CS482/682: Computational Techniques in Biological Sequence Analysis. Spring 2013.
PEAKS was best-known as the peptide de novo sequencing software from mass spectrometry data.
Now it includes many other functions such as protein/peptide identification with a database and protein quantification.
PeaksPTM is an online service to identify modified peptides from MS/MS
without requring the users to specify what PTMs they are looking for.
This is useful because researchers do not usually know all the PTM types
presenting in their biological samples.
CHAMPS (Complete Homology Assisted MS/MS Protein Sequencing)
is software for computing the complete sequence of a protein from the tandem mass spectrometry data
of multiple-enzyme digests of the protein.
SPIDER (Software Protein Identifier) is an online service to identify proteins in
a database by searching the peptide sequence tags obtained by de novo sequencing software using tandem mass spectrometry.
The major difference between SPIDER and similar systems is that SPIDER allows common de novo sequencing
errors in the sequence tags and automatically recover them during the database search.
PatternHunter compares large DNA sequences and reports
all the homologies between them. PatternHunter is much faster and has better quality than
BLAST for DNA homology searches.
Index of abbrevations:
- H. Lin, L. He, and B. Ma. A Combinatorial Approach to the Peptide Feature Matching Problem for Label-Free Quantification. Bioinformatics. Accepted 2013.
- A. Alhaider, A. Abdelgader, A. Turjoman, K. Newell, S. Hunsucker, B. Shan, B. Ma, D. Gibson, and M. Duncan. Through the Eye of an Electrospray Needle: Mass Spectrometric Identification of the Major Peptides & Proteins in the Milk of the One Humped Camel (Camelus dromedarius). Journal of Mass Spectrometry. Accepted 2013.
- L. He, X. Han, and B. Ma. De Novo Sequencing with Limited Number of Post-Translational Modifications per Peptide. Journal of Bioinformatics and Computational Biology. Accepted 2013.
- A. Ibrahima, L. Yang, C. Johnstonc, X. Liu, B. Ma, and N.A. Magarvey. Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery. PNAS 109:19196-19201. 2012.
- S. Sun, F. Yang, Q. Yang, H. Zhang, Y. Wang, D. Bu, and B. Ma. MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions. Journal of Proteome Research. DOI: 10.1021/pr300235v. 2012.
- Z. Chen, B. Ma and L. Wang. A Three-String Approach to the Closest String Problem. Journal of Computer and System Sciences 78(1): 164-178. 2012.
- J. Zhang, L. Xin, B. Shan, W. Chen, M. Xie, D. Yuen, W. Zhang, Z. Zhang, G. Lajoie, and B. Ma. PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification. Molecular & Cellular Proteomics 11. DOI, 10.1074/mcp.M111.010587. 2012.
- B. Ma and R. Johnson. De Novo Sequencing and Homology Searching. Molecular & Cellular Proteomics 11. DOI 10.1074/mcp.O111.014902. 2012.
- X. Han, L. He, L. Xin, B. Shan, B. Ma.
PeaksPTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications.
Journal of Proteomics Research 10(7): 2930-2936. 2011. (Also appeared in RECOMB-CP'2011)
- C. Boucher and B. Ma.
Closest String with Outliers.
BMC Bioinformatics 12 (Suppl 1): S55. 2011.
- L. Zhang and B. Ma.
Efficient Estimation of the Accuracy of the Maximum Likelihood Method for Ancestral State Reconstruction.
Journal of Combinatorial Optimization. 21(4):409-422. 2011.
(Also appeared in APBC'09)
- L. He and B. Ma.
ADEPTS: Advanced Peptide De Novo Sequencing with a Pair of Tandem Mass Spectra.
Journal of Bioinformatics and Computational Biology 8(6): 981-994. 2010.
- Q. Sun, D. Zhang, Y. Fan, K. Zhang, and B. Ma.
Ancient Chinese Zither (Guqin) Music Recovery with Support Vector Machine.
Journal on Computing and Cultural Heritage 3(2). Doi 10.1145/1841317.1841320. 2010
- Z. Zhang, H. Lin, and B. Ma.
ZOOM Lite: Next-generation Sequencing Data Mapping and Visualization Software.
Nucleic Acids Research. 38(suppl 2):W743-W748. 2010.
- X. Liu, L. Xin, B. Shan, and B. Ma.
Better Score Function for Peptide Identification with ETD MS/MS Spectra.
BMC Bioinformatics 11(Suppl 1):S4. 2010.
- Nikhil Bansal, Moshe Lewenstein, Bin Ma, and Kaizhong Zhang.
On the Longest Common Rigid Subsequence Problem.
Algorithmica 56(2): 270-280. 2010.
(Some material appeared in CPM'05)
- B. Ma.
Why Greed Works for Shortest Common Superstring Problem.
Theoretical Computer Science 410(51):5374-5381. 2009.
(Also appeared in CPM'08)
- B. Ma.
Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics.
Journal of Computer Science and Technology 25(1): 107-123. Invited paper. 2009.
- B. Ma and X. Sun.
More Efficient Algorithm for Closest String and Substring Problems.
SIAM J. Computing 39(4): 1432-1443. 2009.
(Also appeared in RECOMB'08)
- B. Ma and H. Yao.
Seed Optimization for I.I.D. Similarities Is No Easier than Optimal Golomb Ruler Design.
Information Processing Letter 109(19): 1120-1124. 2009.
(Also appeared in APBC'08)
- X. Liu, Y. Han, D. Yuen, and B. Ma.
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.
Bioinformatics 25(17):2174-2180. 2009.
- S. Chen, B. Ma, and K. Zhang.
On the similarity metric and the distance metric.
Theoretical Computer Science 410(24-25):2365-2376. 2009.
(Some material appeared in ICBB'07.)
- H. Lin, Z. Zhang, M. Zhang, B. Ma, and M. Li.
ZOOM! Zillions of Oligos Mapped.
Bioinformatics 24(21): 2431-2437. 2008.
- X. Wu, B. Ma, and N. Sarshar. Rainbow Network Problems and Multiple Description Coding.
IEEE Transactions on Information Theory 54(10):4565-4574. 2008.
(Some material appeared in NetCod'05)
- B. Ma, L. Xin, and K. Zhang.
A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method.
Journal of Combinatorial Optimization 16(3):293-306. 2008.
(Also appeared in COCOON'07)
- B. Shan, K. Zhang, B. Ma, C. Zhang, G. Lajoie.
An Algorithm for Determining Glycan Structures from MS/MS Spectra.
Journal of Bioinformatics and Computational Biology 6(1):77-91. 2008.
(Some material appeared in ICBA'04 and APBC'06.)
- B. Ma and M. Li.
On the Complexity of Spaced Seeds.
Journal of Computer Science and System Sciences 73(7):1024-1034. 2007.
(Some material appeared in SODA'06)
- B. Ma, L. Wang and M. Li.
Near Optimal Multiple Alignment within a Band in Polynomial Time.
Journal of Computer Science and System Sciences 73(6):997-1011. 2007.
(Also appeared in STOC'2000, pp. 425--434, Portland, Oregon, 2000.)
- S. Chellappan, W. Gu, X. Bai, D. Xuan, B. Ma, and K. Zhang.
Deploying Wireless Sensor Networks under Limited Mobility Constraints.
IEEE Transactions on Mobile Computing 10:1142-1157. 2007.
(Some material appeared in "The Second IEEE International Conference on Mobile Ad-Hoc and Sensor Systems 2005)
- M. Csuros and B. Ma. Rapid homology search with neighbour seeds. Algorithmica 48(2):187-202.
(Some material appeared in "Rapid homology search with two-stage extension and daughter seeds"
- S. Chellappan, X. Bai, B. Ma, D. Xuan and C. Xu.
Mobility Limited Flip-based Sensor Network Deployment.
IEEE Transactions on Parallel and Distributed Systems. 18(2):199-211. 2007.
(Some material appeared in "Sensor Network Deployment using Flip-based Sensors", MASS'05).
- J. Xu, D. Brown, M. Li, and B. Ma.
Optimizing Multiple Spaced Seeds for Homology Search.
Journal of Computational Biology 13(7): 1355-1368.
(Also appeared in CPM'04, 47-58.)
- B. Ma, L. Wu, and K. Zhang.
Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures.
Journal of Bioinformatics and Computationa Biology 4(3):709-720. 2006.
(Preliminary version appeared in IWBRA'05, 960-967, 2005.)
- C. Xu, and B. Ma.
Software for Computational Peptide Identification from MS/MS.
Drug Discovery Today.
11(13/14):595-600. 2006. (Review article.)
- J. Liu, B. Ma, M. Li: PRIMA: Peptide robust identification from MS/MS spectra.
Journal of Bioinformatics and Computationa Biology 5(1):125-138. 2006.
(Also appeared in APBC'05, 181-190, 2005.)
- Y. Han, B. Ma, and K. Zhang.
SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error.
Journal of Bioinformatics and Computational Biology 3(3):697-716. 2005.
(Also appeared in CSB'04, 206-215.)(Received the Best Paper Award of CSB'04)
- Y. Han, B. Ma, and K. Zhang.
An Automata Approach to Match Gapped Sequence Tags.
Int. J. Found. Comput. Sci. . 16(3): 487-497. 2005.
(Also appeared in CIAA'04 167-177).
- Derek Kisman, Ming Li, Bin Ma, and Li Wang.
TPatternHunter: Gapped, Fast and Sensitive Translated Homology Search.
Bioinformatics 21(4): 542-544. 2005.
- Bin Ma, Kaizhong Zhang, and Chengzhi Liang.
An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum.
Journal of Computer and System Sciences 70: 418-430. 2005. (Also appeared in CPM'03, 266-278.)
- M. Li, X. Chen, X. Li, B. Ma, and P. Vitanyi.
The Similarity Metric. IEEE Transaction Information Thoery.
50: 3250-3264. 2004.
(Also appeared in SODA'03, 863-872.)
- Dan Brown, Ming Li, and Bin Ma. A tutorial of recent developments in the seeding of local alignment.
Journal of Bioinformatics and Computational Biology 2(4): 819-842. 2004.
- M. Li, B. Ma, D. Kisman, and B. Ma.
PatternHunter II: Highly Sensitive and Fast Homology Search.
Journal of Bioinformatics and Computational Biology 2(3): 417-440. 2004. (Also appeared in GIW'03. GIW'03 version).
- U. Keich, M. Li, B. Ma, and J. Tromp.
Computing Optimally Spaced Seeds.
Discrete Applied Mathematics 138(3): 253-263. 2004.
- T. Jiang, G. Lin, B. Ma, and K. Zhang.
The Longest Common Subsequence Problem for Arc-annotated Sequences.
Invited paper, Journal of Discrete Algorithms 2(2): 257-270. 2004.
(also appeared in CPM'00. CPM'00 version).
- Rat Genome Sequencing Project Consortium (B. Ma is a coauthor).
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature 428: 493-521. 2004.
- L. Zhang, B. Ma, L. Wang, and Y. Xu.
Greedy Method for Inferring Tandem Duplication History.
Bioinformatics. 19(12): 1497-1504. 2004. (Also appeared in WABI'02)
- B. Ma, K. Zhang, C. Hendrie, C. Liang, M. Li, A. Doherty-Kirby, and G. Lajoie.
PEAKS: Powerful Software for Peptide De Novo Sequencing by Tandem Mass Spectrometry.
Rapid Communication in Mass Spectrometry 17(20): 2337-2342. 2003. (Also presented in 50th ASMS Conference (2002))
- X. Deng, G. Li, Z. Li, B. Ma, and L. Wang.
Genetic Design of Drug without Side Effects.
SIAM Journal on Computing 32(4): 1073-1090. 2003.
(also appeared in ICALP'02)
- JK. Lanctot, M. Li, B. Ma, S. Wang, and L. Zhang.
Distinguishing String Search Problems.
Information and Computation 185: 41-55. 2003.
(Also appeared in SODA'99. SODA'99 version)
- C.H. Bennett, M. Li, and B. Ma.
Chain Letters and Evolutionary Histories.
Scientific American, June 2003, 76-79.
- Mouse Genome Consortium (B. Ma is a coauthor.).
Initial Sequencing and Comparative Analysis of the Mouse Genome.
Nature 420: 520 - 562. 2002.
- X. Chen, M. Li, B. Ma, and J. Tromp.
DNACompress: Fast and Effective DNA Sequence Compression.
Bioinformatics 18: 1696-1698. 2002.
- D. Jaitly, P. Kearney, G. Lin, and B. Ma.
Methods for Reconstructing the History of Tandem Repeats and Their Application to the Human Genome. Invited paper,
Journal of Computer and System Sciences 65(3): 494-507. 2002.
- M. Li, B. Ma, and L. Wang.
Finding Similar Regions in Many Sequences.
Invited paper, Journal of Computer and System Sciences (Special Issue for STOC'99) 65: 73-96. 2002.
(Also appeared as part of a paper in STOC'99)
- B. Ma, L. Wang, and K. Zhang.
Computing Similarity Between RNA Structures.
Theoretical Computer Sciences 276(1-2): 111-132. 2002.
(Also appeared in CPM'99)
- T. Jiang, G. Lin, B. Ma, and K. Zhang.
A General Edit Distance between Two RNA Structures.
Journal of Computational Biology 9(2): 371-388. 2002.
(also appeared in RECOMB'01)
- B. Ma, J. Tromp, and M. Li.
PatternHunter: Faster and More Sensitive Homology Search.
Bioinformatics 18: 440-445. 2002.
- M. Li, B. Ma, and L. Wang.
On the Closest String and Substring Problems.
Journal of the ACM 49(2): 157-171. 2002. (parts of the paper appeared in STOC'99 and CPM'00)
- B. Ma, M. Li, and L. Zhang.
From Gene Trees to Species Trees.
SIAM Journal on Computing 30: 729-752. 2000.
(Also appeared in RECOMB'98)
- L. Wang, B. Ma, and M. Li.
Fixed Topology Alignment with Recombination.
Discrete Applied Mathematics, special issue on computational molecular biology, 104: 281-300. 2000.
(Also appeared in CPM'98)
- B. Ma and L. Wang.
On the Inapproximability of Disjoint Paths and Minimum Steiner Forest with Bandwidth Constraints.
Journal of Computer and System Sciences 60: 1-12. 2000.
- B. Ma, L. Wang and L. Zhang.
Fitting Distances by Tree Metrics with Incremental Errors.
Journal of Combinatorial Optimization(special issue on computational biology) 3: 213-225. 1999.
- L. Qi, W. Mao and B. Ma,
An algorithm for Ranking Football Teams,
Mathematics in Theory and Practice,1994(2), (in Chinese).
Some conference papers without journal versions
- C. Long, J. Zhang, M. Huang, X. Zhu, M. Li, and B. Ma.
Specialized Review Selection for Feature Rating Estimation.
Web Intelligence'09. 214-221.
- W. Li, B. Ma, K. Zhang. Amino Acid Classification and Hash Seeds for Homology Search.
- X. Liu, B. Ma, and L. Wang.
Voting Algorithms for the Motif Finding Problem.
- Z. Wu, G. Lajoie, and B. Ma.
MSDash: Mass Spectrometry Database and Search.
- B. Ma, Z. Wang, and K. Zhang.
Alignment between Two Multiple Alignments.
COCOON = International Computing and Combinatorics Conference.
MASS = IEEE International Conference on Mobile Ad-Hoc and Sensor Systems.
CIAA = International Conference on Implementation and Application of Automata.
CSB = IEEE Computer Society Bioinformatics Conference.
CPM = Ann. Symposium
on Combinatorial Pattern Matching
STOC = Annual ACM
Symposium on Theory of Computing
SODA = Annual ACM-SIAM
Symposium on Discrete Algorithms
RECOMB =Annual ACM
International Conference of Computational Molecular Biology
International Colloquium on Automata,Languages, and Programming
Workshop on Algorithms in Bioinformatics
ICBA = International Conference on Bioinformatics and its Applications
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