Lee Newberg's Academic Publications

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Journal Publications

Also see PubMed, DBLP, and Google Scholar. *For these journal publications, an asterisk indicates first author or co-first author.

  1. 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)
  2. 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.
  3. 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.
  4. 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)
  5. 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)
  6. 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
  7. 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
  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 Scholar.
  9. 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.
  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.
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. 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)
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. Lee A. Newberg*, Xiaowei Chen, Chinnappa D. Kodira, and Maria I. Zavodszky* (2018) Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PLoS One, 13(3), e0193067. doi: 10.1371/journal.pone.0193067. Google Scholar.
  21. Lee A. Newberg. Multiple contributions to the On-Line Encyclopedia of Integer Sequences.

Journal publications, acknowledged

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Dean Foster, Howard Karloff, and Kenneth E. Shirley (2016) How well does the standard body mass index or variations with a different exponent predict human lifespan?. Obesity, 24(2):469-475. doi: 10.1002/oby.21318. Google Scholar. (Mortality Calculator Web Server)

Presented Talks

  1. 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)
  2. Lee A. Newberg (2002) DNA Contig Reconstruction, Computer Science, and Funding. Computer Science Colloquium Series Rensselaer Polytechnic Institute, Troy, NY.
  3. 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.
  4. Lee A. Newberg (2005) What Is Conservation? The Center for Bioinformatics Wadsworth Center, Albany, NY. February 22, 2005.
  5. 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.
  6. 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.
  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, 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 (ISMB 2009) and Eighth European Conference on Computational Biology (ECCB 2009), International Society for Computational Biology, Stockholm, Sweden. July 2, 2009.
  9. 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.
  10. 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.
  11. 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.
  12. Lee A. Newberg (2011) Gibbs Sampling for Gene Cis-Regulatory Elements. GE Global Research Center, Niskayuna, NY. October 21, 2011.
  13. Lee A. Newberg (2011) Gibbs Sampling and Centroids for Gene Regulation. Albany Chapter, American Statistical Association, Albany, NY. November 30, 2011.

Conference Abstracts and Posters

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  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 Genomics: GTL Contractor-Grantee Workshop III, #53, page 72, U.S. Department of Energy, Washington, DC.
  6. 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)
  7. 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.
  8. 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.
  9. 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.
  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 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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)
  18. 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 Second 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)
  19. 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.
  20. Kareem S. Aggour, Dipen P. Sangurdekar, Vijay S. Kumar, Lee A. Newberg, and Chinnappa D. Kodira (2014) Efficient Next-Generation DNA Sequencing Analysis in Hadoop. Sixth International Conference on Bioinformatics and Computational Biology (BICoB 2014). Las Vegas, NV. (Best Paper Award finalist.)
  21. Chinnappa D. Kodira, Anup Sood, Lee A. Newberg, Alexandra Miller, Fiona Ginty, Elizabeth McDonough, Yunxia Sui, Alexander G. Bordwell, Qing Li, Lakshmi Kaanumalle, Keyur H. Desai, Zhengyu Pang, Edi Brogi, Steven M. Larson, Ingo K. Mellinghoff (2014) In situ genome-wide expression profiling of individual cell types. Sixty-Fourth Annual Meeting of the American Society of Human Genetics (ASHG 2014). San Diego, CA.

Patents

  1. John F. Graf, Brion D. Sarachan, Maria I. Zavodszky, Lee A. Newberg, Chinnappa D. Kodira, US patent S/N 13/917695 (June 14, 2013) Methods of viewing and analyzing high content biological data.
  2. Lee A. Newberg and Chinnappa D. Kodira, US patent S/N 15/659359 (July 25, 2017) Method for identifying expression distinguishers in biological samples.

Technical Reports

  1. 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.
  2. 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.
  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. 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.
  5. 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.
  6. Kareem S. Aggour, Dipen P. Sangurdekar, Vijay S. Kumar, Lee A. Newberg, and Chinnappa D. Kodira (2013) Big Data for Medical Diagnostics: Next-Generation DNA Sequencing in Hadoop. Technical Report 2013GRC962, GE Global Research, Niskayuna, NY.

Theses

  1.   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.
  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 (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.

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. Google Scholar. Lulu book.

Ph.D. thesis committee for:

  1. RPI 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.
  2. RPI 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.
  3. RPI 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. 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.
  5. RPI 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.