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Items: 1 to 50 of 96

1.

A new statistic for efficient detection of repetitive sequences.

Chen S, Chen Y, Sun F, Waterman MS, Zhang X.

Bioinformatics. 2019 Apr 16. pii: btz262. doi: 10.1093/bioinformatics/btz262. [Epub ahead of print]

PMID:
30993316
2.

Generalized correlation measure using count statistics for gene expression data with ordered samples.

Wang YXR, Liu K, Theusch E, Rotter JI, Medina MW, Waterman MS, Huang H, Stegle O.

Bioinformatics. 2018 Feb 15;34(4):617-624. doi: 10.1093/bioinformatics/btx641.

3.

CAFE: aCcelerated Alignment-FrEe sequence analysis.

Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F.

Nucleic Acids Res. 2017 Jul 3;45(W1):W554-W559. doi: 10.1093/nar/gkx351.

4.

Gene coexpression measures in large heterogeneous samples using count statistics.

Wang YX, Waterman MS, Huang H.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16371-6. doi: 10.1073/pnas.1417128111. Epub 2014 Oct 6.

5.

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.

Song K, Ren J, Reinert G, Deng M, Waterman MS, Sun F.

Brief Bioinform. 2014 May;15(3):343-53. doi: 10.1093/bib/bbt067. Epub 2013 Sep 23. Review.

6.

A geometric interpretation for local alignment-free sequence comparison.

Behnam E, Waterman MS, Smith AD.

J Comput Biol. 2013 Jul;20(7):471-85. doi: 10.1089/cmb.2012.0280.

7.

Topological classification and enumeration of RNA structures by genus.

Andersen JE, Penner RC, Reidys CM, Waterman MS.

J Math Biol. 2013 Nov;67(5):1261-78. doi: 10.1007/s00285-012-0594-x. Epub 2012 Oct 2.

PMID:
23053535
8.

Normal and compound poisson approximations for pattern occurrences in NGS reads.

Zhai Z, Reinert G, Song K, Waterman MS, Luan Y, Sun F.

J Comput Biol. 2012 Jun;19(6):839-54. doi: 10.1089/cmb.2012.0029.

9.

New powerful statistics for alignment-free sequence comparison under a pattern transfer model.

Liu X, Wan L, Li J, Reinert G, Waterman MS, Sun F.

J Theor Biol. 2011 Sep 7;284(1):106-16. doi: 10.1016/j.jtbi.2011.06.020. Epub 2011 Jun 25.

10.

Integrative analysis of many weighted co-expression networks using tensor computation.

Li W, Liu CC, Zhang T, Li H, Waterman MS, Zhou XJ.

PLoS Comput Biol. 2011 Jun;7(6):e1001106. doi: 10.1371/journal.pcbi.1001106. Epub 2011 Jun 16.

11.

Sequence alignment as hypothesis testing.

Meng L, Sun F, Zhang X, Waterman MS.

J Comput Biol. 2011 May;18(5):677-91. doi: 10.1089/cmb.2010.0328.

12.

Alignment-free sequence comparison (II): theoretical power of comparison statistics.

Wan L, Reinert G, Sun F, Waterman MS.

J Comput Biol. 2010 Nov;17(11):1467-90. doi: 10.1089/cmb.2010.0056. Epub 2010 Oct 25.

13.

High-resolution human genome structure by single-molecule analysis.

Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10848-53. doi: 10.1073/pnas.0914638107. Epub 2010 Jun 1.

14.

The power of detecting enriched patterns: an HMM approach.

Zhai Z, Ku SY, Luan Y, Reinert G, Waterman MS, Sun F.

J Comput Biol. 2010 Apr;17(4):581-92. doi: 10.1089/cmb.2009.0218.

15.

An integrative modular approach to systematically predict gene-phenotype associations.

Mehan MR, Nunez-Iglesias J, Dai C, Waterman MS, Zhou XJ.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S62. doi: 10.1186/1471-2105-11-S1-S62.

16.

New Generations: Sequencing Machines and Their Computational Challenges.

Schwartz DC, Waterman MS.

J Comput Sci Technol. 2010 Jan 1;25(1):3-9.

17.

Alignment-free sequence comparison (I): statistics and power.

Reinert G, Chew D, Sun F, Waterman MS.

J Comput Biol. 2009 Dec;16(12):1615-34. doi: 10.1089/cmb.2009.0198.

18.

A single molecule scaffold for the maize genome.

Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC.

PLoS Genet. 2009 Nov;5(11):e1000711. doi: 10.1371/journal.pgen.1000711. Epub 2009 Nov 20.

19.

An integrative network approach to map the transcriptome to the phenome.

Mehan MR, Nunez-Iglesias J, Kalakrishnan M, Waterman MS, Zhou XJ.

J Comput Biol. 2009 Aug;16(8):1023-34. doi: 10.1089/cmb.2009.0037.

20.

HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.

Kim JH, Kim WC, Waterman MS, Park S, Li LM.

Bioinformatics. 2009 Sep 15;25(18):2430-1. doi: 10.1093/bioinformatics/btp399. Epub 2009 Jun 27.

21.

The Seventh Asia Pacific Bioinformatics Conference (APBC2009).

Zhang MQ, Waterman MS, Zhang X.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S1. doi: 10.1186/1471-2105-10-S1-S1. No abstract available.

22.

A graph-based approach to systematically reconstruct human transcriptional regulatory modules.

Yan X, Mehan MR, Huang Y, Waterman MS, Yu PS, Zhou XJ.

Bioinformatics. 2007 Jul 1;23(13):i577-86.

PMID:
17646346
23.

Systematic discovery of functional modules and context-specific functional annotation of human genome.

Huang Y, Li H, Hu H, Yan X, Waterman MS, Huang H, Zhou XJ.

Bioinformatics. 2007 Jul 1;23(13):i222-9.

PMID:
17646300
24.

Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi.

Kim JH, Waterman MS, Li LM.

Genome Res. 2007 Jul;17(7):1101-10. Epub 2007 Jun 13.

25.

A quantile method for sizing optical maps.

Li H, Valouev A, Schwartz DC, Waterman MS, Li LM.

J Comput Biol. 2007 Apr;14(3):255-66.

PMID:
17563310
26.

Auditory efferent feedback system deficits precede age-related hearing loss: contralateral suppression of otoacoustic emissions in mice.

Zhu X, Vasilyeva ON, Kim S, Jacobson M, Romney J, Waterman MS, Tuttle D, Frisina RD.

J Comp Neurol. 2007 Aug 10;503(5):593-604.

PMID:
17559088
27.

On the length of the longest exact position match in a random sequence.

Reinert G, Waterman MS.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):153-6.

PMID:
17277422
28.

Accuracy assessment of diploid consensus sequences.

Kim JH, Waterman MS, Li LM.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):88-97.

PMID:
17277416
29.

Gene Aging Nexus: a web database and data mining platform for microarray data on aging.

Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D756-9. Epub 2006 Nov 7.

30.

An algorithm for assembly of ordered restriction maps from single DNA molecules.

Valouev A, Schwartz DC, Zhou S, Waterman MS.

Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15770-5. Epub 2006 Oct 16.

31.

Integrative missing value estimation for microarray data.

Hu J, Li H, Waterman MS, Zhou XJ.

BMC Bioinformatics. 2006 Oct 12;7:449.

32.

Alignment of optical maps.

Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, Waterman MS.

J Comput Biol. 2006 Mar;13(2):442-62.

PMID:
16597251
33.

Refinement of optical map assemblies.

Valouev A, Zhang Y, Schwartz DC, Waterman MS.

Bioinformatics. 2006 May 15;22(10):1217-24. Epub 2006 Feb 24.

PMID:
16500933
34.

An Eulerian path approach to local multiple alignment for DNA sequences.

Zhang Y, Waterman MS.

Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1285-90. Epub 2005 Jan 24.

35.

DNA sequence assembly and multiple sequence alignment by an Eulerian path approach.

Zhang Y, Waterman MS.

Cold Spring Harb Symp Quant Biol. 2003;68:205-12. No abstract available.

PMID:
15338619
36.

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.

Zhang K, Qin Z, Chen T, Liu JS, Waterman MS, Sun F.

Bioinformatics. 2005 Jan 1;21(1):131-4. Epub 2004 Aug 27.

PMID:
15333454
37.

Haplotype reconstruction from SNP alignment.

Li LM, Kim JH, Waterman MS.

J Comput Biol. 2004;11(2-3):505-16.

PMID:
15285905
38.

Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.

Zhang K, Qin ZS, Liu JS, Chen T, Waterman MS, Sun F.

Genome Res. 2004 May;14(5):908-16. Epub 2004 Apr 12.

39.

An Eulerian path approach to global multiple alignment for DNA sequences.

Zhang Y, Waterman MS.

J Comput Biol. 2003;10(6):803-19.

PMID:
14980012
40.

Whole-genome shotgun assembly and comparison of human genome assemblies.

Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, Flanigan MJ, Edwards NJ, Bolanos R, Fasulo D, Halldorsson BV, Hannenhalli S, Turner R, Yooseph S, Lu F, Nusskern DR, Shue BC, Zheng XH, Zhong F, Delcher AL, Huson DH, Kravitz SA, Mouchard L, Reinert K, Remington KA, Clark AG, Waterman MS, Eichler EE, Adams MD, Hunkapiller MW, Myers EW, Venter JC.

Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1916-21. Epub 2004 Feb 9.

41.
42.

Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.

Zhang K, Sun F, Waterman MS, Chen T.

Am J Hum Genet. 2003 Jul;73(1):63-73. Epub 2003 Jun 10.

43.

Distributional regimes for the number of k-word matches between two random sequences.

Lippert RA, Huang H, Waterman MS.

Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):13980-9. Epub 2002 Oct 8.

44.

A dynamic programming algorithm for haplotype block partitioning.

Zhang K, Deng M, Chen T, Waterman MS, Sun F.

Proc Natl Acad Sci U S A. 2002 May 28;99(11):7335-9.

45.

An Eulerian path approach to DNA fragment assembly.

Pevzner PA, Tang H, Waterman MS.

Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9748-53.

46.

Probabilistic and statistical properties of words: an overview.

Reinert G, Schbath S, Waterman MS.

J Comput Biol. 2000 Feb-Apr;7(1-2):1-46. Review.

PMID:
10890386
47.

Estimation for restriction sites observed by optical mapping using reversible-jump Markov Chain Monte Carlo.

Lee JK, DancĂ­k V, Waterman MS.

J Comput Biol. 1998 Fall;5(3):505-15.

PMID:
9773346
48.
49.

A mathematical analysis of in vitro molecular selection-amplification.

Sun F, Galas D, Waterman MS.

J Mol Biol. 1996 May 17;258(4):650-60.

PMID:
8636999
50.

Poisson process approximation for sequence repeats, and sequencing by hybridization.

Arratia R, Martin D, Reinert G, Waterman MS.

J Comput Biol. 1996 Fall;3(3):425-63.

PMID:
8891959

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