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

 

 

Curriculum vitae

 

 

 

Education            B.A.  University of Parma,  Italy, 1984, Biology (Highest Honors)

                              Ph.D. University of Parma, Italy. 1992, Environmental Sciences. Dissertation in theoretical population genetics: evolution of social behavior.           

 

 

Present Position     Assistant Professor, UF Genetics Institute and Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida.

 

 

Professional Experience

 

2006-present        Assistant Professor, University of Florida, Genetics Institute and Department of Molecular Genetics and Microbiology.

2000-2006             Senior Research Scientist at Stanford University, Department of Mathematics.

1995-2000             Research Scientist at Stanford University, Department of           Mathematics.

1991-1995             Post-doctoral Research Associate at Stanford University, Department of Mathematics.

 

 

Professional Memberships

 

1. International Society for Computational Biology (ISCB)

2. Society for Molecular Biology and Evolution (SMBE)

3. American Association for the Advancement of Science (AAAS)

4. American Chemical Society (ACS)

 

 

 

Honors and Awards

 

 

Fellowships:

 

1988-1991: Fellowship of the Italian Ministry of Public Education for a PhD program in Environmental Sciences.

 

 

Invited presentations:

 

1.  Microbiology and Cell Science Seminar Series, UF, 6/1/2010

2.  EMBO Conference Series: The Biology of Molecular Chaperones, Dubrovniki, Croatia, May 23-28, 2009.

3.  NIH/NLM/NCBI - ORISE Program, Bethesda MD, March 25, 2009.

4.  Computational and Systems Biology Summer Institute Seminar Series 2008 - Iowa State University, June 2008.

5.  Zoology Seminar Series. UF Department of Zoology. January 8, 2008.

6.  World Conference of Stress. Budapest, Hungary, Aug 21-25, 2007.

7.  University of Florida Institute for Aging, Gainesville, FL. November 20, 2006.

8.  3rd Georgia Tech – Emory International Conference on Bioinformatics, Atlanta, Georgia, USA, 2001.

 

 

Invited publications

 

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. (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.

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

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

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

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

 

 

Ad hoc reviewer

 

Reviewer for Scientific Journals: 1. Bioinformatics; 2. Gene; 3. Genome Research; 4. BMC Genomics; 5. Journal of Molecular Biology; 6. Journal of Molecular Evolution; 7. Molecular Biology and Evolution; 8. Nucleic Acids Research; 9. Genome Biology and Evolution; 10. BMC Evolutionary Biology; 11. Genetic Testing; 12. Catalan Journal of Ornithology; 13. Genetica; 14. Archaea. 15. Genome Biology and Evolution; 16. Proceedings of the National Academy of Sciences USA; 17. Science; 18. Evolutionary Biology; 19. PLoS ONE.

 

Reviewer for Conferences: 1. Georgia Tech International Conference on Bioinformatics 2000 – Atlanta, GA. 2. Georgia Tech International Conference on Bioinformatics 2005 – Atlanta, GA.

 

Reviewer for Research Grant Applications: 1. Biotechnology and Biological Sciences Research Council – Research Grant Applications. 2. Basic Research and Higher Education Program of the U.S. Civilian Research and Development Foundation – Research Grant Application. 3. NSF New Investigator Awards. 4. NSF Career 7/21/09. 5. Recovery Act Limited Competition: NIH DirectorÕs Opportunity for Research in Five Thematic Areas (RC4);

Teaching

 

Instructor

 

2011-                        Quantitative models of protein evolution and phylogenetics GMS6233. Two-unit course emphasizing the study of the theoretical principles that underlie different models of protein evolution used in phylogenetic analysis. Through this course students develop a critical understanding of the biological assumptions and mathematical tools used to model protein evolution in inferring phylogenetic relations.

 

2007-2010                Genetics and Genomics Graduate Seminar GMS6181. The philosophy of this class is to educate future scientists to critically evaluate scientific research reports, to identify their scientific significance, and to effectively communicate the scientific findings to an audience of peers and senior scientists..

 

Co-instructor

 

2009-Present           Advanced Application of Bioinformatics in Genetic Research GMS6232. In this class students are exposed to computational bioinformatics themes and their application in available tools, and are asked to develop a bioinformatics project under the guidance of the instructors.

 

Invited lecturer

 

2007-Present           Applications of Bioinformatics in Genetics Research

July 2008                  UF Interdisciplinary Center for Ongoing Research/Education.

July 2008                  Computational and Systems Biology Summer Institute - Iowa State Univ.                 

October 2006           Prokaryotic Cell Structure MCB6409.

 

 

Mentoring

 

Postdoctoral associates

 

Dec 2011 – present    Advisor. UF Postdoctoral Associate Dr. Ying Zhang.

 

July 2007 – Feb 2011  Advisor. UF Postdoctoral Associate Dr. Krishanu Mukherjee.

 

Rotation students

 

Aug-Oct 2007             Advisor. UF Genetics and Genomics Graduate Program - Rotation Graduate Student Yifei Yin.

Oct-Dec 2007              Advisor. UF Genetics and Genomics Graduate Program - Rotation Graduate Student Yajie Yang.

Oct-Dec 2007              Advisor. UF Genetics and Genomics Graduate Program - Rotation Graduate Student Hye Won Lee.

 

Dissertation students

 

2008 - Present            Advisor. UF Genetics and Genomics Graduate Program – Graduate Student Hye Won Lee.

2008 - Present            Advisor. UF Interdepartmental Graduate Program (IDP), Genetics Concentration – Graduate Student Steven M. Oden.

 

Other mentoring activities

 

2010 - Present            Graduate committee member. UF Genetics and Genomics Graduate Program – Graduate Student Guangyao Li.

2010 - Present            Graduate committee member. UF Microbiology and Cell Biology Graduate Program – Graduate Student Nikita Nembhard.

2009 - Present            Graduate committee member. UF Genetics and Genomics Graduate Program – Graduate Student Alireza Nazarian.

2008 - Present            Graduate committee member and Mentoring. UF Zoology Graduate Program – Graduate Student Matt Salomon.

2005-2006                   Co-advisor. NYSU, Undergraduate student Craig Stropkay.

2001-2004                   Co-advisor. Stanford University, Postdoctoral student Dr. Rakesh Nigam.

                                   

 

 

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. DOI: 10.1002/9780470015902.a0022865.

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.    Oden S.M.. and Brocchieri L. (2011). N-PACT: A N-Profile Analysis Computational Tool for gene prediction by quantitative and visual assessment of compositional contrasts (In preparation).

2.    Oden S.M.. and Brocchieri L. (2011). Quantitative analysis of genomic compositional contrasts. Improving gene prediction in prokaryote genomes. (In preparation).

3.    Lee H.W. and Brocchieri L. (2011). Reconstruction of bacterial phylogeny from Òswitch positionsÓ in protein evolution. (In preparation).

4.    Mukherjee K. and Brocchieri L. (2011). Ancient origin of chaperonin gene paralogs involved in ciliopathies. Submitted.

5.    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.

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

7.    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.

8.    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.

9.    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.

10. 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.

11. 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.

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

13. 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.

14. 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.

15. 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.

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

17. 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.

18. 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.

19. 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.

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

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

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

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

24. 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.

25. 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.

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

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

28. 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.

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

30. 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.

31. 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.

32. 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.

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

34. 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.

35. 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.

 

 

 

 

 

Abstracts (2007-present)

 

1.    Oden S and L Brocchieri. (2011) N-pact: a tool for quantitative analysis of compositional contrasts in nucleotide sequences for gene identification. CSHL Meeting: Genome Informatics, November 2-5, Cold Spring Harbor, NY.

2.    Lee HW and L Brocchieri. (2011) Reconstruction of bacterial phylogeny from Òswitch positionsÓ in protein evolution. COM Research Day, April 16, Gainesville, FL.

3.    Lee HW, Alsalhi H and L Brocchieri. (2011) Conservation and codon usage in prokaryotes. COM Research Day, April 16, Gainesville, FL.

4.    Oden S and L Brocchieri. (2010) The coding potential of the human genome: global compositional properties identify with statistical significance a plethora of new potential coding regions. Beyond the Genome: the true gene count, human evolution and disease genomics, October 11-13, Boston, MA.

5.    Oden S and L Brocchieri. (2010) Predicting gene-coding regions from global compositional contrasts: an application to archaeal genomes. MCS/MGM Graduate Retreat, August 20-21, Jacksonville, FL.

6.    Lee HW and L Brocchieri. (2010) Phylogenetic information from rare amino acid substitutions for prokaryotic tree reconstruction. MCS/MGM Graduate Retreat, August 20-21, Jacksonville, FL.

7.    Lee HW and L Brocchieri. (2010) Evolutionary relations of Bacteria: information from neutral evolution and from functional differentiation. COM Research Day, April 21, Gainesville, FL.

8.    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, November 12-14. Atlanta, GA.

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

10. 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, FL.

11. 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.

12. 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.

13. 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.

14. 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.

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

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

17. 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.

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

19. 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.

20. 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.

21. 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.

22. 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.

23. 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.

 

 

 

Research Support

1. Funding agency: University of Florida College of Medicine, Department of Molecular Genetics & Microbiology, and Genetics Institute.

Start up funds                   07/01/2006 –

Role:                                  Assistant Professor

Budget:                              $500,000

 

2. Funding agency: NIH

R01 GM087485-01A2       08/01/10-07/31/15

Role:                                  Principal Investigator

New tools for the characterization of gene predictions in prokaryote genomes: application to Pseudomonas aeruginosa genomes.

Development of gene-characterization tools for prokaryote genomes for the identification of genes of unusual composition. Computational results are developed into a gene finder and applied to the experimental identification of short coding sequences in Pseudomonas aeruginosa.

Budget:                              $975,000 / 5 years

 

3. Funding Agency: Computational Biology Working Group, UF

Seed Grant                        07/01/10-06/30/11

Role:                                  Co-Principal Investigator

Tractable computational models for intuitive analysis and design of biomolecular configurations: leveraging multiscale geometry, symmetry and combinatorial constraints.

Budget:                              $50,000 / 1 year

 

Research interests and activities

Genome and sequence annotation, functional characterization and protein evolution. My background as an evolutionary biologist includes a broad range of topics that naturally brought me to embrace a systemic view of evolutionary processes. These include studies on properties of protein structures (residue-type association, protein sequence structural connectivity, amino acid ¹-cloud/cationic interactions) and protein-DNA interactions (computational models of Trp-repressor/DNA-operator interaction from NMR data) and on the evolution of protein families (e.g., RecA, chaperones, homeodomain proteins).

Most recently, I have been interested in developing new methods for gene identification and characterization, and in understanding how different selective processes and mutational biases affect sequence composition and evolution of proteins, genes and genomes. This interest reflects in the following current research projects:

(i)    Identification and statistical characterization of protein-coding genes. We are developing new methodologies based on global compositional properties of coding sequences to identify and characterize with increased reliability genes in genomes of prokaryotes and eukaryotes. Besides providing new bioinformatics tools for improving current annotations, we are interested in identifying the roles of short polypeptides in regulating gene expression and protein functionality in prokaryotes and eukaryotes.

(ii)  Experimental characterization of gene expression. We are currently investigating expression of predicted genes in the human pathogen Pseudomonas aeruginosa by RNA-seq deep-sequencing analyses and by ribosome-profiling analysis. For the latter analysis we are optimizing protocols for its first application to prokaryotic organisms.

(iii) Models of protein evolution and functional differentiation. We are developing and investigating new models of protein evolution that are used as a conceptual framework for reconstruction of phylogenetic trees, for the identification of protein sites of functional relevance, and for investigating the effect of codon usage on translation accuracy and efficiency.

(iv) Genome evolvability. We are interested in studying evolvability as an adaptive process in relation to sequence content, with particular reference to the role of DNA topology in affecting genetic and phenotypic plasticity in the opportunistic human pathogen Pseudomonas aeruginosa, in collaboration with the biochemistry lab of Dr. Silvia Tornaletti.

 

Teaching statement

I am directing a two-unit course in theoretical models of protein evolution in phylogenetic analysis (GMS 6233). I have experience in mentoring undergraduate and graduate students and in teaching as course instructor or invited lecturer graduate courses related to Bioinformatics, Genetics, Genomics and Molecular Evolution. My teaching interests reflect my background in Biological Sciences, Theoretical Population Genetics and Bioinformatics and in this respect I am most qualified and interested in teaching graduate courses in Bioinformatics and in Molecular Evolution. I am also qualified in teaching undergraduate courses related to any aspect of Biological Sciences. My emphasis is on the relevance of bioinformatics and computational methods in exploring and solving biological problems with an evolutionary perspective.

I have experience in mentoring undergraduate and graduate students, and in teaching (as course director, instructor or lecturer) small and medium sized graduate classes. I consider teaching and research as complementary aspects of my academic commitment and I welcome the teaching and mentoring of graduate and undergraduate students as important aspects of my professional and personal growth.