- "Barvinok's Rational Functions: Algorithms and Applications to Optimization, Statistics, and Algebra." Ph.D. Thesis PDF and book.

**Integer Points in Polyhedra**(Matthias Beck, Christian Haase, Bruce Reznick, Michele Vergne, Volkmar Welker, Ruriko Yoshida). American Mathematical Society (26 Jun 2008). ISBN:978-0821841730. Order the book.

- "Genome-wide phylogenomic analysis method using likelihood ratios" (with Q. Kang, C. Schardl, and N. Moore). Submitted.
- "Distributions of topological tree metrics between a species tree and a gene tree" (with Jing Xi and Jin Xie). Annals of Institute of Statistical Mathematics. June 2017, Volume 69, Issue 3, pp 647-671.
- "Semigroups -- A Computational Approach" (with F. Kohl, Y. Lin and J. Rauh). To appear in the proceedings of the 8th Mathematical Society of Japan Seasonal Institute. Available at ARXIV.
- "Multi Loci Phylogenetic Analysis with Gene Tree Clustering" (with K. Fukumizu and Chrysafis Vogiatzis). To appear in Annals of Operations Research. Available at Arxiv.
- "Stochastic safety radius on Neighbor-Joining method and Balanced Minimal Evolution on small trees" (with J. Xi, J. Xie, and S. Forcey). The proceedings of the 10th Workshop on Uncertainty Processing. page 217 to 230. Available at Arxiv.

- "Extremal Positive Semidefinite Matrices whose Sparsity Pattern is given by Graphs Without K_5 Minors" (with L. Solus and C. Uhler). Linear algebra and its Applications. vol. 509, pp. 247-275. 2016. Available at arxiv.
- "Principal Component Analysis and the Locus of the Fr\'echet Mean in the Space of Phylogenetic Trees" (with T. Nye, X. Tang, and G. Weyenberg). Submitted. Available at ARXIV.
- "Normalizing kernels in the Billera-Holmes-Vogtmann treespace" (with G. Weyenberg and D. Howe). To appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics. Available at arxiv.
- "Phylogenetic Tree Distances" (with G. Weyenberg). In: Kliman, R.M. (ed.), Encyclopedia of Evolutionary Biology. vol. 3, pp. 285--290. Oxford: Academic Press.
- "Tropical Fermat-Weber points" (with B. Lin). Submitted. Available at ARXIV.
- "Efficiencies of the NJp, maximum likelihood, and Bayesian methods of phylogenetic construction for compositional and non-compositional genes" (with M. Nei). Molecular Biology and Evolution. 2016. doi: 10.1093/molbev/msw042
- Reviewer for Mathematical Reviews (MathSciNet); 52 reviews all-time including a review for the book Spectral clustering and biclustering.

- "Convexity in Tree Spaces" (with B. Lin, B. Sturmfels, and X. Tang). Submitted. Availavle at Arxiv.
- "Hybrid Schemes for Exact Conditional Inference in Discrete Exponential Families" (with D. Kahle and L. Garcia-Puente). Submitted.
- "HGT alternatives: Trans-species polymorphism, paralogy and loss, and frequency dependent selection in alkaloid biosynthesis genes" (with Christopher L. Schardl, Patrick J. Calie, Simona Florea, Jerzy W. Jaromczyk, Neil Moore, Padmaja Nagabhyru, Juan Pan, Grady Weyenberg, Carolyn A. Young). Appear to Mycological Society of America annual meeting.
- "Reconstructing the phylogeny: computational methods". (With G. Weyenberg.) In the book "Algebraic and Discrete Mathematical Methods for Modern Biology," edited by Robeva. Elsevier. 2015. 293--319.
- "The characteristic imset polytope of Bayesian networks with ordered nodes" (with Jing Xi). SIAM Discrete Math. 2015. 29(2), 697-715. Available at http://arxiv.org/abs/1206.0406

- "Markov degree of the three-state toric homogeneous Markov chain model" (with D. Haws, A. Martin del Campo, and Takemura). Contributions to Algebra and Geometry. 2014, Volume 55, Issue 1, pp 161-188. Available at http://arxiv.org/abs/1204.3070 and LINK.
- "kdetrees: Nonparametric Estimation of Phylogenetic Tree Distributions", (with G. Weyenberg, P. Huggins, C. Schardl, and D. Howe). To appear in Bioinformatics. Bioinformatics. 2014, 30(16), page 2280-2287. doi: 10.1093/bioinformatics/btu258. Available at Bioinformatics and ARXIV.

- "Book review on
*Stochastic Modelling for Systems Biology*by Wilkinson." Journal of the American Statistical Association. 2013. Vol. 108, p. 1554. - "Using HPC for teaching and learning bioinformatics software: Benefits and challenges" (Tyler Parke, Mark Farman, Elizabeth Farnsworth, Derek Fox, Jerzy W Jaromczyk, Jolanta Jaromczyk, Neil Moore, Christopher L Schardl, Ruriko Yoshida and Pat Calie), BMC Bioinformatics, vol 14, Suppl 17:A18. Available at LINK
- "Approximate techniques in solving optimal camera placement problems" (Jian Zhao, Ruriko Yoshida, Sen-ching Samson Cheung, David Haws), International Journal of Distributed Sensor Networks, vol. 2013, Article ID 241913, 15 pages, 2013. doi:10.1155/2013/241913. Available at LINK.
- "Estimating the number of zero-one multi-way tables via sequential importance sampling" (with J. Xi and D. Haws). Annals of Institute of Statistical Mathematics. Volume 65, Issue 4. 2013, Page 763-783. DOI: 10.1007/s10463-012-0392-7. Available at http://arxiv.org/abs/1108.5939 and SPRINGER.
- "Phylogenetic Tree Reconstruction: Geometric Approaches" (with T. Hodge and D. Haws) a book chapter in "Mathematical Concepts and Methods in Modern Biology" edited by T. Hodget and R. Robeva, Elsevier Press. 2013. page 307-340.
- "Livestock Evacuation Planning for Natural and Man-made Emergencies" (with C. Vogiatzis, I. Aviles-Spadoni, P. Pardalos and S. Imamoto), International Journal of Mass Emergency and Disasters. Volume 31, number 1, 2013. p25-37. ABSTRACT
- "Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci", (with Christopher Schardl, Jerzy Jaromczyk, Neil Moore, David Haws, Thomas Bullock, et al.), PLOS Genetics. 2013. DOI.
- "Algebraic methods for molecular phylogenetics." Annals of Institute of Statistical Mathematics. Volume 60, number 2. 2012. p279--288.

- "Prevalence of Anti-Brucella canis Antibodies in 1104 dogs at general animal hospital and 120 dogs at kennel" (with Shigeki Imamoto, Takashi Iwasaki, Kikuo Miyoshi, Shuichiro Watanabe, Youhei Yamashita, Mitsuru Iba, Mikako Imamoto, Shinichi Namba, Takehisa Soma). Journal of Animal Clinical Medicine. 2012. vol.3 p96-102
- "A support vector machine based test for incongruence between sets of trees in tree space" (with David Haws, Peter Huggins, Eric M. O'Neill, David W. Weisrock). 2012. BMC Bioinformatics. Volume 13. Number 210. doi:10.1186/1471-2105-13-210.
- "Chondrocyte response to Tensile and Compressive cyclic loading modalities " (with Srinath Kamineni, Zubair Wani, Kai-Nan An, Zong-Ping Luo), Journal of Musculoskeletal Research (JMR), 2012, Volume 0 Issue 2 1250006 (9 pages) DOI: 10.1142/S0218957712500066. URL
- "Degree bounds for a minimal Markov basis for the three-state toric homogeneous Markov chain model" (with David Haws and Abraham Martin del Campo) in the Proceedings of the Second CREST--SBM International Conference ``Harmony of Groebner Bases and the Modern Industrial Society.'' 2012. 63--98. Available at http://arxiv.org/abs/1108.0481.
- "First steps toward the geometry of cophylogeny" (with P. Huggins and M. Owen) in the Proceedings of the Second CREST--SBM International Conference ``Harmony of Groebner Bases and the Modern Industrial Society.'' 2012. 99 -- 116. Available at http://arxiv.org/abs/0809.1908.
- "Late Removal of Titanium Hardware from the Elbow is Problematic" (with Abdo Bachoura, Christian Lattermann, and Srinath Kamineni). ISRN Orthopedics. Volume 2012 (2012), Article ID 256239, 4 pages.

- "Approximate techniques in solving optimal camera placement problems" (with Jian Zhao, David Haws, and Sen-ching Samson Cheung) in the proceedings of the Eleventh IEEE International Workshop on Visual Surveillance, 2011, 1707--1712.
- "Bayes estimators for phylogenetic reconstruction" (with P Huggins, W. Li, D. Haws, T. Friedrich, J. Liu). 2011. LINK. Volume 60, Issue 4, Systematic Biology. Page 528-540. Available at http://arxiv.org/abs/0911.0645.
- "Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope" (with D. Haws and T. Hodge), 2011. the Bulletin of Mathematical Biology. Volume 73, Number 11, 2627-2648. Available at http://arxiv.org/abs/1004.2073.
- "Experiments with the site frequency spectrum" (Raazesh Sainudiin, Kevin Thornton, Jennifer Harlow, James Booth, Michael Stillman, Ruriko Yoshida, Robert Griffiths, Gil McVean, and Peter Donnelly), 2011, 829-872. Volume 73, issue 4. Bulletin of Mathematical Biology. LINK.

- "Statistical analysis on detecting recombination sites in DNA-beta satellites associated with the old world geminiviruses" (with K. Xu), Front. Psychiatry. 2010. doi: 10.3389/fpsyt.2010.00138 Available at http://arxiv.org/abs/1006.4397
- "Statistical Phylogenetic Tree Analysis Using Differences of Means" (with Elissaveta Arnaoudova, David Haws, Peter Huggins, Jerzy W. Jaromczyk, Neil Moore, Chris Schardl), Front. Psychiatry volume 1 number 47. doi:10.3389/fnins.2010.0004. Available at http://arxiv.org/abs/1004.2101.
- "Phylotree - a toolkit for computing experiments with distance-based methods for genome coevolution" (Elissaveta Arnaoudova, Jerzy W Jaromczyk, Neil Moore, Christopher L Schardl, Ruriko Yoshida). BMC Bioinformatics 2010, 11(Suppl 4):P6 (23 July 2010).
- "Open Problems on Connectivity of Fibers with Positive Margins in Multi-dimensional Contingency Tables" Vol. 1, No. 1, 2010, 13-26 ISSN 1309-3452, J of Algebraic Statistics.
- "Markov bases and subbases for bounded contingency tables" (with Fabio Rapallo), Annals of the Institute of Statistical Mathematics, 62(4), 2010, 785--805. (Available at arxiv:0905.4841 and DOI).
- "Book review on Markov Processes and Applications" the journal of the American Statistical Association, 10, June 2010, 3 - 4.
- "On connectivity of fibers with positive marginals in multiple logistic regression" (with H. Hara and A. Takemura), J of Multivariate Analysis. 101(4), 2010, 909-925. Available at http://dx.doi.org/10.1016/j.jmva.2009.12.014 and http://arxiv.org/abs/0810.1793.
- "Counting Tables using the Double Saddlepoint Approximation" (with J. Booth and V. Zipunnikov), the Journal of Computational and Graphical Statistics, 18(4) December 1, 2009, 915-929. PDF.

- "Computing holes in semi-groups and its applications to transportation problems" (with R. Hemmecke and A. Takemura), Contributions to Discrete Mathematics, Volume 4, Number 1, 2009, 81 - 91. Available at Contributions to Discrete Mathematics
- "A Generating Function for all Magic Squares and the Volume of the Birkhoff Polytope" (with J. Deloera and F. Liu), Journal of Algebraic Combinatorics, 30(1), 2009, 113 -- 139. Available at J of Algebraic Combinatorics.
- "Markov Bases for Two-way Subtable Sum Problems" (with H. Hara and A. Takemura), in the special issue ``THEORETICAL EFFECTIVITY AND PRACTICAL EFFECTIVITY OF GROEBNER BASES'' of the Journal of Pure and Applied Algebra, 213(8), 2009, 1507 - 1521. (Available at arxiv:0708.2312).
- "A Markov Basis for Conditional Test of Common Diagonal Effect in Quasi-Independence Model for Two-Way Contingency Tables" (with H. Hara and A. Takemura). J of Computational Statistics and Data Analysis. 53 (2009) 1006 - 1014. Available at arXiv:0802.2603.
- "Holes in semigroups and their applications to the two-way common diagonal effect model" (with A. Takemura and P. Thomas). In: Proceedings of the 2008 International Conference on Information Theory and Statistical Learning, ITSL 2008, CSREA Press, ISBN: 1-60132-079-5, p67-72. PDF. (Even though this is published in 2008 I am posting this paper here for my convenience reason).

- "Markov Chains, Quotient Ideals, and Connectivity with Positive Margins" (with Y. Chen and I. Dinwoodie). in ``Algebraic and Geometric Methods in Statistics'' dedicated to Professor Giovanni Pistone (P. Gibilisco, E. Riccomagno, M.-P. Rogantin, H. P. Wynn, eds.). 2008. PDF. p99 - 110.
- "Parametric k-best alignment" (with P. Huggins), preprint. Available at arxiv.org/abs/0809.1473.
- "Geometry of Neighbor-Joining Algorithm for Small Trees" (with K. Eickmeyer), the proceedings of Algebraic Biology, Springer LNC Series (2008), p82-96. Available at arXiv:0908.0098.
- "A novel test for significant codivergence between cool-season grasses and their symbiotic fungal endophytes" (with C. L. Schardl, K. D. Craven, A. Lindstrom, S. Speakman, and A. Stromberg). Systematic Biology. Volume 57, Issue 3, (2008), p483 - 498. Available at arXiv:q-bio.PE/0611084.
- "On the optimality of the neighbor-joining algorithm" (With K. Eickmeyer, P. Huggins, and L. Pachter). Algorithms for Molecular Biology. Volume 3, Issue 5, (2008). (Available at arxiv:0710.5142).
- "Indispensable Monomials of Toric Ideals and Markov Bases" (with S. Aoki and A. Takemura). J of Symbolic Computations Volume 43 (2008) p490-509. (Also available at arXiv:math.ST/0511290.)
**Integer Points in Polyhedra**(Matthias Beck, Christian Haase, Bruce Reznick, Michele Vergne, Volkmar Welker, Ruriko Yoshida). American Mathematical Society (26 Jun 2008). ISBN:978-0821841730. Order the book.- "Saturation points on faces of a rational polyhedral cone" (with A. Takemura), in Joint Summer Research Conference proceedings. Contemporary Mathematics. Volume 452. American Mathematical Society (2008), p147--162. Available at arXiv:math.CO/0605479.
- "A generalization of the integer linear infeasibility problem" (with A. Takemura), Discrete Optimization, Volume 5, Issue 1 (2008) p36-52. (Available at Discrete Optimization).

- "On the enumeration of certain weighted graphs" (with B\'ona and Ju), Volume 155, Issue 11, 1 June 2007, p1481-1496, Discrete Applied Math. Available at arXiv:math.CO/0606163.
- "Partitioning the Sample Space on Five Taxa for the Neighbor Joining Algorithm" (with K. Eickmeyer). Preprint. Available at math.CO/0703081.
- "Formulas for the Volumes of the Polytope of Doubly-Stochastic Matrices and its faces" (with J. DeLoera and F. Liu). Preprint. Available at math.CO/0701866.

- "Computing holes in semi-groups" (with R. Hemmecke and A. Takemura). Preprint. Available at arXiv:math.CO/0607599.
- "Beyond Pairwise Distances: Neighbor Joining with Phylogenetic Diversity Estimates" (with D. Levy and L. Pachter), the Molecular Biology and Evolution, 2006 23(3):491-498. MBE site.

- "Applications of Interval Methods to Phylogenetic
trees" (with R. Sainudiin), a chapter contributing
to a book
*Algebraic Statistics for Computational Biology*edited by Lior Pachter and Bernd Sturmfels, (2005) Cambridge University Press, p359 - 374. ASCB site. - "Fairground game computations" (with P. Huggins and
J. B. Kadane),
*Significance*, Letters, Volume 2, Issue 2, (June 2005) p92. PDF. - "A Computational Study of Integer Programming
Algorithms Based on Barvinok's Rational Functions" (with
J. De Loera, D. Haws, R. Hemmecke, P. Huggins),
*the Journal of Discrete Optimization*, Volume 2, Issue 2, (June 30 2005), P 135-144 PDF. - "Short Rational Generating Functions and Their Applications to Integer Programming" (with K. Woods), SIAG/OPT Views and News, vol. 16 (2005) p15 - 19.PDF.
- "Indispensable Monomials of Toric Ideals
and Markov Bases"
(with S. Aoki and A. Takemura), the
*Asian Symposium on Computer Mathematics (ASCM) 2005*edited by S. Pae, H. Park, (2005), p200 -- 202, Korea Institute for Advanced Study. PDF. (Also available at arXiv:math.ST/0511290.) - "Maximum likelihood estimation of phylogenetic
tree and substitution rates via generalized neighbor-joining
and the EM algorithm" (with A. Hobolth),
*Algebraic Biology 2005, Computer Algebra in Biology*, edited by H. Anai and K. Horimoto, vol. 1 (2005) p41 - 50, Universal Academy Press, INC.. PDF. (Also available at arXiv:q-bio.QM/0511034.)

- "Effective Lattice Point Counting in Rational
Convex Polytopes" (with J. De Loera, R. Hemmecke,
J. Tauzer),
*the Journal of Symbolic Computation*, 38 (2004), no. 4, p1273 -- 1302. PDF. **Lattice Point Enumeration: LattE**, (with De Loera, J., Haws, D., Hemmecke, R., Huggins, P., Tauzer, J), software to count the number of lattice points inside a rational convex polytope via Barvinok's cone decomposition, available at www.math.ucdavis.edu/~latte, the GNU General Public License, 2004.- "Short Rational Functions for Toric Algebra
and Applications" (with J. De Loera, D. Haws,
R. Hemmecke, P. Huggins, B. Sturmfels),
*the Journal of Symbolic Computation*, 38 (2004), no. 2, p959--973. PDF. - "Reconstructing trees from dissimilarity maps" (with Levy, D. and Su, F.), RECOMB 2004 meeting abstracts (2004) p. 19. PDF.
- "Three Kinds of Integer Programming Algorithms
based on Barvinok's Rational Functions" (with
J. De Loera, D. Haws, R. Hemmecke, P. Huggins),
*Integer Programming and Combinatorial Optimization: 10th International IPCO Conference*, Springer, (D. Bienstock and G. Nemhauser eds.) p244 -- 255, 2004. PDF. **MJOIN**, software to reconstruct phylogenetic trees from DNA sequences via the Neighbor Joining method with subtree weights, available at http://bio.math.berkeley.edu/mjoin/, the GNU General Public License, 2004.