Luciano Brocchieri, Ph.D.

Assistant Professor

University of Florida

College of Medicine

Department of Molecular Genetics and Microbiology

and Genetics Institute

PO Box 103610

Gainesville, FL 32610-3610

Phone: (352) 273-8131.  Fax: (352) 273-8284.

Email: lucianob@ufl.edu

 

 

Publications

 

Books, Chapter Author

 

1.    Mukherjee K. and Brocchieri L. (2010) Evolution of plant homeobox genes. In: Encyclopedia of Life Sciences. John Wiley and Sons Ltd, Chichester. In press.

2.    Brocchieri L., Zhou G.-P. and Jardetzky O. (2002) 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). Pp 340-366. ACS Symposium series 827.

3.    Karlin S. and Brocchieri L. (1999) Significant segment alignment of pairs of protein sequences from animals, plants, or fungi. In Evolutionary Theory and Processes: Modern Perspectives: Papers in honor of Eviatar Nevo (S.P. Wasser, ed.), Pp 145-157. Klewar Academic Publishers.

 

 

 

Reviewed Journal Articles

 

1.    Mukherjee K., Conway de Macario E., Macario A.J.L. and Brocchieri L. (2010). Chaperonin genes on the rise: more divergent classes and intense duplication activity are revealed by a comprehensive analysis of human and other vertebrate genomes. BMC Evol Biol, 10, 64.

2.    Mukherjee K., Brocchieri L.* and BŸrglin T.* (2009). A comprehensive classification and evolutionary analysis of plant homeobox genes. Mol Biol Evol, 26, 2775-2794.

3.    Brocchieri L., Conway de Macario E. and Macario, A.J.L. (2008). hsp-70 genes in the human genome: conservation and differentiation patterns predict a wide array of overlapping and specialized functions BMC Evol Biol 8, 19.

4.    Brocchieri L., Conway de Macario E. and Macario, A.J.L. (2007). Chaperonomics, a new tool to study ageing and associated diseases. Mec. Ageing Dev. 128, 125-136.

5.    Karlin S., Brocchieri L., Mr‡zek J. and Kaiser D. (2006). Distinguishing features of δ-proteobacterial genomes. Proc Natl Acad Sci USA. 103, 11352-11357.

6.    Macario, A.J.L., Brocchieri L., Shenoy A.R. and 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.

7.    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.

8.    Brocchieri L. and Karlin S. (2005). Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res, 33, 3390-3400.

9.    Brocchieri L., Kledal T.N., Karlin S. and Mocarski E.S. (2005) Predicting coding potential from genome sequence: application to betaherpesviruses infecting rats and mice. J Virol, 79, 7570-7596.

10. Karlin S., Brocchieri L., Campbell, A., Cyert, M. and Mr‡zek, J. (2005). Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. Proc Natl Acad Sci USA, 102, 7309-7314.

11. Karlin S., Mr‡zek, J., Ma J. and Brocchieri L. (2005). Predicted highly expressed genes in archaeal genomes. Proc Natl Acad Sci USA, 102, 7303-7308.

12. Brocchieri L. (2004) Environmental signatures in proteome properties. Proc Natl Acad Sci USA, 101, 8257-8258.

13. Kagawa H.K., Yaoi T., Brocchieri L., McMillan R.A., Alton T., and Trent J.D. (2003) The composition, structure, and stability of a group II chaperonin is temperature regulated in a hyperthermophilic archaeon. Mol Microbiol, 48, 143-156.

14. Karlin S., Brocchieri L., Bergman A., Mr‡zek J., and Gentles A. (2002) Amino acid runs in eukaryotic proteomes and disease associations. Proc Natl Acad Sci USA, 99, 333-338.

15. Karlin S., Brocchieri L., Trent J., Blaisdell B.E., and Mr‡zek J. (2002) Heterogeneity of genome and proteome content in Bacteria, Archaea, and Eukaryotes. Theor Popul Biol, 61, 367-390.

16. Brocchieri L. (2002) Review of: Molecular evolution and phylogenetics, by Nei M and Kumar S. Q Rev Biol 77, 200-201.

17. Brocchieri L. (2001) Phylogenetic inferences from molecular sequences: review and critique. Theor Popul Biol 59, 27-40.

18. Brocchieri L. (2001) Low complexity regions in Plasmodium proteins: in search of a function. Genome Res 11, 195-197.

19. Brocchieri L. and Karlin S. (2000) Conservation among HSP60 sequences in relation to structure, function, and evolution. Prot Sci, 9, 476-486.

20. Karlin S. and Brocchieri L. (2000) Heat shock protein 60 sequence comparisons: duplication, lateral transfer, and mitochondrial evolution. Proc Natl Acad Sci USA, 97, 11348-11353.

21. Karlin S., Brocchieri L., Mr‡zek J., Campbell, A.M., and Spormann A.M. (1999) A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes. Proc Natl Acad Sci USA, 96, 9190-9195.

22. Brocchieri L. and Karlin S. (1998) A symmetric-iterated method for the multiple alignment of protein sequences. J Mol Biol, 276, 249-264.

23. Karlin S. and Brocchieri L. (1998) Heat shock protein 70 family: multiple sequence comparisons, function and evolution. J Mol Evol 47, 565-577.

24. Brendel V., Brocchieri L., Sandler S.J. and Karlin S. (1997) Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J Mol Evol, 44, 28-36.

25. Karlin S. and Brocchieri L. (1996) Evolutionary conservation of RecA genes in relation to protein structure and function. J Bacteriol, 178, 1881-1894. 

26. Chang C.P., Brocchieri L., Shen W.-F., Largman C. and Cleary, M.L. (1996)  Pbx modulation of Hox homeodomain N-terminal arms establishes a gradient of DNA-binding specificities across the Hox locus. Mol Cell Biol, 16, 1734-1745.

27. Brocchieri L., di Pasquale C. and Matessi C. (1996) Conflicts for the production of males in social hymenoptera: a mathematical analysis of long term evolution. Ins Soc Life, 1, 63-69.

28. Brocchieri L. and Karlin S. (1995) How are close residues of protein structures distributed in primary sequence?  Proc Natl Acad Sci USA. 92, 12136-12140.

29. Brocchieri L. and Karlin S. (1994) Geometry of interplanar residue contacts in protein structures. Proc Natl Acad Sci USA, 91, 9297-9301.

30. Karlin S., Zucker M., and Brocchieri L. (1994) Measuring residue associations in protein structures. Possible implications for protein folding. J Mol Biol, 239, 227-248.

31. Brocchieri L., Matessi C. and Marin G. (1992) Inference of pair bonds from capture data based on low variation of the sex ratio among catches. Am Nat, 140: 492-508.

 

* These authors share senior-authorship.

 

Abstracts (2007-present)

 

1.    Oden SM and L Brocchieri. (2009) A new approach to gene finding in prokaryote genomes: a study of gene content in Pseudomonas aeruginosa strains. The 7th biennial Georgia Tech & Oak RIdge National Lab International Conference on Bioinformatics. Atlanta, Georgia, November 12-14.

2.    Oden SM and L Brocchieri. (2009) Comparative analysis of gene content in strains of Pseudomonas aeruginosa. CSHL Meeting: Genome Informatics. Cold Spring Harbor, October 27-30.

3.    Oden SM and L Brocchieri. (2009) A new method for gene prediction: application to comparative analysis of Pseudomonas aeruginosa genomes. Florida Genetics 2009, October 28-29, Gainesville, Florida.

4.    Mukherjee K, E Conway de Macario, AJL Macario and L Brocchieri (2009) Comprehensive analysis of the human genome reveals new hsp60 gene classes and evolutionary relations. Cell Stress Society International - The 4th International Congress on Stress Responses in Biology and Medicine, October 6 - 9, Sapporo, Japan.

5.    Lee HW and L Brocchieri (2009) Mixture models and protein neutral evolution profiles. CSHL Meeting: 74th Symposium: Evolution – The Molecular Landscape. Cold Spring Harbor, May 27 – June 1.

6.    Mukherjee K and L Brocchieri (2009) Bardet-Biedl Syndrome proteins and ciliary transport across the eukaryotic domain. COM Research Day, April 28-29, Gainesville, Florida.

7.    Mukherjee K and L Brocchieri (2009). Ancient origin and functional differentiation of diverged chaperonin genes in eukaryotes. EMBO Conference Series: The Biology of Molecular Chaperones. Cellular Protein Homeostasis in Disease and Aging. May 23-28 May. Dubrovnik, Croatia.

8.    Oden SM and L Brocchieri. (2008) Gene Compositional Characterization of Pseudomonas aeruginosa pathovars. Florida Genetics 2008, October 29-30, Gainesville, Florida.

9.    Lee HW and L Brocchieri. (2008) Models of position-specific constrained neutral evolution of protein families. Florida Genetics 2008, October 29-30, Gainesville, Florida.

10. Mukherjee K and L Brocchieri. (2008). Bardet-Biedl Syndrome proteins constitute an anciently evolved machinery for ciliary transport. Florida Genetics 2008, October 29-30, Gainesville, Florida.

11. Brocchieri L. (2008) Models of constrained neutral evolution and phylogenetic information in molecular sequences. Gordon Conference on Molecular Evolution, February 3-8, Ventura, California.

12. Mukherjee K, E Conway de Macario, L Brocchieri and AJL Macario (2008) Comprehensive analysis of the human genome reveals new hsp60 gene classes and evolutionary relations. Molecular Chaperone and Stress Response, April 30 - May 4, Cold Spring Harbor Laboratory, New York.

13. Mukherjee K and L Brocchieri (2007) Ancient origin and functional differentiation of chaperonin-like genes involved in Bardet-Biedl syndrome. Florida Genetics 2007, November 7-8, Gainesville, Florida.

14. Brocchieri L, E Conway de Macario  and AJL Macario (2007) Evolution and diversity of human Hsp70: implications for health and disease. World Conference of Stress, Aug 21-25. Budapest, Hungary.

15. Maeder D, Brocchieri L, AJL Macario and E Conway de Macario (2007) The extended cct-hsp60 gene family in the human genome. World Conference of Stress, Aug 21-25. Budapest, Hungary.

16. Brocchieri L and D Bloom (2007) Coding potential and G+C content in Simplex virus genomes. 32nd International Herpesvirus Workshop 2007, Jul 7-12, Asheville, North Carolina.