Lee Newberg's Academic Publications

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Journal Publications

Also see PubMed and DBLP.
*An asterisk indicates first author or co-first author.
Note: I stepped away from scientific research, 1993-2002.

  1. Michael J. Palumbo* and Lee A. Newberg* (2010) Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data. Nucleic Acids Research, 38(Web Server Issue), W268-W274. doi: 10.1093/nar/gkq330. Google Scholar. (PhyloScan Web Server)
  2. Matthew J. Harrigan, Heidi Jo Newberg, Lee A. Newberg, Brian Yanny, Timothy C. Beers, Young Sun Lee, and Paola Re Fiorentin (2010) Statistical properties of blue horizontal branch stars in the spheroid: detection of a moving group approximately 50 kpc from the sun. Monthly Notices of the Royal Astronomical Society, 405(3), 1796-1808. doi: 10.1111/j.1365-2966.2010.16552.x. Google Scholar. arXiv: 1002.3607.
  3. Lee A. Newberg* (2009) Error statistics of hidden Markov model and hidden Boltzmann model results. BMC Bioinformatics, 10, article 212. doi: 10.1186/1471-2105-10-212. Google Scholar.
  4. Lee A. Newberg* and Charles E. Lawrence* (2009) Exact calculation of distributions on integers, with application to sequence alignment. Journal of Computational Biology, 16(1), 1-18. doi: 10.1089/cmb.2008.0137. Google Scholar.
  5. Ian C. Jacobi, Heidi J. Newberg, Darren Broder, Rose A. Finn, Anthony J. Milano, Lee A. Newberg, Allan T. Weatherwax, and Douglas C. B. Whittet (2008) Effect of night laboratories on learning objectives for a nonmajor astronomy class. Astronomy Education Review, 7(2), article 301. doi: 10.3847/AER2008021. Google Scholar. (Extended Version).
  6. Lee A. Newberg* (2008) Significance of gapped sequence alignments. Journal of Computational Biology, 15(9), 1187-1194. doi: 10.1089/cmb.2008.0125. Google Scholar. (Sequence Alignment Significance Web Server)
  7. 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 Scholar. (Supplementary Data)
  8. 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 Scholar. (Gibbs Web Server)
  9. 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 Scholar. (Gibbs Web Server)
  10. 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 Scholar. (PhyloScan Web Server)
  11. 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 Scholar. (Effective Species Count / Motif Efficiency Web Server)
  12. 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 Scholar.
  13. 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 Scholar
  14. 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 Scholar
  15. 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 Scholar. (Similar Technical Report)
  16. 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 Scholar. (Similar Technical Report)
  17. 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 Scholar.
  18. 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 Scholar.
  19. Eric S. Lander, Philip Green, Jeff Abrahamson, Aaron Barlow, Mark J. Daly, Stephen E. Lincoln, and Lee A. Newberg (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 Scholar (PDF).

Journal publications, acknowledged

  1. Matthew T. Harrison (2012) Conservative hypothesis tests and confidence intervals using importance sampling. Biometrika. 99(1), 57-69. doi: 10.1093/biomet/asr079. Google Scholar.
  2. 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 Scholar.
  3. Sean Conlan and Lee Ann McCue (2006) Software to perform automated comparisons of pair-wise percent identities for microbial species. Biotechniques, 40(5), 578-582. doi: 10.2144/000112170 (broken). Google Scholar.
  4. Sean Conlan, Charles E. 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 Scholar.
  5. Heidi J. 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 Scholar.
  6. Farid Alizadeh, Richard M. Karp, Deborah K. Weisser, and Geoffrey Zweig (1995) Physical mapping of chromosomes using unique probes. Journal of Computational Biology, 2(2), 159-184. doi: 10.1089/cmb.1995.2.159. Google Scholar.
  7. Heidi Jo Newberg (1992) Measuring q0 Using Supernovae at z ≈ 0.3. Doctoral thesis with Richard A. Muller, Department of Physics, University of California, Berkeley, CA.
  8. 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 Scholar.

Presented Talks

  1. Lee A. Newberg (2011) Gibbs Sampling and Centroids for Gene Regulation. Albany Chapter, American Statistical Association, Albany, NY. November 30, 2011.
  2. Lee A. Newberg (2011) Gibbs Sampling for Gene Cis-Regulatory Elements. GE Global Research Center, Niskayuna, NY. October 21, 2011.
  3. Lee A. Newberg (2011) E-Value Estimation for Non-Local Alignment Scores. Janelia Farm Research Center, Howard Hughes Medical Institute, Ashburn, VA. April 13, 2011.
  4. Lee A. Newberg (2009) Getting Statistical Significance and Bayesian Confidence Limits for Your Hidden Markov Model Results, with Pairwise Alignment of Nucleotide Sequences As an Example. Laboratory for Computational and Structural Biology, Wadsworth Center, Albany, NY. December 7, 2009.
  5. Lee A. Newberg (2009) Getting Statistical Significance and Bayesian Confidence Limits for Your Hidden Markov Model or Score-Maximizing Dynamic Programming Algorithm, with Pairwise Alignment of Sequences As an Example. Center for Computational Molecular Biology Seminar Series, Brown University, Providence, RI. October 7, 2009.
  6. Lee A. Newberg, Bobbie-Jo M. Webb-Robertson, Lee Ann McCue, and Charles E. Lawrence (2009) Global Measures of Uncertainty: Long Overdue in Computational Molecular Biology. Joint Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology and Eighth European Conference on Computational Biology, International Society for Computational Biology, Stockholm, Sweden. July 2, 2009.
  7. Lee A. Newberg and Charles E. Lawrence (2009) Exact Calculation of Distributions on Integers, with Application to Sequence Alignment. Theory Seminar Series, Department of Computer Science, Rensselaer Polytechnic Institute, Troy NY. April 29, 2009.
  8. Lee A. Newberg (2007) OrthoGibbs & PhyloScan: A Comparative Genomics Approach to Locating Transcription Factor Binding Sites. Special Seminar, Wadsworth Center, Albany NY. June 19, 2007.
  9. 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. July, 2006.
  10. Lee A. Newberg (2005) What Is Conservation? The Center for Bioinformatics Wadsworth Center, Albany, NY. February 22, 2005.
  11. 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. March 26, 2004.
  12. Lee A. Newberg (2002) DNA Contig Reconstruction, Computer Science, and Funding. Computer Science Colloquium Series Rensselaer Polytechnic Institute, Troy, NY.
  13. 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 Ann McCue, Lee A. Newberg, William A. Thompson, and Charles E. Lawrence (2012) Multi-Species, Multi-Gene Co-Regulation: Finding DNA Cis-Regulatory Elements for Biofuel Pathways in Alpha-Proteobacteria. Poster and abstract at the 2012 Genomic Science Awardee Meeting X, US Department of Energy, Office of Biological and Environmental Research, Bethesda North Marriott Hotel & Conference Center, Bethesda, MD.
  2. Travis Desell, Lee A. Newberg, Malik Magdon-Ismail, Boleslaw K. Szymanski, and William Thompson (2012) Finding Protein Binding Sites Using Volunteer Computing Grids. Proceedings of the 2011 2nd International Congress on Computer Applications and Computational Science, Advances in Intelligent and Soft Computing, 144, 385-393. doi: 10.1007/978-3-642-28314-7_52. Google Scholar. (Preprint)
  3. Travis J. Desell, Malik Magdon-Ismail, Heidi Jo Newberg, Lee A. Newberg, Boleslaw K. Szymanski, and Carlos A. Varela (2011) A Robust Asynchronous Newton Method for Massive Scale Computing Systems. IEEE International Conference on Computational Intelligence and Software Engineering (CiSE 2011), Wuhan, China. (Preprint)
  4. Luis E. Carvalho, William A. Thompson, Lee A. Newberg, and Charles E. Lawrence (2009) Applications of Centroid Estimation to Regulatory Genomics. Poster at the RECOMB Satellite on Regulatory Genomics, Massachusetts Institute of Technology, Cambridge, MA.
  5. Lee A. Newberg (2009) Computationally Efficient Estimation of the Error Rates of Hidden Markov Model Results. Poster U02 at the joint Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology and Eighth European Conference on Computational Biology, International Society for Computational Biology, Stockholm, Sweden.
  6. Lee Ann McCue, William A. Thompson, Lee A. Newberg, and Charles E. Lawrence (2009) Phylogenetic Footprinting in the Shewanellae. Poster at Genomics: GTL Contractor-Grantee Workshop VII, US Department of Energy, Office of Biological and Environmental Research, Bethesda North Marriott Hotel & Conference Center, Bethesda, MD.
  7. Lee A. Newberg (2008) Estimation of Statistical Significance for Motif Scans by Hidden Markov Models. Poster 177 at the RECOMB Satellite on Regulatory Genomics, Massachusetts Institute of Technology, Cambridge, MA.
  8. Michael J. Palumbo and Lee A. Newberg (2008) PhyloScan II Web Server: Scanning for Cis-Regulatory Elements in Mixed Aligned and Unaligned Sequence Data. Poster 186 at the RECOMB Satellite on Regulatory Genomics, Massachusetts Institute of Technology, Cambridge, MA.
  9. 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.
  10. 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 joint Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology and Sixth European Conference on Computational Biology, International Society for Computational Biology, Vienna, Austria.
  11. Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann McCue, and Charles E. Lawrence (2007) Centroid Methods for High-Dimensional Inference in Computational Biology. Poster at Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
  12. 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. Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
  13. 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.
  14. Lee A. Newberg (2005) Functional DNA Positions Change As Frequently As Do Neutral Ones. In Systems Biology: Global Regulation of Gene Expression, page 61, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. (Similar Technical Report).
  15. 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 Genomics: GTL Contractor-Grantee Workshop III, #53, page 72, U.S. Department of Energy, Washington, DC. (PhyloScan Web Server)
  16. 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)
  17. 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)
  18. 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)
  19. 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, European Organization for Nuclear Research (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. Doctoral thesis with Richard M. Karp, Department of Computer Science, The University of California, Berkeley, CA. Google Scholar.
  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. Google Scholar.
  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. Google Scholar.

Graduate Students

Ph.D. Advisees:

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

Ph.D. thesis committee for:

  1. Andrey Sarayev (2009) Estimation of Credit and Interest Rate Risks for Loan Portfolios. Doctoral thesis with Malik Magdon-Ismail, Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY. Google Scholar.
  2. A. P. Jason de Koning (2007) Experimental Design and the Detection of Adaptive Molecular Divergence in Phylogenetics and Genomics. Doctoral thesis with Caro-Beth Stewart, Department of Biological Sciences, State University of New York, Albany, NY. Google Scholar.
  3. Benjarath Phoophakdee (2007) Trellis: Genome-Scale Disk-Based Suffix Tree Indexing Algorithm. Doctoral thesis with Mohammed Zaki, Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY. Google Scholar.
  4. James Kilbride (2006) Methods for Reformulating Dynamic Programming Algorithms As Representatively Sampled Algorithms. Doctoral thesis with Mukkai S. Krishnamoorthy, Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY. Google Scholar.
  5. Nicholas Markham (2006) Algorithms and Software for Nucleic Acid Sequences. Doctoral thesis with Michael Zuker, Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY. Google Scholar.