Short Bio
I am an Associate Director of Computational Biology at the New York Genome Center (NYGC).
My research interest is in developing novel algorithms and computational systems to analyze DNA sequences,
concentrating on the assembly and alignment of next generation sequencing reads.
Before joining the NYGC, I was a Computational Science Analyst at the Simons Center for Quantitative Biology
(SCQB) of Cold Spring Harbor Laboratory (CSHL)
where I worked with Professor Michael Schatz on micro-assembly algorithms for indels detection.
Before that, I was a Research Scientist at the NYU Bioinformatics Group
of Courant Institute of Mathematical Sciences (CIMS) led by
Professor Bud Mishra, where I worked on several problems at the
core of computational genomics, such as, DNA sequence assembly,
base calling, and metrics for assembly quality evaluation.
I earned my Ph.D. in Computer Science from New York University in 2011.
In 2010 I received the "IBM Ph.D. Fellowship award" for my innovative research in Computational Genomics.
Check out my CV for more details.
Selected publications
(see more in Google Scholar)
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Byrska-Bishop M., Evani U.S, Zhao X., Basile A.O., Abel H.J., Regier A.A., Corvelo A., Clarke W.E., Musunuri R., Nagulapalli K., Fairley S., Runnels A., Winterkorn L., Lowy-Gallego E., The Human Genome Structural Variation Consortium, Flicek P., Germer S., Brand H., Hall I.M., Talkowski M.E., Narzisi G., Zody M.C.
High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.
Cell, Volume 185, Issue 18, 3426 - 3440 (DOI: 10.1016/j.cell.2022.08.004)
Also available in bioRxiv 2021.02.06.430068; 2021 (DOI: 10.1101/2021.02.06.430068).
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Musunuri R., Arora K., Corvelo A., Shah M., Shelton J., Zody MC., Narzisi G.
Somatic variant analysis of linked-reads sequencing data with Lancet. Bioinformatics, Oxford Journals, 2020 (DOI: 10.1093/bioinformatics/btaa888)
Also available in bioRxiv 2020.07.04.158063; 2020 (DOI: 10.1101/2020.07.04.158063).
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Narzisi G, Corvelo A, Arora K, Bergmann E, Shah M, Musunuri R, Emde AK, Robine N, Vacic V, Zody MC.
Genome-wide somatic variant calling using localized colored de Bruijn graphs. Communications Biology, volume 1, Article number: 20, 2018 (DOI:10.1038/s42003-018-0023-9)
Also available in bioRxiv 196311; 2017 (DOI: 10.1101/196311).
GenomeWeb story -
Fan P.D., Narzisi G., Jayaprakash A.D., Venturini E., Robine N., Smibert P., Germer S., Yu H.A., Jordan E.J., Paik P.K., Janjigian Y.Y., Chaft J.E., Wang L., Jungbluth A.A., Middha S., Spraggon L., Qiao H., Lovly C.M., Kris M.G., Riely G.J., Politi K., Varmus H., Ladanyi M.
YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics. Proceedings of the National Academy of Sciences, Jun 2018, 201717782 (DOI: 10.1073/pnas.1717782115).
Also available in bioRxiv 275974 (DOI: 10.1101/275974). -
Dolzhenko E., van Vugt J.J.F.A., Shaw R.J., Bekritsky M.A., van Blitterswijk M., Narzisi G., Ajay S.S., Rajan V., Kingsbury Z., Humphray S.J., Schellevis R.D., Brands W.J., Baker M., Rademakers R., Kooyman M., Tazelaar G.H.P., van Es M.A., McLaughlin R, Sproviero W., Shatunov A., Jones A., Khleifat A.A., Pittman A., Morgan S., Hardiman O., Al-Chalabi A., Shaw C., Smith B., Neo E.J., Morrison K., Shaw P.J., Reeves C., Winterkorn L., Wexler N.S., The US-Venezuela Collaborative Research Group, Housman D.E., Ng C., Li A., Taft R.J., van den Berg L.H., Bentley D.R., Veldink J.H., Eberle M.A.
Detection of long repeat expansions from PCR-free whole-genome sequence data. Genome Research September 8 2017. (DOI: 10.1101/gr.225672.117)
Also available in bioRxiv (DOI: 10.1101/093831). -
Fang H., Bergmann E.A., Arora K., Vacic V., Zody M.C., Iossifov I., O'Rawe J.A., Wu Y., Jimenez Barron L.T., Rosenbaum J., Ronemus M., Lee Y., Wang Z., Dikoglu E., Jobanputra V., Lyon G.J., Wigler M., Schatz M.C., Narzisi G.
Indel variant analysis of short-read sequencing data with Scalpel. Nature Protocols 11, 2529-2548, 2016. (DOI: 10.1038/nprot.2016.150)
Also available in bioRxiv (DOI: 10.1101/028050). -
Narzisi G. and Schatz M.C.
The challenge of small-scale repeats for indel discovery. Front. Bioeng. Biotechnol. 2015 (DOI: 10.3389/fbioe.2015.00008) -
Narzisi G., O'Rawe J.A., Iossifov I., Fang H., Lee Y., Wang Z., Wu Y., Lyon G.J., Wigler M., Schatz M.C.
Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods (DOI: 10.1038/nmeth.3069)
Also available in bioRxiv (DOI: 10.1101/001370).
[Press Release (CSHL)] [Press Release (SFARI)] -
Fang H., Narzisi G., O'Rawe J., Wu Y., Rosenbaum J., Ronemus M., Iossifov I., Schatz M.C., Lyon G.J.
Reducing INDEL calling errors in whole-genome and exome sequencing data. Genome Medicine 2014, 6:89 (DOI: 10.1186/s13073-014-0089-z).
Also available in bioRxiv 2014 (DOI: 10.1101/006148). -
Iossifov I., O'Roak B.J., Sanders S.J., Ronemus M., Krumm N., Levy D., Stessman H.A., Witherspoon K.T., Vives L., Patterson K.E., Smith J.D., Paeper B., Nickerson D.A., Dea J., Dong S., Gonzalez L.E., Mandell J.D., Mane S.M., Murtha M.T., Sullivan C.A., Walker M.F., Waqar Z., Wei L., Willsey A.J., Yamrom B., Lee Y., Grabowska E., Dalkic E., Wang Z., Marks S., Andrews P., Leotta A., Kendall J., Hakker I., Rosenbaum J., Ma B., Rodgers L., Troge J., Narzisi G., Yoon S., Schatz M.C., Ye K., McCombie W.R., Shendure J., Eichler E.E., State M.W. & Wigler M.
The contribution of de novo coding mutations to autism spectrum disorder. Nature (2014) (DOI: 10.1038/nature13908) -
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). -
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). -
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).
Seminars and Lectures
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Somatic variant analysis using localized colored de Bruijn graphs
International Genome Graph Symposium 2022, (IGGSy22), Monte Verita, Ascona, Switzerland - July 3-7, 2022 -
Lancet: somatic variant calling using localized colored DeBruijn graphs
Advances in Genome Biology and Technology 2017, (AGBT2017), Hollywood Beach, Florida, USA, February 13-16 2017. -
Lancet: somatic variant calling using localized colored DeBruijn graphs
Genome Informatics 2016, (GI2016), Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK, 19-22 September 2016. -
Towards accurate germline and somatic indel discovery with Micro-Assembly
Iowa Institute of Human Genetics (IIHG), Bioinformatics Short Course, Iowa City, USA, July 2014. -
From DNA Sequencing to Genomes: the Assembly Challenge
Iowa Institute of Human Genetics (IIHG), Bioinformatics Short Course, Iowa City, USA, July 2014. -
Towards accurate germline and somatic indel discovery with Micro-Assembly
New York Genome Center (NYGC) USA, February 2014. -
Micro-assembly approach to discover INDELs in NGS data
Computational Biology & Bionformatics seminar. Simons Center for Quantitative Biology (CSHL) USA, November 2013. -
SCALPEL - Micro-assembly approach to detect INDELs within exome-capture data
Genome Informatics 2013, (GI2013), USA, October 30 - November 2, 2013. -
Discovering Indels within Human Exome-Capture data
Quantitive Biology Seminar Series 2012, Cold Spring Harbor Laboratory (CSHL) USA, September 2012. -
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.
