Short Bio
I am currently a Scientific Informatics Analyst at the
Simons Center for Quantitative Biology (SCQB)
of Cold Spring Harbor Laboratory (CSHL)
where I am working with Professor Michael Schatz
to develop novel algorithms and computational systems to analyze DNA sequences,
concentrating on the assembly and alignment of next generation
sequencing reads. Applications include analysis of genetic variations in
human genome to identify the genetic causes of various human diseases
including autism, cancer, and other psychiatric conditions.
Before this position, I was appointed as a Research Scientist at the
NYU Bioinformatics Group
of Courant Institute of Mathematical Sciences (CIMS) where, together with Professor
Bud Mishra, I developed novel sequence assembly
and base-calling methods for next generation sequencing data.
I received a Ph.D. in Computer Science from New York University
(NYU) in 2011 and from University of Catania
(UniCT) in 2008 respectively.
I have been awarded an IBM PhD Fellowship
for the 2010-2011 academic year.
Check out my CV for more details.
Here you can find my old home page at NYU.
Research Interests
Thanks to the enormous advances in DNA sequencing technology there is now the potential to perform analyses
that can be directly applied to many different areas in Computational Biology such as, genome-wide association studies,
detecting new polymorphisms, finding rare and de novo mutations.
However the availability and performance of the computational tools required to analyze these data
continue to lag far behind the improvements in technology.
To address this issue, my research has focused on applying techniques and algorithms from Combinatorial Optimization
(such as Branch-and-Bound and Beam Search global search methods)
to solve hard problems in Computational Genomics, with special focus on sequence accuracy.
In particular my main areas of research are: DNA sequence assembly, Base-Calling
and Assembly Validation from next generation sequencing reads.
My research interests also include: Protein Structure Prediction, Multi-objective Optimization,
Evolutionary Computation and Multi-Agent Systems.
Seminars and Lectures
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From DNA Sequencing to Genomes: the Assembly Challenge
2nd Conference on Systems Biology and New Sequencing Techniques
(SBNST):
The Abdus Solam International Centre for Theoretical Physics (ICTP)
Miramare - Trieste, Italy, October 2011.
-
From Sequencing to Sequences: Algorithms and Metrics for Accurate Genome Assembly
SchatzLab: Simons Center for Quantitative Biology,
Cold Spring Harbor Laboratory
(CSHL) USA, August 2011.
-
SUTTA: Scoring-and-Unfolding Trimmed Tree Assembler
Zhang Lab: Computational Biology and Bioinformatics,
Cold Spring Harbor Laboratory
(CSHL) USA, September 2009.
-
A Multi-Objective Evolutionary Approach to the Protein Structure Prediction Problem
Computer-Aided Systems Laboratory
(CASL),
Princeton University USA, December 2007.
Selected Publications
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Iossifov I., Ronemus M., Levy D., Wang Z., Hakker I., Rosenbaum J., Yamrom B., Lee Y., Narzisi G., Leotta A., Kendall J., Grabowska E., Ma B., Marks S., Rodgers L., Stepansky A., Troge J., Andrews P., Bekritsky M., Pradhan K., Ghiban E., Kramer M., Parla J., Demeter R., Fulton L.L., Fulton R.S., Magrini V.J., Ye K., Darnell J.C., Darnell R.B., Mardis E.R., Wilson R.K., Schatz M.C., McCombie R.W., Wigler M.:
De novo gene disruptions in children on the autism spectrum.
Neuron. 74:2 285-299, 2012.
(DOI: 10.1016/j.neuron.2012.04.009).
-
Vezzi F., Narzisi G., and Mishra B.:
Feature-by-Feature - Evaluating De Novo Sequence Assembly.
PLoS ONE 7(2): e31002, February 2012.
(DOI: 10.1371/journal.pone.0031002).
-
Schatz M. C., Phillippy A. M., Sommer D., Delcher A. L., Puiu D., Narzisi G., Salzberg S. L., Pop M.:
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.
Briefings in Bioinformatics, December 2011.
(DOI: 10.1093/bib/bbr074).
-
Narzisi G. and Mishra B.:
Comparing De Novo Genome Assembly: The Long and Short of It.
PLoS ONE 6(4):e19175. April 2011
(DOI: 10.1371/journal.pone.0019175).
-
Narzisi G. and Mishra B.:
Scoring-and-Unfolding Trimmed Tree Assembler: Concepts, Constructs and Comparisons.
Bioinformatics, Oxford Journals, (2011) 27 (2): 153-160
(DOI: 10.1093/bioinformatics/btq646).
[Revision, Feb 10 2011]
-
Menges F., Narzisi G., and Mishra B.:
TotalReCaller: Improved Accuracy and Performance via Integrated Alignment & Base-Calling.
Bioinformatics, Oxford Journals, (2011) 27(17): 2330-2337
(DOI: 10.1093/bioinformatics/btr393).
-
Smith S.W., Portelli I., Narzisi G., Nelson L.S., Menges F., Rekow E.D., Mincer J.S., Mishra B., Goldfrank L.R.:
A Novel Approach to Multi-Hazard Modeling and Simulation.
Disaster Medicine and Public Health Preparedness (DMPHP),
The American Medical Association (AMA), 2009
(DOI: 10.1097/DMP.0b013e3181a88899).
-
Cutello V., Narzisi G., Nicosia G.:
A Multi-Objective Evolutionary Approach to the Protein Structure Prediction Problem.
Journal of the Royal Society Interface, Royal Society Publications London,
vol. 3, issue 6, pp. 139-151, 22 February 2006
(DOI: 10.1098/rsif.2005.0083).
-
Anile A.M., Cutello V., Narzisi G., Nicosia G., Spinella S.:
Determination of protein structure and dynamics combining immune algorithms and pattern search methods.
Natural Computing Int. Journal, Springer 2006
(DOI: 10.1007/s11047-006-9027-3).
Reviewer for
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Giuseppe Narzisi, Ph.D.
Cold Spring Harbor Laboratory
One Bungtown Road
Koch Building 1121
Cold Spring Harbor, NY 11724
E-mail: gnarzisi <at> cshl.edu
Phone: (516) 367-5244
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