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Department of Ecology & Evolutionary Biology tel. (609) 258-1947 Princeton University fax (609) 258-1682 Princeton, NJ 08544-1003 LFL@princeton.edu PERSONAL Born November 6, 1967. EDUCATION Princeton University, A.B. in Molecular Biology, summa cum laude, June, 1989. Harvard University, M.A. in Biology, November, 1991. Harvard University, Ph.D. in Biology from the Department of Cellular and Developmental Biology, June, 1993. Topic of doctoral dissertation: "RNA editing and the evolution of mitochondrial DNA in kinetoplastid protozoa." (Graduate advisors: Walter Gilbert and Richard Lewontin) POSITIONS HELD Princeton University, Associate Professor with Tenure, July 2001 - present. California Institute of Technology, Visiting Associate in Chemical Engineering, Sept. 2001 - Jan. 2002. Princeton University, Assistant Professor of Ecology and Evolutionary Biology, 1994 - 2001. Princeton University, Associate Faculty, Department of Molecular Biology, 1994 - present. Harvard University, Junior Fellow of the Society of Fellows, 1993-1994. Massachusetts General Hospital, Assistant in Molecular Biology, 1993-1994. Harvard University, Parker Graduate Fellow in Cellular and Developmental Biology, 1992-1993. Harvard University, Teaching Fellow (tutorial on Molecular Biology of Protozoa: organized and designed a year long course for advanced undergraduate students) 1991-1992. HONORS & AWARDS Elected Fellow of AAAS in Biological Sciences, 2005. Named "Distinguished scientist of the DNA computing community," Recognition at the 7th annual meeting on DNA Based Computers, June 2001. NSF CAREER Award in Computational Biology, 1999. Sigma Xi's first Young Investigator Award in the life and social sciences, 1999. Elected to Santa Fe Institute Science Board, 1999. Santa Fe Institute Fellow-at-Large, 1999. Burroughs Wellcome Fund New Investigator Award in Molecular Parasitology, 1994. Alfred P. Sloan Foundation grant to Dalhousie University for a Symposium on Evolution of Unusual Molecular Processes in Protists, August 10, 1994 (with Mark Ragan). Harvard University, William F. Milton Fund Award, 1993. Harvard University Society of Fellows, Junior Fellowship, 1992. Alfred P. Sloan Postdoctoral Fellowship in Molecular Studies of Evolution, 1992 (declined). Life Sciences Research Foundation Postdoctoral Fellowship, 1992 (declined). Harvard University Graduate School of Arts and Sciences Merit Fellowship, 1992 (named one of ten "most outstanding third-year graduate students"). Howard Hughes Medical Institute predoctoral fellowship, 1990-1993. National Science Foundation predoctoral fellowship, 1989-1990. Elected to membership in Sigma Xi, a scientific honorary society, 1989. Sigma Xi Book Award (highest distinction) in Molecular Biology, 1989. Genetics Society of America undergraduate research fellowship, 1988. BOOKS Landweber, L. F. and Baum, E. B., eds. (1998) DNA Based Computers II. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.44, American Mathematical Society. Landweber, L. F. and Dobson, A., eds. (1999) Genetics and the Extinction of Species. Princeton University Press. updated 12/7/06 - 2 - Landweber, L. F. and Winfree, E., eds. (2002) Evolution as Computation. Springer-Verlag. REFEREED RESEARCH ARTICLES Kreitman, M. and L. F. Landweber (1989) A strategy for producing single-stranded DNA in the polymerase chain reaction: a direct method for genomic sequencing. Gene Analysis Techniques 6: 84-88. Landweber, L. F. (1992) The evolution of RNA editing in kinetoplastid protozoa. BioSystems 28: 41-45. Landweber, L. F. and M. Kreitman (1993) Producing Single-Stranded DNA in Polymerase Chain Reaction for Direct Genomic Sequencing. Methods in Enzymology 218: 17-26. Landweber, L. F. and W. Gilbert (1993) RNA editing as a source of genetic variation. Nature 363: 179-182. Landweber, L. F., Fiks, A. G., and W. Gilbert (1993) The Boundaries of Partially Edited Cytochrome c Oxidase III Transcripts are Not Conserved in Kinetoplastids: Implications for the Guide RNA Model of Editing. Proc. Natl. Acad. Sci. USA 90: 9242-9246. Landweber, L. F. and W. Gilbert (1994) Phylogenetic analysis of RNA editing: A primitive genetic phenomenon. Proc. Natl. Acad. Sci. USA 91: 918-921. Orr, A. T., Rabets, J. C., Horton, T. L., and L. Landweber. (1997) RNA Editing Missing in Mitochondria. RNA 3: 335-336. Knight, R. D. and L. F. Landweber. (1998) Rhyme or Reason: RNA-Arginine Interactions and the Genetic Code. Chemistry and Biology. 5: R215-220. Landweber, L.F. and I. D. Pokrovskaya. (1999) Emergence of a Dual Catalytic RNA with Metal Specific Cleavage and Ligase Activities: The Spandrels of RNA Evolution. Proc. Natl. Acad. Sci. USA 96: 173-178. Freeland, S. J., Knight, R. D., and L. F. Landweber. (1999). Do Proteins Predate DNA? Science 286: 690-692. Faulhammer, D., Cukras, A. R., Lipton, R. J. and L. F. Landweber (2000) Molecular Computation: RNA Solutions to Chess Problems. Proc. Natl. Acad. Sci. USA. 97:1385-1389. Landweber, L. F., Kuo, T.-C., and E. Curtis (2000) Evolution and Assembly of an Extremely Scrambled Gene. Proc. Natl. Acad. Sci. USA. 97: 3298-3303. Ronneberg, T. A., Landweber, L. F. and S. J. Freeland (2000) Testing a Biosynthetic Theory of the Genetic Code: Fact or Artifact? Proc. Natl. Acad. Sci. USA 97(25): 13690-13695. Knight, R. D. and L. F. Landweber. (2000) Guilt by Association: The Arginine Case Revisited. RNA 6:499-510. Freeland, S. J., Knight, R. D., Landweber, L. F., and L. D. Hurst (2000) Early Fixation of an Optimal Genetic Code. Molecular Biology and Evolution. 17(4): 511-518. Hagedorn, T. R. and L. F. Landweber (2000) Phylogenetic Invariants and Geometry. Journal of Theoretical Biology 205: 365-376. Horton, T. L. and L. F. Landweber (2000) Evolution of Four Types of RNA Editing in Myxomycetes. RNA 6: 1339-1346. Horton, T. L. and L. F. Landweber (2000) Mitochondrial RNAs of Myxomycetes terminate with nonencoded 3' poly(U) tails. Nucleic Acids Research 28(23): 4750-4754. Katz, L. A., Curtis, E., Pfunder, M., and L. F. Landweber (2000) Characterization of Novel Sequences from Distantly Related Taxa by Walking PCR. Mol. Phylogenet. Evol., 14: 318-321. Lozupone, C. A., Knight, R. D., and L. F. Landweber (2001) The Molecular Basis for Nuclear Genetic Code Change in Ciliates. Current Biology, 11: 65-74. Faulhammer, D., Lipton, R. J. and L. F. Landweber (2001) Fidelity of enzymatic ligation for DNA computing. J. Comp. Biol. 7(6):839-48. Ronneberg, T. A., Freeland, S. J., and L. F. Landweber (2001) Genview and Gencode: A Pair of Programs to Test Theories of Genetic Code Evolution. Bioinformatics 17(3):280-1. Knight, R. D., Freeland, S. J., and L. F. Landweber (2001) A Simple Model Based On Mutation and Selection Explains Codon and Amino Acid Usage Trends Within and Across Genomes. Genome Biology 2(4):RESEARCH0010 (genomebiology.com/2001/2/4/research/0010/). Knight, R. D., Landweber, L. F., and M. Yarus (2001) How Mitochondria Redefine the Code. J. Mol. Evol. 53(4-5):299-313. Ruben, A. J., Freeland, S. J., and L. F. Landweber (2002) PUNCH: An Evolutionary Algorithm for Optimizing Bit Set Selection. Lecture Notes in Computer Science 2340:150-160. Doak, T. G., A.R.O. Cavalcanti, N.A. Stover, D.M. Dunn, R. Weiss, G. Herrick, L.F. Landweber. updated 12/7/06 - 3 - (2003) Sequencing the Oxytricha trifallax macronuclear genome: a pilot project. Trends in Genetics 19(11):603-7. Ardell, D. H., C. A. Lozupone, and L. F. Landweber (2003) Polymorphism, Recombination and Alternative Unscrambling in the DNA Polymerase α Gene of the Ciliate Stylonychia lemnae. Genetics 165:1761-77. Cavalcanti, A.R.O., L. F. Landweber. (2004) Gene Unscrambler for detangling scrambled genes in ciliates, Bioinformatics 20(5):800-2. Vlassov, A. V., Johnston, B. H., Landweber, L. F., and S. A. Kazakov (2004) Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world. Nucleic Acids Research 32(9):2966-74. van Noort, D. and Landweber, L. F. (2004) Towards a re-configurable DNA computer. Lecture Notes in Computer Science 2943:190-197. Livstone, M. S. and Landweber, L. F. (2004) Mathematical Considerations in the Design of Microreactor-Based DNA Computers. Lecture Notes in Computer Science 2943:180-189. Chang, W.-J., Stover, N. A., Addis, V. M., and L. F. Landweber. (2004) A Micronuclear Locus Containing Three Protein-coding Genes Remains Linked During Macronuclear Development in the Spirotrichous Ciliate Holosticha. Protist, 155(2):245-255. Cavalcanti, A.R.O., N.A. Stover, L. Orecchia, T.G. Doak and L. F. Landweber (2004) Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma, 113:69-76. Cavalcanti, A.R.O., D. M. Dunn, R. Weiss, L. F. Landweber, T. G. Doak. (2004) Sequence features of Oxytricha trifallax (class Spirotrichia) macronuclear telomeric and subtelomeric sequences, Protist, 155(3): 311-322. van Noort, D., Z. Tang and L. F. Landweber (2004) Fully controllable microfluidics for molecular computers. J. Association Laboratory Automation (JALA) 9(5): 285-290. Cavalcanti, A.R.O., T. H. Clarke, and L. F. Landweber (2005) MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. Nucleic Acids Res. 33 Database Issue:D396-8. Liang, H., J. Wong, Q. Bao, Cavalcanti, A.R.O. and L. F. Landweber (2005) Decoding the decoding region: analysis of eukaryotic release factor stop codon-binding residues, J. Mol. Evol. 60: 337- 44. Liang, H., Cavalcanti, A. R. O., and L. F. Landweber (2005) Conservation of tandem stop codons in yeasts. Genome Biology 6(4):R31-R31.8. Stover, N. A., A. R. O. Cavalcanti, A. J. Li, B. C. Richardson, and L. F. Landweber. (2005) Reciprocal fusions of two genes in the formaldehyde detoxification pathway in ciliates and diatoms. Mol Biol Evol. 22(7):1539-42. Liang, H. and L. F. Landweber (2005) Molecular mimicry: quantitative methods to study structural similarity between protein and RNA. RNA 11(8):1167-72. Vlassov, A. V., Kazakov, S. A. Johnston, B. H. and L. F. Landweber, (2005) The RNA World on Ice: A New Scenario for the Emergence of RNA Information. J. Mol Evol. 61(2):264-73. Chang, W.-J., Bryson, P. D., Liang, H., Shin, M.-K. and L. F. Landweber (2005) The evolutionary origin of a complex scrambled gene. Proc Natl Acad Sci U S A. 102(42):15149-54. Liang, H., L. F. Landweber, and J. R. Fresco (2005) Are stop codons recognized by base triplets in the large ribosomal RNA subunit? RNA 11(10):1478-84. van Noort, D. and L. F. Landweber (2005) Towards a re-programmable DNA computer. Natural Computing 4: 163-175. Kuo, S., W.-J. Chang, and L. F. Landweber (2006) Complex Germline Architecture: Two Genes Intertwined on Two Loci. Mol. Biol. Evol. 23(1):4-6. Liang, H. and L. F. Landweber (2006) A Genome-wide Study of Dual Coding Regions in Human Alternatively Spliced Genes. Genome Research 16(2):190-196. Chang, W.-J., S. Kuo, and L. F. Landweber (2006) A new scrambled gene in the ciliate Uroleptus. Gene 368:72-77. Cavalcanti, A.R.O., N. A. Stover and L. F. Landweber (2006) On the paucity of duplicated genes in Caenorhabditis elegans operons. J. Mol. Evol. 62(6):765-771. McFarland, C.P., W.-J. Chang, S. Kuo, and L. F. Landweber (2006) Conserved linkage of two genes on the same macronuclear chromosome in spirotrichous ciliates. Chromosoma 115(2):129-138. Wong, L.-C. and L. F. Landweber (2006) Evolution of Programmed DNA Rearrangements in a Scrambled Gene. Mol. Biol. Evol. 23(4):756-763. updated 12/7/06 - 4 - Livstone, M. S., R. Weiss, and L. F. Landweber (2006) Automated Design and Programming of a Microfluidic DNA Computer. Natural Computing 5:1-13. Möllenbeck, M., A. R. O. Cavalcanti, F. Jönsson, H. J. Lipps, and L. F. Landweber (2006) Interconversion of germline-limited and somatic DNA in a scrambled gene. J. Mol. Evol. 63(1):69-73. Liang, H., W. Zhou, L. F. Landweber (2006) SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. Nucleic Acids Res. 34:W382-4. Liang, H. and L. F. Landweber. Hypothesis: RNA Editing of MicroRNA Target Sites in Humans? RNA, in press. REFEREED REVIEW ARTICLES OR COMMENTARY Landweber, L. F. and L. A. Katz. (1998) Evolution: Lost Worlds. Trends Ecol. Evol. 13: 93-94. Landweber, L. F., Simon, P. J., and T. A. Wagner. (1998) Ribozyme Design and Early Evolution. BioScience 48: 94-103. Landweber, L. F. (1999) Testing Ancient RNA-Protein Interactions. Proc. Natl. Acad. Sci. USA_96: 11067-11068. Knight, R. D., Freeland, S. J., and L. F. Landweber. (June, 1999) Selection, History, and Chemistry: The Three Faces of the Genetic Code. Trends in Biochemical Sciences_24(6):241-247. Forbes, N. A. and L. F. Landweber. (1999) Computer Science and Meta-Evolution. Trends in Genetics. 15(6):220-221. Landweber, L. F. (1999) Experimental RNA Evolution. Trends Ecol. Evol. 14: 353-358. Kari, L. and L. F. Landweber. (1999) Computing with DNA. Methods in Molecular Biology_132: 413-430. Forbes, N. A. and L. F. Landweber. (1999) Computer Science and the Evolution of Genetic Information. Computing in Science and Engineering_1(5):12-15. Landweber, L. F. (1999) Something Old for Something New: The Future of Ancient DNA in Conservation Biology. In Genetics and the Extinction of Species. L. F. Landweber and A. Dobson, eds. Princeton University Press, 163-186. Knight, R. D., and L. F. Landweber (June 9, 2000) The Early Evolution of the Genetic Code Cell 101(6) 569-572. Freeland, S. J., Knight, R. D., and L. F. Landweber (2000) Measuring adaptation in the genetic code. Trends in Biochemical Sciences_25(2): 44-5. Ruben, A. J. and L. F. Landweber (2000) The Past, Present, and Future of Molecular Computing. Nature Reviews Molecular Cell Biology, inaugural October issue 1: 69-72. Horton, T. L. and L. F. Landweber (2000) Nucleic Acid Biodiversity. In Encyclopedia of Biodiversity. S. A. Levin, ed. Adademic Press 4: 415-426. Faulhammer, D., Lipton, R. J. and L. F. Landweber (2000) When the knight falls: On constructing an RNA computer. In DNA Based Computers V, E. Winfree, D. Gifford, eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, 54: 1-7. Beech, P. L., Landweber, L. F. and P. R. Gilson. (2000) Protist News: Meeting Report: XIIIth Meeting of the International Society for Evolutionary Protistology, Ceské Budejovice, Czech Republic, July 31-August 4, 2000 Protist 151: 299-305. Knight, R. D., Freeland, S. J., and L. F. Landweber (2001) Rewiring the Keyboard: Evolvability of the Genetic Code. Nature Reviews Genetics 2: 49-58. Landweber, L. F. (2002) Custom Codons come in Threes, Fours, and Fives. Chemistry and Biology. 9(2):143. Horton, T. L. and L. F. Landweber (2002) Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes Current Opinion in Microbiology 5: 620-626. Knight, R. D., Landweber, L. F., and M. Yarus (2002) Tests of a Stereochemical Code. In Translation Mechanisms, Lapointe, J. and Brakier-Gingras, L., eds., Landes Bioscience. Livstone, M., van Noort, D., and L. F. Landweber (2003) Molecular computing revisited: a Moore's law? Trends in Biotechnology. 21: 98-101. Cavalcanti, A.R.O. and Landweber LF. (2003) Genetic code: what nature missed. Current Biology 13(22):R884-5. Knight, R. D., Freeland, S. J., and L. F. Landweber (2004) Adaptive Evolution of the Genetic Code. In The Genetic Code and the Origin of Life. Ribas de Pouplana, L., ed., Landes Bioscience. Cavalcanti, A.R.O. and L.F. Landweber (2004) Genetic code. Current Biology 14: R147. Koonin, E. V., L. F. Landweber, D. J. Lipman (2006) A community experiment with fully open and published peer review. Biol Direct 1:1. updated 12/7/06 - 5 - Koonin, E. V., L. F. Landweber, D. J. Lipman, R. Dignon (2006) Reviving a culture of scientific debate. Nature doi:10.1038/nature05005, www.nature.com/nature/peerreview/debate/nature05005.html CONFERENCE PROCEEDINGS AND OTHER PUBLICATIONS Landweber, L. F. and M. Kreitman (1995) Producing Single-Stranded DNA in Polymerase Chain Reaction for Direct Genomic Sequencing. In Recombinant DNA Methodology II, Ray Wu, ed., pp.579-588. Landweber, L. F. and R. J. Lipton. (1997) DNA2DNA Computations: A potential ‘killer app'? In 24th International Colloquium on Automata, Languages and Programming (ICALP), Lecture Notes in Computer Science, pages 672-683, Springer-Verlag. Landweber, L. F. (1998) The Evolution of DNA Computing: Nature's Solution to a Path Problem. IEEE Proceedings of Symposia on Intelligence and Systems '98, May 21-23, 1998. IEEE Computer Society Press, 133-139. Landweber, L. F. and L. Kari. (1998) The Evolution of DNA Computing: Nature's Solution to a Computational Problem. 1998 Genetic Programming Conference Proceedings, John Koza et al., eds., Morgan Kaufmann Publishers, Inc., 700-708. Landweber, L. F. (1998) RNA Based Computing. In DNA Based Computers II, L. F. Landweber and E. B. Baum, eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, 181-189. Landweber, L. F., Lipton, R. J. and M. O. Rabin. (1999) DNA2DNA Computations: A Potential "Killer App"? In DNA Based Computers III, H. Rubin and D.H. Wood, eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, vol 48, 161-172. Landweber, L. F. and L. Kari. (1999) The Evolution of Cellular Computing: Nature's Solution to a Computational Problem, In DNA Based Computers IV, L. Kari, ed. Biosystems 52:3-13 Cukras, A. R., Faulhammer, D., Lipton, R. J. and L. F. Landweber (1999) Chess Games: A Model for RNA Based Computation. In DNA Based Computers IV, L. Kari, ed. Biosystems 52:35-45. Faulhammer, D., Lipton, R. J. and L. F. Landweber (1999) Counting DNA: Estimating the complexity of a test tube of DNA. In DNA Based Computers IV, L. Kari, ed. Biosystems 52:193-6. Landweber, L. F. (1999) The Evolution of Cellular Computing. The Biological Bulletin 196: 324-326. Knight, R. D. and L. F. Landweber (1999) Is the Genetic Code Really a Frozen Accident? New Evidence from In Vitro Selection. In Molecular Strategies in Biological Evolution. Annals New York Acad. Sci, 870:408-410. Curtis, E. and L. F. Landweber (1999) The Evolution of Gene Scrambling in Ciliate Micronuclear Genes. In Molecular Strategies in Biological Evolution. Annals New York Acad. Sci. 870: 349- 350. Kari, L. and L. F. Landweber (1999) L'ordinateur biologique, pour demain? Le Calcul par ADN (Computing with DNA) Les Cahiers de Science & Vie, Octobre, 53: 88-93. Kari, L., Kari, J., and L. F. Landweber. (1999) Reversible molecular computation in ciliates. in Jewels are Forever, Karhumaki, J., Maurer, H., Paun, G., and Rozenberg, G., eds. Springer-Verlag, pp. 353-363. Kari, L., Siromoney, R., Daley, M., Gloor, G., and L. F. Landweber (1999). How to compute with DNA. Proceedings of Foundations of Software Technology and Theoretical Computer Science, C. Pandu Rangan, R. Ramanujam, Eds., Lecture Notes in Computer Science, 1738, Springer Verlag, Berlin, 269-282. Kari, L. and L. F. Landweber (2000) Computational Power of Gene Rearrangement, In DNA Based Computers V, E. Winfree, D. Gifford eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, vol 54: 201-216. Ruben, A. J. and L. F. Landweber (2001) The Past, Present, and Future of DNA Computing. In Biotechnology 2000. B. Alizadeh, ed. Universal Medical Press, San Francisco. Landweber, L. F. and L. Kari (2002) Universal Molecular Computation in Ciliates. In Landweber, L. F. and Winfree, E., eds. Evolution as Computation. Springer-Verlag, Berlin. Kari, L. and L. F. Landweber. (2004) Biocomputation in ciliates. In Cellular Computing, M. Amos, Ed., Oxford University Press, 202-216. Vlassov AV, Johnston BH, Landweber LF, Kazakov SA. (2005) RNA catalysis in frozen solutions. Dokl Biochem Biophys. May-Jun;402:207-9. Cavalcanti, A. R. O., and L. F. Landweber. (2006) Insights into a Biological Computer: Detangling
Category: Biological Sciences & Engineering
Type: Scientist & Engineers
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