Fast algorithms for finding nearest common ancestors
SIAM Journal on Computing
Applications of computer graphics in molecular biology
Computer Graphics Forum
A taxonomy of parallel sorting
ACM Computing Surveys (CSUR)
The role of frame-based representation in reasoning
Communications of the ACM
Discovering the secrets of DNA
Communications of the ACM - Special issue: computing in the frontiers of science and engineering
Structural properties of the string statistics problem
Journal of Computer and System Sciences
Improved string matching with k mismatches
ACM SIGACT News
Rapid dynamic programming algorithms for RNA secondary structure
Advances in Applied Mathematics
A horizontally reconfigurable architecture for extended precision arithmetic
A horizontally reconfigurable architecture for extended precision arithmetic
Efficient string matching with k mismatches
Theoretical Computer Science
Introducing efficient parallelism into approximate string matching and a new serial algorithm
STOC '86 Proceedings of the eighteenth annual ACM symposium on Theory of computing
Sequence alignments with matched sections
SIAM Journal on Algebraic and Discrete Methods
Measurement of protein surface shape by solid angles
Journal of Molecular Graphics
DNA vectorgrams: representation of cancer genes as movements on a 2D cellular lattice
IBM Journal of Research and Development
Scientific discovery: computational explorations of the creative process
Scientific discovery: computational explorations of the creative process
ARIADNE: pattern-directed inference and hierarchical abstraction in protein structure recognition
Communications of the ACM
Comparison of protein structural profiles by interactive computer graphics
Journal of Molecular Graphics
SIAM Journal on Computing
Parallel string matching with k mismatches
Theoretical Computer Science
Studies of frequently recurring substructures in human &agr;-like globin mRNA precursors
Computers and Biomedical Research
Algorithms
Pattern analysis of the genetic code
Advances in Applied Mathematics
A lower bound for the edit-distance problem under an arbitrary cost function
Information Processing Letters
Journal of Molecular Graphics
Journal of Molecular Graphics
RMS: programs for generating raster molecular surfaces
Journal of Molecular Graphics
Full text retrieval based on syntactic similarities
Information Systems
Efficient parallel algorithms
Data structures and algorithms for approximate string matching
Journal of Complexity
Protein folding: computational approaches to an exponential-time problem
Annual review of computer science: vol. 3, 1988
Parallel algorithmic techniques for combinatorial computation
Annual review of computer science: vol. 3, 1988
The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
A greedy approximation algorithm for constructing shortest common superstrings
Theoretical Computer Science - International Symposium on Mathematical Foundations of Computer Science, Bratisl
LOPAL and SCAMP: techniques for the comparison and display of protein structures
Journal of Molecular Graphics
On finding lowest common ancestors: simplification and parallelization
SIAM Journal on Computing
Journal of Chemical Information & Computer Sciences
Matching patterns in strings subject to multi-linear transformations
Theoretical Computer Science
The matching of protein sequences using color intrasequence homology displays
Journal of Molecular Graphics
Computational molecular biology
Computational molecular biology
Size-time complexity of Boolean networks for prefix computations
Journal of the ACM (JACM)
A logical language for data and knowledge bases
A logical language for data and knowledge bases
Partial evaluation of pattern matching in strings
Information Processing Letters
Trees, stars, and multiple biological sequence alignment
SIAM Journal on Applied Mathematics
Speeding up dynamic programming with application to molecular biology
Theoretical Computer Science
Leaf pairs and tree dissections
SIAM Journal on Discrete Mathematics
On the expected sublinearity of the Boyer-Moore algorithm
SIAM Journal on Computing
Preparing a medical informatics research grant proposal: general principles
Computers and Biomedical Research
Software—Practice & Experience
Hardware Algorithms for Determining Similarity Between two Strings
IEEE Transactions on Computers
An Algorithm for Finding a Common Structure Shared by a Family of Strings
IEEE Transactions on Pattern Analysis and Machine Intelligence
Fast parallel and serial approximate string matching
Journal of Algorithms
Approximation algorithms for the shortest common superstring problem
Information and Computation
Rendering volumetric data in molecular systems
Journal of Molecular Graphics
Rapid geometric searching in protein structures
Journal of Molecular Graphics
Atoms with shadows–an area-based algorithm for cast shadows on space-filling molecular models
Journal of Molecular Graphics
Tree graphs of RNA secondary structures and their comparisons
Computers and Biomedical Research
Supercomputers and biological sequence comparison algorithms
Computers and Biomedical Research
Applications of ray tracing in molecular graphics
Journal of Molecular Graphics
Searching techniques for databases of protein secondary structures
Journal of Information Science
An Efficient Implementation of Static String Pattern Matching Machines
IEEE Transactions on Software Engineering
Coordinating the use of qualitative and quantitative knowledge in declarative device modeling
Artificial intelligence, simulation & modeling
Exclusion methods for the determination of protein structure from experimental data
Exclusion methods for the determination of protein structure from experimental data
Speeding up dynamic programming algorithms for finding optimal lattice paths
SIAM Journal on Applied Mathematics
Simple fast algorithms for the editing distance between trees and related problems
SIAM Journal on Computing
Hypothesis formation and qualitative resoning in molecular biology
Hypothesis formation and qualitative resoning in molecular biology
Performance and Architectural Issues for String Matching
IEEE Transactions on Computers
A space-efficient parallel sequence comparison algorithm for a message-passing multiprocessor
International Journal of Parallel Programming
Approximate sequence comparison: a study with histograms
Pattern Recognition
A spelling correction method and its application to an OCR system
Pattern Recognition
Fast hashing of variable-length text strings
Communications of the ACM
A very fast substring search algorithm
Communications of the ACM
PORTREP: A portable repeated string finder
Software—Practice & Experience
Optimal merging and sorting on the EREW PRAM
Information Processing Letters
A linear-time algorithm for concave one-dimensional dynamic programming
Information Processing Letters
Sequence matching with binary codes
Information Processing Letters
An analysis of the Karp-Rabin string matching algorithm
Information Processing Letters
On a cyclic string-to-string correction problem
Information Processing Letters
Journal of Molecular Graphics
A method for the characterization of foldings in protein ribbon models
Journal of Molecular Graphics
Sequence comparison with mixed convex and concave costs
Journal of Algorithms
Parallel computation of multiple biological sequence comparisons
Computers and Biomedical Research
Journal of Computational Chemistry
Optimal Correspondence of String Subsequences
IEEE Transactions on Pattern Analysis and Machine Intelligence
A note on graphing helical parameters of dynamics structure of DNA
Journal of Molecular Graphics
Parallel construction of minimal suffix and factor automata
Information Processing Letters
Informed parsimonious inference of prototypical genetic sequences
COLT '89 Proceedings of the second annual workshop on Computational learning theory
Context-dependent string matching
Sequences
Constant-space string-matching
Sequences
Parallel supercomputing: methods, algorithms and applications
Parallel supercomputing: methods, algorithms and applications
Performance limits for parallel processors
Parallel supercomputing: methods, algorithms and applications
Overview of current developments in parallel architectures
Parallel supercomputing: methods, algorithms and applications
Derivation of efficient parallel programs: an example from genetic sequence analysis
International Journal of Parallel Programming
An improved algorithm for approximate string matching
SIAM Journal on Computing
An optimal O(log n)time parallel string matching algorithm
SIAM Journal on Computing
An O(NP) sequence comparison algorithm
Information Processing Letters
Artificial neural system for gene classification using a domain database
CSC '90 Proceedings of the 1990 ACM annual conference on Cooperation
Linear approximation of shortest superstrings
STOC '91 Proceedings of the twenty-third annual ACM symposium on Theory of computing
Two-dimensional pattern matching with k mismatches
Pattern Recognition
An algorithm for string matching with a sequence of don't cares
Information Processing Letters
Partial sum problem mapping into a hypercube
Information Processing Letters
A review of algorithms for molecular sequence comparison
Computers and Biomedical Research
Computers and Biomedical Research
Journal of Chemical Information & Computer Sciences
The human genome project and informatics
Communications of the ACM
On the exact complexity of string matching: upper bounds
SIAM Journal on Computing
Sparse dynamic programming I: linear cost functions
Journal of the ACM (JACM)
Sparse dynamic programming II: convex and concave cost functions
Journal of the ACM (JACM)
Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
An Algorithm for Reconstructing Protein and RNA Sequences
Journal of the ACM (JACM)
The String-to-String Correction Problem
Journal of the ACM (JACM)
Bounds on the Complexity of the Longest Common Subsequence Problem
Journal of the ACM (JACM)
Bounds for the String Editing Problem
Journal of the ACM (JACM)
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
The Complexity of Some Problems on Subsequences and Supersequences
Journal of the ACM (JACM)
Journal of the ACM (JACM)
Parallel permutation and sorting algorithms and a new generalized connection network
Journal of the ACM (JACM)
Neural networks for molecular sequence database management
CSC '91 Proceedings of the 19th annual conference on Computer Science
Fast parallel sorting algorithms
Communications of the ACM
A fast string searching algorithm
Communications of the ACM
Efficient string matching: an aid to bibliographic search
Communications of the ACM
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
Mathematical Methods for DNA Sequences
Mathematical Methods for DNA Sequences
Sequence Analysis in Molecular Biology: Treasure Trove or Trivial Pursuit
Sequence Analysis in Molecular Biology: Treasure Trove or Trivial Pursuit
Supercomputers and Their Use
Nucleic Acid and Protein Sequence Analysis
Nucleic Acid and Protein Sequence Analysis
Applications of Artificial Intelligence for Chemical Inference: The Dendral Project
Applications of Artificial Intelligence for Chemical Inference: The Dendral Project
The Design and Analysis of Computer Algorithms
The Design and Analysis of Computer Algorithms
SIGGRAPH '78 Proceedings of the 5th annual conference on Computer graphics and interactive techniques
Chemical Discovery as Belief Revision
Machine Learning
Optimal Parallel Pattern Matching in Strings (Extended Summary)
Proceedings of the 12th Colloquium on Automata, Languages and Programming
Efficient dynamic programming using quadrangle inequalities
STOC '80 Proceedings of the twelfth annual ACM symposium on Theory of computing
Optimal parallel algorithms for string matching
STOC '84 Proceedings of the sixteenth annual ACM symposium on Theory of computing
TOWARDS A PROBLEM SOLVING SYSTEM FOR MOLECULAR GENETICS
TOWARDS A PROBLEM SOLVING SYSTEM FOR MOLECULAR GENETICS
Qualitative Process Theory
Algorithms for Constructing a Consensus Sequence
Algorithms for Constructing a Consensus Sequence
Planning with constraints
Discovery and representation of causal relationships from a large time-oriented clinical database: the rx project
A qualitative matching scheme for postulating enzyme kinetic models and experimental conditions: reasoning with constraints
Categorization of macromolecular sequences by minimal length encoding
Categorization of macromolecular sequences by minimal length encoding
Efficient randomized pattern-matching algorithms
IBM Journal of Research and Development - Mathematics and computing
The Noisy Substring Matching Problem
IEEE Transactions on Software Engineering
An optimal parallel algorithm for integer sorting
SFCS '85 Proceedings of the 26th Annual Symposium on Foundations of Computer Science
Efficient string matching in the presence of errors
SFCS '85 Proceedings of the 26th Annual Symposium on Foundations of Computer Science
Speeding up dynamic programming
SFCS '88 Proceedings of the 29th Annual Symposium on Foundations of Computer Science
Approximate string matching in sublinear expected time
SFCS '90 Proceedings of the 31st Annual Symposium on Foundations of Computer Science
Towards a DNA sequencing theory (learning a string)
SFCS '90 Proceedings of the 31st Annual Symposium on Foundations of Computer Science
Some triply-logarithmic parallel algorithms
SFCS '90 Proceedings of the 31st Annual Symposium on Foundations of Computer Science
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Automatic determination of amino acid sequences
IBM Journal of Research and Development
Journal of Computer and System Sciences
Knowledge-Driven Ultrasonic Three-Dimensional Organ Modeling
IEEE Transactions on Pattern Analysis and Machine Intelligence
| Hi-index | 0.98 |
The field of computational molecular biology and genetics is expanding at an enormous rate. Journals such as CABIOS and Nucleic Acids Research routinely publish articles on computational and mathematical aspects of biology. The purpose of this paper is to provide a bibliographic review of the literature in this area related to DNA mapping and sequence analysis. We have focused on computer and mathematical aspects of molecular biology and genetics (interpreted in a broad sense). Authors are solicited for their additions/corrections to this bibliography. Contact us at the above address.