CURRICULUM VITAE

Eugene W. Myers

Research Interests

Developing algorithms and software for the automatic interpretation of images produced by light and electron microscopy of stained samples with a particular emphasis on building 3D and 4D ``atlases'' of brains, developing organisms, and cellular processes. We also continue our long-standing work on selected computational problems in genome sequencing and analysis.

Education

1971-1975
California Institute of Technology
B.S. with Honors in Mathematics, June 1975.
1975-1981
University of Colorado
Ph.D. in Computer Science, May 1981.
A Depth-First Search Characterization of k-Connectivity and Its Application to Connectivity Testing
Advisor: Andrzej Ehrenfeucht

Experience

2005-
Group Leader, HHMI Janelia Farm Research Campus, Ashburn, VA.
2003-2006
Professor of Computer Science & Molecular Biology, University of California, Berkeley, CA.
2003-2005
Staff Scientist, Lawrence Berkeley Labs & Joint Genome Institute, Berkeley, CA.
2000-2002
Vice President of Informatics Research, Celera Genomics, Rockville, MD.
1998-1999
Director of Informatics Research, Celera Genomics, Rockville, MD.
1991-1998
Professor of Computer Science, University of Arizona, Tucson, AZ.
1991-1998
Professor of Molecular & Cellular Biology, University of Arizona, Tucson, AZ.
1990
Acting Department Head, University of Arizona, Tucson, AZ.
1987-1991
Associate Professor, University of Arizona, Tucson, AZ.
1987-1988
Visiting Associate Professor, The Pennsylvannia State University, State College, PA.
1981-1987
Assistant Professor, University of Arizona, Tucson, AZ.
1981
Assistant Professor Adjunct, University of Colorado, Boulder, CO.
1978
Programmer/Analyst, National Center for Atmospheric Research, Boulder, CO.
1977
Student research fellow, Bell Laboratories, Murray Hill, NJ.
1975-1980
Research Assistant, University of Colorado, Boulder, CO.

Publications

Refereed Journals:

  1. H. Gabow and E. Myers, ``Finding All Spanning Trees of Directed and Undirected Graphs,'' SIAM Journal on Computing 7, 3 (1978), 280-287.
  2. E. Myers, ``An Applicative Random-Access Stack,'' Information Processing Letters 17, 5 (1983), 241-248.
  3. E. Myers, ``An O(ElogE+I) Expected-Time Algorithm for the Planar Segment Intersection Problem,'' SIAM Journal on Computing 14, 3 (1985), 625-637.
  4. W. Miller and E. Myers, ``A File Comparison Program,'' Software — Practice & Experience 15, 11 (1985), 1025-1041.
  5. E. Myers and D. Mount, ``Computer Program for the IBM Personal Computer that Searches for Approximate Matches to Short Oligonucleotide Sequences in Long Target DNA Sequences,'' Nucleic Acids Research 14, 1 (1986), 501-508.
  6. E. Myers, ``An O(ND) Difference Algorithm and Its Variations,'' Algorithmica 1, 2 (1986), 251-266.
  7. W. Miller and E. Myers, ``Side-effects in Automatic File Updating,'' Software — Practice & Experience 16, 9 (1986), 809-820.
  8. C. Fraser and E. Myers, ``An Editor for Revision Control,'' ACM Trans. Prog. Lang. and Systems 9, 4 (1987), 277-295.
  9. E. Myers and W. Miller, ``Optimal Alignments in Linear Space,'' CABIOS 4, 1 (1988), 11-17.
  10. J. Hall and E. Myers, ``A Software Tool for Finding Locally Optimal Alignments in Protein and Nucleic Acid Sequences,'' CABIOS 4, 1 (1988), 35-40.
  11. W. Miller and E. Myers, ``Sequence Comparison with Concave Weighting Functions,'' Bull. of Mathematical Biology 50, 2 (1988), 97-120.
  12. W. Miller and E. Myers, ``A Simple Row Replacement Algorithm,'' Software — Practice & Experience 18, 7 (1988), 597-612.
  13. E. Myers and W. Miller, ``Row Replacement Algorithms for Screen Editors,'' ACM Trans. Prog. Lang. and Systems, 11, 1 (1989), 33-56.
  14. E. Myers and W. Miller, ``Approximate Matching of Regular Expressions,'' Bull. of Mathematical Biology 51, 1 (1989), 5-37.
  15. S. Wu, E. Myers, U. Manber, and W. Miller, ``An O(NP) Sequence Comparison Algorithm,'' Information Processing Letters 35, 6 (1990), 317-323.
  16. D. Lipman, E. Myers, W. Miller, S. Altschul, and W. Gish, ``A Basic Local Alignment Search Tool,'' Journal of Molecular Biology 215 (1990), 403-410.
  17. E. Myers and X. Huang, ``An O(N2log N) Restriction Map Comparison and Search Algorithm,'' Bulletin of Mathematical Biology 54, 4 (1992), 599-618.
  18. E. Myers, ``A Four Russians Algorithm for Regular Expression Pattern Matching,'' J. of ACM 39, 2 (1992), 430-448.
  19. G. Mehldau and E. Myers, ``A System for Pattern Matching Applications on Biosequences,'' CABIOS 9, 3 (1993), 299-314.
  20. U. Manber and E. Myers, ``Suffix Arrays: A New Method for On-Line String Searches,'' SIAM Journal on Computing 22, 5 (1993), 935-948. (Also appeared in: Proceedings of the First ACM-SIAM Symposium on Discrete Algorithms (1990), 319-327.)
  21. E. Myers, ``A Sublinear Algorithm for Approximate Keyword Matching,'' Algorithmica 12, 4-5 (1994), 345-374.
  22. C.B. Lawrence, S. Honda, N.W. Parrott, T.C. Flood, L. Gu, S. Larson, M. Jain, and E.W. Myers, ``The Genome Reconstruction Manager: A Software Environment for Supporting High-Throughput DNA Sequencing'' Genomics 23 (1994), 192-201.
  23. J. Knight and E. Myers, ``Super Pattern Matching,'' Algorithmica 13, 1-2 (1995), 211-243.
  24. J. Kececioglu and E. Myers, ``Combinatorial Algorithms for DNA Sequence Assembly,'' Algorithmica 13, 1-2 (1995), 7-51.
  25. E. Myers, ``Approximately Matching Context-Free Languages,'' Information Processing Letters 54, 2 (1995), 85-92. (Also appeared in: Proceedings of the 2nd South American Workshop on String Processing (Valparaiso, Chile 1995), 38-52.)
  26. M. Jain and E.W. Myers, ``A Note on Scoring Clones Given a Probe Ordering,'' J. of Computational Biology 2, 1 (1995), 33-38.
  27. S. Wu, U. Manber, and E. Myers, ``A Subquadratic Algorithm for Approximate Regular Expression Matching,'' J. of Algorithms 19 (1995), 346-360.
  28. J. Knight and E. Myers, ``Approximate Regular Expression Pattern Matching with Concave Gap Costs,'' Algorithmica 14, 1 (1995), 85-121. (Also appeared in: Proceedings of the Third Symposium on Combinatorial Pattern Matching (1992), 67-76.)
  29. E. Myers, ``Toward Simplifying and Accurately Formulating Fragment Assembly,'' J. of Computational Biology 2, 2 (1995), 275-290.
  30. S. Wu, U. Manber, and E. Myers, ``A Sub-Quadratic Algorithm for Approximate Limited Expression Matching,'' Algorithmica 15, 1 (1996), 50-67.
  31. E. Myers, ``Approximate Matching of Network Expressions with Spacers,'' J. of Computational Biology 3, 1 (1996), 33-51. (Also appeared in: Proceedings of the First Latin American Symposium on Theoretical Computer Science (1992), 372-386.)
  32. E. Myers and S. Kannan, ``An Algorithm for Locating Non-Overlapping Regions of Maximum Alignment Score,'' SIAM Journal on Computing 25, 3 (1996), 648-662. (Also appeared in: Proceedings of the Fourth Symposium on Combinatorial Pattern Matching (Padova, Italy 1993), 74-86.)
  33. E. Myers, S. Selznick, Z. Zhang, and W. Miller, ``Progressive Multiple Alignment with Constraints,'' J. of Computational Biology 3, 4 (1996), 563-572 (Also appeared in: Proceedings of the 1st Conference on Computational Molecular Biology (Santa Fe, 1997), 220-225.)
  34. J. Weber and E. Myers, ``Human Whole Genome Shotgun Sequencing,'' Genome Research 7 (1997), 401-409.
  35. E. Anson and E. Myers, ``ReAligner: A Program for Refining DNA Sequence Multi-Alignments,'' J. of Computational Biology 4, 3 (1997), 369-383. (Also appeared in: Proceedings of the 1st Conference on Computational Molecular Biology (Santa Fe, 1997), 9-16.)
  36. M. Jain and E. Myers, ``Algorithms for Computing and Integrating Physical Maps Using Unique Probes,'' J. of Computational Biology 4, 4 (1997), 449-466. (Also appeared in: Proceedings of the 1st Conference on Computational Molecular Biology (Santa Fe, 1997), 151-161.)
  37. G.M. Landau, E.W. Myers, and J.P. Schmidt, ``Incremental String Comparison,'' SIAM Journal on Computing 27, 3 (1998), 557-582.
  38. S. Levy, L. Compagnoni, E.W. Myers, and G.D. Stormo, ``Xlandscape: A tool for the graphical display of word frequencies in sequences,'' BioInformatics 14, 1 (1998), 74-80.
  39. M.F. Sagot and E. Myers, ``Identifying Satellites and Periodic Reptitions in Biological Sequences'', J. of Computational Biology 5, 3 (1998), 539-553. (Also appeared in: 2nd Conference on Computational Molecular Biology, (New York, 1998), 234-242.)
  40. E. Myers, ``Whole-Genome DNA Sequencing,'' IEEE Computational Engineering and Science 3, 1 (1999), 33-43.
  41. E. Myers, ``A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Progamming,'' J. of ACM 46, 3 (1999), 539-553. (Also appeared in: Ninth Combinatorial Pattern Matching Conference (Piscataway, NJ, 1998), 1-13.)
  42. E.W. Myers, G.G. Sutton, A.L. Delcher, I.M Dew, D.P. Fasulo, M.J. Flannigan, S.A. Kravitz, C.M Mobarry, K.H. Reinert, K.A. Remington, E.L. Anson, R.A> Bolanos, H.H. Chou, C.M. Jordan, A.L. Halpern, S. Lonardi, E.M. Beasley, R.C. Brandon, L. Chen, P.J. Dunn, Z. Lai, Y. Lian, D.R. Nusskern, M. Zhan, Q. Zhang, X. Zheng, G.M. Rubin, M.D. Adams, and J.C. Venter ``A Whole-Genome Assembly of Drosophila,'' Science 287 (2000), 2196-2204.
  43. M.D. Adams, ... (194 co-authors) ... E.W Myers, G.M. Rubin, and J.C. Venter ``The Genome Sequence of Drosophila Melanogastor,'' Science 287 (2000), 2185-2195.
  44. J.C. Venter, M.D. Adams, E.W. Myers, ... (273 co-authors) ... X. Zhu, ``The Sequence of the Humane Genome,'' Science 291 (2002), 1304-1351.
  45. E.W Myers, G.G. Sutton, H.O. Smith, M.D. Adams, and J.C. Venter ``On the Sequencing and Assembly of the Human Genome,'' Proc. Natl. Acad. Sciences 99, 7 (2002), 1661-1671.
  46. R.J. Mural, M.D. Adams, E. Myers, ... (179 coauthors)..., and L.D. Stephenson, ``A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome,'' Science 296 (2002), 1661-1671.
  47. J.A. Bailey, ..., E.W. Myers, P.W. Li, and E.E. Eichler, ``Recent Segmental Duplications in the Human Genome,'' Science 297 (2002), 1003-1007.
  48. R.A. Holt, G.M. Subramanian, A. Halpern, ... (121 co-authors) ..., E.W. Myers, M.D. Adams, H.O. Smith, S. Broder, M.J. Gardner, C.M Fraser, E. Birney, P. Bork, P.T. Brey, J.C. Venter, J. Weissenbach, K.C. Kafatos, F.H. Collins, S.L. Hoffman, ``The genome sequence of the malaria mosquito Anopheles gambiae,'' Science 298 (2002), 129-149.
  49. D.H. Huson, K. Reinert, and E. Myers, ``The Greedy Path-Merging Algorithm for Contig Scaffolding,'' J. of ACM 49, 5 (2002), 603-615. (Also appeared in: 5th Conf. on Computational Molecular Biology (Montreal, CA, 2001), 157-163.)
  50. S.E. Celnicker, ... (30-coauthors) ..., E.W. Myers, R.A. Gibbs, and G.M. Rubin ``Finishing a Whole-Genome Shotgun: Release 3 of the Drosophila melanogaster Euchromatic Genome Sequence,'' Genome Biology 3, 12 (2002), research0079.1 - 0079.14
  51. R.A. Hoskins, C.D. Smith, J.W. Carlson, A.B> Carvalho, A. Halpern, J.S. Kaminker, C. Kennedy, C.F. Mungall, B.A. Sullivan, G.G Sutton, J.C. Yasuhara, B.T. Wakimoto, E.W. Myers, S.E. Celniker, G.M. Rubin, and G.H. Karpen ``Heterochromatic Sequences in a Drosophila Whole-Genome Shotgun Assembly,'' Genome Biology 3, 12 (2002), research0085.1 - 0085.16
  52. M.D. Adams, G.G. Sutton, H.O. Smith, E.W Myers, and J.C. Venter ``The Independence of Our Genome Assemblies,'' Proc. Natl. Acad. Sciences 100, 6 (2003), 3025-3026.
  53. A.B. Carvalho, ... , M.D. Adams, E.W. Myers & A.G. Clark ``Y Chromosome and Other Heterochromatic Sequences of the Drosophila melanogaster Genome: How Far Can We Go?,'' Genetica 117 (2003), 227-237
  54. E. Myers and R. Durbin, ``A Table-Driven, Full-Sensitivity Similarity Search Algorithm," J. of Computational Biology 10, 2 (2003), 103-118. (Also appeared in: Proc. Workshop on Algorithms for BioInformatics (Rome, Italy 2002), 331-342.
  55. S. Istrail, G.G. Sutton, ... (33 co-authors) ..., E.W Myers, and J.C. Venter ``Whole Genome Shotgun Assembly and Comparison of Human Genome Asssemblies'', Proc. Natl. Acad. Sciences 101 (2004), 1916-1921.
  56. M. Margulies, M. Egholm, W.E. Altman, ... (57 co-authors) E.W. Myers ..., R.F. Begley, J.M. Rothberg, ``Genome Sequencing in Microfabricated Reactors," Nature 437 (2005), 376-380.
  57. K. Rasmussen, J. Stoye, and E.W. Myers, ``Efficient q-Gram Filters for Finding All e-matches Over a Given Length,'' J. of Computational Biology 13 (2006), 296-308. (Also appeared Conf. on Computational Molecular Biology (Boston, MA, 2005), 615-629.)
  58. C.D. Smith, R.C. Edgar, M.D. Yandell, D.R. Smith, S.E. Celniker, E.W. Myers, G.H. Karpen, ``Improved Repeat Identification and Masking in Dipterans,'' Gene 389 (2007), 1-9.
  59. H. Peng, F. Long, J. Zhou, G. Leung, M. Eisen, and E. Myers, ``Automatic Image Analysis For Gene Expression Patterns of Fly Embryos,'' BMC Cell Biology 8, Supp. 1 (2007).
  60. M.M. Mwangi, S.W. Wu, Z. Yanjiao, K. Sieradzki, H. de Lencastre, P. Richardson, D. Bruce, E. Rubin, E. Myers, E.D. Siggia, A. Tomasz, ``Tracking in vivo Evolution of Multidrug Resistance in S. aureus by Whole Genome Sequencing,'' PNAS 104, 22 (2007), 9451-56.
  61. H. Peng, F. Long, X. Liu, S. Kim, and E. Myers, ``Straightening C. elegans Images,'' Bioinformatics 24, 2 (2007), 234-242.
  62. H. Peng, F. Long, and E. Myers, ``VANO: A Volume-Object Image Annotation System,'' Bioinformatics, to appear.

Volumes and Proceedings:

  1. E. Myers (ed.) Algorithmica: Special Issue on Computational Biology 13, 1-2 (1995).
  2. E. Myers and D. Hirschberg (eds.), Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching, Springer-Verlag Lecture Notes in Computer Science #1075 (Heidelberg, 1996).
  3. E. Myers (ed.), Journal of Computational Biology: Special RECOMB 2002 Issue Volume 10, 3-4 (2003), 237-667.
  4. E. Myers (ed.), Proceeding of the 11th International Conference on Intelligent Systems for Molecular Biology, Oxford University Press, Volume 19 (supplement) (Brisbane 2003).
  5. R. Cassadio and E. Myers (eds.), Proceedings of the 5th Workshop on Algorithms in Bioinformatics, Springer-Verlag Lecture Notes in Bioinformatics #3692 (Mallorca, 2005).

Book Chapters:

  1. E. Myers, ``Advances in Sequence Assembly,'' in Automated DNA Sequencing and Analysis Techniques (C. Ventner, ed.), Academic Press Limited (London, England 1994), 231-238.
  2. E. Myers, ``Algorithmic Advances for Searching Biosequence Databases,'' in Computational Methods in Genome Research (S. Suhai, ed.), Plenum Press (New York, 1994), 121-135.
  3. E. Myers, ``Seeing Conserved Signals: Using algorithms to detect similarities between biosequences,'' in Calculating the Secrets of life: Applications of the Mathematical Sciences in Molecular Biology (E. Lander and M. Waterman, eds.), National Academy Press (Washington, D.C. 1995), 56-89.
  4. E. Myers and J. Weber, ``Is Whole Genome Shotgun Sequencing Feasible?,'' in Computational Methods in Genome Research (S. Suhai, ed.), Plenum Press (New York, 1996), 73-89.

Refereed Conference Proceedings (Not appearing elsewhere):

  1. L. Osterweil and E. Myers, ``BIGMAC II: A FORTRAN Language Augmentation Tool,'' Proceedings of the Fifth International Conference on Software Engineering (1981), 410-421.
  2. E. Myers, ``A Precise Interprocedural Data Flow Algorithm,'' Proceedings of the Eighth ACM Symposium on the Principles of Programming Languages (1981), 219-230.
  3. E. Myers, ``Efficient Applicative Data Types,'' Proceedings of the Eleventh ACM Symposium on the Principles of Programming Languages (1984), 66-75.
  4. C. Fraser, E. Myers, and A. Wendt, ``Analyzing and Compressing Assembly Code,'' Proceedings of the SIGPLAN Symposium on Compiler Construction (1984), 117-121.
  5. E. Myers and W. Miller, ``Chaining Multiple-Alignment Fragments in Sub-Quadratic Time,'' Proceedings of the Sixth ACM-SIAM Symposium on Discrete Algorithms (San Francisco, 1995), 38-47.
  6. E. Myers and M. Jain, ``Going Against the Grain,'' Proceedings of the 3rd South American Workshop on String Processing (Recife, Brazil 1996), 203-213. Published as International Inforatics Series #4 (Carleton University Press).
  7. S. Kurtz and E. Myers, ``Estimating the Probability of Approximate Matches,'' Proceedings of the Eighth Symposium on Combinatorial Pattern Matching (Aarhus, Denmark 1997), 52-64. Published as Springer-Verlag Lecture Notes in Computer Science, #1264.
  8. K. Guimaraes, P. Oliva, and E. Myers, ``Reporting Exact and Approximate Regular Expression Matches,'' Ninth Combinatorial Pattern Matching Conference (Piscataway, NJ 1998), 91-103. Published as Springer-Verlag Lecture Notes in Computer Science, #1448.
  9. E. Anson and E. Myers, ``Algorithms for Whole Genome Shotgun Sequencing,'' 3rd Conference on Computational Molecular Biology, (Lyon, France, 1999), 1-9.
  10. E. Myers, ``A Dataset Generator for Whole Genome Shotgun Sequencing,'' Conf. on Intelligent Systems for Molecular Biology (Heidelberg, Germany, 1999), 202-210.
  11. E. Myers, ``Comparing Sequence Scaffolds,'' 5th Conf. on Computational Molecular Biology (Montreal, CA, 2001), 224-230.
  12. D.H. Huson, K. Reinert, S.A. Kravitz, K.A. Remington, A.L. Delcher, I.M. Dew, M. Flanigan, A.L. Halpern, Z. Lai, C.M. Mobarry, G.G. Sutton, and E.W. Myers, ``Design of a Compartmentalized Shotgun Assembler for the Human Genome,'' Conf. on Intelligent Systems for Molecular Biology (Copenhagen, Denmark 2001), 132-139. Also published as Bioinformatics 17, Supplement 1.
  13. D.H. Huson, A.L. Halpern, Z. Lai, E.W. Myers, K. Reinert, and G.G. Sutton, ``Comparing Assemblies Using Fragments and Mate Pairs,'' Proc. Workshop on Algorithms in BioInformatics (Aarhus, Denmark 2001), 294-306. Also published as Springer-Verlag LNCS #2149.
  14. E. Myers, ``Optimally Separating Sequences,'' Proc. Genome Informatics Workshop 2001 (Tokyo, Japan 2001), 165-174.
  15. H. Peng and E.W. Myers, ``Hybrid-GMM-Matching: Toward Comparing Embryogenesis Staining Pattern Images of D. melanogaster and Finding Co-Regulated Genes,'' 8th Conf. on Computational Molecular Biology (San Diego, CA, 2004), 157-166.
  16. G.M Landau, E.W. Myers, and M. Ziv-Ukelson, ``Two Algorithms for LCS Consecutive Suffix Alignment,'' 15th Combinatorial Pattern Matching Conference (Istanbul, Turkey 2004), 173-193. Published as Springer-Verlag Lecture Notes in Computer Science, #3109.
  17. R. Edgar and E. Myers, ``PILER: identification and classification of genomic repeats,'' Conf. on Intelligent Systems for Molecular Biology (Detroit, Michigan, 2005), 52-58.
  18. R. Sharan and E. Myers, ``A Motif-based Framework for Recognizing Sequence Families,'' Conf. on Intelligent Systems for Molecular Biology (Detroit, Michigan, 2005), 387-393.
  19. E. Myers, ``The Fragment Assembly String Graph,'' European Conf. on Computational Biology (Madrid, Spain, 2005), 79-85. Also published as Bioinformatics 21, Supplement 2.
  20. H. Peng, F. Long, M. Eisien, and E. Myers, ``Clustering Gene Expression Patterns of Fly Embryos,'' Proc. IEEE Symp. on Biomedical Imaging (Washington, DC, 2006), 1144-1147.
  21. T. Lin, E.W. Myers, and E.P. Xing, ``Interpreting Anonymous DNA Samples From Mass Disasters -- Probabilistic Forensic Inference Using Genetic Markers,'' Conf. on Intelligent Systems for Molecular Biology (Forta Leza, Brazil, 2006), 298-306. Also published as Bioinformatics 22(14).
  22. F. Long, H. Peng, and E. Myers, ``Automatic Segmentation of Nuclei in 3D Microscopy Images of C. Elegans,'' Proc. IEEE Symp. on Biomedical Imaging (Washington, DC, 2007), 536-539.
  23. P. Medvedev, K. Georgiou, G. Myers, and M. Brudno, ``Computability Models of Sequence Assembly,'' Proc. Workshop on Algorithms in BioInformatics (Philadelphia, PA 2007), 289-301.
  24. F. Long, H. Peng, X. Liu, S. Kim, and E. Myers, ``Automatic recognition of cells (ARC) for 3D images of C. elegans,'' Proc. 2008 Conf. on Computational Molecular Biology (RECOMB) (Singapore, 2008), 128-139. Also published as Springer-Verlag LNCS #4955.

Other Reports and Thesis (Not appearing elsewhere):

  1. E. Myers, ``The BIGMAC Users Manual,'' Tech. Rep. CU-CS-145-78, Dept. of Computer Science, U. of Colorado, Boulder, CO (1978).
  2. E. Myers, ``A Precise and Efficient Algorithm for Determining Existential Summary Data Flow Information,'' Tech. Rep. CU-CS-175-80, Dept. of Computer Science, U. of Colorado, Boulder, CO (1980).
  3. E. Myers, ``A Depth-First Search Characterization of k-Connectivity and Its Application to Connectivity Testing,'' Ph.D. Thesis, University of Colorado (1981).
  4. E. Myers, ``AVL Dags,'' Tech. Rep. TR82-9, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1982).
  5. E. Myers, ``Incremental Alignment Algorithms and Their Applications,'' Tech. Rep. TR86-22, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1986).
  6. J. Kececioglu and E. Myers, ``A Procedural Interface for a Fragment Assembly Tool,'' Tech. Rep. TR89-5, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1989).
  7. S. Miller and E. Myers, ``A Fragment Assembly Project Environment,'' Tech. Rep. TR91-17, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1991).
  8. E. Myers, ``Sequence Comparison Algorithms in Molecular Biology,'' Tech. Rep. TR91-29, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1991).
  9. S. Larson, M. Jain and E. Myers, ``An Interface for a Fragment Assembly Kernel,'' Tech. Rep. TR93-20, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1993).
  10. S. Larson, M. Jain, E. Anson, and E. Myers, ``An Interface for a Fragment Assembly Kernel (updated),'' Tech. Rep. TR96-04, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1996).
  11. E. Myers, ``A Suite of UNIX Filters for Fragment Assembly,'' Tech. Rep. TR96-07, Dept. of Computer Science, U. of Arziona, Tucson, AZ (1996).

Grants

  1. The Design and Analysis of a Practical and Precise Interprocedural Data Flow Analysis System, Principal Investigator, 1982-1985 ($50,000), NSF grant.
  2. A Programming Systems Laboratory, Co-Principal Investigator with G. Andrews, T. Budd, P. Downey, C. Fraser, R. Griswold, D. Hanson, G. Levin, W. Miller, and R. Schlichting, 1984-1989 ($3,634,000), NSF Coordinated Experimental Research Program.
  3. The Design and Analysis of Efficient Applicative Data Types and Their Applications, Principal Investigator, 1985-1987 ($100,000), NSF grant.
  4. A Workshop on Algorithms for Molecular Genetics, Co-Principal Investigator with W. Miller, March 26-28, 1988 ($30,000), NLM grant.
  5. Efficient Software for the Analysis of Biosequences, Principal Investigator, 1988-1991 ($423,000), NLM grant.
  6. A Laboratory for Programming Languages and Software Systems, Co-Principal Investigator with G. Andrews, R. Griswold, and U. Manber, 1989-1994 ($1,976,000), NSF Institutional Infrastructure Program.
  7. A Workshop on Recognizing Genes and Other Genomic Structure Components, Co-Principal Investigator with M. Turner, C. Burks, and G. Stormo, May 28-June 18, 1990 ($47,000), NSF grant.
  8. Problems in Discrete Pattern Matching, Co-Principal Investigator with U. Manber, 1991-1993 ($134,000), NSF grant.
  9. A Software Environment to Support Large-Scale Sequencing, Subcontract to C. Lawrence at Baylor Medical College, 1991-1994 ($291,000, subcontract only), DOE grant.
  10. Efficient Software for the Analysis of Biosequences, Principal Investigator, 1992-1995 ($554,000), NLM grant.
  11. Computer Upgrade for Sequence Analysis, Co-Principal Investigator with A. Adams, G. Burd, J. Law, M. Wells, and S. Ward, 1994 ($33,000), NSF grant.
  12. A Workshop on Identifying Features in Biological Sequences, Co-Principal Investigator with T. Applequist, C. Burks, and G. Stormo, May 30-June 19, 1994 ($8,000), NSF grant.
  13. A Flexible Sequence Reconstructor for Large Scale DNA Sequencing Projects, Principal Investigator, 1994-1997 ($403,000), DOE grant.
  14. A Laboratory for Scalable Systems, Co-Principal Investigator with L. Peterson, 1995-2000 ($1,000,000), NSF grant.
  15. Efficient Software for the Analysis of Biosequences, Principal Investigator, 1996-1999 ($639,000), NLM grant.
  16. A Flexible Sequence Reconstructor for Large Scale DNA Sequencing Projects, Principal Investigator, 1997-1998 ($192,000), DOE grant.
  17. Making the Most of Sequencing: Improved Assembly, Improved Protocols, and True Comparative Annotation Tools, Principal Investigator, 2003-2005 ($330,000), LRDR program grant, LBNL.
  18. A Computational Systems Biology Program for Drosophila, Principal Investigator, 2004-2009 (EU 750,000), Max Planck and Alexander von Humboldt Socieities.

Professional Activities

Awards:

  • Honorary Doctorate (ETH, Zurich, 2006)
  • Leopoldina (German Academy of Science, 2006)
  • University of Colorado Distinguished Engineering Alumni Award (2005)
  • International Max Plank Research Prize (2004)
  • National Academy of Engineering (2003)
  • ACM Paris Kanellakis Theory and Practice Award (2002)
  • Genome Technology Magazine most influtential in BioInformatics (2001)
  • Newcomb Cleveland Best Paper of the Year Award, Science (2000)
  • IEEE 3rd Millenium Achievement Award (2000)
  • Faculty of Science Distinguished Teaching Award (U. of Arizona, 1989)
  • University of Colorado Fellowship (U. of Colorado, 1976-1979)
  • Honeywell Outstanding Junior Engineer (Caltech, 1974)
  • Tau Beta Pi (Caltech, 1974)

Boards & Panels:

  • Helicos, Science Advisory Board, 2006-present.
  • Membership Peer Committee (Section 5: Computer Science), NAE, 2006-present.
  • Hawaii IDeA Network for Biomedical Research Excelence, External Advisory Committee, 2004-2006.
  • Genome Canada, Review Panel (2004).
  • 454 Corporation, Science Advisory Board, 2003-2006.
  • Genomatica, Science Advisory Board, 2003-present.
  • ARC Centre in Bioinformatics, U. of Queensland, Advisory Board and Honorary Professor, 2003-present.
  • Alan Wilson Centre for Molecular Ecology and Evolution, New Zealand, External Advisory Panel, 2003-present.
  • International Socitey for Computational Biology, Board Member, 1998-2001.
  • Paracel, Science Advisory Board, 2000-2002.
  • Adhoc Review Committee for the National Center for Human Genome Research, Aug. & Dec., 1995.
  • Biomedical Library Review Committee, NLM, 1989-1993.
  • Working group on training, Office for Human Genome Research, NIH (1989).
  • DOE Human Genome Computational Task Force (1989).
  • Los Alamos National Laboratory, Affiliate (1989-1993).

Editor:

  • Lecture Notes in BioInformatics, Editorial Board, 2003-present.
  • Bioinformatics, ISMB 2003 Supplement, 2003.
  • Journal of Computatioan Biology, RECOMB '02 Special Issue.
  • Kluwer ``Computational Biology'' book series, 1999-present.
  • Journal of Computational Biology, Associate Editor, 1997-present.
  • BioInformatics, Editorial Board, 1994-2005.
  • Journal of Computational Biology, Editorial Board, 1993-present.
  • Algorithmica, Special Issue on Computational Biology, Vol. 13, Nos. 1-2.
  • RAIRO Informatique Theorique et Applications, Editorial Board, 1998-present.
  • GENECombis, Editorial Board, 1995-1998.

Meeting Organizer:

  • Program Co-Chair, 5th Workshop on Algorithms in Bioinformatics, WABI 2005 (Mallorca, Spain 2005).
  • Program Chair, 11th Conference on Intelligent Systems in Molecular Biology, ISMB 2003 (Brisbane, Austrailia 2003).
  • Co-chair, RECOMB satellite meeting on Assembly Algorithms (Stanford, CA, 2002).
  • Program Chair, 6th Conference on Computational Molecular Biology, RECOMB 2002 (Washington, D.C. 2002).
  • Organizer, RECOMB satellite meeting on Assembly Algorithms (Los Angeles, CA, 2001).
  • Co-chair, 7th Combinatorial Pattern Matching Conference (Laguna Beach, CA, 1996).
  • ``A Workshop on Identifying Signals in Biological Sequences,'' with C. Burks and G. Stormo (Aspen, Colorado, 1994), with C. Burks and W. Pearson (Aspen, Colorado, 1995).
  • ``IMA Summer Program: Molecular Biology,'' with M. Waterman, T.P. Speed, J.P. Mesirov, K. Schulten, D.W. Sumners (Minneapolis, Minnesota, 1994).
  • ``A Workshop on Recognizing Genes and Other Genomic Structure Components,'' with C. Burks and G. Stormo (Aspen, Colorado, 1990), with C. Burks and C. Fields (Aspen, Colorado, 1991).
  • ``A Workshop on Algorithms for Molecular Genetics,'' with W. Miller (Washington, D.C., 1988).

Program Committees:

  • 7th Workshop on Algorithms in Bioinformatics, WABI 2007 (Philadelphia, PA).
  • 6th Workshop on Algorithms in Bioinformatics, WABI 2006 (Zurich, Switzerland).
  • Conference on Computational Molecular Biology, RECOMB 2006 (Venice, Italy).
  • Conference on Computational Molecular Biology, RECOMB 2005 (Boston, MA).
  • Intelligent Systems for Molecular Biology, ISMB 2004 (Glasgow, Scotland).
  • Genome Informatics Workshop 2001, 2002, 2003, 2004 & 2005 (Tokyo, Japa).
  • 9th Computing and Combinatorics Conference, COCOON 2003 (Big Sky, MT).
  • European Conference on Computational Biology, ECCB 2003 (Paris, France).
  • Workshop on Algorithms in Bioinformatics, WABI 2002 (Rome, Italy).
  • Computational Genomics V (Reston, VA 2001).
  • Intelligent Systems for Molecular Biology, ISMB 1999 (Heidelberg, Germany).
  • Computational Genomics III (Baltimore, MD, 1999).
  • 10th Combinatorial Pattern Matching Conference, CPM 1999 (Warwick, England).
  • 1998 Workshop on Implementing Automata (Rouen, France, 1998).
  • Latin American Conference on Theoretical Informatics (Campinas, Brazil, 1998).
  • 2nd Conference on Computational Molecular Biology, RECOMB 1998 (New York, NY).
  • 1st Conference on Computational Molecular Biology, RECOMB 1997 (Sante Fe, NM).
  • 1997 Workshop on Implementing Automata (London, Ontario, 1997).
  • Latin American Conference on Theoretical Informatics 1995 (Vina del Mar, Chile, 1995).
  • Intelligent Systems for Molecular Biology, ISMB 1994 (Stanford, CA).
  • 5th Combinatorial Pattern Matching Conference (Asilomar, CA, 1994).
  • 4th Combinatorial Pattern Matching Conference (Padova, Italy, 1993).
  • 3rd Combinatorial Pattern Matching Conference (Tucson, AZ, 1992).

Educational Activities

Students:

  • Gerhard Mehldau, ``A Rule-Based P.L. Applied to Image Recognition,'' M.S. 1986.
  • Gerhard Mehldau, ``A Pattern Matching System for Biosequences,'' Ph.D. 1991.
  • John Kececioglu, ``Exact and Approximate Algorithms for DNA Sequence Reconstruction,'' Ph.D. 1991.
  • Jim Knight, ``Discrete Pattern Matching Over Sequences and Interval Sets,'' Ph.D. 1993.
  • Mudita Jain, ``Algorithms for Physical Mapping Using Unique Probes,'' Ph.D. 1996.
  • Eric Anson, ``Algorithms for Whole Genome Shotgun Sequencing,'' Ph.D. 1999.

Courses taught:

  • Data structures, Algorithms, Theory of computation, Computer graphics, First and second semester introductions to programming (PASCAL, C, etc.), Computer architecture, Software tools, Theory seminar, Advanced courses on special topics in algorithm analysis (probabilistic algorithms and algorithms for molecular biology).
  • Member of the Applied Mathematics Program, 1982-92.
  • Instructor for ``Essential Computational Genomics,'' at Cold Spring Harbor Laboratories, October '91, '92, & '94.
  • Instructor for ``Mathematics in Molecular Biology,'' a SIMMS tutorial workshop, Stanford '91 & Reutgers '92.