, 115, 2007.
2006

"Multiscale Strip Constructions and Their Application to Gene
Expression and ChIPonchip Data,"
(with G. Lerman, J. McQuown, A. Blais, B.D. Dynlacht, and G. Chen),
Bioinformatics, (Advanced Access), December 2006.

"Mapping Tumor Suppressor Genes using Multipoint
Statistics from CopyNumber Variation Data,"
(with I. Ionita and R. Daruwala),
American Journal of Human Genetics, 79(1):1322,
July 2006.

"Validation of S. pombe sequence assembly by microarray hybridization,"
(with J. West, J. Healy, M. Wigler, and W. Casey),
Journal of Computational Biology,
13(1): 120, Jan 2006.
DataSet A: Raw Intensity
Ratios 
DataSet B: EM processed
average log ratios 
DataSet C: All probe
sequences

"Quantitative analysis of germline mitosis in adult
C. elegans,"
(with J. Maciejowski, N. Ugel, M. Isopi, and J. Hubbard),
Developmental Biology,
292(1):142151, 1 April 2006.

"Interpreter of Maladies: Redescription Mining Applied to Biomedical Data analysis,"
(with P. Waltman and A. Pearlman), Pharmacogenomics,
7(3):503509, Apr 2006.

"CLARITY: Algorithms for Semantic Comparison of Timecourse
Transcriptomic Data,"
(with S. Kleinberg),
International Symposium on Computational Biology &
Bioinformatics: ISBB 06, Bhubaneswar, India,
December 1517, 2006.

"PLANAR: RNA Sequence Alignment using NonAffine Gap Penalty and
Secondary Structure,"
(with O. Gill and N. Ramakrishnan),
International Symposium on Computational Biology &
Bioinformatics: ISBB 06, Bhubaneswar, India,
December 1517, 2006.

"COMBAT: Search Rapidly For Highly Similar ProteinCoding Sequences
Using Bipartite Graph Matching,"
(with B. Sun, J. Schwartz and O. Gill),
International Conference on Computational Science,
(2): 654661, 2006.

"SEPA: Approximate NonSubjective Empirical pValue Estimation for
Nucleotide Sequence Alignment,"
(with O. Gill),
International Conference on Computational Science,
(2): 638645, 2006.

"Remembrance of Experiments Past: A Redescription Based Tool for
Discovery in Complex Systems,"
(with S. Kleinberg, M. Antoniotti, S. Tadepalli, and
N. Ramakrishnan),
Interational Conference on Complex Systems,
Quincy, Boston, MA, June 2006.

"Algorithmic Algebraic Model Checking III: Approximate Methods,"
(with V. Mysore),
7th International Workshop on Verification of
InfiniteState Systems, INFINITY 05, San Francisco,
California, USA, August 27, 2005.
Electr. Notes Theor. Comput. Sci., 149(1):6177,
2006.

"MultiObjective Evolutionary Optimization of Agent Based
Models: An Application to Emergency Response Planning,"
(with G. Narzisi and V. Mysore),
The IASTED InternationalConference on Computational
Intelligence, CI 2006, pp. 224230,
November 2022, San Francisco, CA, 2006.

"Complexities, Catastrophes and Cities: AgentBased Analysis of
LargeScale Urban Emergency Response,"
(with G. Narzisi et al.),
Interational Conference on Complex Systems,
Quincy, Boston, MA, June 2006.

"Emergency Response Planning for a Potential Sarin Gas
Attack in Manhattan using Agentbased Models,"
(with V. Mysore, G. Narzisi et al.),
Agent Technology for Disaster Management Notification,
ATDM 06, 8th May 2006, Hakodate, Japan.
2005

"A Coherent Framework for Multiresolution Analysis of Biological
Networks with Memory: RAS pathway, Cell Cycle and Immune System,"
(with P. Barbano, M. Spivak, J. Feng, and M. Antoniotti),
Proc. National Academy of Science U S A,
102(18):62456250, 2005.

"On LargeSegmental Duplications in Human Genome and Their Statistical Analysis,"
(with Y. Zhou),
Proc. National Academy of Science U S A,
102(11):40514056, 2005.

"Multiple Biological Model Classification: From System Biology to
Synthetic Biology,"
(with M. Antoniotti et al.),
BioConcur'04, 2nd Workshop on Concurrent Models in
Molecular Biology, The Royal Society, London,
Transactions on Computational Systems Biology,
2005.

"The Importance of Being Bounded,"
(with A. Casagrande, V. Mysore, and C. Piazza),
1st International Conference on Algebraic Biology: Computer
Algebra in Biology, AB 05, Tokyo, Japan, 2830, November 2005.

"SemiAlgebraic Constant Reset Hybrid Automata  SACoRe,"
(with A. Casagrande, and C. Piazza),
44th IEEE Conference on Decision and Control, and European
Control Conference ECC 2005, CDC 05, Seville, Spain. 1215,
December 2005.

"Stability of Hybrid Systems and Related Questions from Systems
Biology," (In honor of Professor Pravin Varaiya on his 65th birthday),
(with C. Piazza),
Advances in Control, Communication Networks, and
Transportation Systems: In Honor of Pravin
Varaiya,E.H. Abed (Ed.),
Systems and Control: Foundations and Applications
Series, Birkhauser, Boston, 2005.

"Algorithmic Algebraic Model Checking II: Decidability of
SemiAlgebraic Model Checking and its Applications to Systems Biology,"
(with V. Mysore and C. Piazza),
Automated Technology for Verification and Analysis:
(Taipei, Taiwan, October 4  7, 2005), ATVA 2005:
217233, 2005.

"Algorithmic Algebraic Model Checking I: Challenges from Systems Biology,"
(with C. Piazza, M. Antoniotti, V. Mysore, A. Policriti, and
F. Winkler),
17th International Conference on Computer Aided
Verification, (The University of Edinburgh, Scotland, UK,
July 6  10 , 2005), CAV 2005:519, 2005.

"Reconstructing Formal Temporal Models of Cellular Events using the GO
Process Ontology,""
(with M. Antoniotti and N. Ramakrishnan),
Proceedings of the Eighth Annual BioOntologies
Meeting,
(ISMB'05 Satellite Workshop), Detroit, MI, June 2324 2005.

"GOALIE, A Common Lisp Application to Discover Kripke Models:
Redescribing Biological Processes from TimeCourse Data"
(with M. Antoniotti and N. Ramakrishnan),
International Lisp Conference, ILC 2005,
Stanford University, June 1922, 2005.

"Fast and Cheap Genome wide Haplotype Construction via Optical
Mapping,"
(with T.S. Anantharaman and V. Mysore.),
The Pacific Symposium on Biocomputing:,
(Eds. R.B. Altman, A.K. Dunker, L. Hunter & T.E.Klein),
PSB 2005:38596, World Scientific, January, 2005.

"Simpathica: A Computational Systems Biology Tool within the Valis
Bioinformatics Environment,"
(with M. Antoniotti, S. Paxia and N. Ugel),
Computational Systems Biology,
(Ed. E. Eiles and A. Kriete), Elsevier, 2005.

"MultiAgent Modeling and Analysis of the Brazilian FoodPoisoning
Scenario,"
(with V. Mysore, O. Gill, R.S. Daruwala, M. Antoniotti, and
V. Saraswat),
The Agent 2005 Conference on Generative Social Processes,
Models, and Mechanisms. Agent 2005, Argonne
National Laboratory, & The University of Chicago, 1315,
October 2005.

"Improved Estimation of The Relationships Between Random Vectors,"
(with M. Sobel),
4th National Hawaii International Conference on Statistics,
Mathematics and Related Fields,
Honolulu, Hawaii, January 2005.
2004

"Taming the Complexity of Biochemical Models through
Bisimulation and Collapsing: Theory and Practice,"
(with M. Antoniotti, C.Piazza, A. Policriti and M. Simeoni),
Theoretical Computer Science, 325(1): 4567,
2004.

"A Versatile Statistical Analysis Algorithm to Detect Genome Copy
Number Variation,"
(with R.S. Daruwala, A. Rudra, H. Ostrer, R. Lucito, and M. Wigler),
Proc. National Academy of Science U S A,
101(46): 162927, 2004.

"Distribution of Short Paired Duplications in Mammalian Genomes."
(with E. Thomas et al.),
Proc. National Academy of Science U S A,
101(28):1034910354, 2004.

"Computational Real Algebraic Geometry."
CRC Handbook of Discrete and Computational Geometry:
(Second Edition), pp. 740764, CRC Press, Boca Raton, FL,
April, 2004.
(In pdf,
Index,
Authors)

"Aligning Sequences with NonAffine Gap Penalty:
PLAINS Algorithm, a Practical Implementation, and its
Biological Applications in Comparative Genomics,"
(with O.H. Gill, and Y. Zhou),
ICBA2004 Conference, December 1719, 2004.

"Models of Genome Evolution,"
(with Y. Zhou),
Modeling in Molecular Biology,
G. Ciobanu, G. Rozenberg (Eds.),
Natural Computing Series, pages 287304,
Lecture Notes in Computer Science, 2004.

"Systems Biology and Automata,"
(with A. Policriti),
3rd Workshop on Computation of Biochemical Pathways
and Genetic Networks, Villa Bosch, Heidelberg, October
67, 2003, Springer Verlag, 2004.

"Turning CARTwheels: An Alternating Algorithm for Mining Redescriptions,"
(with N. Ramakrishnan, D. Kumar, M. Pott, and R.F. Helms), The
Tenth ACM SIGKDD International Conference on Knowledge
Discovery and Data Mining, SIGKDD 2004, Seattle
Washington.2225, August, 2004.

"Systems Biology, Automata, and Languages,"
(with A. Policriti),
Bioinformatics Italian Society Meeting, BITS 2004, Padova,
March 2004.

"TimeFrequency Feature Detection for TimeCourse Microarray Data,"
(with J. Feng and P.E. Barbano),
19th ACM Symposium on Applied Computing (SAC 2004), pages
128132, Nicosia, Cyprus, March 1417, 2004.
2003

"A Sense of Life: Computational & Experimental Investigations with
Models of Biochemical & Evolutionary Processes,"
(with R. Daruwala, Y. Zhou, N. Ugel, A. Policriti,
M. Antoniotti, S. Paxia, M. Rejali, A. Rudra, V. Cherepinsky,
N. Silver, W. Casey, C. Piazza, M. Simeoni, P. Barbano,
M. Spivak, JW. Feng, O. Gill, M. Venkatesh, F. Cheng, B. Sun,
I. Ioniata, T.S. Anantharaman, E.J.A. Hubbard, A. Pnueli,
D. Harel, V. Chandru, R. Hariharan, M. Wigler, F. Park,
S.C.. Lin, Y. Lazebnik, F. Winkler, C. Cantor, A. Carbone,
and M. Gromov),
OMICS  A Journal of Integrative Biology,
(Special Issue on BioCOMP, Ed.: S. Kumar), 7(3): 253268,
2003.

"ShrinkageBased Similarity Metric for Cluster Analysis of Microarray Data,"
(with V. Cherepinsky, J. Feng and M. Rejali),
Proc. National Academy of Science,
100(17): 96689673, 2003.
 NYU
Technical Report (long; in .pdf)

"Optical Mapping,"
Encyclopedia of the Human Genome,
4: 448453,
Nature Publishing Group, Macmillan Publishers Limited,
London, UK, June, 2003.

"Model Building and Model Checking for Biochemical Processes,"
(with M. Antoniotti, A. Policriti and N. Ugel),
Cell Biochemistry and Biophysics (CBB),
38(3): 271286, Humana Press, June, 2003.

"A Nearly LinearTime General Algorithm for BiAllele Haplotype Phasing,"
(with W. Casey),
High Performance ComputingHiPC 2003,
(Eds. T.M. Pinkston & V.K. Prasanna),
Proceedings of the 10th International Conference in Hyderabad,
India, Lecture Notes in Computer Scuence,
LNCS 2913: 204215, SpringerVerlag, NY, December 2003.

"Life's Duplicities: Sex, Death, and Valis."
High Performance ComputingHiPC 2003,
(Eds. T.M. Pinkston & V.K. Prasanna),
Proceedings of the 10th International Conference in Hyderabad,
India, Lecture Notes in Computer Scuence,
LNCS 2913: 1, SpringerVerlag, NY, December 2003.

"Modelling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing,"
(with M. Antoniotti, C. Piazza, A. Policriti and M. Simeoni),
International workshop on Computational Methods in Systems
Biology, CMSB'03, (Ed. C. Priami), Lecture Notes in
Computer Science, LNCS: 2602: 5774, SpringerVerlag,
2003.
(In pdf)

"Foundations of a Query and Simulation System for the Modeling of
Biochemical and Biological Processes."
(with M. Antoniotti, F. Park, A. Policriti and N. Ugel),
The Pacific Symposium on Biocomputing: PSB 2003,
(Eds. R.B. Altman, A.K. Dunker, L. Hunter, T.A. Jung & T.E.Klein),
pp 116127, World Scientific, January, 2003.
(In pdf)

Designer Molecules for Biosensor Applications,
(with J.T. Schwartz),
Banbury Workshop, Cold Spring Harbor Laboratory,
National Science Foundations, 40pp, 2003.
2002

"A WholeGenome Shotgun Optical Map of Yersinia pestis Strain KIM,"
(with S. Zhou, et al.),
Appl Environ Microbiol,
68(12):63216331, 2002.

"A Random Walk Down the Genomes: DNA Evolution in VALIS,"
(with S. Paxia, A. Rudra and Y. Zhou).
Computer, 35(7):7379, IEEE Press, July,
2002.

"Wild by Nature,"
(with M. Wigler),
Science,
296: 14071408, 24 May 2002.

"Comparing Genomes,"
Special issue on "Biocomputation:" Computing in
Science and Engineering. , pp 4249, January/February
2002.

"Simulating Large Biochemical and Biological Processes and Reasoning
about their Behavior."
(with M. Antoniotti, F. Park, A. Policriti and N. Ugel),
3rd International Conference on Systems Biology,
ICSB 2002, Karolinska Institutet, Stockholm, Sweden,
2002.
(In pdf)

"xSsystems: eXtended Ssystems and Algebraic Differential Automata
for Modeling Cellular Behavior,"
(with M. Antoniotti, A. Policriti and N. Ugel),
High Performance ComputingHiPC 2002,
(Eds. S. Sahni, V.K. Prasanna & U. Shukla),
LNCS 2552:431442, SpringerVerlag, December 2002.
(In pdf)

"A Symbolic Approach to Modelling Cellular Behaviour,"
High Performance ComputingHiPC 2002,
(Eds. S. Sahni, V.K. Prasanna & U. Shukla),
LNCS 2552:725732, SpringerVerlag, December 2002.
(In pdf)
2001

"Shotgun Optical Maps of the Whole Escherichia coli 0157:H7 Genome,"
(with A. Lim et al.),
Genome Research,
11(9): 15841593, 2001.

"Placing Probes along the Genome using Pairwise Distance Data,"
(with W. Casey and M. Wigler),
Algorithms in Bioinformatics, First
International Workshop, WABI 2001 Proceedings, LNCS 2149:5268,
SpringerVerlag, 2001.
(In pdf)

"A Probabilistic Analysis of False Positives in Optical Map Alignment
and Validation,"
(with T.S. Ananatharaman),
Algorithms in Bioinformatics, First
International Workshop, WABI 2001 Proceedings, LNCS 2149:2740,
SpringerVerlag, 2001.
(In pdf)
2000

"Detecting Gene Copy Number Fluctuations in Tumor Cells by Microarray
Analysis of Genomic Representations,"
(with R. Lucito et al.),
Genome Research,
10(11): 17261736, 2000.

"Optical Mapping of BAC Clones from the Human Y Chromosome DAZ
Locus,"
(with J. Giacalone et al.),
Genome Research,
10(9): 14211429, 2000.

"Partitioning SingleMolecule Maps into Multiple Populations:
Algorithms And Probabilistic Analysis,"
(with L. Parida),
Discrete Applied Mathematics (The Computational Molecular
Biology Series),104(l3):203227,
August, 2000.
(In pdf)

"On the Other Hands: Geometric Ideas in Robotics,"
In Geometry at Work: Papers in Applied Geometry,
(Eds. C.A. Gorini et al.),
53:105117,
Mathematical Association of America, Cambridge University
Press, 2000.
(In pdf)

"On the Dynamic Finger Conjecture for Splay Trees.
Part I: Splay Sorting log nBlock Sequences,"
(with R. Cole, J. Schmidt and A. Siegel),
SIAM Journal of Computing,
30(1):143, 2000.

"Reactive Robotics I: Reactive Grasping with a Modified
Gripper and Multifingered Hands,"
(with M. Teichmann),
International Journal of Robotics Research,
19(7):697708, 2000.

"Computational Differential Algebra,"
In Geometrical Foundations of Robotics,
(Ed. Jon Selig), Lecture 8:111145,
WorldScientific, Singapore, 2000.

"Probabilistic Algorithms for Efficient Grasping and Fixturing,"
(with M. Teichmann),
Algorithmica,
26:345363, 2000.
1999

"A Shotgun SequenceReady Optical Map of the Whole
Plasmodium falciparum Genome,"
(with Z. Lai et al.),
Nature Genetics,
23(3):309313,
1999.

"Optical PCR: Genomic Analysis by LongRange PCR and Optical Mapping,"
(with J. Skiadas et al.),
Mammalian Genome,
10:10051009,
1999.

"Whole Genome Shotgun Optical Mapping of Deinococcus
radiodurans,"
(with J. Lin et al.),
Science,
285(5433):15581562,
1999.

"Optical Mapping and Its Potential for LargeScale Sequencing
Projects,"
(with C. Aston and D.C. Schwartz),
Trends in Biotechnology,
17:297302,
1999.

"Genomics via Optical Mapping III: Contiging Genomic DNA and Variations,"
(with T.S. Anantharaman and D.C. Schwartz),
Proceedings 7th Intl. Cnf. on Intelligent Systems for
Molecular Biology: ISMB '99 ,
7:1827, AAAI Press, 1999.

"Optical Mapping of Plasmodium falciparum Chromosome 2,"
(with J. Jing et al.),
Genome Research,
9:175181, 1999.
1998

"The Santa Fe Bar Problem Revisited: Theoretical and Practical
Implications,"
(with A. Greenwald and R. Parikh),
The Proceedings of the Summer Festival on Game Theory:
International Conference,
1998.

"Partitioning K Clones: Inapproximability Results and a
Practical Solution to the KPopulations Problem,"
(with L. Parida),
Proceedings of the Second Annual Conference on
Computational Molecular Biology,
RECOMB 98:192201, 1998.

"New Approaches to Genomic Analysis Using Single Molecules,"
(with D.C. Schwartz et al.),
Proceedings of the Second Annual Conference on
Computational Molecular Biology,
RECOMB 98:248250, 1998.

"Automated High Resolution Optical Mapping Using Arrayed, Fluid
Fixated, DNA Molecules,"
(with J. Jing, et al.),
Proc. National Academy of Science,
95:80468051, 1998.

"High Resolution Restriction Maps of Bacterial Artificial Chromosomes
Constructed by Optical Mapping,"
(with W. Cai, et al.),
Proc. National Academy of Science,
95:33903395, 1998.
1997

"Computational Real Algebraic Geometry,"
In CRC Handbook of Discrete and Computational Geometry:
537558, CRC Press, Boca Raton, FL, 1997.

"Genomics via Optical Mapping II: Ordered Restriction Maps,"
(with T.S. Anantharaman and D.C. Schwartz),
Journal of Computational Biology,
4(2):91118, 1997.
(In pdf)

"The Power of Friction: Quantifying the "Goodness" of Frictional
Grasps,"
(with M. Teichmann),
In Algorithms for Robotic Motion and Manipulation:
311320, A.K. Peters, Wellesley, MA, 1997.

"CATS: A Complex Adaptive Traffic Simulator,"
(with F. Archetti, E. Messina and F. Stella),
Transportation Systems 97,
1997.
1996

"Bidirectional Edges Problem: Part I, A Simple Algorithm,"
Algorithmica,
15:256286,
1996.

"NPcompleteness of the Supervisor Synthesis Problem for
Unrestricted CTL Specifications,"
(with M. Antoniotti),
Workshop on Discrete Event Systems,
WODES 96, 1996.

"Hybrid Controllers for Robotics,"
In Robotics and Manufacturing: Recent Trends in Research and
Applications,
6:435440, 1996.

"CAFE: A Complex Adaptive Financial Environment,"
(with R. Even),
IEEE/IAFE Conference on Computational Intelligence for
Financial Engineering,
CIFEr 96:2025, 1996.
1995

"Mapping the Genome One Molecule at a Time  Optical Mapping,"
(with A.H. Samad et al.),
Nature,
378:516517, 1995.

"Grasp Metrics: Optimality and Complexity,"
In Algorithmic Foundations of Robotics: 137166,
A.K. Peters, Wellesley, MA, 1995.

"Discrete Event Models + Temporal logic = Supervisory Controller:
Automatic Synthesis of Locomotion Controllers,"
(with M. Antoniotti),
1995 IEEE International Conference on Robotics and
Automation,
ICRA 95, 1995.

"Applying Temporal Logic Verification and Synthesis to Manufacturing
Systems,"
(with M. Antoniotti and M. Jafari),
IEEE System Man and Cybernetics Conference,
1995.
1994

"A Solution to Kronecker's Problem,"
(with G. Gallo),
Applicable Algebra in Engineering, Communication and
Computing,
5(6):343370, 1994.

"The Complexity of Resolvent Resolved,"
(with G. Gallo),
in
Proceedings of the Fifth Annual ACMSIAM Symposium on Discrete
Algorithms
,
SODA 94:280289,
1994.

"Reactive Algorithms for Grasping Using a Modified Parallel Jaw
Gripper,"
(with M. Teichmann),
in
Proceedings of the 1994 IEEE International Conference on
Robotics and Automation
,
ICRA 94, 1994.

"Reactive Algorithms for 2 and 3 Finger Grasping,"
(with M. Teichmann),
in
Proceedings of the 1994 International Workshop on
Intelligent Robots and Systems,
IRS 94, 1994.

"Automatic Synthesis Algorithms for Supervisory Controllers,"
(with M. Antoniotti),
Proceedings of the Fourth International Conference on
Computer Integrated Manufacturing and Automation
Technology,
151156, 1994.

"Three Finger Optimal Planar Grasp,"
(with M. Teichmann),
in
Proceedings of the 1994 International Workshop on
Intelligent Robots and Systems,
IRS 94, 1994.

"New Findings from the Spider Web Algorithm: Toward A Digital Morse
Theory,"
(with J. Cox and D. Karron),
Proceedings of the Visualization in Biomedical Computing
Conference,
VBC 94, 1994.
1993

Algorithmic Algebra,
In
Texts and Monographs in Computer Science Series,
SpringerVerlag, New York, 1993. XIV, 416 pp., 9 illus.
[Amazon.com entry]

"The SpiderWeb Algorithm for Surface Construction from Medical Volume
Data: Geometric Properties of its Surfaces,"
(with D. Karron and J. Cox),
Innovation et Technologie en Biologie et Medecine,
14(6), 1993.

ED I: NYU Educational Robot
(with M. Antoniotti)
Courant Technical Report No. TR1993643,
Courant Institute of Mathematical Sciences, August 1993, 82pp.
1992

"Quantitative Steinitz's Theorem with Applications to Multifingered
Grasping,"
(with D. Kirkpatrick and C.K. Yap),
Discrete & Computational Geometry,
7(3):295318, 1992.

"A Linear Time Algorithm for Finding an Ambitus,"
(with R.E. Tarjan),
Algorithmica,
7(5/6):521554,
1992.

"Real Algebraic Numbers are in NC,"
(with F. Cucker, P. Pedersen and M.F. Roy),
Applicable Algebra in Engineering, Communication and
Computing,
3(2):7998, 1992.

"Quantifying the Advantage of Knowing the Future When Scheduling
Sporadic Tasks,"
(with S. Baruah et al.),
Real Time Systems Journal,
4(2):125144, 1992.

"Recent Progress in Characteristic Set Computation: Complexity & Open
Problems,"
(with G. Gallo),
in
Proceedings of the International Workshop on Mathematics
Mechanization,
2837, 1992.

"On Immobility,"
(with M. Teichmann),
Laboratory Robotics and Automation,
4:145153,
1992.
1991

"WuRitt Characteristic Sets and Their Complexity,"
(with G. Gallo),
Dimacs Series in Discrete Mathematics and Theoretical
Computer Science,
6:111136, 1991.

"Efficient Algorithms and Bounds for WuRitt Characteristic Sets,"
(with G. Gallo),
In Effective Methods in Algebraic Geometry,
Progress in Mathematics,
94:119142, Birkhauser Boston, Inc., 1991.

"Automatic Verification of Sequential Circuits Using Temporal Logic,"
(with M. Browne, E.M. Clarke and D. Dill),
IEEE tutorial on Formal Verification of Hardware
Designs:166175,
IEEE Computer Society Press, 1991.

"An NL Hierarchy,"
(with J. Chen and J. Cox),
Information Processing Letter,
39(1):2126, 1991.

"Some Constructions in Rings of Differential Polynomials,"
(with G. Gallo and F. Ollivier),
in
Proceedings of the Applied Algebra, Algebraic Algorithms,
Error Correcting Codes Symposium
,
AAECC 9, LNCS 539:171182, 1991.

"Online Scheduling in the Presence of Overload,"
(with S. Baruah, G. Koren, A. Raghunathan, L. Rosier and
D. Shasha),
in
Proceedings: 32nd Annual Symposium on Foundations of
Computer Science
FOCS 91:100110, 1991.

"WorkholdingAnalysis and Planning,"
in
Proceedings: IEEE/RSJ International Workshop on Intelligent
Robots and Systems
,
IROS 91, 1:5357,
1991.
Also see
"An Algorithmic Approach to Fixturing."

"Dexterous Manipulation: A Geometric Approach,"
Advances in Robot Kinematics,
XIV:1727, 1991.
1990

"Fully Parallel Algorithm for Implementing Path Expressions,"
(with A. Dinning),
Journal of Parallel and Distributed Computing,
10(3):205221, 1990.

"Fine Manipulation with Multifinger Hands,"
(with J.W. Hong, G. Lafferriere and X. Tan),
in
1990 IEEE International Conference on Robotics and Automation
ICRA 90:15681573, 1990.

"Arithmetic of Real Algebraic Numbers is in NC,"
(with P. Pedersen),
in
Proceedings of the International Symposium on Symbolic and
Algebraic Computation
,
ISSAC 90:120126, Tokyo, 1990.

"Quantitative Steinitz's Theorem with Applications to Multifingered
Grasping,"
(with D. Kirkpatrick and C.K. Yap),
in
Proceedings of the TwentySecond ACM Symposium on Theory of
Computing,
STOC 90:341351, 1990.
1989

"Notes on Gröbner Bases,"
(with C.K. Yap),
Information Sciences,
48:219252,
1989.
Also see
DubeMishraYap (1)
,
DubeMishraYap (2)

"Some Discussion of Static Gripping and Its Stability,"
(with N. Silver),
IEEE Transactions on Systems, Man and Cybernetics,
19(4):783796, 1989.
1987
1986

"Automatic Verification of Sequential Circuits Using Temporal Logic,"
(with M. Browne, E.M. Clarke and D. Dill),
IEEE Transactions on Computers,
c35(12):10351044, 1986.

"Compiling Path Expressions into VLSI Circuits,"
(with T.S. Anantharaman, E.M. Clarke and M.J. Foster),
Distributed Computing,
1(2):150166, 1986.
1985

Some Graph Theoretic Issues in VLSI Design,
Ph.D. Thesis, Computer Science Department,
CarnegieMellon University, September, 1985. 138 pp. +
Appendix.

"Hierarchical Verification of Asynchronous Circuits using Temporal
Logic,"
(with E.M. Clarke),
Theoretical Computer Science,
38:269291, 1985.

"Compiling Path Expressions into VLSI Circuits,"
(with T.S. Anantharaman, E.M. Clarke and M.J. Foster),
in
Proceedings of ACM Symposium on Principles of Programming
Languages,
POPL 85, 1985.
1984

"An Efficient Algorithm to find All 'Bidirectional' Edges of an
Undirected Graph,"
in
Proceedings of the 25th Annual Symposium on Foundations of
Computer Science,
FOCS 84:207216, 1984.
1983

"Automatic Verification of Asynchronous Circuits,"
(with E.M. Clarke),
in Logics of Programs,
(Editors: E.M. Clarke and D. Kozen),
Lecture Notes in Computer Science,
164: 101115, SpringerVerlag, Berlin, 1983.

"Extensions to Attribute Gramars,"
(with J.R. Nestor, W.L. Scherlis and W.A. Wulf),
TL 8386,
Tartan Laboratories, 1983.
1980

"Formation of Routh's Array in the Presence of a Row of Zeroes,"
Journal of the Institute of Electronics and
Telecommunication Engineers,
26(11), 1980.
1979

Design of Waveguide, Cavity and a Coupling Arrangement Using
Centered
Circular Aperture to Operate at a Fixed Frequency of 8GHz.
National Design and Research Forum,
Institute of Engineers, India,
1979. 55 pp.