Nir Yakoby

Education

  • 2001 Ph.D., Hebrew University, Israel
  • 1994 B.Sc., Hebrew University, Israel

Professional Experience

  • 2020- Professor, Biology Department, Rutgers University
  • 2016-2022 – Director, Center for Computational and Integrative Biology, Rutgers University
  • 2021 (Fall)- Acting Chair, Biology Department, Rutgers University
  • 2014-2020 – Associate Professor, Biology Department, Rutgers University
  • 2014-2016 – Grad. Program Director, Center for Computational and Integrative Biology, Rutgers University
  • 2008-2014 – Assistant Professor, Biology Department, Rutgers University
  • 2004-2008 – Post-doctoral Associate, Lewis-Sigler Institute for Integrative Genomics, Princeton University
  • 2000-2004 – Post-doctoral Fellow, Biotech Center, Rutgers University

Research Interests

Signaling networks and cell fate determination. Mechanisms underlying cell communication systems. Drosophila oogenesis, pattern formation and morphogenesis. Bone morphogenetic protein and epidermal growth factor receptor pathways’ dynamics. The evolution of morphologies. The evolution of gene regulation. 

Scholarships & Awards

  1. The Rutgers University Board of Trustees Research Fellowship for Scholarly Excellence, 2014
  2. NSF-CAREER Award IOS-1149144, 2012
  3. Postdoctoral Poster Award, Genetics Society of America, 48th Drosophila Annual Meeting, 2007
  4. Vaadia-BARD Post-doctoral Fellowship, number FI-302-2000, 2000
  5. Outstanding Student Lecture. Israel Phytopathological Society 20th Convention, 1999
  6. Future Leadership in Orchards. The Fruit Board of Israel and Agricultural Ministry, 1998-2000
  7. Avigad and his daughter Dovrat. The Association of Trustees and Friends of Agricultural Research at the Volcani Center, 1998
  8. Yehuda Horin. The Association of Trustees and Friends of Agricultural Research at the Volcani Center, 1996
  9. The Fruit Board of Israel Scholarship, 1995

List of Publications

  1. C.A. Stevens, H.L. Stott, S.V. Desai, and N. Yakoby. Shared cis-regulatory modules control expression of the tandem paralogs midline and H15 in the follicular epithelium. Development (accepted Oct. 11th, 2022)
  2. C.J. Sottolano, N.T. Revaitis, A.J. Geneva, and N. Yakoby. Nebulous without white: annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa. G3 (accepted July 27th, 2022).
  3. M.A.Herman, B.R. Aiello, J.D. DeLong, H. Garcia-Ruiz, A.L. González, E. Hwang, C. McBeth, E.A, Stojković, M.A. Trakselis, and N. Yakoby.  A unifying framework for understanding biological structures and functions across levels of biological organization. Integrative and Comparative Biology, icab167, https://doi.org/10.1093/icb/icab167 Published 24 July 2021.
  4. C.A. Stevens, N.T. Revaitis, R. Caur, and N. Yakoby. The ETS-transcription factor Pointed is sufficient to regulate the posterior fate of the follicular epithelium. Development. :dev.189787 doi: 10.1242/dev.189787. Published 7 October 2020.
  5. N.T. Revaitis, M.G. Niepielko, R.A. Marmion, E.A. Klein, B. Piccoli, N. Yakoby. Quantitative analyses of EGFR localization and trafficking dynamics in the follicular epithelium. 2020. Development. Jul 17;dev.183210. doi: 10.1242/dev.183210.
  6. R.A. Marmion, N. Yakoby. In locus analysis of patterning evolution in the BMPR2 Wishful thinking. 2018. Development,145: dev161083 doi: 10.1242/dev.161083 Published 9 July.
  7. N. T. Revaitis, R.A. Marmion, M. Farhat, V. Ekiz, W. Wang, N. Yakoby. Simple expression domains are regulated by discrete CRMs during Drosophila oogenesis. 2017. G3 7:2705-2718; early online June 20, 2017. doi:10.1534/g3.117.043810.
  8. G. Pyrowolakis, V. Veikkolainen, N. Yakoby, S.Y. Shvartsman. Gene regulation during Drosophila eggshell patterning. 2017. PNAS Jun 6;114(23):5808-5813. doi: 10.1073/pnas.1610619114. 
  9. F. Rossi, N.P. Duteil, N. Yakoby, B. Piccoli. Control of reaction-diffusion equations on time-evolving manifolds. 2016. Proceedings of the IEEE Conference on Decision and Control 2016, 1614-1619.
  10. M.G. Niepielko, N. Yakoby. Evolutionary changes in TGF-alpha distribution underlie morphological diversity in Drosophila eggshells. 2014. Development 15;141(24):4710-4715.
  11. M.G. Niepielko, R. A. Marmion, K. Kim, D. Luor, C. Ray, N. Yakoby. Chorion Patterning: A window into gene regulation and Drosophila species-relatedness. 2014. Molecular Biology & Evolution. 31 (1):154-164.
  12. R.A. Marmion, M. Jevtic, A. Springhorn, G. Pyrowolakis, and N. Yakoby. The Drosophila BMPRII, Wishful thinking, is required for eggshell patterning. 2013. Developmental Biology. 375:45-53.
  13. M.G. Niepielko, K. Ip, J.S. Kanodia, D. Lun, and N. Yakoby. The evolution of BMP signaling in Drosophila oogenesis: a receptor-based mechanism. 2012. Biophysical Journal. 102:1722-1730.
  14. J.J. Zartman, L.S. Cheung, M.G. Niepielko, C. Bonini, B. Haley, N. Yakoby, and S.Y. Shvartsman. Pattern formation by a moving morphogen source. 2011. Physical Biology. Aug;8(4):045003. Epub 2011 Jul 12.
  15. M.G. Niepielko, Y. Hernáiz-Hernández, and N. Yakoby. BMP signaling dynamics in the follicle cells of multiple Drosophila species. 2011. Developmental Biology. 354:151-159.
  16. J. Lembong, N. Yakoby, and S.Y. Shvartsman. Modeling of epithelial patterning by interacting signaling pathways. 2009. PNAS. 9:3213-3218.
  17. J.J. Zartman, J.S. Kanodia, N. Yakoby, X. Schafer, C. Watson, K. Schlichting, C. Dahmann and S.Y. Shvartsman. Expression patterns of cadherin genes in Drosophila oogenesis. 2009. Gene Expression Patterns. 9(1):31-36
  18. J. J. Zartman, N. Yakoby, C. A. Bristow, X. Zhou, K. Schlichting, K. Dahmann, and S. Y. Shvartsman. Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis. 2008. Developmental Biology. 322:289-301.
  19. N. Yakoby, C.A. Bristow, D. Gong, X. Schafer, J. Lembong, J.J. Zartman, M. Halfon, T. Schupbach, and S.Y. Shvartsman. A combinatorial code for pattern formation in Drosophila oogenesis. 2008. Developmental Cell. 15:725-737.
  20. J. Lembong, N. Yakoby, and S.Y. Shvartsman. Spatial regulation of BMP signaling by patterned expression. 2008. Tissue Engineering. 14:1469-1477.
  21. N. Yakoby, J. Lembong, T. Schüpbach, and S. Y. Shvartsman. Drosophila eggshell is patterned by sequential action of feedforward and feedback loops. 2008. Development. 135:343-351.
  22. S. Komarnytsky, N. Borisjuk, N. Yakoby, A. Garvey, and I. Raskin. Co-secretion of proteinase inhibitor stabilizes antibodies produced by plant roots. 2006. Plant Physiology. 141:1185-1193.
  23. N. Yakoby, A.S., Garvey, and I. Raskin. Tobacco ribosomal DNA spacer element enhances BBI expression in tomato plants. 2006. Plant Cell Reports. 25:573-581.
  24. L.A. Goentoro, N. Yakoby, J. Goodhouse, T. Schüpbach, and S.Y. Shvartsman. Fluorescence-based quantitative analysis of GAL4/UAS systems in Drosophila oogenesis. 2006. Genesis. 44:66-74.
  25. N. Yakoby, C.A. Bristow, I. Gouzman, M.P. Rossi, Y. Gogotsi, T. Schüpbach, and S.Y. Shvartsman. Systems-level questions in Drosophila oogenesis. 2005. IEE Systems Biology. 152:169-302.
  26. N. Yakoby, and I. Raskin. A simple method to determine trypsin and chymotrypsin inhibitory activity. Journal of Biochemical and Biophysical Methods. 2004. 59:241-251.
  27. D. Prusky, and N. Yakoby. Pathogenic fungi: leading or led by ambient pH? Molecular Plant Pathology. 2003. 6:509-516.
  28. I. Raskin, D.M. Ribnicky, S. Komarnytsky, N. Ilic, A. Poulev, N. Borisjuk, A. Brinker, D.A. Moreno, C. Ripoll, N. Yakoby, J.M O’Neal, T. Cornwell, I. Pastor, and B. Fridlender. Plants and human health in the twenty-first century. Trends in Biotechnology. 2002. 12:522-531.
  29. N. Yakoby, D. Beno-Moualem, I. Kobiler, and D. Prusky. The analysis of fruit protection mechanisms provided by reduced pathogenicity mutants of Colletotrichum gloeosporioidesobtained by restriction enzyme mediated integration. Phytopathology. 2002. 92:1196-1201.
  30. N. Yakoby, D. Beno-Moualem, N. T. Keen, A. Dinoor, O. Pines, and D. Prusky.
    Colletotrichum gloeosporioides pelB is an important virulence factor in avocado fruit fungus interactions. Molecular Plant Microbe Interactions. 2001. 14:988-995.
  31. D. Prusky, D. Eshel, I. Kobiler, N. Yakoby, D. Beno-Moualem, M. Akerman, Y. Zuthi, and R. Ben Arie. Post-harvest chlorine treatments for the control of the persimmon black spot disease caused by Alternaria Alternata. Post-harvest Biology and Technology. 2001. 22:271-277.
  32. N. Yakoby, R. Zhou, I. Kobiler, A. Dinoor, and D. Prusky. Development of
    Colletotrichum gloeosporioides restriction enzyme mediated integration mutants as biocontrol agents against anthracnose disease in avocado fruit. Phytopathology. 2001. 91:143-148.
  33. N. Yakoby, S. Freeman, A. Dinoor, N.T. Keen, and D. Prusky. Expression of pectate lyase from Colletotrichum gloeosporioidesin C. magna promotes pathogenicity. Molecular Plant Microbe Interactions. 2000. 13:887-891.
  34. N. Yakoby, I. Kobiler, A. Dinoor, and D. Prusky. pH regulation of pectate lyase secretion modulates the attack of Colletotrichum gloeosporioides on avocado fruits. Applied and Environmental Microbiology. 2000. 66:1026-1030.

Chapter in Book

  1. D. Prusky, I. Kobiler, A. Dinoor, D. Beno-Moualem, and N. Yakoby. Mechanisms of defense of unripe avocado fruits against Colletotrichum gloeosporioides attack. pp. 232-244. Colletotrichum: Host Specificity, Pathology and Host Pathogen Interaction of Colletotrichum. eds: D. Prusky., S. Freeman, M.B. Dickman. American Phytopathological Society Press, St. Paul, MN. 2000.