Gene Myers

Brief Bio:Gene.BlauenWunder

In 2012 Gene Myers joined a growing group of computational biologists in Dresden as the founding director of a new Systems Biology Center that is being built as part of an extension of the Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). Previously Gene had been a group leader at the HHMI Janelia Farm Research Campus (JFRC) since its inception in 2005. Gene came to the JFRC from UC Berkeley where he was on the faculty of Computer Science from 2003 to 2005. He was formerly Vice President of Informatics Research at Celera Genomics for four years where he and his team determined the sequences of the Drosophila, Human, and Mouse genomes using the whole genome shotgun technique that he advocated in 1996. Prior to that Gene was on the faculty of the University of Arizona for 17 years and he received his Ph.D in Computer Science from the University of Colorado in 1981. His research interests include the design and analysis of algorithms for problems in computational molecular biology, image analysis of bioimages, and light microscopy with a focus on building models of the cell and cellular systems from imaging data. He is best known for the development of BLAST -- the most widely used tool in bioinformatics, and for the paired-end whole genome shotgun sequencing protocol and the assembler he developed at Celera that delivered the fly, human, and mouse genomes in a three year period. He has also written many seminal papers on the theory of sequence comparison. He was awarded the IEEE 3rd Millenium Acheivement Award in 2000, the Newcomb Cleveland Best Paper in Science award in 2001, and the ACM Kanellakis Prize in 2002. He was voted the most influential in bioinformatics in 2001 by Genome Technology Magazine and was elected to the National Academy of Engineering in 2003. In 2004 he won the International Max-Planck Research Prize and in 2005 was selected as one of two distinguished alumni (with David Haussler) at his alma-mater, the University of Colorado. In 2006 Gene was inducted into Leopoldina, the German Academy of Science and awarded an honarary doctorate at ETH, Zurich.

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 ItsApplication to Connectivity Testing
Advisor: Andrzej Ehrenfeucht

Experience:

2012-
Director, MPI Molecular Cell Biology and Genetics, Dresden, Germany.
2005-2012
Group Leader, HHMI Janelia Farm Research Campus, Ashburn, VA.
2003-2005
Professor of Computer Science &amp Molecular Biology, University of California, Berkeley, CA.
2003-2005
Staff Scientist, Lawrence Berkeley Labs &amp 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.

Awards:

  • ISCB Senior Scientist Award (2014)
  • Linné Lecture, Uppsala Universität, Sweden (2013)
  • Fellow of the ISCB (Intl. Soc. for Comp. Biology, 2010)
  • 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)
  • Fellow of the ACM (Assoc. Comp. Machinery, 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)

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 (2001), 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 theHuman 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 Identificationand 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. D.J. Begun, A.K. Holloway, K. Stevenes, L.W. Hillier, Y.P. Poh, M.W. Hahn, P.M. Nista, C.D. Jones, A.D. Kern, C.N. Dewey, L.Pachter, E. Myers, and C.H. Langley, "Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans,'' PLoS Biology 5, 11 (2007), 2534-2559.
  62. H. Peng, F. Long, X. Liu, S. Kim, and E. Myers,  "Straightening C. elegans Images,'' Bioinformatics 24, 2 (2007), 234-242.
  63. H. Peng, F. Long, and E. Myers,  "VANO: A Volume-Object Image Annotation System,'' Bioinformatics 25, 5 (2009), 695-697.
  64. F. Long, H. Peng, X. Liu, S.K. Kim, and E. Myers,  "A 3D Digital Atlas of C. elegans and its application to single-cell analysis,''Nature Methods 6, 9 (2009), 667-672. Supplement
  65. X. Liu, F. Long, H. Peng, S.J. Aerni, M. Jiang, A. Sanchez-Blanco, J.I. Murray, E. Preston, B. Mericle, S. Batzoglu, E.W. Myers, and S.K. Kim, "Analysis of gene regulation and cell fate from single-cell gene expression profiles in C. elegans,'' Cell, 139 (2009), 623-633.
  66. S.C. Lam, Z. Ruan, T. Zhao, F. Long, A. Jenett, J. Simpson, E.W. Myers, and H. Peng, ``Segmentation of Center Brains and Optic Lobes in 3D Confocal Images of Adult Fruit Fly Brains,'' Methods, 50, 2 (2010), 63-69.
  67. D. O'Connor, N. Clack, D. Huber, T. Komiyama, E.W. Myers, and K. Svoboda, ``Vibrissa-based object localization in head-fixed mice,'' J. of Neuroscience, 30, 5 (2010), 1947-1967.
  68. H. Peng, Z. Ruan, F. Long, J.H. Simpson, and E.W. Myers, ``V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets,'' Nature Biotechnology 28, 4 (2010), 348-353.
  69. E. Giladi, J. Healy, G. Myers, C. Hart, P. Kapranov, D. Lipson, S. Roels, E. Thayer, S. Letovsky, ``Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families,'' J. Of Computational Biology, 71, 10 (2010), 1279-1293.
  70. H. Peng, F. Long, T. Zhao, and E. Myers, ``Proof-Editing is the Bottleneck For 3D Neuron Reconstruction: The Problem and Solutions,'' Neuroinformatics, 17 (2010), 1-3.
  71. T. Zhao, J. Xie, F. Amat, N. Clack, P. Ahammad, H. Peng, F. Long, and E. Myers, ``Automated Reconstruction of Neuronal Morphology Based on Local Geometrical and Global Structural Models,'' Neuroinformatics 9, 2-3 (2011), 247-261.
  72. H. Peng, P. Chung, F. Long, L. Qui, A. Jenett, E.W. Myers, and J.H. Simpson, ``BrainAligner Automates 3D Registration of the Neuropil of Drosophila Brains,'' Nature Methods 8, 5 (2011), 493-498.
  73. M. Decker, S. Jaensch, A. Pozniakovsky, A. Zinke, K.F. O'Connell, W. Zachariae, E. Myers, and A.A. Hyman, ``Limiting amounts of centrosome material set centrosome size in C.elegans embryos,'' Current Biology 21, 15 (2011), 1259-1267.
  74. L. Qu, F. Long, X. Liu, E. Myers, S. Kim, and H. Peng, ``Simultaneous Recognition and Segmentation of Cells: Application in C. elegans,'' Bioinformatics 27, 20 (2011), 2895-2902.
  75. J. Kim, T. Zhao, R.S. Petralia, Y. Yu, H. Peng, E. Myers, and J.C. Magee, ``mGRASP Enables Mapping Synaptic Connectivity with Light Microscopy,'' Nature Methods 9 (2012), 96-102.
  76. E.W. Myers, ``Why Bioimage Informatics Matters,'' Nature Methods 9 (2012), 659-660.
  77. N.G. Clack, D.H. O'Connor, D. Huber, L. Petreanu, A. Hires, S. Peron, K. Svoboda, E.W. Myers, ``Automated Tracking of Whiskers in Videos of Head-Fixed Rodents,'' PLoS Computational Biology 8 (2012).
  78. A. Jenett, G.M. Rubin GM, T.T. Ngo, D. Shepherd, C. Murphy, H. Dionne, B.D. Pfeiffer, A. Cavallaro, D. Hall, J. Jeter, N. Iyer, D. Fetter, J.H. Hausenfluck, H. Peng, E.T. Trautman,R.R. Svirskas, E.W. Myers, Z.R. Iwinski, Y. Aso, G.M. Depasquale, A. Enos, P. Hulamm, S.C. Lam,H.H. Li, T.R. Laverty, F. Long, L. Qu, S.D. Murphy, K. Rokicki, T. Safford, K. Shaw, J.H. Simpson, A. Sowell, S. Tae, Y. Yu, C.T. Zugates, ``A GAL4-Driver Line Resource for Drosophila Neurobiology,'' Cell Reports 2 (2012), 991-1001.
  79. L. Pammer, D.H. O'Connor, S.A. Hires, N.G. Clack, D. Huber, E.W. Myers, and K. Svoboda, ``The Mechanical Variables Underlying Object Localization Along the Axis of the Whisker,'' J. of Neuroscience 33, 16 (2013), 6726-6741.
  80. F. Amat, E.W. Myers, and P.J. Keller, ``Fast and Robust Optical Flow for Time-Lapse Microscopy Using Super-Voxels,'' Bioinformatics 29, 3 (2013), 373-380.
  81. S. Navlakha, P. Ahammad, and E.W. Myers, ``Unsupervised Segmentation of Noisy Electron Microscopy Images Using Salient Watersheds and Region Merging,'' BMC Bioinformatics 14, 294 (2013).
  82. H.H. Yu, T. Awasaki, M.D. Schroeder, F. Long, J.S. Yang, Y. He, P. Ding, J.C. Kao, G.Y. Wu, H. Peng, G. Myers, T. Lee1, ``Clonal Development and Organization of the Adult Drosophila Central Brain,'' Current Biology 23, 8 (2013), 633-643.
  83. J.C. Rah, E. Bas, J. Colonell, Y. Mischenko, W. Karsh, R.D. Fetter, E.W. Myers, D.B. Chklovskii, K. Svoboda, T.D. Harris, and J.T.R. Isaac, ``Thalamocortical Input onto Layer 5 Pyramidal Neurons Measured Using Quantitative Large-Scale Array Tomography,'' Frontiers in Neural Circuits (2013), doi: 10.3389/fncir.2013.00177.
  84. J.C. Pearson, S.T. Crews, H. Peng, E. Myers, C.Q. Doe, ``Atlas-Builder Softward and the eNeuro Atlas: Resources for Developmental Biology and Neuroscience,'' Development, 14 ,12 (2014), 2524-2532.
  85. S. Preibisch, F. Amat, E. Myers, and P. Tomancak, ``Efficient Bayesian-Based Multi-View Deconvolution,'' Nature Methods 11, (2014), 645-648.
  86. H. Peng, J. Tang, H. Xiao, A. Bria, J. Zhou, V. Butler, Z. Zhou, P.T. Gonzalez-Bellido, S.W. Oh, J. Chen, A. Mitra, G.A. Ascoli, R.W. Tsien, H. Zeng, G. Iannello, M. Hawrylycz, E.W. Myers, and F. Long, ``Virtual Finger Boosts 3d Imaging and Microsurgery, and Terabyte Volume Image Visualization and Analysis,'' Nature Communications 5 (2014).
  87. F. Amat, D. Mossing, W. Lemon, K. McDole, K. Branson, E. Myers, P.J. Keller, ``Fast, Accurate Cell Lineage Reconstructions from Large-Scale Fluorescence Microscopy Data,'' Nature Methods 11, 9 (2014).
  88. M. Merkel, A. Sagner, R. Etourney, F.S. Gruber, C. Blasse, E. Myers, S. Eaton, F. Juelicher, ``The Balance of Prickle/Spiny-Legs Isoforms Controls the Amount of Coupling Between Core and Fat PCP Systems,'' Current Biology 24 (2014), 1-13.

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 andFinding 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.
  25. S. Jaensch, M. Decker, A.A. Hyman, and E.W. Myers, ``Automated Tracking and Analysis of Centrosomes in Early Caenorhabditis elegans Embryos,'' Conf. on Intelligent Systems for Molecular Biology (Boston, MA, 2010), 113-120.  Also published as Bioinformatics 26(12).
  26. J. Xie, T. Zhao, T. Lee, E. Myers, and H. Peng, ``Automatic Neuron Tracing in Volumetric Microscopy Images with Anisotropic Path Searching,'' Proc. of Medical Image Computing and Computer Assisted Intervention (MICCAI) (Beijing, 2010), 472-479.
  27. H. Peng, F. Long, and G. Myers, ``Automatic 3D Neuron Tracing Using All-Paths Pruning,'' Conf. on Intelligent Systems for Molecular Biology (Vienna, 2011), 239-247.  Also published as Bioinformatics 27(12).
  28. M. Liu, H. Peng, A.K. Roy-Chowdhury, and E. Myers, ``3D Neuron Tip Detection in Volumetric Microscopy Images,'' Conf. on Bioinformatics & Biomedicine (Atlanta, GA 2011).
  29. E. Bas, M.G. Uzunbas, D. Metaxsas, and E. Myers, ``Contextual Grouping in a Concept: A Multistage Decision Strategy for EM Segmentation,'' Conf. on Bioinformatics & Biomedicine (Barcelona, Spain 2012).
  30. E.W. Myers, ``What's Behind Blast,'' Models and Algorithms for Genome Evolution (MAGE) Conference, Computational Biology 19 (Spring-Verlag 2013), 3-15.
  31. E. Myers, ``Efficient Alignment Discovery amongst Noisy Long Reads,'' Proc. Workshop on Algorithms for BioInformatics (Wroclaw, Poland 2014), 52-67.  Also appeared as Springer Verlag LNCS #8791.
  32. D. Kainmueller, F. Jug, C. Rother, E. Myers, ``Active Graph Matching for Automatic Joint Segmentation and Annotation of C. elegans,'' Conf. on Medical Image Computing and Computer-Assisted Intervention (MICCAI, Boston, MA 2014), 81-88.  Also published as Springer-Verlag LNCS #8673.
  33. F. Jug, T. Pietzsch, D. Kainmueller, J. Funke, M. Kaiser, E. van Nimwegen, C. Rother, E. Myers, ``Optimal Join Segmentation and Tracking of Escherichia Coli in the Mother Machine,'' BAMBI 2014, presented.
  34. F. Jug, T. Pietzsch, D. Kainmueller, E. Myers, ``Tracking by Assignment Facilitates Data Curation,'' IMIC 2014, presented.

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. L. Osterweil and E. Myers, ``BIGMAC II: A FORTRAN Language Augmentation Tool,'' Tech. Rep. CU-CS-179-80, Dept. of Computer Science, U. of Colorado, Boulder, CO (1980).
  4. E. Myers, ``A Depth-First Search Characterization of k-Connectivity and Its Application to Connectivity Testing,'' Ph.D. Thesis, University of Colorado (1981).
  5. E. Myers, ``AVL Dags,'' Tech. Rep. TR82-9, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1982).
  6. E. Myers, ``Incremental Alignment Algorithms and Their Applications,'' Tech. Rep. TR86-22, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1986).
  7. 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).
  8. S. Miller and E. Myers, ``A Fragment Assembly Project Environment,'' Tech. Rep. TR91-17, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1991).
  9. E. Myers, ``Sequence Comparison Algorithms in Molecular Biology,'' Tech. Rep. TR91-29, Dept. of Computer Science, U. of Arizona, Tucson, AZ (1991).
  10. 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).
  11. 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).
  12. E. Myers, ``A Suite of UNIX Filters for Fragment Assembly,'' Tech. Rep. TR96-07, Dept. of Computer Science, U. of Arziona, Tucson, AZ (1996).