Bud Mishra: Selected Publications

Fall 2009

Selected Publications

NYU Technical Report

2021

"PHENSIM: Phenotype Simulator," (with S Alaimo, RV Rapicavoli, GP Marceca, A La Ferlita, OB Serebrennikova, PN Tsichlis, A Pulvirenti, A Ferro), Accepted, PLOS Computational Biology, (2021). Also in bioRxiv 2020.01.20.912279; doi:https://doi.org/10.1101/2020.01.20.912279, (2020).
"Rapid Identification of Druggable Targets and the Power of the PHENotype SIMulator for Effective Drug Repurposing in COVID." (with Maria N, et alia) Res Sq. 2021. April 14.
"How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology." (with Casey W and Massey S) Interface: JRS (2021).
Also appears as Res Sq. 2020. Aug 6:rs.3.rs-51959.
"Coins, Covid, Keynes and K-Shaped Recovery." (with Martinez P and Huang WW) Online/Virtual (2021)
"To Mock a Mockingbird: Studies in Biomimicry." (with Enaganti, I) arXiv (2021).
arXiv:2104.13228 [q-bio.PE]
"Lotka-Volterra Equations in the Presence of Mimicry." (with Enaganti, Inavamsi) bioRxiv (2021).
http://biorxiv.org/content/early/2021/03/25/2021.03.25.436931
"Efficient Agony Based Transfer Learning Algorithms for Survival Forecasting." (with Tamaskar A and Bannon J) BioRxiv (2021).
BIORXIV/2021/432695
"Creolizing the Web." (with Tamaskar A, Rinberg R and Chakraborty S) arXiv (2021) 2102.12382.

2021 (Unpublished/Submitted/Under-review)

"Cryptomarket MicroStructure for a Biomedical MegaFund," (with Qianru Qi), In Review, 2021.
"NanZam I: Rapid Karyotyping via Nanomapping," (with J. Bannon and J. Reed), Submitted (under review). 2021.
"Optimizing Behavior in Acquisition," (with W. Casey, A. Moore and W. Novak), To Be Submitted. 2021.

2020

"Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs," (with K Hadi, X Yao, JM Behr, et al., M Imielinski) Cell. 2020 Oct 1; 183(1):197-210. (2020). doi: 10.1016/j.cell.2020.08.006. PMID: 33007263.
"Decidability in Robot Manipulation Planning," (with M Vendittelli, A Cristofaro, J-P Laumond), to appear in Autonomous Robots, DOI: 10.1007/s10514-020-09957-2. (2020)
Also appeared as M Vendittelli, J-P Laumond, B Mishra, "Decidability in Robot Manipulation Planning," 2018. https://arxiv.org/abs/1811.0358
"Anergy to Synergy− The Energy Fueling the RXCOVEA Framework," (with E Bischof, JAC Broek, CR Cantor, et al.) International Journal for Multiscale Computational Engineering, pages 329-333, (2020)
"Tech and the City: Axialization, Institutionalization and Disruption," Jnl EAI, 2020.
"tamaso ma jyotirgamaya: Seeking the Self Amidst Covids’ Cytokine Cyclones," (with R.x. Covea), Jnl IISc, 2020.
"Prospero's Books: A Distributed Architecture for AI." ICDCIT 2020: 41-49 Also see: ``System, Method and Computer-Accessible Medium for Artificial Intelligent Market Microstructure.'' Provisional Patent.
Correction to: "Exposing the Probabilistic Causal Structure of Discrimination." (with Francesco Bonchi, Sara Hajian, Daniele Ramazzotti), Int. J. Data Sci. Anal. 9(3): 373 (2020)

2019

"Identitity, Deception and Signaling: The Game Theory of Sybil Attacks," (with Will Casey et al.), Comm. ACM, January 2019.
"Origin of Biomolecular Networks," (with H. Janwa, SE. Massey and J. Velev), Frontiers, 2019. Supp.Mat. [Invited Paper]
Editorial: Network Bioscience. (with Antoniotti M, and Pellegrini M.), Front Genet. 2019 Nov 20;10:1160. doi: 10.3389/fgene.2019.01160. eCollection 2019.

2018

"Origin of Biomolecular Games: Deception & Molecular Evolution," (with S. Massey), Interface: Jnl. Roy. Soc., 5 September 2018. DOI: 10.1098/rsif.2018.0429, 2018.
"Nanotechnologies for Rapid, Sensitive Detection of Structural Variants in Lymphomas and Leukemias," (with Andrey Mikheikin, et al.), International Society for Laboratory Hematology, ISLH 18, Brussels, Belgium, May 9-12, 2018. [Plenary Abstract]
"BURPA or Bust! How to build a Bio-Unified Research Project Agency?" (Extended Abstract) (with Q. Qi et al.), 2nd Workshop on Trusted Smart Contracts, Financial Cryptography 2018, February 26–March 2, 2018, Curaçao, Springer-Verlag 2018. [Invited Plenary Paper]
"Causal Data Science for Financial Stress Testing," (with G. Gao and D. Ramazzotti), Jnl. of Computational Science, 6: 294-304, 2018.
"Social Influence Detection by Probabilistic Causation and Spatial Proximity," (with D. Ramazzotti, F. Bonchi and F. Gullo), CIKM 2018: International Conference on Information and Knowledge Management, 22-26 October 2018, Lingotto, Turin, Italy, 2018. (Also in ArXiv.)
"Inherent Moral Hazards in Acquisition: Improving Contractor Cooperation in Government As The Integrator (GATI) Programs," (with W. Novak et al.), Naval Postgraduate School’s 15th Annual Acquisition Research Dymposium. New Dimensions in Managing Systems of Systems, ARD 18, May 9-10, 2018 in Monterey, California. 2018. [Invited Panel Presentation]

2017

"DNA ‘Nanomapping’ Using CRISPR-Cas9 as a Programmable Nanoparticle," (with A Mikheikin, A Olsen, K Leslie, F Russell-Pavier, L Picco, O Payton, JK Gimzewski, and J Reed), Nature Communications, November 2017.
"Simulating Heterogeneous Tumor Cell Populations," (with A. Sundstrom, and D Bar-Sagi), PLOS ONE, PONE-D-15-48781R3, 2017.
"Design of the TRONCO BioConductor Package for TRanslational ONCOlogy," (with M. Antoniotti, G. Caravagna, L. De Sano, A. Graudenzi, G. Mauri and D. Ramazzotti), R Journal, 2017.
"Malware FingerPrinting under Uncertainty," (with K. Ghosh et al.), The 4th IEEE International Conference on Cyber Security and Cloud Computing , IEEE CSCloud 2017, New York, USA, June 26-28, 2017. [CSCloud 2017 Best Paper Award]
"Efficient Simulation of Financial Stress Testing Scenarios with Suppes-Bayes Causal Networks," (with G. Gao and D. Ramazzotti), International Conference on Computational Science, ICCS 2017, Zürich, Switzerland, 12-14 June, 2017. [ICCS 2017 Best Paper Award]
"Exposing the Probabilistic Causal Structure of Discrimination," (with F. Bonchi, S. Hajian and D. Ramazzotti), International Journal of Data Science and Analytics, JDSA-D-16-00043R2, 2017.DOI:10.1007/s41060-016-0040-z
"Computational and Quantitative Real Algebraic Geometry." (with S Basu), CRC Handbook of Discrete and Computational Geometry: (Third Edition), CRC Press, Boca Raton, FL, 2017.

2016

"Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth 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 Sanz-Pamplona, 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 Bar-Sagi), 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.]
"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.
"High-Speed 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:ac-2015-04023j.R2
“Visualizing a Malware Distribution Network,” (with S Peryt, JA Morales, W Casey, A Volkmann, and Y Cai), VizSEC 2016: 1-4, 2016.
"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): 161-174, 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.

2015

"CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional 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 Bio-inspired Information and Communications Technologies, BICT 2015, NYC, NY, (December 3-5, 2015), 2015. [BICT 2015 Best Paper Award]
"Compliance Control: Managed Vulnerability Surface in Social-Technological 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 12-16, 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 20-23, 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 Bio-inspired Information and Communications Technologies, BICT 2014, Boston, MA, (December 1-3, 2014), 2014.
"Agent Based Trace Learning in a Recommendation-Verification 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 28-30, 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, 3-5 August 2014, Bogazici University, Istanbul, Turkey, 2014.
"Improving Detection of Driver Genes: Power-law 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 Low-Cycle-Number 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 1-3, 2014.
"Algorithms in Stringomics (I): Pattern-Matching against "Stringomes"," (with P. Ferragina), BIORXIV/2014/001669, January 2014.

2013

"What Can Information-Asymmetric 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 Base-Calling and Mapping," BIORXIV/2013/000489, November 2013.
"Genomics via Optical Mapping I: 0-1 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. )
"Feature-by-Feature - 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. Soon-Shiong), Biomarkers in Oncology: Predictions and Prognosis, (edited by Heinz-Josef Lenz, MD), Springer-Verlag, 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 Intra-Molecular 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): 73-77, 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), Springer-Verlag, NY, August 2012.

2011

"TotalReCaller: Improved Accuracy and Performance via Integrated Alignment & Base-Calling,'' (with F. Menges and G. Narzisi), Bioinformatics, 27(17):2330-7. (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.
"Scoring-and-Unfolding Trimmed Tree Assembler: Concepts, Constructs and Comparisons," (with G. Narzisi), Bioinformatics, 27(2):153-60, Jan 2011.
(Epub doi: 10.1093/bioinformatics/btq646.)
"Prediction of Protein Functions with Gene Ontology and Inter-Species Protein Homology Data," (with A. Mitrofanova and V. Pavlovic), IEEE/ACM Transaction on Computational Biology and Bioinformatics, 8(3): 775-784 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. 295-315, Oxford University Press, Oxford, 2011.
"Jacob T. Schwartz," Memorial Tributes, pp: 297-301, National Academy of Engieering, 2011.

2010

"On a Novel Coalescent Model for Genome-Wide Evolution of Copy Number Variations," [Invited Paper], (with A. Mitrofanova), International Journal of Data Mining and Bioinformatics (IJDMB), 4(3): 300-315, 2010.
(Also appeared in The Twenty-Third Annual ACM Symposium on Applied Computing, SAC 2008, Ceara, Brazil, 16-20 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):12511-6, 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 9-13, 2010), KR-10():, AAAI, 2010. ("The Temporal Logic of Token Causes," TR.)

2009

"Metamorphosis: The Coming Transformation of Translational Systems Biology" (with S. Kleinberg), Queue, 7(9):40-52, ACM, 2009.
"The Temporal Logic of Causal Structures," (with S. Kleinberg), Uncertainty in Artificial Intelligence, UAI 2009: 303-312, 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):575-97, 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):339-356, 2009.
(Also appeared in The Sixth Asia Pacific Bioinformatics Conference, APBC2008, Kyoto, Japan, 14-17 January 2008.)
"Predicting Malaria Interactome Classifications from Time-Course Transcriptomic Data along the Intra-Erythrocytic 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(1-2): 49-66, Mar 31 2009.
"A Novel Approach to Multi-Hazard 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 Gomory-Hu Tree," (with A. Mitrofanova and M. Farach-Colton), The Pacific Symposium on Biocomputing:, (Eds. R.B. Altman, A.K. Dunker, L. Hunter & T.E.Klein), PSB 2009: 215-226, 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 Intergenic-Spacers in rDNA Analyzed by Dropout-Alignment of DNA sequences," (with S. Ryu et al.), Journal of Molecular Evolution, 66(4): 368-383, April, 2008.
"Transposable Element-driven 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):1484-9, June 2008.
"Inclusion Dynamics Hybrid Automata," (with A. Casagrande, C. Piazza, and A. Policriti), Information and Computation, 2008.
"Decidable Compositions of O-minimal Automata," (with A. Casagrande, P. Corvaja, and C. Piazza), ATVA 2008, Seoul, South Korea on Oct 20-23, 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): 197-205, 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 Inter-Variable Correlation," (with M. Sobel), Communications in Statistics, 37(15):2315-2330, 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 E-Mail Social Networks: A New Stochastic Agent-Based Approach," (with F. Menges and G. Narzisi), Winter Simulation Conference '08, WSC 08, Miami, Florida, December 7-10, 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, 1-15, 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): 1-12, 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 Semi-algebraic O-Minimal 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. 668-671, 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 Time-course Gene Expression Profiles into Semi-Algebraic 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 GO-annotated 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 Multi-Agent Systems, HOLOMAS 2007, Regensburg, Germany, September 3 - 5, 2007.

2006

"Multiscale Strip Constructions and Their Application to Gene Expression and ChIP-on-chip Data," (with G. Lerman, J. McQuown, A. Blais, B.D. Dynlacht, and G. Chen), Bioinformatics, 23(3):314-20, December 2006.
"Mapping Tumor Suppressor Genes using Multipoint Statistics from Copy-Number Variation Data," (with I. Ionita and R. Daruwala), American Journal of Human Genetics, 79(1):13-22, July 2006.
"Validation of S. pombe sequence assembly by micro-array hybridization," (with J. West, J. Healy, M. Wigler, and W. Casey), Journal of Computational Biology, 13(1): 1-20, 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):142-151, 1 April 2006.
"Interpreter of Maladies: Redescription Mining Applied to Biomedical Data analysis," (with P. Waltman and A. Pearlman), Pharmacogenomics, 7(3):503-509, Apr 2006.
"CLARITY: Algorithms for Semantic Comparison of Time-course Transcriptomic Data," (with S. Kleinberg), International Symposium on Computational Biology & Bioinformatics: ISBB 06, Bhubaneswar, India, December 15-17, 2006.
"PLANAR: RNA Sequence Alignment using Non-Affine Gap Penalty and Secondary Structure," (with O. Gill and N. Ramakrishnan), International Symposium on Computational Biology & Bioinformatics: ISBB 06, Bhubaneswar, India, December 15-17, 2006.
"COMBAT: Search Rapidly For Highly Similar Protein-Coding Sequences Using Bipartite Graph Matching," (with B. Sun, J. Schwartz and O. Gill), International Conference on Computational Science, (2): 654-661, 2006.
"SEPA: Approximate Non-Subjective Empirical p-Value Estimation for Nucleotide Sequence Alignment," (with O. Gill), International Conference on Computational Science, (2): 638-645, 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 Infinite-State Systems, INFINITY 05, San Francisco, California, USA, August 27, 2005. Electr. Notes Theor. Comput. Sci., 149(1):61-77, 2006.
"Multi-Objective 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. 224-230, November 20-22, San Francisco, CA, 2006.
"Complexities, Catastrophes and Cities: Agent-Based Analysis of Large-Scale 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 Agent-based 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 Multi-resolution 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):6245-6250, 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):4051-4056, 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, 28-30, November 2005.
"Semi-Algebraic 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. 12-15, 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 Semi-Algebraic 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: 217-233, 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 2005:5-19, 2005.
"Reconstructing Formal Temporal Models of Cellular Events using the GO Process Ontology,"" (with M. Antoniotti and N. Ramakrishnan), Proceedings of the Eighth Annual Bio-Ontologies Meeting, (ISMB'05 Satellite Workshop), Detroit, MI, June 23-24 2005.
"GOALIE, A Common Lisp Application to Discover Kripke Models: Redescribing Biological Processes from Time-Course Data" (with M. Antoniotti and N. Ramakrishnan), International Lisp Conference, ILC 2005, Stanford University, June 19-22, 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 2005:385-96, 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.
"Multi-Agent Modeling and Analysis of the Brazilian Food-Poisoning 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, 13-15, 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): 45-67, 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): 16292-7, 2004.
"Distribution of Short Paired Duplications in Mammalian Genomes." (with E. Thomas et al.), Proc. National Academy of Science U S A, 101(28):10349-10354, 2004.
"Computational Real Algebraic Geometry." CRC Handbook of Discrete and Computational Geometry: (Second Edition), pp. 740-764, CRC Press, Boca Raton, FL, April, 2004. (In pdf, Index, Authors)
"Aligning Sequences with Non-Affine Gap Penalty: PLAINS Algorithm, a Practical Implementation, and its Biological Applications in Comparative Genomics," (with O.H. Gill, and Y. Zhou), ICBA2004 Conference, December 17-19, 2004.
"Models of Genome Evolution," (with Y. Zhou), Modeling in Molecular Biology, G. Ciobanu, G. Rozenberg (Eds.), Natural Computing Series, pages 287-304, 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.22-25, August, 2004.
"Systems Biology and Automata," (with A. Policriti), 3rd Workshop on Computation of Biochemical Pathways and Genetic Networks, Villa Bosch, Heidelberg, October 6-7, 2003, Springer Verlag, 2004.
"Time-Frequency Feature Detection for Time-Course Microarray Data," (with J. Feng and P.E. Barbano), 19th ACM Symposium on Applied Computing (SAC 2004), pages 128-132, Nicosia, Cyprus, March 14-17, 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, J-W. 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): 253-268, 2003.
"Shrinkage-Based Similarity Metric for Cluster Analysis of Microarray Data," (with V. Cherepinsky, J. Feng and M. Rejali), Proc. National Academy of Science, 100(17): 9668-9673, 2003.

NYU Technical Report (long; in .pdf)
"Optical Mapping," Encyclopedia of the Human Genome, 4: 448-453, 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): 271-286, Humana Press, June, 2003.
"A Nearly Linear-Time General Algorithm for Bi-Allele Haplotype Phasing," (with W. Casey), High Performance Computing--HiPC 2003, (Eds. T.M. Pinkston & V.K. Prasanna), Proceedings of the 10th International Conference in Hyderabad, India, Lecture Notes in Computer Scuence, LNCS 2913: 204-215, Springer-Verlag, NY, December 2003.
"Life's Duplicities: Sex, Death, and Valis." High Performance Computing--HiPC 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, Springer-Verlag, 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: 57-74, Springer-Verlag, 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 116-127, 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 Whole-Genome Shotgun Optical Map of Yersinia pestis Strain KIM," (with S. Zhou, et al.), Appl Environ Microbiol, 68(12):6321-6331, 2002.
"A Random Walk Down the Genomes: DNA Evolution in VALIS," (with S. Paxia, A. Rudra and Y. Zhou). Computer, 35(7):73-79, IEEE Press, July, 2002.
"Wild by Nature," (with M. Wigler), Science, 296: 1407-1408, 24 May 2002.
"Comparing Genomes," Special issue on "Biocomputation:" Computing in Science and Engineering. , pp 42-49, 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)
"xS-systems: eXtended S-systems and Algebraic Differential Automata for Modeling Cellular Behavior," (with M. Antoniotti, A. Policriti and N. Ugel), High Performance Computing--HiPC 2002, (Eds. S. Sahni, V.K. Prasanna & U. Shukla), LNCS 2552:431-442, Springer-Verlag, December 2002. (In pdf)
"A Symbolic Approach to Modelling Cellular Behaviour," High Performance Computing--HiPC 2002, (Eds. S. Sahni, V.K. Prasanna & U. Shukla), LNCS 2552:725-732, Springer-Verlag, December 2002. (In pdf)

2001

"Genomics via Optical Mapping IV: Sequence Validation via Optical Map Matching," (with M. Antoniotti et al.), CIMS TR-811, 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): 1584-1593, 2001.
"Placing Probes along the Genome using Pair-wise Distance Data," (with W. Casey and M. Wigler), Algorithms in Bioinformatics, First International Workshop, WABI 2001 Proceedings, LNCS 2149:52-68, Springer-Verlag, 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 2149:27-40, Springer-Verlag, 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): 1726-1736, 2000.
"Optical Mapping of BAC Clones from the Human Y Chromosome DAZ Locus," (with J. Giacalone et al.), Genome Research, 10(9): 1421-1429, 2000.
"Partitioning Single-Molecule Maps into Multiple Populations: Algorithms And Probabilistic Analysis," (with L. Parida), Discrete Applied Mathematics (The Computational Molecular Biology Series),104(l-3):203-227, 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.), 53:105-117, Mathematical Association of America, Cambridge University Press, 2000. (In pdf)
"On the Dynamic Finger Conjecture for Splay Trees. Part I: Splay Sorting log n-Block Sequences," (with R. Cole, J. Schmidt and A. Siegel), SIAM Journal of Computing, 30(1):1-43, 2000.
"Reactive Robotics I: Reactive Grasping with a Modified Gripper and Multi-fingered Hands," (with M. Teichmann), International Journal of Robotics Research, 19(7):697-708, 2000.
"Computational Differential Algebra," In Geometrical Foundations of Robotics, (Ed. Jon Selig), Lecture 8:111-145, World-Scientific, Singapore, 2000.
"Probabilistic Algorithms for Efficient Grasping and Fixturing," (with M. Teichmann), Algorithmica, 26:345-363, 2000.

1999

"A Shotgun Sequence-Ready Optical Map of the Whole Plasmodium falciparum Genome," (with Z. Lai et al.), Nature Genetics, 23(3):309-313, 1999.
"Optical PCR: Genomic Analysis by Long-Range PCR and Optical Mapping," (with J. Skiadas et al.), Mammalian Genome, 10:1005-1009, 1999.
"Whole Genome Shotgun Optical Mapping of Deinococcus radiodurans," (with J. Lin et al.), Science, 285(5433):1558-1562, 1999.
"Optical Mapping and Its Potential for Large-Scale Sequencing Projects," (with C. Aston and D.C. Schwartz), Trends in Biotechnology, 17:297-302, 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 , 7:18-27, AAAI Press, 1999.
"Optical Mapping of Plasmodium falciparum Chromosome 2," (with J. Jing et al.), Genome Research, 9:175-181, 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 K-Populations Problem," (with L. Parida), Proceedings of the Second Annual Conference on Computational Molecular Biology, RECOMB 98:192-201, 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 98:248-250, 1998.
"Automated High Resolution Optical Mapping Using Arrayed, Fluid Fixated, DNA Molecules," (with J. Jing, et al.), Proc. National Academy of Science, 95:8046-8051, 1998.
"High Resolution Restriction Maps of Bacterial Artificial Chromosomes Constructed by Optical Mapping," (with W. Cai, et al.), Proc. National Academy of Science, 95:3390-3395, 1998.

1997

"Computational Real Algebraic Geometry," In CRC Handbook of Discrete and Computational Geometry: 537-558, 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):91-118, 1997. (In pdf)
"The Power of Friction: Quantifying the "Goodness" of Frictional Grasps," (with M. Teichmann), In Algorithms for Robotic Motion and Manipulation: 311-320, 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, 15:256-286, 1996.
"NP-completeness 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, 6:435-440, 1996.
"CAFE: A Complex Adaptive Financial Environment," (with R. Even), IEEE/IAFE Conference on Computational Intelligence for Financial Engineering, CIFEr 96:20-25, 1996.

1995

"Mapping the Genome One Molecule at a Time -- Optical Mapping," (with A.H. Samad et al.), Nature, 378:516-517, 1995.
"Grasp Metrics: Optimality and Complexity," In Algorithmic Foundations of Robotics: 137-166, 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):343-370, 1994.
"The Complexity of Resolvent Resolved," (with G. Gallo), in Proceedings of the Fifth Annual ACM-SIAM Symposium on Discrete Algorithms , SODA 94:280-289, 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, 151-156, 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, Springer-Verlag, 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. TR1993-643, 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):295-318, 1992.
"A Linear Time Algorithm for Finding an Ambitus," (with R.E. Tarjan), Algorithmica, 7(5/6):521-554, 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):79-98, 1992.
"Quantifying the Advantage of Knowing the Future When Scheduling Sporadic Tasks," (with S. Baruah et al.), Real Time Systems Journal, 4(2):125-144, 1992.
"Recent Progress in Characteristic Set Computation: Complexity & Open Problems," (with G. Gallo), in Proceedings of the International Workshop on Mathematics Mechanization, 28-37, 1992.
"On Immobility," (with M. Teichmann), Laboratory Robotics and Automation, 4:145-153, 1992.

1991

"Wu-Ritt Characteristic Sets and Their Complexity," (with G. Gallo), Dimacs Series in Discrete Mathematics and Theoretical Computer Science, 6:111-136, 1991.
"Efficient Algorithms and Bounds for Wu-Ritt Characteristic Sets," (with G. Gallo), In Effective Methods in Algebraic Geometry, Progress in Mathematics, 94:119-142, Birkhauser Boston, Inc., 1991.
"An NL Hierarchy," (with J. Chen and J. Cox), Information Processing Letter, 39(1):21-26, 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 539:171-182, 1991.
"On-line 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 91:100-110, 1991.
"Workholding--Analysis and Planning," in Proceedings: IEEE/RSJ International Workshop on Intelligent Robots and Systems , IROS 91, 1:53-57, 1991.
Also see "An Algorithmic Approach to Fixturing."
"Dexterous Manipulation: A Geometric Approach," Advances in Robot Kinematics, XIV:17-27, 1991.

1990

"Fully Parallel Algorithm for Implementing Path Expressions," (with A. Dinning), Journal of Parallel and Distributed Computing, 10(3):205-221, 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 90:1568-1573, 1990.
"Arithmetic of Real Algebraic Numbers is in NC," (with P. Pedersen), in Proceedings of the International Symposium on Symbolic and Algebraic Computation , ISSAC 90:120-126, Tokyo, 1990.
"Quantitative Steinitz's Theorem with Applications to Multifingered Grasping," (with D. Kirkpatrick and C.-K. Yap), in Proceedings of the Twenty-Second ACM Symposium on Theory of Computing, STOC 90:341--351, 1990.

1989

"Notes on Gröbner Bases," (with C.-K. Yap), Information Sciences, 48:219-252, 1989.
Also see Dube-Mishra-Yap (1) , Dube-Mishra-Yap (2)
"Some Discussion of Static Gripping and Its Stability," (with N. Silver), IEEE Transactions on Systems, Man and Cybernetics, 19(4):783-796, 1989.

1987

"On the Existence and Synthesis of Multifinger Positive Grips," (with J.T. Schwartz and M. Sharir), Algorithmica, 2(4):541-558, 1987.

1986

"Automatic Verification of Sequential Circuits Using Temporal Logic," (with M. Browne, E.M. Clarke and D. Dill), IEEE Transactions on Computers, c-35(12):1035-1044, 1986.
"Compiling Path Expressions into VLSI Circuits," (with T.S. Anantharaman, E.M. Clarke and M.J. Foster), Distributed Computing, 1(2):150-166, 1986.

1985

Some Graph Theoretic Issues in VLSI Design, Ph.D. Thesis, Computer Science Department, Carnegie-Mellon University, September, 1985. 138 pp. + Appendix.
"Hierarchical Verification of Asynchronous Circuits using Temporal Logic," (with E.M. Clarke), Theoretical Computer Science, 38:269-291, 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 84:207-216, 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: 101-115, Springer-Verlag, Berlin, 1983.
"Extensions to Attribute Gramars," (with J.R. Nestor, W.L. Scherlis and W.A. Wulf), TL 83-86, 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.