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William Bruno, PhD - Publications

Theoretical Biology & Biophysics Los Alamos National Laboratory, Los Alamos, NM, United States 
Theoretical and computational molecular evolution, ion channel models

39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2013 Bruno WJ, Ullah G, Mak DO, Pearson JE. Automated maximum likelihood separation of signal from baseline in noisy quantal data. Biophysical Journal. 105: 68-79. PMID 23823225 DOI: 10.1016/j.bpj.2013.02.060  1
2012 Berendzen J, Bruno WJ, Cohn JD, Hengartner NW, Kuske CR, McMahon BH, Wolinsky MA, Xie G. Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. Bmc Research Notes. 5: 460. PMID 22925230 DOI: 10.1186/1756-0500-5-460  1
2012 Ullah G, Bruno WJ, Pearson JE. Simplification of reversible Markov chains by removal of states with low equilibrium occupancy. Journal of Theoretical Biology. 311: 117-29. PMID 22820127 DOI: 10.1016/j.jtbi.2012.07.007  1
2012 Srinivasan T, Bruno WJ, Wan R, Yen A, Duong J, Dean D. In vitro recombinants of antibiotic-resistant Chlamydia trachomatis strains have statistically more breakpoints than clinical recombinants for the same sequenced loci and exhibit selection at unexpected loci. Journal of Bacteriology. 194: 617-26. PMID 22123249 DOI: 10.1128/JB.06268-11  1
2009 Maljkovic Berry I, Athreya G, Kothari M, Daniels M, Bruno WJ, Korber B, Kuiken C, Ribeiro RM, Leitner T. The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data. Epidemics. 1: 230-9. PMID 21352769 DOI: 10.1016/j.epidem.2009.10.003  1
2009 Dean D, Bruno WJ, Wan R, Gomes JP, Devignot S, Mehari T, de Vries HJ, Morré SA, Myers G, Read TD, Spratt BG. Predicting phenotype and emerging strains among Chlamydia trachomatis infections. Emerging Infectious Diseases. 15: 1385-94. PMID 19788805 DOI: 10.3201/eid1509.090272  1
2008 Hraber P, Kuiken C, Waugh M, Geer S, Bruno WJ, Leitner T. Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index. The Journal of General Virology. 89: 2098-107. PMID 18753218 DOI: 10.1099/vir.0.83657-0  1
2007 Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T. Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases. Journal of Virology. 81: 10625-35. PMID 17634235 DOI: 10.1128/JVI.00985-07  1
2007 Gomes JP, Bruno WJ, Nunes A, Santos N, Florindo C, Borrego MJ, Dean D. Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots. Genome Research. 17: 50-60. PMID 17090662 DOI: 10.1101/gr.5674706  1
2006 Hraber PT, Fischer W, Bruno WJ, Leitner T, Kuiken C. Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes. Virology Journal. 3: 103. PMID 17169155 DOI: 10.1186/1743-422X-3-103  1
2006 Bruno WJ, Pearson JE. Transformations that preserve detailed balance in Markov models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1574-8. PMID 17147480 DOI: 10.1089/cmb.2006.13.1574  1
2006 Macken CA, Webby RJ, Bruno WJ. Genotype turnover by reassortment of replication complex genes from avian influenza A virus. The Journal of General Virology. 87: 2803-15. PMID 16963738 DOI: 10.1099/vir.0.81454-0  1
2006 Yang J, Bruno WJ, Hlavacek WS, Pearson JE. On imposing detailed balance in complex reaction mechanisms. Biophysical Journal. 91: 1136-41. PMID 16698778 DOI: 10.1529/biophysj.105.071852  1
2006 Gomes JP, Nunes A, Bruno WJ, Borrego MJ, Florindo C, Dean D. Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: evidence for serovar Da recombination and correlation with tissue tropism. Journal of Bacteriology. 188: 275-86. PMID 16352844 DOI: 10.1128/JB.188.1.275-286.2006  1
2005 Bruno WJ, Yang J, Pearson JE. Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics. Proceedings of the National Academy of Sciences of the United States of America. 102: 6326-31. PMID 15843461 DOI: 10.1073/pnas.0409110102  1
2005 Joslyn CA, Bruno WJ. Weighted pseudo-distances for categorization in semantic hierarchies Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3596: 381-395.  1
2004 Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, ... ... Bruno WJ, et al. The sequence and analysis of duplication-rich human chromosome 16. Nature. 432: 988-94. PMID 15616553 DOI: 10.1038/nature03187  1
2004 Gomes JP, Bruno WJ, Borrego MJ, Dean D. Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer. Journal of Bacteriology. 186: 4295-306. PMID 15205432 DOI: 10.1128/JB.186.13.4295-4306.2004  1
2004 Dutilh BE, Huynen MA, Bruno WJ, Snel B. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. Journal of Molecular Evolution. 58: 527-39. PMID 15170256 DOI: 10.1007/s00239-003-2575-6  1
2001 Holmes I, Bruno WJ. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics (Oxford, England). 17: 803-20. PMID 11590097  1
2001 Kishino H, Thorne JL, Bruno WJ. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution. 18: 352-61. PMID 11230536  1
2000 Pollock DD, Bruno WJ. Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition. Molecular Biology and Evolution. 17: 1854-8. PMID 11110901  1
2000 Holmes I, Bruno WJ. Finding regulatory elements using joint likelihoods for sequence and expression profile data. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 202-10. PMID 10977081  1
2000 Bruno WJ, Socci ND, Halpern AL. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Molecular Biology and Evolution. 17: 189-97. PMID 10666718  1
1999 Bruno WJ, Halpern AL. Topological bias and inconsistency of maximum likelihood using wrong models. Molecular Biology and Evolution. 16: 564-6. PMID 10331281  1
1999 Koshi JM, Bruno WJ. Major structural determinants of transmembrane proteins identified by principal component analysis. Proteins. 34: 333-40. PMID 10024020 DOI: 10.1002/(SICI)1097-0134(19990215)34:3<333::AID-PROT6>3.0.CO;2-2  1
1999 Percus JK, Percus OE, Bruno WJ, Torney DC. Asymptotics of pooling design performance Journal of Applied Probability. 36: 951-964.  1
1998 Halpern AL, Bruno WJ. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Molecular Biology and Evolution. 15: 910-7. PMID 9656490  1
1998 Bruno WJ, Sun F, Torney DC. Optimizing nonadaptive group tests for objects with heterogeneous priors Siam Journal On Applied Mathematics. 58: 1043-1059.  1
1998 Knill E, Bruno WJ, Torney DC. Non-adaptive group testing in the presence of errors Discrete Applied Mathematics. 88: 261-290.  1
1997 Arvestad L, Bruno WJ. Estimation of reversible substitution matrices from multiple pairs of sequences. Journal of Molecular Evolution. 45: 696-703. PMID 9419247 DOI: 10.1007/PL00006274  1
1996 Bruno WJ. Modeling residue usage in aligned protein sequences via maximum likelihood. Molecular Biology and Evolution. 13: 1368-74. PMID 8952081  1
1995 Xie G, Lobb R, Bruno WJ, Torney DC, Gatewood JM. Single-base sequencing and similarity comparisons. Genomics. 30: 445-9. PMID 8825629 DOI: 10.1006/geno.1995.1263  1
1995 Bruno WJ, Knill E, Balding DJ, Bruce DC, Doggett NA, Sawhill WW, Stallings RL, Whittaker CC, Torney DC. Efficient pooling designs for library screening. Genomics. 26: 21-30. PMID 7782082 DOI: 10.1016/0888-7543(95)80078-Z  1
1993 McCormick MK, Buckler A, Bruno W, Campbell E, Shera K, Torney D, Deaven L, Moyzis R. Construction and characterization of a YAC library with a low frequency of chimeric clones from flow-sorted human chromosome 9. Genomics. 18: 553-8. PMID 8307565 DOI: 10.1016/S0888-7543(05)80355-6  1
1992 Pearson JE, Bruno WJ. Pattern formation in an N+Q component reaction-diffusion system. Chaos (Woodbury, N.Y.). 2: 513-524. PMID 12780000 DOI: 10.1063/1.165893  1
1992 Bruno WJ, Bialek W. Vibrationally enhanced tunneling as a mechanism for enzymatic hydrogen transfer. Biophysical Journal. 63: 689-99. PMID 1420907 DOI: 10.1016/S0006-3495(92)81654-5  1
1991 Joseph JS, Bruno W, Bialek W. Bleaching of the bacteriochlorophyll monomer band: Can absorption kinetics distinguish virtual from two-step electron transfer in bacterial photosynthesis? Journal of Physical Chemistry. 95: 6242-6247.  1
1989 Bialek W, Bruno WJ, Joseph J, Onuchic JN. Quantum and classical dynamics in biochemical reactions. Photosynthesis Research. 22: 15-27. PMID 24424675 DOI: 10.1007/BF00114763  1
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