NYU Bioinformatics group applies algorithmic, statistical, and mathematical techniques to solve problems of interest to biology, biotechnology and biomedicine. The group focuses on bioinformatics, computational biology and systems biology with many active projects in areas ranging from single molecules to entire populations: Analysis of Single-Molecule/Single-Cell Data, SPM-based Transcriptomic Profiling, Whole-Genome Haplotype Sequencing using SMASH (Single Molecule Approaches to Haplotype Sequencing), SUTTA (Scoring and Unfolding Trimmed Tree Assembler) assembly algorithm, Analysis of Spatio-Temporal Data, Model Checking and Model Building for Systems Biology, GOALIE-based Phenomenological Models and their Verification, Causality Analysis, Causal Models and their Verification, Analysis of EHR (Electronic Health Record Data) and Disease Models (e.g., Chronic Fatigue Syndrome, Congestive Heart Failure, Deep Vein Thrombosis, etc.), Models of Cancer, Applications to Pancreatic Cancer, Polymorphisms and Biomarkers, Strategies for Group Testing, Epidemiological and Bio-Warfare Models, Planning with Large Agent Networks against Catastrophes (PLAN C), Population Genomics, and Genome Wide Association Studies (GWAS).
The group has received its funding from Air Force, Army, CCPR, DARPA, NIH, NIST, NSF, NYSTAR, etc. and various other governmental and commercial entities. Currently, the group is part of an NSF funded “Expedition in Computing” project (CMACS: Center for Modeling and Analysis of Complex Systems at CMU) and collaborates widely, both nationally and internationally. The group is highly multi-disciplinary, attracting researchers and students from mathematics, statistics, computer science, and biology who team up with physicians, physicists, and chemists as well as professionals in their own disciplines.
- Scoring-and-Unfolding Trimmed Tree Assembler: Concepts, Constructs and Comparisons, (with G. Narzisi), Bioinformatics (2011) 27(2): 153-160.
- 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.
- Mapping the Genome One Molecule at a Time -- Optical Mapping, (with A.H. Samad et al.), Nature, 378:516-517, 1995.
- Quantifying the mechanisms for segmental duplications in mammalian Genomes by Statistical Analysis and Modeling, (with Y. Zhou), Proc. National Academy of Science USA, 102(11):4051-4056, 2005.
- Wild by Nature, (with M. Wigler), Science, 296: 1407-1408, 24 May 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.
- Competitive Hybridization Models, (with V.Cherepinsky, and G. Hashmi), Phys. Rev. E, 82, 051914 (17 pages) 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, 2010.
- Intelligently Deciphering Unintelligible Designs: Algorithmic Algebraic Model Checking in Systems Biology, (Invited Paper), Interface: Journal of the Royal Society, 2009.
- 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.
- 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.
- On the Existence and Synthesis of Multifinger Positive Grips, (with J.T. Schwartz and M. Sharir), Algorithmica, 2(4):541-558, 1987.
- A Linear Time Algorithm for Finding an Ambitus, (with R.E. Tarjan), Algorithmica, 7(5/6):521-554, 1992.
- 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.
- Hierarchical Verification of Asynchronous Circuits using Temporal Logic, (with E.M. Clarke), Theoretical Computer Science, 38:269-291, 1985.
Bud Mishra has been elected a Fellow of the American Association for the Advancement of Science. [link]
Researchers at NYU’s Courant Institute of Mathematical Sciences have developed a novel algebraic model of DNA “hybridization,” a process central to most biotechnology devices that monitor changes in cell’s gene expression or characterize a cell’s genome. Their work provides an additional tool for understanding how biological systems function and could enhance methods and designs of technologies used in cancer and genetics research. The full article can be found at NYU Today.
GOALIE uses techniques from mathematical optimization, data mining, and computational biology to reconstruct temporal models of cellular processes from gene expression data. The full article and interview can be found at GenomeWeb (BioInform).
Researchers at Virginia Tech, New York University, and Italy’s University of Milan have created a data mining algorithm they call GOALIE that can automatically reveal how biological processes are coordinated in time. The full article can be found at Futurity.
A team of researchers led by Bud Mishra is currently working to create computer-based models charting the growth of pancreatic cancer. The full article can be found at Washington Square News.
A new and novel computer modeling platform developed through intensive, multidisciplinary collaboration at New York University can help hospitals and cities to be more prepared for catastrophic public health scenarios. The full article can be found at Science Daily.
Bud Mishra was named a Fellow of the IEEE in January 2009, for "contributions to the mathematical modeling of robotic grasping". [link]
A new release of GOALIE, our novel microarray experiments analysis tool, which leverages the GO Ontology, has been made available for download. The new version contains a GANTT Charts viewer that gives a snapshot of the relevant up- and down-regulated biological processes resulting from GOALIE's temporal enrichment analysis. [link]