David Fenyő Explained

David Fenyö
Doctoral Advisor:	Bo Sundqvist
Academic Advisors:	Brian Chait
Workplaces:	Rockefeller University NYU

David Fenyö is a Hungarian-Swedish-American computational biologist, physicist and businessman. He is currently professor in the Department of Biochemistry and Molecular Pharmacology at NYU Langone Medical Center.^{[1] [2]} Fenyö's research focuses on the development of methods to identify, characterize and quantify proteins and in the integration of data from multiple modalities including mass spectrometry, sequencing and microscopy.^{[3] [4] [5] [6]}

Career and research

Fenyö studied engineering physics, with a focus on mathematical and numerical methods, at Uppsala University in Sweden. After receiving an M.Sc. in 1987, he joined the laboratory of Bo Sundqvist at Uppsala University, and studied the mechanisms of ion–solid interaction both experimentally,^[7] theoretically^[8] and using molecular dynamics^{[9] [10] [11]} and Monte Carlo simulations.^[12] He graduated with a Ph.D. in Physics in 1991.

He then went on to complete his postdoctoral work at Rockefeller University with Brian Chait where he developed algorithms to analyze proteomics data obtained using mass spectrometry,^{[13] [14]} developed a statistical method for protein identification,^{[15] [16]} and applied modeling and simulations to optimize proteomics experimental design^[17] and study replication in yeast^[18]

In 1997, Fenyö co-founded the bioinformatics start-up ProteoMetrics, LLC, and served as the President of the company until 2002 during which he developed software systems for automated analysis of large-scale proteomics data.^[19] Subsequently, he served as the Director of Proteomics at Genomic Solutions, and as Staff Scientist and Product Manager at Amersham Biosciences and GE Healthcare before returning to Rockefeller University in 2005 and joining the faculty of NYU in 2010.

Fenyö is a member of the Editorial Advisory Boards of Molecular and Cellular Proteomics and Proteome Science. He serves on the scientific advisory boards of The Global Proteome Machine, BC Proteome Network, Proteome Software, Protein Metrics and Denator AB. He is also a member of the board of directors for US Human Proteome Organization (USHUPO) and serves as the treasurer.

Notes and References

1. Web site: David Fenyö, Ph.D. NYU CENTER FOR HEALTH INFORMATICS AND BIOINFORMATICS . www.med.nyu.edu . dead . https://web.archive.org/web/20150303131108/http://www.med.nyu.edu/chibi/about-us/faculty/david-fenyo-phd . 2015-03-03.
2. Web site: David Fenyo Biochemistry and Molecular Pharmacology . www.med.nyu.edu . dead . https://web.archive.org/web/20150806033851/http://www.med.nyu.edu/biomolpharm/research/biochemistry-macromolecules/david-fenyo . 2015-08-06.
3. Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyö D, "An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer", Mol Cell Proteomics 2015.
4. M. Askenazi, K.V. Ruggles, D. Fenyö: PGx: Putting Peptides to BED, J Proteome Res. 2015
5. P.C. Fridy, Y. Li, S. Keegan, M.K. Thompson, I. Nudelman, J.F. Scheid, M. Oeffinger, M.C. Nussenzweig, D. Fenyö, B.T. Chait, M.P. Rout, "A robust pipeline for rapid production of versatile nanobody repertoires", Nature Methods 11 (2014) 1253-1260. .
6. Agullo-Pascual E, Reid DA, Keegan S, Sidhu M, Fenyö D, Rothenberg E, Delmar M. "Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque", Cardiovasc Res. 100 (2013) 231-240.
7. Fenyö D, Hedin A, Håkansson P, Sundqvist BU: Radial Velocity Distribution of Ions Ejected from Organic Solids by Fast Heavy Ion Bombardment. International Journal of Mass Spectrometry and Ion Processes 100 (1990) 63
8. Johnson RE, Sundqvist BU, Hedin A, Fenyö D: Sputtering by Fast Ions Using a Sum of Impulses. Physical Review B40 (1989) 49.
9. D. Fenyö*, B. U. R. Sundqvist, B. Karlsson & R. E. Johnson, "Molecular Dynamics Study of Sputtering of Large Molecules", Physical Review B. 42 (1990) 1895.
10. Fenyö D,* Johnson RE: Computer Experiments on Molecular Ejection from an Amorphous Solid: Comparison to an Analytic Continuum Mechanical Model. Physical Review B. 46 (1992) 5090-5099.
11. Fenyö D*: Sputtering by a Sum of Impulses: The Effect of Finite Track Width. Physical Review B 47 (1993) 8263-8264.
12. Fenyö D*, Håkansson P, Sundqvist BU: On the Ejection of Hydrogen Ions from Organic Solids Impacted by MeV Ions. Nuclear Instruments and Methods B84 (1994) 31
13. D. Fenyö, W. Zhang, R.C. Beavis & B.T. Chait, "Internet-Based Analytical Chemistry Resources - A Model Project", Analytical Chemistry 68 (1996) A721-6
14. D. Fenyö, J. Qin, & B.T. Chait, "Protein Identification Using Mass Spectrometric Information", Electrophoresis 19 (1998) 998-1005.
15. J. Eriksson, B.T. Chait, and D. Fenyö, "A Statistical Basis for Testing the Significance of Mass Spectrometric Protein Identification Results", Analytical Chemistry 72 (2000) 999-1005.
16. D. Fenyö & R.C. Beavis, "A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes", Anal Chem. 75 (2003) 768-74.
17. J. Eriksson & D. Fenyö, "Predicting the Success Rate of Proteome Analysis by Modeling Protein Abundance Distributions and Experimental Designs", Nature Biotechnology, 25 (2007) 651-655.
18. M.D. Sekedat, D. Fenyö, A.J. Tackett, J.D. Aitchison, B.T. Chait, "Direct Genome-Wide View of DNA Replication Fork Progression in S. cerevisiae, From the Perspective of the GINS Complex", Molecular Systems Biology, 6 (2010) 353.
19. H.I. Field, D. Fenyö, R.C. Beavis, "RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database", Proteomics. 2 (2002) 36-47.