Michael C. Wendl


Published Research (Journal Articles in Print)

  1. Bell, D. et al. (2011) ``Integrated Genomic Analyses of Ovarian Carcinoma'', Nature, 474 (7353), 609-615. Pubmed (PMID 21720365)

  2. Wendl, M. C. et al. (2011) ``PathScan: A Tool for Discerning Mutational Significance in Groups of Putative Cancer Genes'', Bioinformatics, 27 (12), 1595-1602. Pubmed (PMID 21498403)

  3. Ding, L., Wendl, M. C., Koboldt, D. C., and Mardis, E. R. (2010) ``Analysis of Next-Generation Genomic Data in Cancer: Accomplishments and Challenges'', Human Molecular Genetics, 19 (R2), 188-196. Pubmed (PMID 20843826)

  4. Altshuler, D. L. et al. (2010) ``A Map of Human Genome Variation from Population-Scale Sequencing'', Nature, 467 (7319), 1061-1073. Pubmed (PMID 20981092)

  5. Ding, L., et al. (2010) ``Genome Remodelling in a Basal-Like Breast Cancer Metastasis and Xenograft'', Nature, 464 (7291), 999-1005. Pubmed (PMID 20393555)

  6. Wendl, M. C. and Wilson, R. K. (2009) ``The Theory of Discovering Rare Variants via DNA Sequencing'', BMC Genomics, 10 (article number 485). Pubmed (PMID 19843339)

  7. Wendl, M. C. and Wilson, R. K. (2009) ``Statistical Aspects of Discerning Indel-Type Structural Variation via DNA Sequence Alignment'', BMC Genomics, 10 (article number 359). Pubmed (PMID 19656394)

  8. Chen, K. et al. (2009) ``BreakDancer: An Algorithm for High-Resolution Mapping of Genomic Structural Variation'', Nature Methods, 6 (9), 677-681. Pubmed (PMID 19668202)

  9. Ding, L., et al. (2008) ``Somatic Mutations Affect Key Pathways in Lung Adenocarcinoma'', Nature, 455 (7216), 1069-1075. Pubmed (PMID 18948947)

  10. Chin, L. et al. (2008) ``Comprehensive Genomic Characterization Defines Human Glioblastoma Genes and Core Pathways'', Nature, 455 (7216), 1061-1068. Pubmed (PMID 18772890)

  11. Wendl, M. C. and Wilson, R. K. (2008) ``Aspects of Coverage in Medical DNA Sequencing'', BMC Bioinformatics, 9 (article number 239). Pubmed (PMID 18485222)

  12. Wendl, M. C. (2008) ``Random Covering of Multiple One-Dimensional Finite Domains with an Application to DNA Sequencing'', SIAM Journal on Applied Mathematics, 68 (3), 890-905.

  13. Wendl, M. C. et al. (2007) ``Design and Implementation of a Generalized Laboratory Data Model'', BMC Bioinformatics, 8 (article number 362). Pubmed (PMID 17897463)

  14. Wendl, M. C. (2007) ``Algebraic Correction Methods for Computational Assessment of Clone Overlaps in DNA Fingerprint Mapping'', BMC Bioinformatics, 8 (article number 127). Pubmed (PMID 17442113)

  15. Chen, K., McLellan, M. D., Ding, L., Wendl, M. C., Kasai, Y., Wilson, R. K., and Mardis, E. R. (2007) ``PolyScan: Automatic Indel and SNP Detection in Human Resequence Data'', Genome Research, 17 (5), 659-666. Pubmed (PMID 17416743)

  16. Mitreva, M., Wendl, M. C., Martin, J., Wylie, T., Yin, Y., Larson, A., Parkinson, J., Waterston, R. H., and McCarter, J. P. (2006) ``Codon Usage Patterns in Nematoda: Analysis Based on Over 25 Million Codons in Thirty-Two Species'', Genome Biology, 7 (article number 75). Pubmed (PMID 16907990)

  17. Wendl, M. C. (2006) ``A General Coverage Theory for Shotgun DNA Sequencing'', Journal of Computational Biology, 13 (6), 1177-1196. Pubmed (PMID 16901236)

  18. Wendl, M. C. (2006) ``Occupancy Modeling of Coverage Distribution for Whole Genome Shotgun DNA Sequencing'', Bulletin of Mathematical Biology, 68 (1), 179-196. Pubmed (PMID 16794926)

  19. Wendl, M. C. and Barbazuk, W. B. (2005) ``Extension of Lander-Waterman Theory for Sequencing Filtered DNA Libraries'', BMC Bioinformatics, 6 (article number 245). Pubmed (PMID 16216129)

  20. Mikkelsen, T. J. et al. (2005) ``Initial Sequence of the Chimpanzee Genome and Comparison with the Human Genome'', Nature, 437 (7055), 69-87. Pubmed (PMID 16136131)

  21. Wendl, M. C. (2005) ``Probabilistic Assessment of Clone Overlaps in DNA Fingerprint Mapping via a priori Models'', Journal of Computational Biology, 12 (3), 283-297. Pubmed (PMID 15857243)

  22. Hillier, L. W., et al. (2005) ``Generation and Annotation of the DNA Sequences of Human Chromosomes 2 and 4'', Nature, 434 (7034), 724-731. Pubmed (PMID 15815621)

  23. International Human Genome Sequencing Consortium [Z. Abdellah, et al.] (2004) ``Finishing the Euchromatic Sequence of the Human Genome'', Nature, 431 (7011), 931-945. Pubmed (PMID 15496913)

  24. Wendl, M. C. and Yang, S. P. (2004) ``Gap Statistics for Whole Genome Shotgun DNA Sequencing Projects'', Bioinformatics, 20 (10), 1527-1534. Pubmed (PMID 14962917)

  25. Wendl, M. C. (2003) ``Collision Probability Between Sets of Random Variables'', Statistics & Probability Letters, 64 (3), 249-254.

  26. Hillier, L. W., et al. (2003) ``The DNA Sequence of Human Chromosome 7'', Nature, 424 (6945), 157-164. Pubmed (PMID 12853948)

  27. Wendl, M. C. and Waterston, R. H. (2002) ``Generalized Gap Model for Bacterial Artificial Chromosome Clone Fingerprint Mapping and Shotgun Sequencing'', Genome Research, 12 (12), 1943-1949. Pubmed (PMID 12466299)

  28. Waterston, R. H. et al. (2002) ``Initial Sequencing and Comparative Analysis of the Mouse Genome'', Nature, 420 (6915), 520-562. Pubmed (PMID 12466850)

  29. Wendl, M. C. and Agarwal, R. K. (2002) ``Viscous Dissipation in Finite Thin-Gap Couette Devices'', Journal of Heat Transfer, 124 (1), 200-203.

  30. Wendl, M. C. (2001) ``Mathematical Analysis of Coaxial Disk Cellular Shear Loading Devices'', Review of Scientific Instruments, 72 (11), 4212-4217.

  31. Wendl, M. C., Marra, M. A., Hillier, L. W., Chinwalla, A. T., Wilson, R. K., and Waterston, R. H. (2001) ``Theories and Applications for Sequencing Randomly Selected Clones'', Genome Research, 11 (2), 274-280. Pubmed (PMID 11157790)

  32. Wendl, M. C., Korf, I., Chinwalla, A. T., and Hillier, L. W. (2001) ``Automated Processing of Raw DNA Sequence Data'', IEEE Engineering in Medicine and Biology, 20 (4), 41-48. Pubmed (PMID 11494768)

  33. Lander, E. S. et al. (2001) ``Initial Sequencing and Analysis of the Human Genome'', Nature, 409 (6822), 860-921. Pubmed (PMID 11237011)

  34. Wendl, M. C. and Agarwal, R. K. (2000) ``Couette Flow Profiles for Two Non-Classical Taylor-Couette Cells'', Journal of Fluids Engineering, 122 (2), 435-438.

  35. Wendl, M. C. (1999) ``General Solution for the Couette Flow Profile'', Physical Review E, 60 (5), 6192-6194. Pubmed (PMID 11970531)

  36. Wendl, M. C. (1999) ``A Method for Obtaining Benchmark Navier-Stokes Solutions'', International Journal for Numerical Methods in Fluids, 31 (3), 657-660.

  37. C. elegans Sequencing Consortium [R. H. Waterston, et al.] (1998) ``Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology'', Science, 282 (5396), 2012-2018. Pubmed (PMID 9851916)

  38. Wendl, M. C., Dear, S., Hodgson, D., and Hillier, L. (1998) ``Automated Sequence Preprocessing in a Large-Scale Sequencing Environment'', Genome Research, 8 (9), 975-984. Pubmed (PMID 9750196)

  39. Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) ``Base-calling of Automated Sequencer Traces Using PHRED. I. Accuracy Assessment'', Genome Research, 8 (3), 175-185. Pubmed (PMID 9521921)

Book Chapters

  1. Wendl, M. C., Wallis, J. W., Yang, S. P., Chinwalla, A. T. and Hillier, L. W. (2005) ``Genome Assembly'', In Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, Edited by P. F. R. Little, John Wiley & Sons, Volume 3, pp. 1047-1058.

  2. Wendl, M. C., Fulton, R. S., Graves, T., Mardis, E. R., and Wilson, R. K. (2005) ``The Mouse Genome Sequencing Project: An Overview'', Ch. 16 in The Mouse in Animal Genetics and Breeding Research, Edited by E. J. Eisen, World Scientific, New Jersey, U. S. A., pp. 341-352.

  3. Wendl, M. C., Chinwalla, A. T., and Hillier, L. W. (2003) ``Software for Genomic Sequencing'', Ch. 12 in Genome Mapping and Sequencing, Edited by I. Dunham, Horizon Scientific Press, Wymondham Norfolk, U. K., pp. 357-395.

  4. Wendl, M. C. and Agarwal, R. K. (2003) ``Mass Conservation and the Accuracy of Non-Staggered Grid Incompressible Flow Schemes'', In Numerical Simulations of Incompressible Flows, Edited by M. M. Hafez, World Scientific, New Jersey, U. S. A. pp. 86-97.

  5. Wendl, M. C. (2001) ``Mathematics and Numeracy'', In Encyclopedia of the United States in the Nineteenth Century, Edited by P. Finkelman, Charles Scribner's Sons, New York, U. S. A. Volume 2, pp. 273-274.

Op-Ed Pieces

  1. Wendl, M. C. (2009) ``Technology Takes on Deadlines for Fetal Human Rights'', Nature, 458 (7235), 147. Pubmed (PMID 19370011)

  2. Wendl, M. C. (2007) ``H-Index: However Ranked, Citations Need Context'', Nature, 449 (7161), 403. Pubmed (PMID 17898746)

  3. Wendl, M. C. (2005) ``Bioweapons Could Kill More in One Strike than Guns'', Nature, 437 (7056), 192. Pubmed (PMID 16148911)

  4. Wendl, M. C. (2005) ``The Question of Forbidden Knowledge'', Science, 308 (5728), 1549. Pubmed (PMID 15957206)

  5. Wendl, M. C. and Dooling, D. J. (2003) ``Open-Source Answer to Bibliography Problem'', Nature, 424 (6952), 995. Pubmed (PMID 12944940)

  6. Wendl, M. C. (1997) ``Computer Testing Not Yet Mature'', American Physical Therapy Association Bulletin, 12 (16), 16.


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Mike Wendl 2011-10-07