Gomes JP, Bruno WJ, Nunes A, Santos N, Florindo C, Borrego MJ, & Dean D (2006) "Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots." Genome Res. 2007 Jan;17(1):50-60. Epub 2006 Nov 7
Hraber PT, Fischer W, Bruno WJ, Leitner T & Kuiken C (2006) "Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes." Virol J. Dec 14;3(1):103
Bruno WJ & Pearson JE (2006) "Transformations that preserve detailed balance in Markov models." J Comput Biol. Nov;13(9):1574-8.
Macken CA, Webby RJ & Bruno WJ (2006) "Genotype turnover by reassortment of replication complex genes from avian influenza A virus." J Gen Virol. Oct;87(10):2803-15.
Yang J, Bruno WJ, Hlavacek WS & Pearson JE (2006) "On imposing detailed balance in complex reaction mechanisms." Biophys J. Aug 1;91(3):1136-41.
Gomes JP, Nunes A, Bruno WJ, Borrego MJ, Florindo C, & Dean D. (2006) "Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: evidence for serovar Da recombination and correlation with tissue tropism." J Bacteriol. Jan;188(1):275-86.
W. J. Bruno , Yang J. & Pearson J. E., (2005) "Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics." Proceedings of the National Academy of Sciences (PNAS) USA. 102:6326-31. Epub 2005 Apr 20
I. Holmes & W. J. Bruno, ``Evolutionary HMMs: a Bayesian approach to multiple alignment." Bioinformatics. 17: 803-20 (2001).
H. Kishino, J. L. Thorne & W. J. Bruno, ``Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution" Mol Biol Evol. 18 352-361 (2001).
W. J. Bruno, N. D. Socci, & A. L. Halpern, ``Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction,'' Mol. Biol. Evol., 17 (1): 189-197 (2000) .
W. J. Bruno & A. L. Halpern, ``Topological Bias and Inconsistency of Maximum Likelihood Using Wrong Models,'' Mol. Biol. Evol., 16 (4) 564-566 (1999) [summary].
A. Halpern & W. J. Bruno, ``Evolutionary Distances for Protein-Coding Sequences: Modeling Site-Specific Residue Frequencies'', Mol. Biol. Evol. 15 (7) 910-917 (1998) .
W. J. Bruno, ``Modeling Residue Usage in Aligned Protein Sequences via Maximum Likelihood'', Mol. Biol. Evol. 13 (10) 1368-1374 (1996) .
W. J. Bruno, E. Knill, D. J. Balding, D. C. Bruce, N. A. Doggett, W. W. Sawhill, R. L. Stallings, C. C. Whittaker & D. C. Torney, ``Efficient Pooling Designs for Library Screening,'' Genomics, 26, 21-30 (1995).
J. Pearson & W. J. B., ``Pattern Formation in an N+Q Component Reaction-Diffusion System,'' CHAOS, 2, 513-524 (1992).
W. J. Bruno & W. Bialek, ``Vibrationally Enhanced Tunneling as a Mechanism for Enzymatic Proton Transfer,'' Biophys. J. 63, 689-699 (1992).
C. A. Joslyn & W.J. Bruno "Weighted Pseudo-Distances for Categorization in Semantic Hierarchies", Conceptual Structures: Common Semantics for Sharing Knowledge, Lecture Notes in AI, v. 3596, eds. F. Dau, M.-L. Mugnier, and G. Stumme, 381-395 (2005).
J. Martin et al., (2004) "The sequence and analysis of duplication-rich human chromosome 16." Nature. 432: 988-94.
Bas E. Dutilh, Martijn A. Huynen, W. J. Bruno & Berend Snel (2004), "The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise", J Mol Evol 58: 527-539.
Gomes J.P., W. J. Bruno, M.J. Borrego & D. Dean, "Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer." J Bacteriol. 186(13):4295-306 (2004).
I. Holmes & W. J. Bruno, ``Finding regulatory elements using joint likelihoods for sequence and expression profile data," Proc Int Conf Intell Syst Mol Biol. (ISMB) 8 202-210 (2000).
D. D. Pollock & W. J. Bruno, ``Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition," Mol Biol Evol. 17 1854--1858 (2000).
J. Koshi & W. J. Bruno, ``Major structural determinants of transmembrane proteins identified by principal component analysis," Proteins, 34 333-340 (1999) [abstract].
W. J. Bruno, G.-C. Rota & D. C. Torney, "Probability Set Functions," Annals of Combinatorics, 3 13-26 (1999).
W. J. Bruno, F. Sun, & D. C. Torney, ``Optimizing Non-Adaptive Group Tests for Objects with Heterogeneous Priors'', SIAM J. Appl. Math. 58 1043-1059 (1998) [abstract].
L. Arvestad & W. J. Bruno, ``Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences'', J. Mol. Evol. 45 696-703 (1997) [abstract].
D. J. Balding, W. J. Bruno, E. Knill, & D. C. Torney, ``A Comparative Study of Non-Adaptive Pooling Designs,'' in ``Genetic Mapping and DNA Sequencing, IMA Volumes in Mathematics and its Applications,'' T. Speed and M. S. Waterman (eds.) Volume 31, pp. 133-155. Springer-Verlag, Berlin.
G. Xie, R. Lobb, W. J. Bruno, D. C. Torney, & J. M. Gatewood, ``Single-base Sequencing and Similarity Comparisons,'' Genomics 30, 445-449 (1995).
N. A. Doggett, L. A. Goodwin, J. G. Tesmer, L. J. Meincke, D. C. Bruce, L. M. Clark, M. R. Altherr, A. A. Ford, H.-C. Chi, B. L. Marrone, J. L. Longmire, S. A. Lane, S. A. Whitmore, M. G. Lowenstein, R. D. Sutherland, M. O. Mundt, E. H. Knill, W. J. Bruno, C. A. Macken, D. C. Torney, J. R. Wu, J. Griffith, G. R. Sutherland, L. L. Deaven, D. F. Callen & R. K. Moyzis, ``An Integrated Physical Map of Human Chromosome 16,'' Nature, 377, Suppl. 335-366 (1995).
M. K. McCormick, A. Buckler, W. Bruno, E. Campbell, K. Shera, D. Torney, L. Deaven & R. Moyzis, ``Construction and Characterization of a YAC Library with a Low Frequency of Chimeric Clones from Flow Sorted Human Chromosome 9,'' Genomics 18, 553-558 (1993).
W. J. Bruno, ``Patterns that Grow,'' CNLS Newsletter, 82, 1-10 (1992). arxiv.org.
J. S. Joseph, W. Bruno & W. Bialek, ``Bleaching of the Bacteriochlorophyll Monomer Band: Can Absorption Kinetics Distinguish Virtual from Two-Step Electron Transfer in Bacterial Photosynthesis?'' J. Phys. Chem. 95, 6242-6247 (1991).
W. Bialek, W. J. Bruno, J. Joseph & J. N. Onuchic, ``Quantum and Classical Dynamics in Biochemical Reactions,'' Photosyn. Res. 22, 15-27 (1989).
H. H. Sample, W. J. Bruno, S. B. Sample & E. K. Sichel, ``Reverse-field reciprocity for conducting specimens in magnetic fields,'' J. Appl. Phys. 61, 1079-84 (1987).
Bill Bruno