Lee Newberg's Academic Publications

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Journal Publications

Also see PubMed and DBLP.
* indicates first author or co-first author.

  1. Lee A. Newberg* and Charles E. Lawrence (2009) Exact Calculation of Distributions on Integers, with Application to Sequence Alignment. J Comput Biol, 16(1), in press.
  2. Lee A. Newberg* (2008) Significance of gapped sequence alignments. J Comput Biol, 15(9), 1187-1194. doi: 10.1089/cmb.2008.0125. (Sequence Alignment Significance Web Server)
  3. Lee A. Newberg* (2008) Memory-efficient dynamic programming backtrace and pairwise local sequence alignment. Bioinformatics, 24(16), 1772-1778. doi: 10.1093/bioinformatics/btn308 google: dnsJk5vHpNMJ.
  4. Lee A. Newberg*, William A. Thompson*, Sean Conlan, Thomas M. Smith, Lee Ann McCue, and Charles E. Lawrence (2007) A phylogenetic Gibbs sampler that yields centroid solutions for cis regulatory site prediction. Bioinformatics, 23(14), 1718-1727. doi: 10.1093/bioinformatics/btm241 google: SnIOwPMtubMJ. (Gibbs Web Server)
  5. William A. Thompson*, Lee A. Newberg*, Sean Conlan, Lee Ann McCue, and Charles E. Lawrence (2007) The Gibbs Centroid Sampler. Nucleic Acids Research, 35(Web Server Issue), W232-W237. doi: 10.1093/nar/gkm265 google: LKeIBgTvWF4J. (Gibbs Web Server)
  6. C. Steven Carmack*, Lee Ann McCue*, Lee A. Newberg*, and Charles E. Lawrence (2007) PhyloScan: Identification of transcription factor binding sites using cross-species evidence. Algorithms for Molecular Biology, 2(1), article 1. doi: 10.1186/1748-7188-2-1 google: ZSHpoF9s-oEJ. (PhyloScan Web Server)
  7. Lee A. Newberg*, Lee Ann McCue, and Charles E. Lawrence (2005) The relative inefficiency of sequence weights approaches in determining a nucleotide position weight matrix. Statistical Applications in Genetics and Molecular Biology, 4(1), article 13. doi: 10.2202/1544-6115.1135 google: qLfhcMrgZf8J. (Effective Species Count / Motif Efficiency Web Server)
  8. Lee A. Newberg* and Charles E. Lawrence (2004) Mammalian genomes ease location of human DNA functional segments but not their description. Statistical Applications in Genetics and Molecular Biology, 3(1), article 23. doi: 10.2202/1544-6115.1065 google: tge8U2NCbsUJ.
  9. Lee A. Newberg* (1996) The number of clone orderings. Discrete Applied Mathematics, 69(3), 233-245. doi: 10.1016/0166-218X(96)00093-5. google: qZ-D4JF8rIsJ
  10. Richard M. Karp* and Lee A. Newberg* (1995) An algorithm for analysing probed partial digestion experiments. Computer Applications in the Biosciences, 11(3), 229-235. doi: 10.1093/bioinformatics/11.3.229. google: EfTMo66ycf8J
  11. Farid Alizadeh*, Richard M. Karp*, Lee A. Newberg*, and Deborah K. Weisser* (1995) Physical mapping of chromosomes: A combinatorial problem in molecular biology. Algorithmica, 13(1-2), 52-76. doi: 10.1007/BF01188581 google: RJpCS5uqB-gJ. (Similar Technical Report)
  12. Lee A. Newberg* and David S. Wolfe* (1994) String layouts for a redundant array of inexpensive disks. Algorithmica, 12(2-3), 209-224. doi: 10.1007/BF01185211 google: s0BlySGCs5EJ. (Similar Technical Report)
  13. Lee A. Newberg* (1994) Finding a most likely clone ordering from oligonucleotide hybridization data. Genomics, 21(3), 602-611. doi: 10.1006/geno.1994.1320 google: pGKbJMirlL0J.
  14. Lee A. Newberg* and Dalit Naor (1993) A lower bound on the number of solutions to the probed partial digest problem. Advances in Applied Mathematics, 14(2), 172-183. doi: 10.1006/aama.1993.1009 google: 5QOr-rOPtV0J.
  15. Eric S. Lander, Philip Green, Jeff Abrahamson, Aaron Barlow, Mark J. Daly, Stephen E. Lincoln, and Lee A. Newburg [sic] (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1(2), 174-181. doi: 10.1016/0888-7543(87)90010-3 google: rfcZTMTt7IsJ.

Journal Publications, Acknowledged

  1. Acknowledged in Luis E. Carvalho and Charles E. Lawrence (2008) Centroid estimation in discrete high-dimensional spaces with applications in biology. Proceedings of the National Academy of Sciences, USA, 105(9), 3209-3214. doi: 10.1073/pnas.0712329105. google: eYgM8ORYxiYJ
  2. Acknowledged in Sean Conlan, Charles Lawrence, and Lee Ann McCue (2005) Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes. Applied and Environmental Microbiology, 71(11), 7442-7452. doi: 10.1128/AEM.71.11.7442-7452.2005. google: BP309aEvnkEJ
  3. Acknowledged in Heidi Jo Newberg and Brian Yanny (1997) Three-dimensional parameterization of the stellar locus with application to QSO color selection. The Astrophysical Journal Supplement Series, 113, 89-104 doi: 10.1086/313051. google: r1XQtXM2PvAJ
  4. Acknowledged in Eric S. Lander and Philip Green (1987) Construction of multilocus genetic linkage maps in humans. Proceedings of the National Academy of Sciences, USA, 84(8), 2363-2367. doi: 10.1073/pnas.84.8.2363 google: ip5yQVV6JqAJ.

Presented Talks

  1. Lee A. Newberg (2007) OrthoGibbs & PhyloScan: A comparative genomics approach to locating transcription factor binding sites. Special Seminar, Wadsworth Center, Albany NY.
  2. Sean P. Conlan, William Thompson, Lee Ann McCue, Lee A. Newberg, Thomas M. Smith, and Charles E. Lawrence (2006) OrthoGibbs: A Phylogenetically-Aware Gibbs Recursive Sampler for Locating Transcription Factor Binding Sites (a.k.a. A Phylogenetic Gibbs Recursive Sampler for Locating Transcription Factor Binding Sites) Phylogenomics Conference Sainte-Adèle, Québec, Canada
  3. Lee A. Newberg (2005) What Is Conservation? The Center for Bioinformatics Wadsworth Center, Albany, NY.
  4. Lee A. Newberg and Charles E. Lawrence (2004) How Much Is Another Mammal Worth? In The First Annual RECOMB Satellite Workshop on Regulatory Genomics, page 13 The University of California, San Diego, CA.
  5. Lee A. Newberg (2002) DNA Contig Reconstruction, Computer Science, and Funding. Computer Science Colloquium Series Rensselaer Polytechnic Institute, Troy, NY.
  6. Farid Alizadeh, Richard M. Karp, Lee A. Newberg, and Deborah K. Weisser (1993) Physical Mapping of Chromosomes: A Combinatorial Problem in Molecular Biology. In Proceedings of The Fourth Annual ACM-SIAM Symposium on Discrete Algorithms. ACM Press, Austin, TX. (Similar Technical Report)

Conference Abstracts and Posters

  1. Lee A. Newberg, William A. Thompson, Sean P. Conlan, Thomas M. Smith, Lee Ann McCue, and Charles E. Lawrence (2008) Understanding Gene Regulation in Mycobacterium tuberculosis: The Phylogenetic Gibbs Centroid Sampler for Cis-Regulatory Element Discovery. Poster 96 at Poster Day 2008, New York State Department of Health, Albany, NY.
  2. Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann McCue, and Charles E. Lawrence (2007) The Phylogenetic Gibbs Centroid Sampler for Cis-Regulatory Element Discovery. Poster J11 at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology and Sixth European Conference on Computational Biology, International Society for Computational Biology, Vienna, Austria.
  3. Sean P. Conlan, William Thompson, Lee Ann McCue, Lee A. Newberg, Thomas M. Smith, and Charles E. Lawrence (2006) A Phylogenetic Gibbs Recursive Sampler for Locating Transcription Factor Binding Sites and Lee A. Newberg (2006) A New Nucleotide Substitution Model for Use with Felsenstein's Algorithm. Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
  4. Lee A. Newberg (2005) Functional DNA Positions Change As Frequently As Neutral Ones. In Systems Biology: Global Regulation of Gene Expression, page 61, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. (Similar Technical Report)
  5. C. Steven Carmack, Lee Ann McCue, Lee A. Newberg, and Charles E. Lawrence (2005) PhyloScan: A New Tool for Identifying Statistically Significant Transcription Factor Binding Sites by Combining Cross-Species Evidence. In 2005 Genomics: GTL Workshop, #53, page 72, U.S. Department of Energy, Washington, DC. (PhyloScan Web Server)
  6. Lee A. Newberg and Charles E. Lawrence (2004) Mammalian Genomes Ease the Location of Human Transcription Factor Binding Sites but Do Not Ease Their Description. In Systems Biology: Genomic Approaches to Transcriptional Regulation, page 82, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. (Extended Abstract)
  7. Lee A. Newberg, Jerome J. Jahnke, John A. Kruper, and David Micklos (1996) Implementing a Student Allele Database via the World Wide Web. In Proceedings of The World Conference on Educational Multimedia and Hypermedia, Association for the Advancement of Computing in Education, Boston, MA. (Preprint)
  8. Lee A. Newberg, Richard O. Rouse III, and John A. Kruper (1995) Integrating the World-Wide Web and Multi-User Domains to Support Advanced Network-Based Learning Environments. In Proceedings of The World Conference on Educational Multimedia and Hypermedia, Association for the Advancement of Computing in Education, Graz, Austria. (Preprint)
  9. Acknowledged in John Kruper and Marc Lavenant (1994) The Phoenix Project at the University of Chicago: Developing a Secure, Distributed Hypermedia Authoring Environment Built on the World Wide Web. In Proceedings of The First International Conference on the World-Wide Web, CERN, Geneva, Switzerland. (Preprint)

Technical Reports

  1. Lee A. Newberg (2007) Effective species count and motif efficiency: The value of comparative genomics in characterizing conserved sequence positions. Technical Report 07-09, Rensselaer Polytechnic Institute Department of Computer Science, Troy, NY. (Effective Species Count / Motif Efficiency Web Server)
  2. Lee A. Newberg (2005) Functional DNA Positions Change As Frequently As Do Neutral Ones. Technical Report 05-08, Rensselaer Polytechnic Institute Department of Computer Science, Troy, NY.
  3. Lee A. Newberg, Lee Ann McCue, and Charles E. Lawrence (2003) The Relative Inefficiency of Sequence Weights in Determining a Nucleotide Consensus Distribution. Technical Report 03-10, Rensselaer Polytechnic Institute Department of Computer Science, Troy, NY.
  4. Farid Alizadeh, Richard M. Karp, Lee A. Newberg, and Deborah K. Weisser (1992) Physical Mapping of Chromosomes: A Combinatorial Problem in Molecular Biology. Technical Report 92-066, International Computer Science Institute, Berkeley, CA.
  5. Lee A. Newberg and David S. Wolfe (1991) Strings Layout in Redundant Disk Arrays. Technical Report 91/625, Computer Science Department, University of California, Berkeley, CA.

Theses

  1.   Lee A. Newberg (1993) Finding, Evaluating, and Counting DNA Physical Maps. PhD thesis with Richard M. Karp, Department of Computer Science, The University of California, Berkeley, CA.
  2.   Lee A. Newberg (1991) The k-Server Problem with Distinguishable Servers. Master's thesis with Richard M. Karp, Department of Computer Science, The University of California, Berkeley, CA.
  3.   Lee A. Newberg (1986) Monte Carlo Simulation of the Nuclear to Quark Matter Deconfinement Transition of Three Quark Nucleons. Undergraduate thesis with Charles J. Horowitz, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA.

Graduate Students

  1. RPI Thomas M. Smith (2006) A Computational System for Identifying Cis-Regulatory Elements in Closely Related Genomes. Ph.D thesis with Lee A. Newberg, Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY. (Available upon request.)