Fall 2009
Selected Publications
NYU Technical Report
2016

"Rates and Mechanisms of Bacterial Mutagenesis from MaximumDepth Sequencing,"
(with J Jee, A Rasouly, I Shamovsky, Y Akivis, S Steinman, and E Nudler),
Nature, 2016.

"Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer
Progression,"
(with G Caravagna, A Graudenzi, D Ramazzotti, R SanzPamplona,
L De Sano, et al.),
Proc. National Academy of Science of USA, 2016.
[Also in Arxiv: arXiv:1509.07918, CoRR abs/1509.07918, 2015.]

"Histological Image Processing Features Induce a Quantitative
Characterization of Chronic Tumor Hypoxia,"
(with A. Sundstrom, E Grabocka and D BarSagi),
PLOS ONE, 11(4): e0153623. doi:10.1371/journal.pone.0153623, 2016.

"TRONCO: an R Package for the Inference of Cancer Progression Models
from Heterogeneous Genomic Data,"
(with L De Sano, G Caravagna, D Ramazzotti, A Graudenzi, G
Mauri, et al.),
Bioinformatics, doi:
10.1093/bioinformatics/btw035, 2016.
[ Also in Arxiv:arXiv:1509.07304, CoRR
abs/1509.07304, 2015.]

"Design of the TRONCO BioConductor Package for TRanslational ONCOlogy,"
(with M Antoniotti, G Caravagna, L De Sano, A Graudenzi, G
Mauri, et al.), bioRxiv: 027524, 2015.

"Cancer megafunds with in silico and in vitro validation: Accelerating
Cancer Drug Discovery via Financial Engineering without Financial Crisis"
(with X Yang, E Debonneuil and A Zhavoronkov),
Oncotarget, 2016;
doi: 10.18632/oncotarget.9808.

"HighSpeed AFM Reveals Contamination in DNA Purification
Systems,"
(with A Mikheikin, A Olsen, L Picco, O Payton, J Gimzewski and
J Reed),
Analytical Chemistry
2016; doi:ac201504023j.R2

"Threats from Inside: Dynamic Utility (Mis)Alignments in an Agent
based Model,"
(with W Casey and J Morales),
Journal of Wireless Mobile Networks, Ubiquitous Computing,
and Dependable Applications (JoWUA), 2016.

"Epistatic Signaling and Minority Games, the Adversarial Dynamics in
Social Technological Systems,"
(with W Casey, R Weaver, J Morales and E Wright),
Mobile Networks and Applications 21(1): 161174, 2016.

"Compliance Signaling Games: Toward Modeling the Deterrence of Insider
Threats,"
[Invited Paper],
(with W. Casey, J. Morales, E. Wright and Q. Zhu),
Computational and Mathematical Organization Theory (CMOT), 2016.

"Computational and Quantitative Real Algebraic Geometry."
(with S Basu),
CRC Handbook of Discrete and Computational Geometry:
(Third Edition), CRC Press, Boca Raton, FL,
April, 2016.
2016 (Unpublished/Submitted)

"Efficient Simulation of Financial Stress Testing Scenarios with
SuppesBayes Causal Networks,"
(with G. Gao and D. Ramazzotti), 2016.

"Identitity, Deception and Signaling: The Game Theory of Sybil Attacks,"
(with Will Casey et al.), 2016.

"Survival Analysis Using Probabilistic Graphical Models and
Probabilistic Causation,"
(with I. Korsunsky et al.), 2016.

"I2V: Steps to Creolize the Web,"
(with S. Chakraborty et al.), 2016.

"Games of Deception,"
(with Will Casey et al.), 2016.

"Social Influence Detection by Probabilistic Causation and Spatial
Proximity,"
(with D. Ramazzotti, F. Bonchi and F. Gullo), 2016.

"Structural and Topical Behavior Modeling  Addressing the Insider
Threat Problem with Utility Alignments,"
(with Jose Andre Morales and William Casey),2016.
2015

"CAPRI: Efficient Inference of Cancer Progression Models from
Crosssectional Data,"
(with D. Ramazzotti, G. Caravagna, L. Olde Loohuis,
A. Graudenzi, I. Korsunsky, G. Mauri and
M. Antoniotti), Bioinformatics, 2015.

"Gappy Total Recaller: Efficient Algorithms and Data Structures for Accurate Transcriptomics,"
[Invited Paper]
11th International Conference on Distributed Computing and
Internet Technology, ICDCIT 2015,
Bhubaneswar, Odisha, India, February, 2015.

"Exposing the Probabilistic Causal Structure of Discrimination,"
(with F. Bonchi, S. Hajian and D. Ramazzotti), Arxiv:
arXiv:1510.00552, CoRR abs/1510.00552 2015.

"Identity Deception and Game Deterrence via Signaling Games,"
(with Will Casey, Parisa Memarmoshrefi, Ansgar Kellner, Jose
Andre Morales),
9th International Conference on Bioinspired Information and
Communications Technologies, BICT 2015,
NYC, NY, (December 35, 2015), 2015.
[BICT 2015 Best Paper Award]

"Compliance Control: Managed Vulnerability Surface in
SocialTechnological Systems via Signaling Games,"
(with Will Casey, Jose Andre Morales and Quanyan Zhu),
ACM MIST 2015,
7th ACM CCS International Workshop on Managing Insider
Security Threats (In Conjunction with ACM CCS 2015),
Denver, Colorado, USA, October 1216, 2015.
[MIST 2015 Best Paper Award]

"Sandboxing and Reasoning on Malware Infection Trees,"
(with Krishnendu Ghosh, Jose Andre Morales and William Casey),
MALCON 2015,
Malware Conference,
Fajardo, Puerto Rico, USA, October 2023, 2015.
2014

"Cyber Security via Minority Games with Epistatic Signaling,"
(with W. Casey, R. Weaver, L. Metcalf, J.A. Morales and E. Wright),
8th International Conference on Bioinspired Information and
Communications Technologies, BICT 2014,
Boston, MA, (December 13, 2014), 2014.

"Agent Based Trace Learning in a RecommendationVerification System
for Cyber Security,"
(with W. Casey, J.A. Morales, E. Wright, M. Appel,
J. Gennari, L. Metcalf, J. Spring and R. Weaver),
9th IEEE International Conference on Malicious and Unwanted Software,
MALCON 2014, Fajardo, Puerto Rico, October 2830, 2014.

"Cyber Security via Signaling Games: Toward a Science of Cyber Security,"
[Invited Paper]
(with W. Casey, et al.),
10th International Conference on Distributed Computing and
Internet Technology,
ICDCIT 2014
Bhubaneswar, Odisha, India, February, 2014.

"Decidability of Robot Manipulation Planning: Three Disks in a Plane,"
(with M. Venditelli and J.P. Laumond),
The Eleventh International Workshop on the Algorithmic Foundations of
Robotics, WAFR 2014, 35 August 2014, Bogazici University, Istanbul, Turkey, 2014.

"Improving Detection of Driver Genes: Powerlaw Null Model of Copy
Number Variation in Cancer"
(with L. Olde Loohuis and A. Witzel),
IEEE Transactions on Computational Biology and
Bioinformatics, August 2014.
DOI 10.1109/TCBB.2014.2351805

"Inferring Tree Causal Models of Cancer Progression with Probability Raising,"
(with L.O. Loohuis, G. Caravagna, A. Graudenzi, D. Ramazzotti,
G.C. Mauri and M. Antoniotti), PLoS One, August, 2014

"Systems Biology of Cancer: A Challenging Expedition for Clinical and
Quantitative Biologists,"
[Invited Paper],
(with I. Korsunsky et al.),
Special Issue on Model Checking and Symbolic Methods in
Biology,
Frontiers in Bioinformatics and Computational Biology,
NPG, July 2014.

"Cancer Hybrid Automata: Model, Beliefs & Therapy,"
(with L. Olde Loohuis and A. Witzel),
Special Issue on "Hybrid Systems and Biology,"
Information and Computation,
January 27 2014.
(Epub http://dx.doi.org/10.1016/j.ic.2014.01.013)

"AFM Detection Enables Multiplexed LowCycleNumber PCR for Biomarker
Assays,"
(with A. Mikheikin, A. Olsen, K. Leslie, J.K. Gimzewski and J. Reed),
Analytical Chemistry, June 2014.
DOI: 10.1021/ac500896k

"Atomic Force Microscopy for Measuring Gene Expression from Single Cells,"
(with A. Mikheykin, et al.),
ASME 2014 3rd Global Congress on Nanoengineering for Medicine
and Biology,
San Francisco, CA, USA, February, 2014.

"On Algorithmic Complexity of Biomolecular Sequence Assembly Problem,"
(with G. Narzisi and M. Schatz), 1st International Conference
on Algorithms for Computational Biology (AlCoB 2014),
Tarragona, Spain, July 13, 2014.

"Algorithms in Stringomics (I): PatternMatching against "Stringomes","
(with P. Ferragina),
BIORXIV/2014/001669,
January 2014.
2013

"What Can InformationAsymmetric Games Tell Us About the Context of
Crick's 'Frozen Accident'?"
(with J. Jee et al.),
Journal of the Royal Society Interface,
August, 2013.

"Inferring Causal Models of Cancer Progression with a Shrinkage
Estimator and Probability Raising,"
(with L.O. Loohuis, G. Caravagna, A. Graudenzi, D. Ramazzotti,
G.C. Mauri and M. Antoniotti),
BIORXIV/2013/000919 & arXiv/2013/0854800,
November 2013.

"Malaria: The Painful Faces Ask, Can We Not Cure?"
[Invited Vision Paper],
The Rising Indian,
2013.

"Gappy TotalReCaller for RNASeq BaseCalling and Mapping,"
BIORXIV/2013/000489, November 2013.

"Genomics via Optical Mapping I: 01 Laws for Single Molecules,"
(with T.S. Anantharaman),
BIORXIV/2013/000844, November 2013.
2012

"The Genome Question: Moore vs. Jevons,"
[Invited Vision Paper],
J. of Computing (of the Computer Society of India),
March, 2012.
(watch GoogleTechTalk Video)

''Reevaluating Assembly Evaluations with Feature Response Curves: GAGE
and Assemblathons,''
(with F. Vezzi and G. Narzisi),
PLoS ONE, 7:(12): e52210.
December, 2012.
(Epub doi:10.1371/journal.pone.0052210.)
(Supplementary Materials.
)

"FeaturebyFeature  Evaluating De novo Sequence Assembly,"
(with F. Vezzi and G. Narzisi),
PLoS ONE, 7(2): e31002.
January, 2012.
(Epub doi:10.1371/journal.pone.0031002)

"Modeling Hospitalization Outcomes with Random Decision Trees and
Bayesian Feature Selection,''
(with T. Nguyen), Kaggle Academic Paper, 2012.

"Towards Cancer Hybrid Automata,"
(with L. Olde Loohuis and A. Witzel),
First International Workshop on Hybrid Systems and Biology:
HSB 2012, Newcasle upon Tyne, UK, September 3, 2012.

"Focus on Personalized Molecular based Medicine,"
(with LHT. Van der Ploeg, C. Eitner, J. Burrows, T. Tombler,
V. Poponin, D. Knauer, I. Ichetovkin, R. Pinnola, G. Endress
and P. SoonShiong),
Biomarkers in Oncology: Predictions and Prognosis,
(edited by HeinzJosef Lenz, MD), SpringerVerlag, NY, January
2012.

"Image Analysis and Length Estimation of Biomolecules Using AFM,''
(with A. Sundstrom, S. Cirrone, S. Paxia, C. Hsueh, R. Kjolby,
J.K. Gimzewski and J. Reed),
IEEE Transactions on Information Technology in
Biomedicine, 16(), July, 2012.
(Epub doi:10.1109/TITB.2012.2206819.)

"Identifying Individual DNA Species in a Complex Mixture by
Precisely Measuring the Spacing between Sparse IntraMolecular
Landmarks,"
(with J. Reed, C. Hsueh, M. Ling, and J.K. Gimzewski),
J. R. Soc. Interface,
(Published online before print) March 28, 2012.
(Epub doi:10.1098/brsif.2012.0024.)

"Discovering the Ebb and Flow of Ideas from Text Corpora,''
(with J. Jee, L.C. Klippel, M.S. Hossain and N. Ramakrishnan),
Discovery Analytics, IEEE Computer,
45(1): 7377, Jan 2012.

"Mathematics' Mortua Manus: Discovering Dexterity,"
[Invited Paper], From Linear Operators to Computational Biology,
(Jack Schwartz Memorial Volume: Ed. M. Davis and E. Schoenberg),
SpringerVerlag, NY, August 2012.
2011

"TotalReCaller: Improved Accuracy and Performance via Integrated
Alignment & BaseCalling,''
(with F. Menges and G. Narzisi),
Bioinformatics, 27(17):23307. (Epub 2011 Jun
30), September 1 2011.

"Comparing De Novo Genome Assembly: The Long and Short of It,"
(with G. Narzisi),
PLoS One, 6(4): e19175, April 2011.

"ScoringandUnfolding Trimmed Tree Assembler: Concepts, Constructs
and Comparisons,"
(with G. Narzisi),
Bioinformatics, 27(2):15360, Jan 2011.
(Epub doi: 10.1093/bioinformatics/btq646.)

"Prediction of Protein Functions with Gene Ontology and InterSpecies Protein Homology
Data,"
(with A. Mitrofanova and V. Pavlovic),
IEEE/ACM Transaction on Computational Biology and
Bioinformatics, 8(3): 775784
May/June, 2011.

"Sarve Santu Niramaya: Computational Biology's Promises for India,"
[Invited Vision Paper], Homi Bhabha and the Computer
Revolution, (Ed. R.K. Shyamasundar and M.A. Pai), pp. 295315, Oxford University
Press, Oxford, 2011.

"Jacob T. Schwartz,"
Memorial Tributes, pp: 297301, National Academy of
Engieering, 2011.
2010

"On a Novel Coalescent Model for GenomeWide Evolution of Copy Number
Variations,"
[Invited Paper],
(with A. Mitrofanova),
International Journal of Data Mining and
Bioinformatics (IJDMB), 4(3): 300315, 2010.
(Also appeared in
The TwentyThird Annual ACM Symposium on Applied Computing,
SAC 2008, Ceara, Brazil, 1620 March 2008.)

"Competitive Hybridization Models,"
(with V.Cherepinsky, and G. Hashmi),
Phys. Rev. E (Stat Nonlin Soft Matter
Phys.), 82(5 Pt 1):051914 (17 pages), 2010.
(Also, highlighted in Virtual Journal of
Biol. Phys. Res., Am. Phys. Soc. & Am. Inst. Phys., November 2010.)

"Reverse Engineering Dynamic Temporal Models of Biological Processes
and their Relationships,"
(with N. Ramakrishnan et al.),
Proc. National Academy of Science U S A,
107(28):125116, 2010.

"Investigating Causal Relationships in Stock Returns with Temporal
Logic Based Methods,"
(with S. Kleinberg and P. Kolm), arXiv:1006.1791 (June 2010),
(Also submitted for jouranl publication), June, 2010.

"The Temporal Logic of Token Causes,"
(with S. Kleinberg), Principles of Knowledge Representation
and Reasoning (Toronto, Canada, May 913, 2010), KR10():, AAAI,
2010.
("The Temporal Logic of Token Causes," TR.)
2009

"Metamorphosis: The Coming Transformation of Translational Systems Biology"
(with S. Kleinberg), Queue, 7(9):4052, ACM,
2009.

"The Temporal Logic of Causal Structures,"
(with S. Kleinberg),
Uncertainty in Artificial Intelligence, UAI
2009: 303312, AUAI Press, Corvallis, Oregon, 2009.

"Intelligently Deciphering Unintelligible Designs:
Algorithmic Algebraic Model Checking in Systems Biology"
,
[Invited Paper],
Interface: Journal of the Royal
Society, 6(36):57597, Apr 2009.

"Where Biology Meets Computing,"
[Invited Technical Perspective],
Communications of the ACM, 52(3), March 2009.
(Epub: doi:10.1145/1467247.1467270)

"Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics,"
[Invited Paper]
(with S. Tadepalli, N. Ramakrishnan, L.T. Watson, and
R.F. Helm),
Journal of Bioinformatics and Computational Biology
(JBCB), 7(2):339356, 2009.
(Also appeared in The Sixth Asia Pacific Bioinformatics Conference,
APBC2008, Kyoto, Japan, 1417 January 2008.)

"Predicting Malaria Interactome Classifications from TimeCourse
Transcriptomic Data along the IntraErythrocytic Developmental
Cycle,"
(with A. Mitrofanova, S. Kleinberg, J. Carlton and S. Kasif),
Artificial Intelligence in Medicine, AIIM, 2009.

"The Apoptotic Machinery As A Biological Complex System: Analysis Of
Its Omics And Evolution, Identification Of Candidate Genes For
Fourteen Major Types Of Cancer And Experimental Validation in
CML And Neuroblastoma"
,
(with C. Di Pietro et al.),
BMC Medical Genomics, 2: 20, Apr 2009.

"Mathematical Modeling of the formation of Apoptosome in Intrinsic
Pathway of Apoptosis,"
(with S. Ryu et al.),
Systems and Synthetic Biology Journal, 2(12):
4966, Mar 31 2009.

"A Novel Approach to MultiHazard Modeling and Simulation,"
(with S.W. Smith et al.),
Disaster Medicine and Public Health Preparedness,
The American Medical Association (AMA), 2009.

"Efficient and Robust Prediction Algorithms for Complexes using GomoryHu Tree,"
(with A. Mitrofanova and M. FarachColton),
The Pacific Symposium on Biocomputing:,
(Eds. R.B. Altman, A.K. Dunker, L. Hunter & T.E.Klein),
PSB 2009: 215226, World Scientific, January, 2009.
2008

"Atomic Force Microscope Observation of Branching in Single Transcript
Molecules Derived from Human Cardiac Muscle,"
(with J. Reed, C. Hsueh and J. Gimzewski),
Nanotechnology, 19 384021 (8pp),
2008.

"On Evolution of the IntergenicSpacers in rDNA Analyzed by
DropoutAlignment of DNA sequences,"
(with S. Ryu et al.),
Journal of Molecular Evolution, 66(4): 368383, April, 2008.

"Transposable Elementdriven Duplications during Hominoid Genome
Evolution"
[Invited Paper],
Encyclopedia of Life Sciences (ELS), John Wiley, 2008.

"Copy Number Variant Analysis of Human Embryonic Stem Cells,"
(with H. Wu et al.),
Stem Cells, 26(6):14849, June 2008.

"Inclusion Dynamics Hybrid Automata,"
(with A. Casagrande, C. Piazza, and A. Policriti),
Information and Computation, 2008.

"Decidable Compositions of Ominimal Automata,"
(with A. Casagrande, P. Corvaja, and C. Piazza),
ATVA 2008, Seoul, South Korea on Oct 2023, 2008.

"Systems Biology via Redescription and Ontologies (III): Protein
Classification using Malaria Parasite's Temporal
Transcriptomic Profiles,"
,
(with A. Mitrofanova et al.),
2008 IEEE International Conference on Bioinformatics and
Biomedicine, BIBM'08, 2008.

"Systems Biology via Redescription and Ontologies(II): A Tool for
Discovery in Complex Systems,"
(with S. Kleinberg et al.),
Proceedings of the International Conference on Complex
Systems, 2008.

"Systems Biology via Redescription and Ontologies (I): Finding Phase
Changes with Applications to Malaria Temporal Data,"
(with S. Kleinberg and K. Casey),
Systems and Synthetic Biology Journal (SSB),
1(4): 197205, 2008.

"Multiple Testing of Causal Hypotheses,"
(Full Paper),
(with S. Kleinberg),
International Conference: Causality and Probability in the
Sciences, CAPITS 2008,
Keynes College, University of Kent, Canterbury, UK, September 2008.

"Deriving Kripke Structures from Time Series Segmentation Results"
,
(With S. Tadepalli et al.),
Workshop on Discrete Event Systems,
WODES'08 meeting, Sweden,
2008.

"A New Approach to the Estimation of InterVariable Correlation,"
(with M. Sobel),
Communications in Statistics,
37(15):23152330, 2008

"Integrative Protein Function Transfer using Factor Graphs and
Heterogeneous Data Sources,"
(with A. Mitrofanova and V. Pavlovic),
2008 IEEE International Conference on Bioinformatics and
Biomedicine, BIBM'08, 2008.

"Modeling and Simulation of EMail Social Networks: A New Stochastic
AgentBased Approach,"
(with F. Menges and G. Narzisi), Winter Simulation Conference
'08, WSC 08, Miami, Florida, December 710, 2008.

"Complexities, Catastrophes and Cities: Emergency Dynamics in Varying
Scenarios and Urban Topologies,"
(with G. Narzisi et al.),
Proceedings of the International Conference on Complex
Systems, 2008.
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.

"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, 3(2): 112,
2007.

"Algebraic Systems Biology: Theses and Hypotheses,"
[Invited Paper],
Algebraic Biology, AB '2007, Linz, Austria, July 2007.

"Algorithmic Algebraic Model Checking IV:
Characterization of Metabolic Networks,"
(with V. Mysore),
Algebraic Biology, AB '2007, Linz, Austria, July
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.

"Composing Semialgebraic OMinimal Automata,"
(with A. Casagrande, P. Corvaja, and C. Piazza),
Hybrid Systems: Computation and Control, HSCC
2007, [A. Bemporad, A. Bicchi, and G. Buttazzo (Eds.)],
LNCS 4416, pp. 668671, 2007.

"Systems Biology via Redescription and Ontologies: Untangling the
Malaria Parasite Life Cycle,"
(with S. Kleinberg and K. Casey),
Life System Modeling and Simulation, LSLMS 07,
Sanghai, China, September 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),
Algebraic Biology, AB '2007, Linz, Austria, July
2007.

"Discovering Relations among GOannotated Clusters by Graph Kernel
Methods,"
(with I. Zoppis, D. Merico, M. Antoniotti, G. Mauri),
2007 International Symposium on Bioinformatics Research and
Applications, ISBRA '07, Atlanta, GA, 2007.

"Resilience in the Face of Disaster: Accounting for Varying Disaster
Magnitudes, Resource Topologies, and (Sub)Population
Distributions in PLAN C Emergency Planning Tool,"
(with G. Narzisi, J.S. Mincer and S. Smith),
3rd International Conference on Industrial Applications of
Holonic and MultiAgent Systems, HOLOMAS 2007,
Regensburg, Germany, September 3  5, 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, 23(3):31420, 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.

"Quantifying the mechanisms for segmental duplications in mammalian
Genomes by Statistical Analysis and Modeling,"
(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.

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

"Genomics via Optical Mapping IV: Sequence Validation via Optical Map Matching,"
(with M. Antoniotti et al.),
CIMS TR811, Courant Institute of Mathematical Sciences, NYU, March 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.

"NC Algorithms for Real Algebraic Numbers,"
(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.

"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
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
1979