Bud Mishra: Notes

Spring 2002

Abstracts, Notes & Comments

Selected Recent Abstracts

2009

"SUTTA: Scoring and Unfolding Trimmed-Tree Assembler," (with G. Narzisi), NHGRI Grantee Meeting, San Diego, 29-31 March 2009.
POSTER

2008

"Multiple Testing of Causal Hypotheses," (with S. Kleinberg), International Conference: Causality and Probabilty in the Sciences, CAPITS 2008, Keynes College, University of Kent, Canterbury, UK, 8-19 September 2008.
"PSST: A Web-Based System for Tracking Political Statements," (Extended Abstract), (with S. Kleinberg), The 17th International World Wide Web Conference, WWW 2008Beijing, China, 21-25 April 2008.
"Algebra, Automata, Algorithms, Biology & Beyond," International conference in memory of Giuseppa Carra` Ferro, Catania, Italy, 26-28 March 2008.
"Logic in the Time of Malaria: Segmenting Time Course Data to Understand the Plasmodium Falciparu Life Cycle," (with S. Kleinberg and K. Casey), The Sixth Asia Pacific Bioinformatics Conference, APBCPoster2008, Kyoto, Japan, 14-17 January 2008.

2007

"Genetic Fingerprints of Human Embryonic Stem Cells by Copy Number Variant Analysis," (with H.Wu, K.J. Kim, K. Mehta, S. Paxia, A. Sundstrom, T.S. Anantharaman, A.I. Kuraishy, T. Doan, J. Ghosh, A. Pyle, A. Clark, W. Lowry, G. Fan, T. Baxter, Y. Sun and M.A. Teitell), The Institute for Stem Cell and Regenerative Medicine (ISCRM) Meeting, University of Washington, Seattle, November 5 2007.
"Automated Abstraction-Refinement of Hybrid Automata for Monotonic CTL Model Checking," (with R. Gentilini and K. Schneider), Comutation and Logic in the Real World, CiE 2007, University of Siena, Italy, June 18-23, 2007.
"SMASH: Single Molecule Approach to Sequencing by Hybridization," (With T.S. Anantharaman, V. Demidov, A. Lim, S. Paxia and J. Reed), Advances in Genome Biology & Technology Conference, AGBT 2007, Marco Island, Florida, February 8-11, 2007.
"Whole Genome Scanning and Oncogenomics with BuddhaCGH Software Pipeline," (With S. Paxia, T.S. Anantharaman and I. Ionita-Laza), Oncogenomics 2007: Dissecting Cancer Through Genome Research, Pointe Hilton Tapatio Cliffs Resort, Phoenix, Arizona. January 31 - February 3, 2007.

2006

"Choosing the Optimal Platform and Analysis for Prostate Cancer Array CGH," (With A. Pearlman, T. Anantharaman, and H. Ostrer), American Society of Human Genetics 2006 Annual Meeting, New Orleans, LA, October 9 - 12, 2006.
"Quantitative analysis of germline mitosis in adult C. elegans," (With J. Maciejowski, N. Ugel, M. Isopi and E.J.A. Hubbard), Model Organisms to Human Biology 2006 Conference, San Diego, California, January 5 -7, 2006.
"Single Molecule Approaches to Genomic Analysis," (With T.S. Anantharaman, C. Cantor, V. Demidov, C.W. Dykes, J. Gimzewski, B.B. Magee, P.T. Magee, M. Place, T. Rast, J. Reed and M. Teitell), Advances in Genome Biology & Technology Conference, AGBT 2006, Marco Island, Florida, February 8-11, 2006.
"Tolque: A Tool for Algorithmic Algebraic Model Checking," (With V. Mysore, A. Casagrande and C. Piazza), The Ninth International Workshop on Hybrid Systems : Computation and Control (HSCC 2006), Santa Barbara, California, March 29-31, 2006.

2005
"A computational approach to characterize germline proliferation," (With J. Maciejowski, N. Ugel, M. Isopi and E.J.A. Hubbard), Fifteenth International C. elegans Meeting, University of California at Los Angeles, June 25 - 29, 2005

2004
"A Novel Alignment-Independent Phylogenomic Method," (With Y. Zhou) New England Molecular Evolutionary Biologists 15th Annual Meeting, Tufts University, Medford, Massachusetts, November 6, 2004.
"Computational Approaches to Understand Germline Stem Cell Behavior in C. elegans," (With J. Maciejowski, N. Ugel, M. Isopi, E.J.A. Hubbard) Germ Cells Meeting, Cold Spring Harbor Lab, October, 2004.
"Competitive Hybridization Model," (With V. Cherepinsky et al.) STATPHYS 22, Bangalore, July, 2004.
"Genome Evolution by Substitutions, Duplications and Deletions," (With Y. Zhou) STATPHYS 22, Bangalore, July, 2004.
"Design of an optimal microarray hybridization experiment for genotyping, or solving HLA typing as an optimization problem on a weighted graph," (with V. Cherepinsky), SIAM Life Sciences, July 2004.
"Probabilistic Error Bounds with Application to Genotyping Microarray Design," (with V. Cherepinsky), AWM Minisymposium on Mathematical Biology (MS9), July 2004.
"Modeling and Simulation of the Behavior of Proliferating C. elegans Germ Cells," (with J. Maciejowski et al.), The East Coast Worm Meeting, Yale Univ, June 2004.

2003
"Multi-resolution Analysis of Biological Networks with 'Memory': RAS pathway, Cell Cycle and Immune System," (with P. Barbano et al.), The Fourth International Georgia Tech Conference on Bioinformatics, Atlanta, GA, November 2003.
Modeling and Simulating Genome Evolution by Duplication , (with Y. Zhou et al.), 2003 CSH meeting on Genome Informatics, CSHL, LI, May 2003.
Time/Frequency Analysis Of Complex Biological Systems , (with P. Barbano et al.), 2003 CSH meeting on Genome Informatics, CSHL, LI, May 2003.
Competitive Hybridization Model , (with V. Cherepinsky et al.), 2003 CSH meeting on Genome Informatics, CSHL, LI, May 2003.

2002
Bayesian Inference for Cluster Analysis of Microarray Data , (with V. Cherepinsky et al.), 2nd Cold Spring Harbor Laboratory/Wellcome Trust Conference: Genome Informatics, Hinxton, UK, September 4-8, 2002.
Bayesian Inference for Cluster Analysis of Microarray Data , (with V. Cherepinsky et al.), AWM minisymposium at SIAM 2002 Annual Meeting, Philadelphia, July 5-10, 2002.
"Detecting and Modeling Long Range Correlation in Genomic Sequences" , (with Y. Zhou et al.), International Conference on Complex Systems (ICCS2002), Nashua, NH, June 9-14, 2002. Organized by New England Complex Systems Institute.
"Single Molecule Sequencing Approach to Find Expressed mRNA" , (with M. Merjan), 15th annual meeting on Genome Sequencing & Biology, CSHL, LI,, May 2002.
"A Versatile MicroArray Data Base: Goals, Design, and Implementation" , (with M. Rejali et al.), 15th annual meeting on Genome Sequencing & Biology, CSHL, LI,, May 2002.
"Genome Evolution Models, Gene Grammar and Valis Genome Analysis Tool" , (with Y. Zhou et al.), 15th annual meeting on Genome Sequencing & Biology, CSHL, LI,, May 2002.
"Correspondence mapping algorithms" (with J.A. West et al.), 15th annual meeting on Genome Sequencing & Biology, CSHL, LI,, May 2002.
"Haplotyping with Phased RFLPs---Algorithms and Mathematical Models" (with W. Casey et al.), 15th annual meeting on Genome Sequencing & Biology, CSHL, LI,, May 2002.
"Mathematically Modeling Stem Cells Populations" , (with M. Antoniotti et al.), 15th annual meeting on Genome Sequencing & Biology, CSHL, LI,, May 2002.
"Validation and Scaffolding of Microbes Sequence Data with Optical Maps" , (with M. Antoniotti et al.), 15th annual meeting on Genome Sequencing & Biology, CSHL, LI,, May 2002.
"Optical Mapping: New Technologies and Applications" , (with David C. Schwartz et al.), Ninth DOE Genome Contractor and Grantee Workshop, Oakland, CA, January 2002.
"Correspondence Mapping Algorithms" , (with L. Cassier et al.), Ninth DOE Genome Contractor and Grantee Workshop, Oakland, CA, January 2002.
"Optical Map Based Sequence Validation of Microbes" , (with M. Antoniotti et al.), Ninth DOE Genome Contractor and Grantee Workshop, Oakland, CA, January 2002.
"A Random Walk Down the Genomes: a Case Study of DNA Evolution in VALIS" , (with Y. Zhou et al.), Ninth DOE Genome Contractor and Grantee Workshop, Oakland, CA, January 2002.
"Goals, Design, and Implementation of a Versatile MicroArray Data Base" , (with M. Rejali et al.), Ninth DOE Genome Contractor and Grantee Workshop, Oakland, CA, January 2002.
"Haplotyping with Phased RFLPs: Algorithms and Mathematical Models" (with William Casey et al.), Ninth DOE Genome Contractor and Grantee Workshop, Oakland, CA, January 2002.

2001
"Design and Implementation of a Versatile MAML-compatible Microarray Database," (with M. Rejali et al.), Fifth Annual Conference On Computational Genomics,TIGR, Baltimore, MD, November 2001.
"Algorithms for Combining Sequence Data With Optical Maps: Examples from P. falciparum and E. coli," (with M. Antoniotti et al.), 13th International Genome Sequencing and Analysis Conference, San Diego, October 2001.Text
"Algorithms and Analysis for Combining Sequences and Maps: Application to the Malaria Parasite Plasmodium falciparum," , (with M. Antoniotti et al.), WABI 2001, 1st Workshop on Algorithms in BioInformatics, Poster Volume, 26-28, August 2001. (In pdf).

Miscellenia

"Analysis of Algorithms." (Feb 1986).