# Papers

Fernando De Tera'n, Ross A. Lippert, Yuji Nakatsukasa, and Vanni Noferini.
*Flanders theorem for many matrices under commutativity assumptions*
Linear Algebra and Its Applications (December 2013)

from Linear Algebra and Its Applications
Ross A. Lippert, Cristian Predescu, et al.
*Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure*
Journal of Chemical Physics. (October 2013).

From JCP
Cristian Predescu, Ross A. Lippert, et al.
*Computationally efficient molecular dynamics integrators with improved sampling accuracy*
Molecular Physics. (April 2012).

From MP
From me
Michael P. Eastwood, Kate A. Stafford, Ross A. Lippert, et al.
*Equipartition and the Calculation of Temperature in Biomolecular Simulations.*
J. Chem. Theory Comput. (May 2010).

From JCTC
Ross A. Lippert
*Fixing multiple eigenvalues by a minimal perturbation.*
Linear Algebra and its Applications 432 (2010) 1785-1817.

From LAA
From me
Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, David E. Shaw
*Improved twiddle access for fast fourier transforms.*
IEEE Transactions on Signal Processing,
Volume 58 Issue 3, (March 2010) 1122-1130.

From ACM
Ross A. Lippert, Gil Strang
*The Jordan forms of AB and BA.*
ELA volume 18 (2009), pages 281-288.

From ELA
Ryan M. Rifkin, Ross A. Lippert
*Notes on Regularized Least Squares.* (2007)

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, issue 4 (January 2007), page 046101.

from DESRES
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
In response to errors pointed out by readers, I have produced
a revision as of Feb 2011
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. Halld?rsson, 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. Halld?rsson, 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. Halld?rsson, 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 (.pdf)
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 the
sg_min code
is available.

from me (.pdf)
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 (.pdf)
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)
or (.pdf)
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.