Publications

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

Books

  1. Linear Algebra with its Applications with R. CRC Press, Taylor and Francis. 2021. Available at CRC Press
  2. 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.

2024

  1. "Tropical Geometric Tools for Machine Learning: the TML package" (with D. Barnhill, G. Aliatimis and K. Miura). Journal of Software for Algebra and Geometry 14-1 (2024), 133--174. DOI 10.2140/jsag.2024.14.133.
  2. "Tropical neural networks and its applications to classifying phylogenetic trees" (with Georgios Aliatimis and Keiji Miura). 2024 International Joint Conference on Neural Networks (IJCNN), Yokohama, Japan, 2024, pp. 1-9, doi: 10.1109/IJCNN60899.2024.10650971. Available at Arxiv.
  3. "Tropical Logistic Regression Model on Space of Phylogenetic Trees" with Georgios Aliatimis, Burak Boyaci and James A. Grant. Bull Math Biol 86, 99 (2024). https://doi.org/10.1007/s11538-024-01327-8. Available at arxiv.
  4. "Tropical Density Estimation of Phylogenetic Trees" (with K. Miura, D. Barnhill, and D. Howe). IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2024. doi: 10.1109/TCBB.2024.3420815. Available at arxiv.
  5. "Connecting Tables with Allowing Negative Cell Counts" (with D Barnhill). Journal of Statistical Theory. 18, 28 (2024). https://doi.org/10.1007/s42519-024-00381-8 Available at arxiv.
  6. "Tropical Linear Algebra and its Applications to Phylogenomics", (with D. Barnhill). To appear in the book "Mathematical Concepts and Methods in Modern Biology" edited by T. Hodget and R. Robeva. Elsevier Press.
  7. "Tropical Fermat-Weber Polytropes" (with D. Barnhill, J. Sabol, and K. Miura). Submitted. Available at Arxiv.
  8. "Tropical Decision Boundaries for Neural Networks Are Robust Against Adversarial Attacks" (with C. Teska, K. Pasque, K. Miura, J. Huang). Submitted. Available at Arxiv.

2023

  1. "Hit and Run Sampling from Tropically Convex Sets" (with K. Miura and D. Barnhill). Algebraic Statistics 14-1 (2023), 37--69. DOI 10.2140/astat.2023.14.37. Available at ARXIV.
  2. "Advice from our Advisor: Jes\'us A. De Loera: Consejo de nuestra asesor: Jes\'us A. De Loera" (with J. Haddock). American Mathematical Society. 2023. Article DOI: 10.1090/noti2754.
  3. "Clustering Methods Over the Tropically Convex Sets" with D. Barnhill. Mathematics 2023, 11, 3433. https://doi.org/10.3390/math11153433
  4. "Imputing phylogenetic trees using tropical polytopes over the space of phylogenetic trees". Mathematics. 2023; 11(15):3419. https://doi.org/10.3390/math11153419. Available at arxiv
  5. "Routing Against Uncertainty: U.S. Marine Corps Rapid Planning and Logistics Routing Against Uncertainty" (with C. Vogiatzis and K. Marler). Hybrid Fleet: The Path Forward for Human Machine Teaming (Special Issue). Naval Engineers Journal, March 2023, Volume 135, No. 1. Pages: 115--125.
  6. "Maximum Inscribed and Minimum Enclosing Tropical Balls of Tropical Polytopes and Applications to Volume Estimation and Uniform Sampling" with D. Barnhill and K. Miura. Submitted. Available at arXiv.
  7. "Tropical Support Vector Machines and its Applications to Phylogenomics" (With X. Tang and H. Wang). Algebraic Statistics 14-2 (2023), 133--165. DOI 10.2140/astat.2023.14.133 Available at arxiv.
  8. "Pl\"ucker Coordinates of the best-fit Stiefel Tropical Linear Space to a Mixture of Gaussian Distributions" (with K. Miura). DOI: 10.1007/s41884-023-00098-w Information Geometry. Available at arXiv.
  9. "Tropical Support Vector Machines: Evaluations and Extension to Function Spaces", (with M. Takamori, H. Matsumoto and K. Miura). Neural Networks. Neural Networks. Volume 157, January 2023, Pages 77-89. DOI. 2022. Available at Arxiv.

2022

  1. "Stochastic Safety Radius on UPGMA", with Lillian Paul and Peter Nesbitt. Algorithms 2022, 15, 483. https://doi.org/10.3390/a15120483
  2. "Triceps Brachii Insertional Footprint: Under-estimated Complexity" (with Srinath Kamineni, Joseph Pooley, Abdo Bachoura and Jason Cummings). Shoulder and Elbow. First published online November 10, 2022. https://doi.org/10.1177/17585732221135633
  3. "Tropical Geometric Variation of Tree Shapes" (with A. Monod, and B. Lin). Discrete and Computational Geometry. 68, pages 817–849. 2022. DOI:10.1007/s00454-022-00410-y Available at arxiv.
  4. "SARS-CoV-2 Dissemination using a Network of the United States Counties" (with Chrysafis Vogiatzis, David Wren, and Patrick Urrutia). Operations Research Forum. 3. 29. DOI: 10.1007/s43069-022-00139-7. 2022. Available at ARXIV
  5. "Solving reward-collecting problems with UAVs: a comparison of online optimization and Q-learning" (with Y. Liu, C. Vogiatzis, and E. Morman). Journal of Intelligent & Robotic Systems. DOI 10.1007/s10846-021-01548-2. 104. 35. 2022. Available at arXiv.
  6. "Tree Topologies along a Tropical Line Segment" With S. Cox. The special issue of the Vietnam Journal of Mathematics dedicated to Bernd Sturmfels on the occasion of his 60th birthday. Vietnam Journal of Mathematics, 50:395-419. 2022. https://doi.org/10.1007/s10013-021-00526-3 Available at arXiv.
  7. "Tropical Data Science" In: Arai K. (eds) Intelligent Systems and Applications. IntelliSys 2021. Lecture Notes in Networks and Systems, vol 295. Springer, Cham. 2022. https://doi.org/10.1007/978-3-030-82196-8_26. Available at arxiv.
  8. "Network Classification with Missing Information" (with C. Vu). In: Arai K. (eds) Intelligent Systems and Applications. IntelliSys 2021. Lecture Notes in Networks and Systems, vol 295. Springer, Cham. 2022. https://doi.org/10.1007/978-3-030-82196-8_13

2021

  1. "Red Cell Analysis for Mobile Networked Control Systems" (with L. Wigington and D. Horner). In in Articles: Emerging Technology. https://cimsec.org/emerging-technologies-week-kicks-off-on-cimsec/
  2. "Phylogenetic Analysis and Molecular Evolution (PAME)" (with Robert Page). PRIMUS.PRIMUS. Volume 32 Issue 3, 386-415. 2021. https://doi.org/10.1080/10511970.2021.1919257
  3. "Tropical Balls and its Applications to K Nearest Neighbor over the Space of Phylogenetic Trees." Mathematics, 9(7), 2021, 779; https://doi.org/10.3390/math9070779 (registering DOI). Available at the journal website.

2020

  1. "Tropical principal component analysis on the space of phylogenetic trees" (with Robert Page and Leon Zhang). Bioinformatics. Volume 36, Issue 17, 1 September 2020. Pages 4590-4598. Available at Arxiv.
  2. "imPhy: Imputing Phylogenetic Trees with Missing Information using Mathematical Programming" (with N. Yasui, C. Vogiatzis, and K. Fukumizu). IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 17, Issue 4, 2020. p.1222--1230. Article.
  3. "Tropical Geometry of Phylogenetic Tree Space: A Statistical Perspective" (with A. Monod, B. Lin, and Q. Kang). Submitted. ARXIV
  4. "CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths" (with Q. Kang, C. Shardl, and N. Moore). IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 17, Issue 3, 2020. p.981-989.

2019

  1. "Sequential Importance Sampling for Logistic Regression Model" (with P. Saluke and H. Hara). A book chapter for "Computational Models for Biomedical Reasoning and Problem Solving" edited by Chung-Hao Chen and Sen-Ching Samson Cheung. DOI: 10.4018/978-1-5225-7467-5.ch009 2019.
  2. ""Old Wine in New Bottles," and Some More New Wine - Stephen Fienberg's Influence on Algebraic Statistics"(with S. Petrovi\'c and A. Slavkovic). Journal of Algebraic Statistics, Issue in honor of Stephen E. Fienberg Volume 10, No. 1, 2019, pp. i--vi.
  3. Book review on a second edition manuscript titled ``Discrete Mathematics'' by Jean Gallier from Springer.
  4. "Multi Loci Phylogenetic Analysis with Gene Tree Clustering" (with K. Fukumizu and C. Vogiatzis). Annals of Operations Research. 2019. Volume 276, Issue 1–2, pp 293–313. https://doi.org/10.1007/s10479-017-2456-9. Available at Arxiv.
  5. "Age and Gender-Related Collagen Alterations in the Transverse Carpal Ligament of Carpal Tunnel Syndrome (CTS)" Srinath Kamineni; Satya Alluri; Hamza Ashfaq; Yoshida Ruriko. International Archives of Orthopaedic Surgery. Volume 2, issue 1. 2019.
  6. "Tropical Principal Component Analysis and its Application to Phylogenetics" (with L. Zhang and X. Zhang). Bulletin of Mathematical Biology. 2019. 81(2), 568-597. SITE. Also available at arxiv.

2018

  1. "Network Similarity using Distribution of Distance Matrices" with R. Gara. DOI: 10.1109/ASONAM.2018.8508321. Conference: 2018 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM). 2018.
  2. "Tropical Fermat-Weber points" (with B. Lin). 2018. SIAM J. Discrete Math. 32-2 (2018), pp. 1229-1245. Available at ARXIV.
  3. "Estimating Tropical Principal Components using Metropolis Hasting Algorithm" with Qiwen Kang. ICMS 2018 proceedings. 2018: Mathematical Software – ICMS 2018 pp 272--279.
  4. "Semigroups -- A Computational Approach" (with F. Kohl, Y. Lin and J. Rauh). Advanced Studies in Pure Mathematics 77, 2018 The 50th Anniversary of Groebner Bases page 155-170. Available at ARXIV.

2017

  1. "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). Volume 104, Issue 4, 1 December 2017, Pages 901--922, Biometrika Biometrika. asx047. Available at ARXIV.
  2. "Analysis of expert and student shiphandlers’ eyegaze during shiphandling scenario: Implications for the COVE-ITS system" (with Q. Kennedy, P. McDowell, and S. Aleem). Submitted.
  3. "Convexity in Tree Spaces" (with B. Lin, B. Sturmfels, and X. Tang). SIAM J. Discrete Math. 31 (2017), no. 3, 2015-2038. Availavle at Arxiv.
  4. "Hybrid Schemes for Exact Conditional Inference in Discrete Exponential Families" (with D. Kahle and L. Garcia-Puente). Annals of Institute of Statistical Mathematics. DOI:10.1007/s10463-017-0615-z. 2017. LINK
  5. "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.
  6. "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.
  7. "Normalizing kernels in the Billera-Holmes-Vogtmann treespace" (with G. Weyenberg and D. Howe). IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 14 , Issue 6, PP 1359 -- 1365, DOI:10.1109/TCBB.2016.2565475. 2017. Available at arxiv.

2016

  1. "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.
  2. "Phylogenetic Tree Distances" (with G. Weyenberg). In: Kliman, R.M. (ed.), Encyclopedia of Evolutionary Biology. vol. 3, pp. 285--290. Oxford: Academic Press.
  3. "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. 33 (6): pp. 1618-1624. 2016. doi: 10.1093/molbev/msw042
  4. Reviewer for Mathematical Reviews (MathSciNet); 52 reviews all-time including a review for the book Spectral clustering and biclustering.

2015

  1. "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.
  2. "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.
  3. "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

2014

  1. "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.
  2. "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.

2013

  1. "Book review on Stochastic Modelling for Systems Biology by Wilkinson." Journal of the American Statistical Association. 2013. Vol. 108, p. 1554.
  2. "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
  3. "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.
  4. "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.
  5. "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.
  6. "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
  7. "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.
  8. "Algebraic methods for molecular phylogenetics." Annals of Institute of Statistical Mathematics. Volume 60, number 2. 2012. p279--288.

2012

  1. "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
  2. "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.
  3. "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
  4. "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.
  5. "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.
  6. "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.

2011

  1. "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.
  2. "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.
  3. "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.
  4. "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.

2010

  1. "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
  2. "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.
  3. "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).
  4. "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.
  5. "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).
  6. "Book review on Markov Processes and Applications" the journal of the American Statistical Association, 10, June 2010, 3 - 4.
  7. "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.
  8. "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.

2009

  1. "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 arxiv
  2. "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.
  3. "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).
  4. "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.
  5. "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).

2008

  1. "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.
  2. "Parametric k-best alignment" (with P. Huggins), preprint. Available at arxiv.org/abs/0809.1473.
  3. "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.
  4. "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.
  5. "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).
  6. "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.)
  7. 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.
  8. "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.
  9. "A generalization of the integer linear infeasibility problem" (with A. Takemura), Discrete Optimization, Volume 5, Issue 1 (2008) p36-52. (Available at Discrete Optimization).

2007

  1. "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.
  2. "Partitioning the Sample Space on Five Taxa for the Neighbor Joining Algorithm" (with K. Eickmeyer). Preprint. Available at math.CO/0703081.
  3. "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.

2006

  1. "Computing holes in semi-groups" (with R. Hemmecke and A. Takemura). Preprint. Available at arXiv:math.CO/0607599.
  2. "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.

2005

  1. "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.
  2. "Fairground game computations" (with P. Huggins and J. B. Kadane), Significance, Letters, Volume 2, Issue 2, (June 2005) p92. PDF.
  3. "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.
  4. "Short Rational Generating Functions and Their Applications to Integer Programming" (with K. Woods), SIAG/OPT Views and News, vol. 16 (2005) p15 - 19.PDF.
  5. "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.)
  6. "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.)

2004

  1. "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.
  2. 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.
  3. "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.
  4. "Reconstructing trees from dissimilarity maps" (with Levy, D. and Su, F.), RECOMB 2004 meeting abstracts (2004) p. 19. PDF.
  5. "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.
  6. 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.