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American scientist and professor at the University of Southern California

Michael Watermanphilosophy Degrees

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Philosophy

According to Wikipedia, Michael Spencer Waterman is a Professor of Biology, Mathematics and Computer Science at the University of Southern California , where he holds an Endowed Associates Chair in Biological Sciences, Mathematics and Computer Science. He previously held positions at Los Alamos National Laboratory and Idaho State University.

- Identification of common molecular subsequences. (1981) (10319)
- The B73 Maize Genome: Complexity, Diversity, and Dynamics (2009) (3594)
- Genomic mapping by fingerprinting random clones: a mathematical analysis. (1988) (935)
- Comparison of biosequences (1981) (697)
- Introduction to computational biology (1995) (575)
- Some Biological Sequence Metrics (1976) (395)
- A dynamic programming algorithm for haplotype block partitioning (2002) (360)
- A New Algorithm for DNA Sequence Assembly (1995) (326)
- Mathematical Methods for DNA Sequences (1989) (320)
- A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. (1987) (308)
- RNA secondary structure: a complete mathematical analysis (1978) (289)
- Introduction to computational biology - maps, sequences, and genomes: interdisciplinary statistics (1998) (278)
- Probabilistic and Statistical Properties of Words: An Overview (2000) (252)
- Sequence alignment and penalty choice. Review of concepts, case studies and implications. (1994) (252)
- Secondary Structure of Single-Stranded Nucleic Acidst (1978) (237)
- A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations. (1992) (233)
- General methods of sequence comparison (1984) (228)
- Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. (1985) (214)
- On the similarity of dendrograms. (1978) (213)
- Whole-genome shotgun assembly and comparison of human genome assemblies (2004) (195)
- Alignment-Free Sequence Comparison (I): Statistics and Power (2009) (193)
- The statistical distribution of nucleic acid similarities. (1985) (192)
- Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. (2004) (191)
- An algorithm for assembly of ordered restriction maps from single DNA molecules (2006) (176)
- High-resolution human genome structure by single-molecule analysis (2010) (175)
- Additive evolutionary trees. (1977) (171)
- Pattern recognition in several sequences: consensus and alignment. (1984) (166)
- Rapid and accurate estimates of statistical significance for sequence data base searches. (1994) (160)
- Sequence Comparison Significance and Poisson Approximation (1994) (155)
- Comparative biosequence metrics (2005) (149)
- New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing (2014) (148)
- RNA Secondary Structure (1995) (143)
- A Single Molecule Scaffold for the Maize Genome (2009) (141)
- The Erdos-Renyi Law in Distribution, for Coin Tossing and Sequence Matching (1990) (134)
- A Phase Transition for the Score in Matching Random Sequences Allowing Deletions (1994) (134)
- Benchmarking of alignment-free sequence comparison methods (2019) (134)
- On some new sequences generalizing the Catalan and Motzkin numbers (1979) (132)
- HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms (2005) (127)
- Linear Trees and RNA Secondary Structure (1994) (122)
- Multiple sequence alignment by consensus. (1986) (115)
- Efficient sequence alignment algorithms. (1984) (114)
- An extreme value theory for long head runs (1986) (113)
- Distributional regimes for the number of k-word matches between two random sequences (2002) (111)
- Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation (2011) (110)
- Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics (2010) (110)
- Parametric sequence comparisons. (1992) (108)
- DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections (2014) (102)
- Rapid dynamic programming algorithms for RNA secondary structure (1986) (102)
- Technical Note - Determining All Optimal and Near-Optimal Solutions when Solving Shortest Path Problems by Dynamic Programming (1984) (100)
- Systematic discovery of functional modules and context-specific functional annotation of human genome (2007) (99)
- Genomic mapping by anchoring random clones: a mathematical analysis. (1991) (93)
- Spaces of RNA Secondary Structures (1993) (93)
- A dynamic programming algorithm to find all solutions in a neighborhood of the optimum (1985) (90)
- A graph-based approach to systematically reconstruct human transcriptional regulatory modules (2007) (89)
- Computational Genome Analysis: An Introduction (2005) (88)
- THE ERDOS-RENYI STRONG LAW FOR PATTERN MATCHING WITH A GIVEN PROPORTION OF MISMATCHES (1989) (86)
- Alignment of Optical Maps (2005) (85)
- Estimating the repeat structure and length of DNA sequences using L-tuples. (2003) (82)
- Line geometries for sequence comparisons (1984) (81)
- A method for fast database search for all k-nucleotide repeats. (1994) (81)
- Biological information signal processor (1991) (81)
- Combinatorics of RNA Hairpins and Cloverleaves (1979) (80)
- Statistical characterization of nucleic acid sequence functional domains. (1983) (80)
- Phase transitions in sequence matches and nucleic acid structure. (1987) (80)
- Mapping DNA by stochastic relaxation (1987) (78)
- Open combinatorial problems in computational molecular biology (1995) (78)
- Interval graphs and maps of DNA. (1986) (76)
- On the statistical significance of nucleic acid similarities (1984) (76)
- Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. (2007) (75)
- Sequence alignments in the neighborhood of the optimum with general application to dynamic programming. (1983) (74)
- COMPUTATION OF GENERATING FUNCTIONS FOR BIOLOGICAL MOLECULES (1980) (73)
- New Stratigraphic Correlation Techniques (1980) (72)
- Multiple filtration and approximate pattern matching (1995) (71)
- A new approach to fragment assembly in DNA sequencing (2001) (71)
- The accuracy of DNA sequences: estimating sequence quality. (1992) (71)
- Poisson Process Approximation for Sequence Repeats and Sequencing by Hybridization (1996) (68)
- An Extreme Value Theory for Sequence Matching (1986) (65)
- Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries. (1990) (65)
- Estimating statistical significance of sequence alignments. (1994) (62)
- Critical Phenomena in Sequence Matching (1985) (61)
- An Erdös-Rényi law with shifts (1985) (57)
- Haplotype reconstruction from SNP alignment (2003) (57)
- Topological classification and enumeration of RNA structures by genus (2013) (56)
- Zinc finger gene clusters and tandem gene duplication (2001) (56)
- A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations (1997) (55)
- Gene Aging Nexus: a web database and data mining platform for microarray data on aging (2006) (55)
- Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. (2003) (53)
- Renewal theory for several patterns (1985) (53)
- CAFE: aCcelerated Alignment-FrEe sequence analysis (2017) (50)
- A local algorithm for DNA sequence alignment with inversions. (1992) (47)
- Consensus methods for DNA and protein sequence alignment. (1990) (47)
- The Continuing Case of the Florida Dentist (1992) (44)
- Neighborhood size in the Simulated Annealing Algorithm (1988) (44)
- New powerful statistics for alignment-free sequence comparison under a pattern transfer model. (2011) (44)
- An Eulerian path approach to local multiple alignment for DNA sequences. (2005) (43)
- Computational Methods for SNPs and Haplotype Inference (2002) (41)
- Integrative missing value estimation for microarray data (2006) (40)
- An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences (2003) (39)
- Stochastic scrabble: large deviations for sequences with scores (1988) (39)
- A Restricted Least Squares Problem (1974) (39)
- Some ergodic properties of multi-dimensional f-expansions (1970) (35)
- Gene coexpression measures in large heterogeneous samples using count statistics (2014) (34)
- Multiple solutions of DNA restriction mapping problems (1991) (34)
- Overlapping genes and information theory. (1981) (33)
- Genetic mapping and DNA sequencing (1996) (33)
- Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data (2003) (32)
- The match game: New stratigraphic correlation algorithms (1987) (32)
- Refinement of optical map assemblies (2006) (32)
- Whole genome amplification of single cells: mathematical analysis of PEP and tagged PCR. (1995) (30)
- A Mathematical Analysis ofin VitroMolecular Selection – Amplification (1996) (29)
- The distribution of restriction enzyme sites in Escherichia coli. (1990) (28)
- Proceedings of the second annual international conference on Computational molecular biology (1998) (28)
- Stanislaw M. Ulam's contributions to theoretical theory (1985) (28)
- Locating maximum variance segments in sequential data (1977) (28)
- Parametric and ensemble sequence alignment algorithms. (1994) (28)
- Algorithms for restriction map comparisons (1984) (28)
- Estimation of probability densities by empirical density functions (1978) (27)
- Approximations to Profile Score Distributions (1994) (26)
- Genomic mapping by end-characterized random clones: a mathematical analysis. (1995) (26)
- Regulatory pattern identification in nucleic acid sequences. (1983) (26)
- Interval graphs and maps of DNA (1986) (26)
- Levenshtein Distance, Sequence Comparison and Biological Database Search (2020) (25)
- [52] Computer analysis of nucleic acid sequences (1988) (25)
- Dynamic programming algorithms for restriction map comparison (1992) (24)
- Poisson, compound Poisson and process approximations for testing statistical significance in sequence comparisons. (1992) (24)
- On the number of alignments ofk sequences (1990) (24)
- A local algorithm for DNA sequence alignment with inversions (1992) (24)
- A systolic array processor for biological information signal processing (1991) (22)
- A mathematical analysis of in vitro molecular selection-amplification. (1996) (21)
- Frequencies of restriction sites. (1983) (21)
- Pattern analysis of the genetic code (1988) (20)
- Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002, Washington, DC, USA, April 18-21, 2002 (2002) (19)
- Poisson, compound poisson and process approximations for testing statistical significance in sequence comparisons (1992) (19)
- New Generations: Sequencing Machines and Their Computational Challenges (2010) (19)
- Some remarks on Kuzmin's theorem for F-expansions (1973) (18)
- An Integrative Network Approach to Map the Transcriptome to the Phenome (2008) (18)
- A Phase Transition for the Minimum Free Energy of Secondary Structures of a Random RNA (1997) (17)
- Computer analysis of nucleic acid sequences. (1988) (17)
- A Fast Filtration Algorithm for the Substring Matching Problem (1993) (16)
- Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo (1998) (16)
- Protein constraints induced by multiframe encoding (1980) (15)
- An integrative modular approach to systematically predict gene-phenotype associations (2010) (14)
- A Bayesian Model for Determining the Optimal Test Stress for a Single Test Unit (1978) (14)
- The Power of Detecting Enriched Patterns: An HMM Approach (2010) (14)
- Computer methods for locating kinetoplastid cryptogenes. (1992) (14)
- Proceedings of the seventh annual international conference on Research in computational molecular biology (2003) (14)
- Matrix Longest Common Subsequence Problem, Duality and Hibert Bases (1992) (14)
- Applications of combinatorics to molecular biology (1996) (13)
- Matching rectangles in d-dimensions: Algorithms and laws of large numbers (1985) (13)
- Symmetries for Conditioned Ruin Problems (1977) (12)
- [Poisson Approximation and the Chen-Stein Method]: Comment (1990) (12)
- Genomic sequence databases. (1990) (12)
- Generalized Sequence Alignment and Duality (1993) (11)
- A Geometric Interpretation for Local Alignment-Free Sequence Comparison (2013) (10)
- Some applications of information theory to cellular automata (1984) (10)
- Chimeric alignment by dynamic programming: algorithm and biological uses (1997) (10)
- Generalized correlation measure using count statistics for gene expression data with ordered samples (2018) (10)
- Accuracy Assessment of Diploid Consensus Sequences (2007) (10)
- Sequence Alignment as Hypothesis Testing (2011) (9)
- Shotgun optical mapping: a comprehensive statistical and computational analysis (2006) (9)
- A Kuzmin theorem for a class of number theoretic endomorphisms (1971) (8)
- Sequence alignments with matched sections (1986) (8)
- Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000 (1997) (8)
- Enumeration of linear chord diagrams (2010) (8)
- A central limit theorem for the parsimony length of trees (1996) (8)
- Error Analysis of a Computation of Euler's Constant* (1974) (7)
- Percentiles for the Gamma Distribution (1977) (7)
- On the Length of the Longest Exact Position Match in a Random Sequence (2007) (7)
- Self-descriptive strings (1982) (7)
- Dynamic programming algorithms for picture comparison (1985) (7)
- Time warps, string edits, and macromolecules: The theory and practice of sequence comparison : David Sankoff and Joseph B. Kruskal, Editors, Addison Wesley Publishing Company, 1983, 382 pp., $31.95 hardback (1985) (7)
- Mathematical Support for Molecular Biology (1999) (7)
- The Seventh Asia Pacific Bioinformatics Conference (APBC2009) (2009) (7)
- Ergodic computations with continued fractions and Jacobi's algorithm (1972) (6)
- Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution (2020) (6)
- Parametric and ensemble sequence alignment algorithms (1994) (6)
- DNA sequence assembly and multiple sequence alignment by an Eulerian path approach. (2003) (6)
- Optimal choice of word length when comparing two Markov sequences using a χ2-statistic (2017) (6)
- Moments of Absorption Time for a Conditioned Random Walk (1979) (6)
- Ergodic Computations with Continued Fraction and Jacobi's Algorithm (1972) (5)
- A new statistic for efficient detection of repetitive sequences (2018) (5)
- Local matching of random restriction maps (2001) (5)
- Calculating the Secrets of Life (1995) (5)
- Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads (2012) (5)
- How Alike are Two Trees (1980) (5)
- Decimals and Partial Quotients of Euler's Constant and ln2 (1974) (5)
- Multidimensional greatest common divisor and Lehmer algorithms (1977) (4)
- RECOMB 99 : proceedings of the Third annual international conference on computational molecular biology : April 11-14, 1999, Hotel de Lyon Metropole, Lyon, France (1999) (4)
- Statistical Significance of Local Alignments with Gaps (2007) (4)
- RECOMB 2000 : proceedings of the Fourth annual international conference on computational molecular biology : April 8-11, 2000, Tokyo, Japan (2000) (4)
- Probability Distributions for DNA Sequence Comparisons (1986) (4)
- RECOMB 98 : proceedings of the Second Annual International Conference on Computational Molecular Biology : March 22-25, 1998, Holiday Inn Manhattan, New York, NY (1998) (4)
- A Jacobi algorithm and metric theory for greatest common divisors (1977) (4)
- Alignment Networks and Electrical Networks (1996) (4)
- C1 . Least souares with nonnegative regression coefficients (1977) (4)
- Simple Maximum Likelihood Methods for the Optical Mapping Problem (2001) (4)
- The expected fraction of clonable genomic DNA (1990) (4)
- Refinement of Optical Map Assemblies ( original paper ) (2006) (3)
- Probability and Statistics for Sequence Patterns (1995) (3)
- Dynamic Programming Alignment of Two Sequences (2018) (3)
- Computational methods for SNPs and Haplotype inference : DIMACS/RECOMB satellite workshop, Piscataway, NJ, USA, November 21-22, 2002 : revised papers (2004) (3)
- Whole Genome Amplification and Branching Processes (1997) (3)
- Whither computational biology. (1994) (3)
- A Quantile Method for Sizing Optical Maps (2007) (3)
- Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings (2005) (3)
- Eulerian path methods for multiple sequence alignment (2003) (2)
- Some Mathematics for DNA Restriction Mapping (1989) (2)
- Statistics in molecular biology : An example from detection of chimeric 16 S rRNA artifactsGeorge (1997) (2)
- Hierarchical analysis of influenza A hemagglutinin gene sequences. (1982) (2)
- On the approximation of invariant measures for continued fractions (1976) (2)
- Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings (2006) (2)
- Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data (2002) (2)
- Research in Computational Molecular Biology (vol. # 3500) : 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings (2005) (2)
- Topics in computational genome analysis: i. matching restriction maps and ii. evolution of gene families by duplication (2000) (2)
- HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome (2009) (2)
- A Set of Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection via Haplotype Data or Genotype Data (2003) (2)
- On the random distribution of nucleoli in metabolic cells. (1977) (2)
- Modeling and optimizing a gas—water reservoir: Enhanced recovery with waterflooding (1979) (2)
- CAFE : aCcelerated Alignment-FrEe sequence analysis : Supplementary Material (2017) (2)
- Diploid genome reconstruction from shotgun sequencing (2006) (1)
- Pooling strategies for establishing physical genome maps using FISH (1997) (1)
- Probabilistic Aspects of Sequence Repeats and Sequencing by Hybridization (1997) (1)
- Pattern recognition in several sequences: Consensus and alignment (1984) (1)
- Benchmarking of alignment-free sequence comparison methods (2019) (1)
- Predicting Progress in Shotgun Sequencing with Paired Ends (2002) (1)
- The exponential family of probability distributions generated by Ơ-finite measures (1966) (1)
- Research in Computational Molecular Biology (2008) (1)
- Genomes, Maps and Sequences (1994) (1)
- The Human Genome Project: the Beginning of the Beginning (2021) (1)
- How do you spell DNA? (1984) (1)
- F-expansions of rationals (1975) (1)
- Cantor's Series for Vectors (1975) (1)
- A Note on the Reparametrization of an Exponential Family (1971) (1)
- Multiple Hypothesis Testing for Sequence Comparisons (2018) (0)
- Prrnred in Bctrum Spaces of RNA Secondary Structures (2003) (0)
- C8. Asymptotics for gamma and beta percentiles (1978) (0)
- Some Molecular Biology (1995) (0)
- Computational Biology Support: RECOMB Conference Series (Conference Support) (2006) (0)
- - Optical Mapping: a high-throughput single-molecule system for genome-wide restriction mapping - Thesis: "Shotgun optical mapping: a comprehensive statistical and computational analysis" (2012) (0)
- Topological classification and enumeration of RNA structures by genus (2012) (0)
- The algorithms of Euclid and Jacobi (1976) (0)
- Preface: Special RECOMB'97 Issues (1997) (0)
- Selected Papers from RECOMB'97 - Preface (1997) (0)
- Special RECOMB 2002 Issue (2004) (0)
- Multiple Sequence Alignment (2018) (0)
- Hierarchical analysis of inflnenza A hemagghitinin gene sequences (2005) (0)
- DNA Locus ECOACE ECOAMPCFR ECOBGLO ECOBIO ECOCARAB ECODMS ECOGLTA ECOGLTB ECOHISPUR ECOHLY ECOILVGE ECOLAC ECOLPXA ECOMALB ECONRDA ECONUSA ECOPHOS ECOPURLA ECORBS ECORECC ECORGNB ECORPLN ECORPLRPO ECORPOS 10 ECORPSRPO ECOTGP ECOTHR ECOTHRINF ECOUHP ECOUNCC (2005) (0)
- Physical Genome Maps: Oceans, Islands and Anchors (1995) (0)
- Parallelizing and Analyzing the Behavior of Sequence Alignment Algorithm on a Cluster of Workstations for Large Datasets (2015) (0)
- Probability and Statistics for Sequence Alignment (2018) (0)
- Designer algorithms for cryptogene searches (1993) (0)
- A CENTRAL LIMIT THEOREM LENGTH OF TREES FOR THE PARSIMONY (1995) (0)
- Remarks on invariant measures for number theoretic transformations (1975) (0)
- Trees and Sequences (2018) (0)
- Stan Ulam and Computational Biology (2006) (0)
- Sequence analysis Refinement of optical map assemblies (2006) (0)
- Statistical Analysis of SNP Alignment From Homologous Chromosomes (2004) (0)
- Sources and Perspectives (2018) (0)
- F-Expansions of rationals (1975) (0)
- Jacobi's Solution of Linear Diophantine Equations (1975) (0)
- Whole Genome Optical Mapping (2005) (0)
- DOUBLE-END CLONE SEQUENCE ASSEMBLY : SOME STATISTICAL ISSUES (2010) (0)
- Cloning and Clone Libraries (1995) (0)
- A New Computational Method for Detection of Chimeric 16s Rrna Artifacts Generated by Pcr Ampliication from Mixed Bacterial Populations Running Title::computational Detection of 16s Chimeras] (2007) (0)
- An Erdos-Rhyi taw with Shifts (1985) (0)
- Databases and Rapid Sequence Analysis (1995) (0)
- Computational genome analysis by alignment (2005) (0)
- Comparative biosequence metrics (2005) (0)
- RNA Secondary Structures with Given Motif Specification: Combinatorics and Algorithms (2023) (0)
- Sequence Comparison and Statistical Significance in Molecular Biology (Abstract) (1993) (0)
- Algorithms for DDP (1995) (0)
- Breathing Mathematics into Genes (2010) (0)
- Mathematical Sciences and The New Biology (2000) (0)

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