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The similarity metric
- Ming Li, Xin Chen, Xin Li, Bin Ma, P. Vitányi
- Computer Science, BiologyIEEE Transactions on Information Theory
- 20 November 2001
A new "normalized information distance" is proposed, based on the noncomputable notion of Kolmogorov complexity, and it is demonstrated that it is a metric and called the similarity metric.
From Gene Trees to Species Trees
- Bin Ma, Ming Li, Louxin Zhang
- Computer ScienceSIAM journal on computing (Print)
- 1 May 2000
This paper studies various algorithmic issues in reconstructing a species tree from gene trees under the duplication and the mutation cost model and proposes a heuristic method that is significantly better than the existing program in Page's GeneTree 1.0 that starts the search from a random tree.
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.
- B. Ma, Kaizhong Zhang, G. Lajoie
- Biology, Computer ScienceRapid Communications in Mass Spectrometry
- 30 October 2003
A new de novo sequencing software package, PEAKS, is described, to extract amino acid sequence information without the use of databases, using a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum.
PatternHunter: faster and more sensitive homology search
A new homology search algorithm 'PatternHunter' is presented that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed.
Clustering by compression
- Ming Li, Xin Chen, Xin Li, Bin Ma, P. Vitányi
- Computer ScienceIEEE International Symposium on Information…
- 2003
A general mathematical theory of universal similarity is developed and tested on real-world applications in a wide range of fields, including the first completely automatic construction of the phylogeny tree based on whole mitochondrial genomes and a language tree for over 50 Euro-Asian languages.
An information-based sequence distance and its application to whole mitochondrial genome phylogeny
- Ming Li, J. Badger, Xin Chen, S. Kwong, P. Kearney, Haoyong Zhang
- BiologyBioinform.
- 1 February 2001
A sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a program to estimate this distance is presented.
Computability
- T. Jiang, Ming Li, B. Ravikumar, Kenneth W. Regan
- MathematicsAlgorithms and Theory of Computation Handbook
- 1 February 2022
It is proved the existence of stationary solutions of the Euler equations in Euclidean space, of Beltrami type, that can simulate a universal Turing machine and disclose a certain degree of independence within different hierarchies of complexity.
Distinguishing string selection problems
- J. Lanctôt, Ming Li, Bin Ma, Shaojiu Wang, Louxin Zhang
- Mathematics, Computer ScienceACM-SIAM Symposium on Discrete Algorithms
- 25 August 2003
DNACompress: fast and effective DNA sequence compression
While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs.
Patternhunter Ii: Highly Sensitive and Fast Homology Search
Extending the single optimized spaced seed of PatternHunter(20) to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman,…
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