Peter Huggins

Peter Huggins

Recently moved to
Dept of Statistics
University of Kentucky

Previously at
Lane Center for Computational Biology
Carnegie Mellon University

Send email to [first name] dot [last name] at

Research Interests

During my PhD I worked on algebraic statistics and computational geometry, with applications in sequence evolution. More recently I've been thinking about statistics and machine learning in computational biology.


18.   Parametric k-best alignment

17.   A support vector machine based test for incongruence between sets of trees in tree space
(joint work with D. Haws, E. M. O'Neill, D. W. Weisrock, and R. Yoshida)

16.   Identification of Differentially Expressed Thyroid Hormone Responsive Genes from the Brain of the Mexican Axolotl (Ambystoma mexicanum)
Comparative Biochemistry and Physiology, in press
(joint work with C. K. Johnson, A. Schoergendorfer, S. Putta, A. Bathke, A. J. Stromberg and S. R. Voss)

15.   Parametric analysis of alignment and phylogenetic uncertainty
Bulletin of Mathematical Biology 73(4):795-810 (2011)
(joint work with N. Eriksson and A. Malaspinas)

14.   Bayes estimators for phylogenetic reconstruction
Systematic Biology, in press
(joint work with W. Li, D. Haws, T. Friedrich, J. Liu and R. Yoshida)

13.   Statistical phylogenetic tree analysis using diļ¬€erences of means
Frontiers in Neuroscience (2010)
(joint work with E. Arnaoudova, D. Haws, J. Jaromczyk, C. Schardl and R. Yoshida)

12.   Cross species analysis of microarray expression data
Bioinformatics (2009); doi: 10.1093/bioinformatics/btp247
(joint work with Y. Lu and Z. Bar-Joseph)

11.   First steps toward the geometry of cophylogeny
(joint work with M. Owen and R. Yoshida)

10.   Selecting universities: personal preference and rankings
(joint work with L. Pachter)

9.   On the optimality of the neighbor-joining algorithm
Algorithms for Molecular Biology, Volume 3 (2008)
(joint work with K. Eickmeyer, L. Pachter and R. Yoshida)

8.   Towards the human genotope
Bulletin of Mathematical Biology, Volume 69, Number 8, (2007), p 2723--2725.
(joint work with L. Pachter, B. Sturmfels)

7.   iB4e: A Software Framework for Parametrizing Specialized LP Problems
A Iglesias, N Takayama (Eds.): Mathematical Software - ICMS 2006, Second International Congress on Mathematical Software, Castro Urdiales, Spain, September 1-3, 2006, Proceedings. Lecture Notes in Computer Science 4151 Springer 2006, ISBN 3-540-38084-1 (pp. 245-247)

6.   Parametric alignment of Drosophila genomes
PLoS Computational Biology, Volume 2, Number 6 (2006) p e73.
(joint work with C. Dewey, L. Pachter, B. Sturmfels, and K. Woods)

5.   The hyperdeterminant and triangulations of the 4-cube
Mathematics of Computation, in press.

(joint work with B. Sturmfels, J. Yu, and D. Yuster)

4.   Fairground game computations
Significance, Letters, Volume 2, Issue 2, (June 2005) p92.
(joint with J. B. Kadane and R. Yoshida)

3.   A computational study of integer programming algorithms based on Barvinok's rational functions
Discrete Optimization, Volume 2, Issue 2, 30 June 2005, Pages 135-144
(joint work with J.A. De Loera, D. Haws, R. Hemmecke, and R. Yoshida.)

2.   Three kinds of integer programming algorithms based on Barvinok's rational functions
Integer Programming and Combinatorial Optimization: 10th International IPCO Conference. Lecture Notes in Computer Science, Volume 3064, Jan 2004, Pages 244-255
(joint work with J.A. De Loera, D. Haws, R. Hemmecke, and R. Yoshida)

1.   Short rational functions for toric algebra and applications
Journal of Symbolic Computation, Volume 38, Issue 2, August 2004, Pages 959-973
(joint work with J.A. De Loera, D. Haws, R. Hemmecke, B. Sturmfels, and R. Yoshida)


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