RESUME
CURRICULUM VITAE
Published Papers & Software
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Papers

Ryan M. Rifkin, Ross A. Lippert Notes on Regularized Least Squares

  • MIT libraries


    • Ross A. Lippert, Kevin J. Bowers, Brent A. Gregersen, Ron O. Dror, Michael P. Eastwood, John L. Klepeis, Istvan Kolossvary, and David E. Shaw. A common, avoidable source of error in molecular dynamics integrators J. Chemical Physics, volume 126, issue4 (January), page 046101.

  • last submission


    • Ross A. Lippert. Discrete approximations to continuum optimal flow problems Studies in Applied Mathematics, volume 117, issue 4, 321-334.

  • last submission
  • from Studies in Applied Mathematics


    • Ryan M. Rifkin and Ross A. Lippert. Value Regularization and Fenchel Duality J. of Machine Learning Research, volume 8 (March), 441-439 (2007).

  • from me
  • from JMLR


    • Ross A. Lippert and Normand A. Modine and Alan F. Wright The optimized effective potential with finite temperature J. of Physics: Condensed Matter, volume 18, 4295-4304 (2006).

  • from me
  • from JoP (limited time)


    • Ross A. Lippert and Ryan M. Rifkin. Infinite-sigma Limits for Tikhonov Regularization J. of Machine Learning Research 7(May):855--876 (2006).

  • latest submission
  • from JMLR


    • Ross A. Lippert and Ryan M. Rifkin. Asymptotics of Gaussian Regularized Least Squares Neural Information Processing Systems (NIPS) 2005. Accepted.

  • tech report version
  • with slight corrections
  • from NIPS


    • Ross A. Lippert, Clark M. Mobarry, Brian P. Walenz. A space-efficient construction of the Burrows Wheeler Transform for genomic data J. of Computational Biology. Volume 12, number 7, pp943-951. Sept. 2005

  • something close to a preprint
  • online at JCB


    • Ross A. Lippert. Fixing Two Eigenvalues by a Minimal Perturbation. Linear Algebra and its Applications. Vol 406C.(2005), pp 177-200

  • no pre-print, but something close
  • Preprint from ScienceDirect (subscription required)


    • Francisco M. De La Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V. Halldórsson, Xiaoping Su, Ross A. Lippert, et al. The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Research. Published March 21, 2005, 10.1101/gr.3241705

  • from Genome Research


    • Ross A. Lippert. Space-Efficient Whole Genome Comparisons with Burrows-Wheeler Transforms. J. of Computational Biology. Volume 12, Number 4 (2005), pp407--415

  • No preprint just yet but here is something close
  • We have Bob Harris to thank for the errata.


    • Bert Gold, Francis Kalush, Julie Bergeron, Kevin Scott, Nandita Mitra, Kelly Wilson, Nathan Ellis, Helen Huang, Michael Chen, Ross Lippert, Bjarni V. Halldorsson, Beth Woodworth, Thomas White, Andrew G. Clark, Fritz F. Parl, Samuel Broder, Michael Dean and Kenneth Offit. Estrogen Receptor Genotypes and Haplotypes Associated with Breast Cancer Risk Cancer Research 64, 8891-8900, December 15 (2004).

  • from Cancer Research.


    • Nathan Edwards and Ross A. Lippert. Sequence database compression for peptide identification from tandem mass spectra. 4th Workshop on Algorithms in Bioinformatics (WABI 2004), Bergen, Norway (2004).

  • from Nathan

    • Bjarni Halldorsson, Vineet Bafna, Ross A. Lippert, Russell Schwartz, Francisco De La Vega, Andrew Clark, Sorin Istrail. Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies. Genome Research 14:1633-1640 (2004).

  • from me (.pdf)


    • Olaf Delgado Friedrichs, Aaron L. Halpern, Ross Lippert, Christian Rausch, Stephan C. Schuster, Daniel H. Huson. Syntenic Layout of Two Assemblies of Related Genomes. Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, Germany, October 4-6, 2004}.

  • from me (.pdf)


    • Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail. Finding anchors for genomic sequence comparison. Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004).

  • from me (.pdf)


    • Sorin Istrail, Granger G. Sutton, Liliana Florea, Aaron L. Halpern, Clark M. Mobarry, Ross Lippert, et al. Whole-genome shotgun assembly and comparison of human genome assemblies. PNAS (February 17, 2004). vol. 101, no. 7. pages 1916-1921.

  • from PNAS online


    • Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross A. Lippert, Shibu Yooseph, Sorin Istrail. Combinatorial Problems Arising in SNP and Haplotype Analysis. DMTCS 2003: 26-47

  • from Springer


    • Ross A. Lippert. A matrix model for the beta-Jacobi ensemble. J. Math. Phys. 44(10) 4807 (01 Oct 2003).

  • from me (.ps.gz)
  • from J. Math. Phys.


    • Nathan Edwards, Ross A. Lippert. Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry. WABI 2002: 68-81.

  • from me (.ps.gz)


    • Ross A. Lippert, Russell S. Schwartz, Giuseppe Lancia, and Sorin Istrail. Algorithmic Strategies for the Single Nucleotide Polymorphism Haplotype Assembly Problem. Briefings in Bioinformatics, vol. 3 no. 1. 2002. pages 23-31.

  • from me (.pdf)


    • Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross A. Lippert, Shibu Yooseph, Sorin Istrail. A Survey of Computational Methods for Determining Haplotypes. Computational Methods for SNPs and Haplotype Inference 2002: 26-47

  • from Springer


    • Ross A. Lippert, Haiyan Huang, and Michael S. Waterman. Distributional regimes for the number of k-word matches between two random sequences. PNAS (October 29, 2002). vol. 99 no. 22. pages 13980-13989.

  • from PNAS


    • Nickolay Trendafilov and Ross A. Lippert. The multimode Procrustes problem. Linear Algebra and its Applications, 2002, 349 (1-3), pages. 245-264.

  • from Nickolay Trendafilov (.pdf)

    • Guisseppe Lancia, Vineet Bafna, Sorin Istrail, Ross A. Lippert, and R. Schwartz. SNPs Problems, Complexity, and Algorithms. ESA 2001. pages 182-193.

  • from me (.pdf)
  • a slightly different copy from me (.ps.gz)


    • J.C. Venter, et al. The sequence of the human genome. Science, 291:1304--1351, 2001. (I'm something like 100th author on this).

  • from Science


    • D. Raczkowski, C.Y. Fong, P.A. Schultz, R.A. Lippert, and E.B. Stechel. Unconstrained and constrained minimization, linear scaling, and the Grassmann manifold: theory and application to electronic structure. Phys. Rev. B. vol. 64, 155203 (2001).

  • from me (.ps.gz)
  • from Dave Raczkowski (.pdf)


    • Sorin Istrail, Alan Hurd, Ross A. Lippert, Brian Walenz, Serafim Batzoglou, John H. Conway, Fredrick W. Peyerl. Prediction of Self-Assembly of Energetic Tiles and Dominos: Experiments, Mathematics and Software. SAND Report, March 2000.

  • from Sandia Labs (.pdf)

    • Ross A. Lippert and Alan Edelman. Nonlinear eigenvalue problems with orthogonality constraints. Chapter 8.3 in Templates for the Solution of Algebraic Eigenvalue Problems: A Practical Guide. SIAM (Nov 2000). Also code is available.

  • from me (.ps.gz)
  • from Alan Edelman (.ps)


    • Ross A. Lippert and Mark P. Sears. Asymptotic convergence for iterative optimization in electronic structure Phys. Rev. B. (May 15, 2000) Volume 61, Issue 19, pp. 12772-12785.

  • from Phys. Rev. B.


    • Tomas A. Arias and Ross A. Lippert. Novel fast algorithms for wavelet calculations of electronic structure American Physical Society, Annual March Meeting, March 16-20, 1998 Los Angeles, CA. from ADSABS at Harvard


    PhD Thesis, Nonlinear Eigenvalue Problems, (MIT 1998)

  • from me (.ps.gz)


    • Ross A. Lippert, Tomas Arias, and Alan Edelman. Multiscale Computation with Interpolating Wavelets. J. of Comp. Phys. 140, pp.278-310, (1998).

  • from me (.ps.gz)
  • from Phys. Rev. B (different formats)


    • Ross A. Lippert and Alan Edelman. The Computation and Sensitivity of Double Eigenvalues. Advances in Computational Mathematics 202 of Lecture Notes in Pure and Applied Mathematics, (1998).

  • from me (.ps.gz)
  • from Alan Edelman (.ps)


    • R. A. Lippert. A Probabilistic Interpretation of the Hurwitz Zeta Fundtion. Advances in Mathematics. (Feb 1993) vol. 97, no. 2. pages 278-284.


    Software

    BBBWT: tools for Burrows-Wheeler transforms in support of my publications on it.


    SG_MIN: a set of MATLAB routines for doing optimization on Stiefel and Grassmann manifolds.


    xspringies: I modified a version of the venerable toy, xspringies, to solve sparse eigenvalue problems interactively. This has been used at least twice in biology applications.


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