Bud Mishra

Justin Jee, Lee Case Klippel, M. Shahriar Hossain, Naren Ramakrishnan, Bud Mishra: Discovering the Ebb and Flow of Ideas from Text Corpora. IEEE Computer 45(2): 73-77 (2012)

Andrew Sundstrom, Silvio Cirrone, Salvatore Paxia, Carlin Hsueh, Rachel Kjolby, James K. Gimzewski, Jason Reed, Bud Mishra: Image Analysis and Length Estimation of Biomolecules Using AFM. IEEE Transactions on Information Technology in Biomedicine 16(6): 1200-1207 (2012)

Loes Olde Loohuis, Andreas Witzel, Bud Mishra: Towards Cancer Hybrid Automata. HSB 2012: 137-151

Samantha Kleinberg, Bud Mishra: The Temporal Logic of Causal Structures. CoRR abs/1205.2634 (2012)

Francesco Vezzi, Giuseppe Narzisi, Bud Mishra: Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons. CoRR abs/1210.1095 (2012)

Giuseppe Narzisi, Bud Mishra: Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons. Bioinformatics 27(2): 153-160 (2011)

Fabian Menges, Giuseppe Narzisi, Bud Mishra: TotalReCaller: improved accuracy and performance via integrated alignment and base-calling. Bioinformatics 27(17): 2330-2337 (2011)

Antonina Mitrofanova, Vladimir Pavlovic, Bud Mishra: Prediction of Protein Functions with Gene Ontology and Interspecies Protein Homology Data. IEEE/ACM Trans. Comput. Biology Bioinform. 8(3): 775-784 (2011)

Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra: Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. Artificial Intelligence in Medicine 49(3): 167-176 (2010)

Antonina Mitrofanova, Bud Mishra: On a novel coalescent model for genome-wide evolution of Copy Number Variations. IJDMB 4(3): 300-315 (2010)

Samantha Kleinberg, Bud Mishra: The Temporal Logic of Token Causes. KR 2010

Bud Mishra: Technical perspective - Where biology meets computing. Commun. ACM 52(3): 96 (2009)

Satish Tadepalli, Naren Ramakrishnan, Layne T. Watson, Bud Mishra, Richard F. Helm: Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics. J. Bioinformatics and Computational Biology 7(2): 339-356 (2009)

Samantha Kleinberg, Bud Mishra: Metamorphosis: the Coming Transformation of Translational Systems Biology. ACM Queue 7(9): 40 (2009)

Antonina Mitrofanova, Martin Farach-Colton, Bud Mishra: Efficient and Robust Prediction Algorithms for Protein Complexes Using Gomory-Hu Trees. Pacific Symposium on Biocomputing 2009: 215-226

Samantha Kleinberg, Bud Mishra: The Temporal Logic of Causal Structures. UAI 2009: 303-312

Alberto Casagrande, Carla Piazza, Alberto Policriti, Bud Mishra: Inclusion dynamics hybrid automata. Inf. Comput. 206(12): 1394-1424 (2008)

Srinivas Akella, Nancy M. Amato, Wesley H. Huang, Bud Mishra: Special Issue on the Seventh International Workshop on Algorithmic Foundations of Robotics. I. J. Robotic Res. 27(11-12): 1173-1174 (2008)

Alberto Casagrande, Pietro Corvaja, Carla Piazza, Bud Mishra: Decidable Compositions of O-Minimal Automata. ATVA 2008: 274-288

Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra: Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic Profiles. BIBM 2008: 278-283

Antonina Mitrofanova, Vladimir Pavlovic, Bud Mishra: Integrative Protein Function Transfer Using Factor Graphs and Heterogeneous Data Sources. BIBM 2008: 314-318

Antonina Mitrofanova, Bud Mishra: Population genetics of human copy number variations: models and simulation of their evolution along and across the genomes. SAC 2008: 1309-1310

Fabian Menges, Bud Mishra, Giuseppe Narzisi: Modeling and simulation of e-mail social networks: A new stochastic agent-based approach. Winter Simulation Conference 2008: 2792-2800

Samantha Kleinberg, Bud Mishra: Psst: a web-based system for tracking political statements. WWW 2008: 1143-1144

Magnus Egerstedt, Bud Mishra (Eds.): Hybrid Systems: Computation and Control, 11th International Workshop, HSCC 2008, St. Louis, MO, USA, April 22-24, 2008. Proceedings. Lecture Notes in Computer Science 4981, Springer 2008, isbn 978-3-540-78928-4

Srinivas Akella, Nancy M. Amato, Wesley H. Huang, Bud Mishra (Eds.): Algorithmic Foundation of Robotics VII, Selected Contributions of the Seventh International Workshop on the Algorithmic Foundations of Robotics, WAFR 2006, July 16-18, 2006, New York, NY, USA. Springer Tracts in Advanced Robotics 47, Springer 2008, isbn 978-3-540-68404-6

Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D. Dynlacht, Guangliang Chen, Bud Mishra: Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data. Bioinformatics 23(3): 314-320 (2007)

Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra: From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Computational Biology 3(2) (2007)

Bud Mishra: Algebraic Systems Biology: Theses and Hypotheses. AB 2007: 1-14

Alberto Casagrande, Kevin Casey, Rachele Falchi, Carla Piazza, Benedetto Ruperti, Giannina Vizzotto, Bud Mishra: Translating Time-Course Gene Expression Profiles into Semi-algebraic Hybrid Automata Via Dimensionality Reduction. AB 2007: 51-65

Venkatesh Mysore, Bud Mishra: Algorithmic Algebraic Model Checking IV: Characterization of Metabolic Networks. AB 2007: 170-184

Giuseppe Narzisi, Joshua S. Mincer, Silas Smith, Bud Mishra: Resilience in the Face of Disaster: Accounting for Varying Disaster Magnitudes, Resource Topologies, and (Sub)Population Distributions in the PLAN C Emergency Planning Tool. HoloMAS 2007: 433-446

Alberto Casagrande, Pietro Corvaja, Carla Piazza, Bud Mishra: Composing Semi-algebraic O-Minimal Automata. HSCC 2007: 668-671

Italo Zoppis, Daniele Merico, Marco Antoniotti, Bud Mishra, Giancarlo Mauri: Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods. ISBRA 2007: 158-169

Venkatesh Mysore, Bud Mishra: Algorithmic Algebraic Model Checking III: Approximate Methods. Electr. Notes Theor. Comput. Sci. 149(1): 61-77 (2006)

Joseph West, John Healy, Michael Wigler, William Casey, Bud Mishra: Validation of S. Pombe Sequence Assembly by Microarray Hybridization. Journal of Computational Biology 13(1): 1-20 (2006)

Giuseppe Narzisi, Venkatesh Mysore, Bud Mishra: Multi-objective evolutionary optimization of agent-based models: An application to emergency response planning. Computational Intelligence 2006: 228-232

Ofer H. Gill, Bud Mishra: SEPA: Approximate Non-subjective Empirical p-Value Estimation for Nucleotide Sequence Alignment. International Conference on Computational Science (2) 2006: 638-645

Bing Sun, Jacob T. Schwartz, Ofer H. Gill, Bud Mishra: COMBAT: Search Rapidly for Highly Similar Protein-Coding Sequences Using Bipartite Graph Matching. International Conference on Computational Science (2) 2006: 654-661

Corrado Priami, Anna Ingólfsdóttir, Bud Mishra, Hanne Riis Nielson (Eds.): Transactions on Computational Systems Biology VII. Lecture Notes in Computer Science 4230, Springer 2006, isbn 3-540-48837-5

Venkatesh Mysore, Carla Piazza, Bud Mishra: Algorithmic Algebraic Model Checking II: Decidability of Semi-algebraic Model Checking and Its Applications to Systems Biology. ATVA 2005: 217-233

Carla Piazza, Marco Antoniotti, Venkatesh Mysore, Alberto Policriti, Franz Winkler, Bud Mishra: Algorithmic Algebraic Model Checking I: Challenges from Systems Biology. CAV 2005: 5-19

Thomas S. Anantharaman, Venkatesh Mysore, Bud Mishra: Fast and Cheap Genome Wide Haplotype Construction via Optical Mapping. Pacific Symposium on Biocomputing 2005

Marco Antoniotti, Carla Piazza, Alberto Policriti, Marta Simeoni, Bud Mishra: Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice. Theor. Comput. Sci. 325(1): 45-67 (2004)

Frank Chongwoo Park, Byungsoo Park, Munsang Kim, Bhubaneswar Mishra: Noise sensitivity analysis of statistically consistent optimal structure from motion. IROS 2004: 3698-3703

Naren Ramakrishnan, Deept Kumar, Bud Mishra, Malcolm Potts, Richard F. Helm: Turning CARTwheels: an alternating algorithm for mining redescriptions. KDD 2004: 266-275

Jiawu Feng, Paolo Emilio Barbano, Bud Mishra: Time-frequency feature detection for time-course microarray data. SAC 2004: 128-132

Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti, Marta Simeoni: Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing. CMSB 2003: 57-74

Bud Mishra: Life's Duplicities: Sex, Death, and Valis. HiPC 2003: 1

Will Casey, Bud Mishra: A Nearly Linear-Time General Algorithm for Genome-Wide Bi-allele Haplotype Phasing. HiPC 2003: 204-215

Marco Antoniotti, F. Park, Alberto Policriti, Nadia Ugel, Bud Mishra: Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. Pacific Symposium on Biocomputing 2003: 116-127

Salvatore Paxia, Archisman Rudra, Yi Zhou, Bud Mishra: A Random Walk Down the Genomes: DNA Evolution in Valis. IEEE Computer 35(7): 73-79 (2002)

Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bud Mishra: XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior. HiPC 2002: 431-442

Bhubaneswar Mishra: A Symbolic Approachto Modeling Cellular Behavior. HiPC 2002: 725-732

Thomas S. Anantharaman, Bud Mishra: False Positives in Genomic Map Assembly and Sequence Validation. WABI 2001: 27-40

Will Casey, Bud Mishra, Michael Wigler: Placing Probes along the Genome Using Pairwise Distance Data. WABI 2001: 52-68

Marek Teichmann, Bud Mishra: Probabilistic Algorithms for Efficient Grasping and Fixturing. Algorithmica 26(3-4): 345-363 (2000)

Laxmi Parida, Bud Mishra: Partitioning single-molecule maps into multiple populations: algorithms and probabilistic analysis. Discrete Applied Mathematics 104(1-3): 203-227 (2000)

Marek Teichmann, Bud Mishra: Reactive Robotics I: Reactive Grasping with a Modified Gripper and Multifingered Hands. I. J. Robotic Res. 19(7): 697-708 (2000)

Richard Cole, Bud Mishra, Jeanette P. Schmidt, Alan Siegel: On the Dynamic Finger Conjecture for Splay Trees. Part I: Splay Sorting log n-Block Sequences. SIAM J. Comput. 30(1): 1-43 (2000)

Thomas S. Anantharaman, Bud Mishra, David C. Schwartz: Genomics via Optical Mapping III: Contiging Genomic DNA. ISMB 1999: 18-27

Laxmi Parida, Bud Mishra: Partitioning K clones: hardness results and practical algorithms for the K-populations problem. RECOMB 1998: 192-201

David C. Schwartz, Thomas S. Anantharaman, C. Aston, Bud Mishra, V. Clarke, D. Gebauer, S. Delobette, E. Dimalanta, J. Edington, J. Evenzehav, J. Giacalone, C. Hiort, E. Huff, J. Jing, Z. Lai, E. Lee, J. Lin, B. Porter, R. Qi, Y. Skiadis: New approaches to genomic analysis using single molecules. RECOMB 1998: 248-250

Thomas S. Anantharaman, Bud Mishra, David C. Schwartz: Genomics via Optical Mapping II: Ordered Restriction Maps. Journal of Computational Biology 4(2): 91-118 (1997)

Thomas S. Anantharaman, Bud Mishra: Statistical Algorithms and Software for Genomics. COMPSAC 1997: 434-437

Bhubaneswar Mishra: Bidirectional Edges Problem: Part I-A Simple Algorithm. Algorithmica 15(3): 256-286 (1996)

Marco Antoniotti, Bud Mishra: Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers. ICRA 1995: 1441-1446

Giovanni Gallo, Bhubaneswar Mishra: A Solution to Kronecker's Problem. Appl. Algebra Eng. Commun. Comput. 5: 343-370 (1994)

Marek Teichmann, Bud Mishra: Reactive Algorithms for Grasping Using a Modified Parallel Jaw Gripper. ICRA 1994: 1931-1936

Giovanni Gallo, Bhubaneswar Mishra: The Complexity of Resolvent Resolved. SODA 1994: 280-289

Bhubaneswar Mishra: Algorithmic algebra. Texts and monographs in computer science, Springer 1993, isbn 978-3-540-94090-6, pp. I-XII, 1-416

Felipe Cucker, Hervé Lanneau, Bud Mishra, Paul Pedersen, Marie-Françoise Roy: NC Algorithms for Real Algebraic Numbers. Appl. Algebra Eng. Commun. Comput. 3: 79-98 (1992)

Bhubaneswar Mishra, Robert Endre Tarjan: A Linear-Time Algorithm for Finding an Ambitus. Algorithmica 7(5&6): 521-554 (1992)

David G. Kirkpatrick, Bhubaneswar Mishra, Chee-Keng Yap: Quantitative Steinitz's Theorems Applications to Multifingered Grasping. Discrete & Computational Geometry 7: 295-318 (1992)

Sanjoy K. Baruah, Gilad Koren, D. Mao, Bhubaneswar Mishra, Arvind Raghunathan, Louis E. Rosier, Dennis Shasha, Fuxing Wang: On the Competitiveness of On-Line Real-Time Task Scheduling. Real-Time Systems 4(2): 125-144 (1992)

Jianer Chen, Jim Cox, Bud Mishra: An NL Hierarchy. Inf. Process. Lett. 39(1): 21-26 (1991)

Giovanni Gallo, Bhubaneswar Mishra, François Ollivier: Some Constructions in Rings of Differential Polynomials. AAECC 1991: 171-182

Sanjoy K. Baruah, Gilad Koren, Bhubaneswar Mishra, Arvind Raghunathan, Louis E. Rosier, Dennis Shasha: On-line Scheduling in the Presence of Overload. FOCS 1991: 100-110

Anne Dinning, Bhubaneswar Mishra: A Fully Parallel Algorithm for Implementing Path Expressions. J. Parallel Distrib. Comput. 10(3): 205-221 (1990)

Bhubaneswar Mishra, Paul Pedersen: Arithmetic with Real Algebraic Numbers is in NC. ISSAC 1990: 120-126

David G. Kirkpatrick, Bhubaneswar Mishra, Chee-Keng Yap: Quantitative Steinitz's Theorems with Applications to Multifingered Grasping. STOC 1990: 341-351

Bud Mishra, Chee-Keng Yap: Notes on Gröbner bases. Inf. Sci. 48(3): 219-252 (1989)

Bhubaneswar Mishra, Jacob T. Schwartz, Micha Sharir: On the Existence and Synthesis of Multifinger Positive Grips. Algorithmica 2: 541-558 (1987)

Thomas S. Anantharaman, Edmund M. Clarke, Michael J. Foster, Bud Mishra: Compiling Path Expressions Into VLSI Circuits. Distributed Computing 1(3): 150-166 (1986)

Michael C. Browne, Edmund M. Clarke, David L. Dill, Bud Mishra: Automatic Verification of Sequential Circuits Using Temporal Logic. IEEE Trans. Computers 35(12): 1035-1044 (1986)

Thomas S. Anantharaman, Edmund M. Clarke, Michael J. Foster, Bud Mishra: Compiling Path Expressions into VLSI Circuits. POPL 1985: 191-204

Bhubaneswar Mishra: An Efficient Algorithm to Find all `Bidirectional' Edges of an Undirected Graph. FOCS 1984: 207-216

Edmund M. Clarke, Bud Mishra: Automatic Verification of Asynchronous Circuits. Logic of Programs 1983: 101-115