David Fenyő

David Fenyö
Alma mater
Scientific career
Fields
InstitutionsRockefeller University
NYU
Doctoral advisorBo Sundqvist
Other academic advisorsBrian Chait

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.

References

  1. ^ "David Fenyö, Ph.D. | NYU CENTER FOR HEALTH INFORMATICS AND BIOINFORMATICS". www.med.nyu.edu. Archived from the original on 2015-03-03.
  2. ^ "David Fenyo | Biochemistry and Molecular Pharmacology". www.med.nyu.edu. Archived from the original on 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 (2015). "An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer". Mol Cell Proteomics. 15 (3): 1060–71. doi:10.1074/mcp.M115.056226. PMC 4813688. PMID 26631509.
  4. ^ M. Askenazi, K.V. Ruggles, D. Fenyö: "PGx: Putting Peptides to BED, J Proteome Res. 2015
  5. ^ Fridy, P.C.; Li, Y.; Keegan, S.; Thompson, M.K.; Nudelman, I.; Scheid, J.F.; Oeffinger, M.; Nussenzweig, M.C.; Fenyö, D.; Chait, B.T.; Rout, M.P. (2014). "A robust pipeline for rapid production of versatile nanobody repertoires". Nature Methods. 11 (12): 1253–1260. doi:10.1038/nmeth.3170. PMC 4272012. PMID 25362362.
  6. ^ Agullo-Pascual, E; Reid, DA; Keegan, S; Sidhu, M; Fenyö, D; Rothenberg, E; Delmar, M (2013). "Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque". Cardiovasc Res. 100 (2): 231–240. doi:10.1093/cvr/cvt191. PMC 3797628. PMID 23929525.
  7. ^ Fenyö, D; Hedin, A; Håkansson, P; Sundqvist, BU (1990). "Radial Velocity Distribution of Ions Ejected from Organic Solids by Fast Heavy Ion Bombardment". International Journal of Mass Spectrometry and Ion Processes. 100: 63. doi:10.1016/0168-1176(90)85068-D.
  8. ^ Johnson, RE; Sundqvist, BU; Hedin, A; Fenyö, D (1989). "Sputtering by fast ions based on a sum of impulses". Phys. Rev., B Condens. Matter. 40 (1): 49–53. doi:10.1103/physrevb.40.49. PMID 9990881.
  9. ^ Fenyö, D; Sundqvist, BU; Karlsson, BR; Johnson, RE (1990). "Molecular-dynamics study of electronic sputtering of large organic molecules". Phys. Rev., B Condens. Matter. 42 (4): 1895–1902. doi:10.1103/physrevb.42.1895. PMID 9995630.
  10. ^ Fenyö, D; Johnson, RE (1992). "Computer Experiments on Molecular Ejection from an Amorphous Solid: Comparison to an Analytic Continuum Mechanical Model". Physical Review B. 46 (9): 5090–5099. doi:10.1103/physrevb.46.5090. PMID 10004283.
  11. ^ Fenyö, D (1993). "Sputtering by a Sum of Impulses: The Effect of Finite Track Width". Physical Review B. 47 (13): 8263–8264. doi:10.1103/physrevb.47.8263. PMID 10004839.
  12. ^ Fenyö, D; Håkansson, P; Sundqvist, BU (1994). "On the Ejection of Hydrogen Ions from Organic Solids Impacted by MeV Ions". Nuclear Instruments and Methods. B84: 31. doi:10.1016/0168-583X(94)95699-5.
  13. ^ Fenyö, D.; Zhang, W.; Beavis, R.C.; Chait, B.T. (1996). "Internet-Based Analytical Chemistry Resources - A Model Project". Analytical Chemistry. 68: A721–6. doi:10.1021/ac9621579.
  14. ^ Fenyö, D.; Qin, J.; Chait, B.T. (1998). "Protein Identification Using Mass Spectrometric Information". Electrophoresis. 19 (6): 998–1005. doi:10.1002/elps.1150190615. PMID 9638946.
  15. ^ Eriksson, J.; Chait, B.T.; Fenyö, D. (2000). "A Statistical Basis for Testing the Significance of Mass Spectrometric Protein Identification Results". Analytical Chemistry. 72 (5): 999–1005. doi:10.1021/ac990792j. PMID 10739204.
  16. ^ Fenyö, D.; Beavis, R.C. (2003). "A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes". Anal Chem. 75 (4): 768–74. doi:10.1021/ac0258709. PMID 12622365.
  17. ^ Eriksson, J.; Fenyö, D. (2007). "Predicting the Success Rate of Proteome Analysis by Modeling Protein Abundance Distributions and Experimental Designs". Nature Biotechnology. 25 (6): 651–655. doi:10.1038/nbt1315. PMID 17557102.
  18. ^ Sekedat, M.D.; Fenyö, D.; Tackett, A.J.; Aitchison, J.D.; Chait, B.T. (2010). "Direct Genome-Wide View of DNA Replication Fork Progression in S. cerevisiae, From the Perspective of the GINS Complex". Molecular Systems Biology. 6: 353. doi:10.1038/msb.2010.8. PMC 2858444. PMID 20212525.
  19. ^ Field, H.I.; Fenyö, D.; Beavis, R.C. (2002). "RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database". Proteomics. 2 (1): 36–47. doi:10.1002/1615-9861(200201)2:1<36::AID-PROT36>3.0.CO;2-W. PMID 11788990.
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