Dr. Luciano Brocchieri

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University of Florida
College of Medicine
Molecular Genetics and Microbiology
UF Genetics Institute
Assistant ProfessorAppointed: 2006
Professional Headshot of Luciano Brocchieri

Mailing Address

UF Genetics Institute
University of Florida
P.O. Box 103610
Gainesville, Florida 32610-3610
United States

Contact Information

Phone: (352) 273-8131
Fax: (352) 273-8284
lucianob@ufl.edu
http://www.mgm.ufl.edu/faculty/lbrocchieri.htm

Qualifications

Ph.D., University of Parma, Environmental Sciences - Theoretical Population Genetics, 1992.

Expertise and Research Interests

Bioinformatics. Analysis of molecular evolution and functionality. Determination of phylogenetic relations through sequence analysis: phylogenetic and functional signals in molecular sequences. Methods for reconstructing phylogenetic trees from molecularsequence data. Methods of multiple alignment of molecular sequences for the determination of protein evolutionary and functional relations. Amino acid usage and distribution in structure and sequence. Genomics and proteomics of herpesviridae. Codon usage: mutational bias and selective pressure. Prediction of transcription and translation levels. Gene duplication in eukaryotic and microbial genomes. Principles of protein structure conformation and stability. Amino acid usage: selection at the protein and nucleic acid levels. Origin and phylogenetic relations of eubacterial, archaeal, and eukaryotic species and their organelles. Conservation and functionality of the heat shock chaperonin HSP60, the heat shock chaperone protein HSP70, and the replication/repair protein RecA. Principles of protein/DNA interaction: the tryptophan repressors, molecular modelling and analysis of NMR data; Pbx/Hox/DNA interaction model using homology modelling and experimental data.

Other Expertise

Mathematical theory of evolution: Theoretical models for the long term evolution of social behavior with non linear costs and benefits (doctorate in theoretical population genetics); long term evolution of reproductive strategies in social hymenoptera. Behavioral sciences, behavioral evolution. Experimental studies on the evolution of animal behavior: aggression and dominance in mice societies; fixed action patterns and genetic control in the predatory response of birds of prey. Ecology: Bentonic communities in sub-alpine lakes.

Future Research

Research in genomics and proteomics: comparison and analysis of gene content and distribution in eukaryotic and prokaryotic genomes. Chaperonomics, the study of chaperone proteins using genomic information. Genomics and proteomics of Herpesviridae. New methods for ascertaining the evolutionary relations among species and functional relations among proteins using biomolecular data. Relations of genomic biases, transcription, efficiency of translation, and other selective processes at the DNA and protein level in determining codon usage and amino acid composition in prokaryotes and eukaryotes.

Industrial Relevance

Sequence and structure analysis of protein and DNA. Gene prediction. Gene expression regulation. Functional analysis of proteins.

Keywords

COS Keywords:

Bioinformatics, Evolution, Genomics, Mathematics.

Additional Terms:

Bioinformatics, Evolution, Genomics, Protein Function.

Languages

(Reading, Writing, Speaking)

English: (Fluent, Fluent, Fluent)
Italian: (Fluent, Fluent, Fluent)

Honors and Awards

2002, Invited speaker International Conference on Research Trends in Science and Technology, Beiruth and Byblos, Lebanon,
2002-2003, Invited speaker Multi-Conference on Systematics, Cybernetics and Informatics, Orlando, Florida, USA,
2001, Invited speaker 3rd Georgia Tech - Emory International Conference on Bioinformatics, Atlanta, Georgia, USA,
2001-2003, Invited speaker Scuola Superiore G. Reiss Romoli (SSGRR) Conferences, L' Aquila, Italy,
1988-1991, Fellowship for a PhD program, Ministry of Public Education, University of Parma, Italy, Environmental Sciences, theroretical population genetics
1987-1988, Fondazione Airone Fellowship, G. Mondadori Publisher, Behavioral evolution

Previous Positions

2000-2005, Senior Research Scientist, Stanford University, Humanity and Sciences, Mathematics
1995-2000, Research Scientist, Stanford University, School of Humanities and Sciences, Mathematics
1991-1995, Postdoctoral Research Associate, Stanford University, School of Humanities and Sciences, Mathematics

Funding Received

  • : Fondazione Airone Fellowship, G. Mondadori Publisher, Behavioral evolution, to .

Publications

  • Macario AJL, Brocchieri L, Shenoy AR, Conway de Macario E (2006) Evolution of a protein-folding machine: genomic and evolutionary analyses reveal three distinct lineages of the archaeal hsp70(dnaK) gene., J. Mol. Evol., 63, 74-86
  • Karlin S, Brocchieri L, Mrazek J, Kaiser D (2006) Distinguishing features of delta-proteobacterial genomes., Proc. Natl. Acad. Sci. U.S.A., 103, 1352-11357
  • Karlin S, Mrazek J, Ma J, Brocchieri L (May 2005) Predicted highly expressed genes in archaeal genomes., Proc. Natl. Acad. Sci. U.S.A., 102 (20), 7303-8 Abstract
  • Karlin S, Brocchieri L, Campbell A, Cyert M, Mrazek J (May 2005) Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes., Proc. Natl. Acad. Sci. U.S.A., 102 (20), 7309-14 Abstract
  • Brocchieri L, Kledal TN, Karlin S, Mocarski ES (2005) Predicting coding potential from genome sequence: application to betaherpesviruses infecting rats and mice., J. Virol., 79, 7570-7596
  • Brocchieri, L (2005) Review of: The Phylogenetic Handbook. A practical approach to DNA and Protein Phylogeny, by Marco Salemi and Anne-Mieke Vandamme (Eds)., Q. Rev. Biol., 80, 110
  • Brocchieri L, Karlin S (2005) Protein length in eukaryotic and prokaryotic proteomes., Nucleic Acids Research, 33 (10), 3390-400 Abstract
  • Brocchieri L, Environmental signatures in proteome properties, Proceedings of the National Academy of Sciences of the United States of America., 101(22), 8257-8, Jun 2004 Abstract
  • Kagawa HK, Yaoi T, Brocchieri L, McMillan RA, Alton T, Trent JD, The composition, structure and stability of a group II chaperonin are temperature regulated in a hyperthermophilic archaeon, Molecular Microbiology, 48(1), 143-56, April 2003 Abstract
  • Karlin S, Brocchieri L, Trent J, Blaisdell BE, Mrazek J, Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes, Theoretical Population Biology, 61(4), 367-90, June 2002 Abstract
  • Karlin S, Brocchieri L, Bergman A, Mrazek J, Gentles AJ, Amino acid runs in eukaryotic proteomes and disease associations, Proceedings of the National Academy of Sciences (USA), 99(1), 333-8, January 2002 Abstract
  • Brocchieri L, Review of: Molecular evolution and phylogenetics, by Nei M and Kumar S, Quarterly Reviews of Biology, 77, 200-201, 2002
  • Brocchieri L., Zhou G.-P. and Jardetzky O., Allostery and induced fit. NMR and molecular modeling study of the trp repressor ? mtr DNA complex. In Structures and mechanisms. From ashes to enzymes (Eaton GR, Wiley DC and Jardetzky O, eds), ACS Symposium series, 827, 340-366, 2002
  • Brocchieri L, Phylogenetic inferences from molecular sequences: review and critique, Theoretical Population Biology, 59(1), 27-40, February 2001 Abstract
  • Brocchieri L, Low complexity regions in Plasmodium proteins: in search of a function, Genome Research, 11, 195-197, 2001
  • Karlin S, Brocchieri L, Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution, Proceedings of the National Academy of Sciences (USA), 97(21), 11348-53, October 2000 Abstract
  • Brocchieri L, Karlin S, Conservation among HSP60 sequences in relation to structure, function, and evolution, Protein Science : a Publication of the Protein Society, 9(3), 476-86, March 2000 Abstract
  • Karlin S, Brocchieri L, Mrazek J, Campbell AM, Spormann AM, A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes., Proceedings of the National Academy of Sciences (USA), 96(16), 9190-5, 3 Aug 1999 Abstract
  • Karlin S, Brocchieri L, Heat shock protein 70 family: multiple sequence comparisons, function, and evolution, Journal of Molecular Evolution, 47(5), 565-77, November 1998 Abstract
  • Brocchieri L, Karlin S, A symmetric-iterated multiple alignment of protein sequences., Journal of Molecular Biology, 276(1), 249-64, 13 1998 Abstract
  • Brendel V, Brocchieri L, Sandler S J, Clark A J, Karlin S, Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms., Journal of Molecular Evolution, 44(5), 528-41, 1997 Abstract
  • Karlin S, Brocchieri L, Evolutionary conservation of RecA genes in relation to protein structure and function., Journal of Bacteriology, 178(7), 1881-94, 1996 Abstract
  • Chang C P, Brocchieri L, Shen W F, Largman C, Cleary M L, Pbx modulation of Hox homeodomain amino-terminal arms establishes different DNA-binding specificities across the Hox locus., Molecular and Cellular Biology, 16(4), 1734-45, 1996 Abstract
  • Brocchieri L, Karlin S, How are close residues of protein structures distributed in primary sequence?, Proceedings of the National Academy of Sciences (USA), 92(26), 12136-40, 19 1995 Abstract
  • Brocchieri L, Karlin S, Geometry of interplanar residue contacts in protein structures., Proceedings of the National Academy of Sciences (USA), 91(20), 9297-301, 27 1994 Abstract
  • Karlin S, Zuker M, Brocchieri L, Measuring residue associations in protein structures. Possible implications for protein folding., Journal of Molecular Biology, 239(2), 227-48, 3 1994 Abstract

Profile Details

Last Updated: 8/2/2006

COS Expertise ID #435408
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