Howard Sirotkin
Associate Professor
PhD, Albert Einstein College of Medicine
Howard.Sirotkin@stonybrook.edu
Life Sciences Building
Office: Room 512
Lab: Room 505
Phone: (631) 632-4818
Fax: (631) 632-6661
Training
Howard Sirotkin attended the University of Florida from 1987 to 1991 and was awarded a B.S. degree in Microbiology in 1991. He attended Albert Einstein College of Medicine from 1991 to 1996 and received an M.S. in Molecular Genetics in 1993 and a Ph.D. in Molecular Genetics in 1996 and was a postdoctoral fellow from 1996 to 1997. He continued his postdoctoral studies at New York University’s School of Medicine from 1997 to 1999 and from 1999 to 2001 was a postdoctoral fellow in Developmental Biology at Stanford University School of Medicine. He became an assistant professor of Neurobiology & Behavior at the State University of New York at Stony Brook in 2002, and in 2008 was promoted to the rank of associate professor with tenure.
Research
During embryonic development, a single cell divides and differentiates to form the
multitude of cell types found in a mature organism. How each cell type executes this
complex program to generate the proper varieties of cells in the correct numbers and
at the appropriate locations is poorly understood. We seek to unravel the mysteries
of neural development and investigate disease states where these processes have failed.
Our research falls into four broad areas:
(1) Elucidating the molecular interactions that govern proliferation and differentiation of neural stem cells and progenitors.
(2)Developing animal models for human neurological disorders including Autism, Parkinson’s and epilepsy.
(3)Pioneering technologies to engineer chromosomes and modulate gene expression.
(4) Determining the neurodevelopmental consequences of environmental pollutants including PFAS "forever chemicals".
My laboratory utilizes the zebrafish as a model organism. Several attributes make the zebrafish an ideal system for this analysis: embryos are transparent which allows for in vivo observations of cell movement and gene expression, development occurs external to the mother which facilitates cellular manipulations (transplants and gain/loss of function assays) and most importantly, it is a powerful genetic system. Because all vertebrates share fundamental similarities in the organization of their body plans, understanding the genetic networks that control zebrafish neural development will provide important insights into development of other species including humans.
Publications
Sanchez-Lievanos, K.R., Zhang, D., Simpson, S.M., Wujayahena, M.K., Rizzo, G., Aguilar, J.M.N, Abayam L.M., Dovi, J.M., Sirotkin, H.I. Crawley, M.R., Cook, T.R. and Aga, D. (2025). “Synthesis and Evaluation of Cationic Porphyrin-Based Organic Nanocages for the Removal of 38 PFAS from Water: Experimental, Theoretical, and Eco-toxicological Insights.” ACS ES&T Engineering 5, (3): 701-713. DOI: 10.1021/acsestengg.4c00639
Basharat, R.*, Rizzo, G.*, Zoodsma, J.D., Wollmuth, L.P. and Sirotkin, H.I. 2025. Optimizing prime editing in zebrafish. The CRISPR Journal. doi: 10.1177/25731599251380500
Nebet, E.R., Aprea, C., Zoodsma, J., Raab, W., Sirotkin, H.I. and Wollmuth, L.P. 2025 Conservation of human NMDA receptor subunits and disease variants in zebrafish. BMC Genomics In Press.
Napoli, A.J., Laderwager, S, Zoodsma, J.D, Biju, B., Mucallari, O., Schubel, S., Aprea, C., Sayed, A., Morgan, K., Napoli, A., Flanagan, S., Wollmuth, L.P, and Sirotkin, H.I. “Regulation of Neurogenesis by NMDARs in zebrafish.” Sci Reports 14, Article 3395 (2024). DOI: 10.1038/s41598-024-53910-7
Zoodsma, J.D, Gomes, C, Sirotkin, H.I. and Wollmuth. “Behavioral assays dissecting NMDA receptor function in zebrafish” Springer Methods Book Chapter. Methods in Molecular Biology: NMDA receptors. (2024). Nail Burnashev & Pierre Szepetowski.
Zoodsma, J.D, Boonkanon, C., Running, L., Basharat, R., Atilla-Gokcumen, G.E., Aga, D., and Sirotkin*, H.I. “PFOS negatively impacts prey capture in zebrafish”. Environ Toxicol and Chem. 2023 PMCID: PMC38204661.
Zoodsma, J.D, Keegan, E., Moody, G.R., Bhandiwad, A.A., Napoli, A.J., Burgess, H.A., Wollmuth*, L.P, and Sirotkin*, H.I. “Disruption of grin2B, an ASD-associated gene, produces social deficits in zebrafish.” Molecular Autism (2022) 13(1):38. doi: 10.1186/s13229-022-00516-3.
Brunelle, L.D, Huang, I.J., Angeles, L.F., Logan Running, L., Sirotkin, H.I., McElroy, A.E., and Aga, D.S. (2022). “Comprehensive Assessment of Chemical Residues in Surface and Wastewater Using Passive Sampling, Chemical, Biological and Fish Behavioral Assays.” Sci Total Enviro. Mar 1;828:154176. doi: 10.1016
Angeles, L., Rachel A Mullen, R.A., Huang, I., Khunjar, W., Christopher Wilson, C., Sirotkin. H.I., McElroy A.E. and Aga, D (2020). Assessing pharmaceutical removal and reduction in toxicity provided by advanced wastewater treatment systems.” Environ Sci: Water Research Technol 6, 62-77. DOI:10.1039
Zoodsma, J.D., Chan, K., Bhandiwad A., Golann D., Liu G., Syed S., Napoli A,. Burgess H.A., Sirotkin H.I.* and Wollmuth, L.P*. (2020). “A Model to Study NMDA Receptors in Early Nervous System Development.” J. Neuroscience 40(18):3631-3645. doi: 10.1523/J NEUROSCI.3025-19.2020. *co-senior authors
Wint, J. and Sirotkin H.I. (2020) “Lrrk2 Modulation of Wnt Signaling During Zebrafish Development.” J. Neuroscience Research 98(10):1831-1842 doi: 10.1002/jnr.24687.
Huang, I., Sirotkin, H.I., and McElroy A. (2020). “Comparative transcriptomics implicate mitochondrial and neurodevelopmental impairments in larval zebrafish (Danio rerio) exposed to two selective serotonin reuptake inhibitors (SSRIs).” Ecotoxicology and Environmental Safety. 203:110934. doi: 10.1016/j.ecoenv.2020.110934.
Huang, I., Sirotkin, H.I., and McElroy A. (2019). Varying the exposure period and duration of neuroactive pharmaceuticals and their metabolites modulates effects on the visual motor response in zebrafish (Danio rerio) larvae. Neurotoxicol and Teratol 72:39-48. DOI 10.1016/j.ntt.2019.01.006
Monestime, C., Taibi, A, Gates, K, Jiang, K. and Sirotkin H.I. (2019). CoRest1 regulates neurogenesis in a stage-dependent manner. Dev Dyn. 248(10):918-930 PMID:31301200
Moravec, C.E., Yousef, H., Kinney, B.A., Salerno-Eichenholz, R., Monestime, C., Martin, B. L., Sirotkin H.I., (2017). Zebrafish sin3b mutants are viable but have size, skeletal and locomotor defects. Dev Dyn 246(11):946-955. PMID: 28850761
Moravec, C.E., Li E. Samuel, J., Weng, W., Wood, I.C., Sirotkin H.I., (2016) Maternal Rest/Nrsf Regulates Zebrafish Behavior Through snap25a/b. J Neurosci 36, 9407-19PMID: 27605615
Moravec, C.E., Li E., Maaswinkle, H., Kritzer, M.F., Weng, W., Sirotkin H.I., (2015). Rest Mutant zebrafish swim erratically and display atypical spatial preferences. Behav Brain Res. 284:238-48. doi: 10.1016
Kim, L., He, L., Maaswinkel, H., Zhu, L., Sirotkin, H. and Weng, W. (2014) Anxiety, hyperactivity and stereotypy in a zebrafish model of fragile X syndrome and autism spectrum disorder. Prog Neuropsychopharmacol Biol Psychiatry. 2014 Mar 27. doi: 10.1016/j.pnpbp.2014.03.007.
Taibi, A.V., Mandavawala, K. P., Noel, J., Okoye, E.V., Milano, C.R., Martin, B. L., and Sirotkin, H.I. (2013) Zebrafish churchill regulates developmental gene expression and cell migration. Dev Dyn. 2013 Feb 27. doi: 10.1002/dvdy.23958
Wang, H.J., Zare H., Mousavi, K., Wang C., Moravec, C.E., Sirotkin, H.I., Ge, K. and Sartorelli V. (2013). The Histone Chaperone Spt6 Coordinates Histone H3K27 Demethylation to Regulate Gene Expression and Myogenesis EMBO J. 2013 32(8):1075-86. doi: 10.1038/emboj.2013.54
Xie X, Mathias JR, Smith MA, Walker SL, Teng Y, Distel M, Köster RW, Sirotkin, H.I., Saxena MT, Mumm JS. (2012). Silencer-delimited transgenesis:NRSE/RE1 sequences promote neural-specific transgene expression in a NRSF/REST dependant manner. BMC Biol. 10(1):93. PMID: 23198762
Kok, F.O., Taibi, A., Wanner, S.J., Xie, X., Moravec, C.E., Love, C.E., Prince, V.E., Mumm, J. S., Sirotkin H.I., (2012). Zebrafish rest regulates developmental gene expression but not neurogenesis. Development 139(20): 3838-48.
Gates K.P., Mentzer L., Karlstrom R.O., Sirotkin H.I. (2010). The transcriptional repressor REST/NRSF modulates hedgehog signaling. Dev Biol. 2010 Feb 1. PMID: 20122919
Kok, F.O., Shepherd I.T., Sirotkin H.I., (2009). Churchill and Sip1a repress fibroblast growth factor signaling during zebrafish somitogenesis. Dev Dyn. Dec 23 epub. PMID: 20034103
Londin, E.R., Mentzer, L., Gates, K.P., and Sirotkin, H.I., (2007). Expression and regulation of the zinc finger transcription factor Churchill during zebrafish development. Gene Expr Patterns 7(6):645-50.
Kok, F., Oster, E., Mentzer, L., Hsieh, J.C., Henry, C and Sirotkin, H.I., (2007). The role of the Spt6 chromatin remodeling factor in zebrafish embryogenesis. Dev Biol. 307(2):214-26.
Londin, E.R., Mentzer, L. and Sirotkin, H.I., (2007) Churchill regulates cell movement and mesoderm specification by repressing Nodal signaling. BMC Dev Bio. 7:120.
Bell, M. A., Ellis, K. E., and Sirotkin, H. I. (2007) Variation of pelvic limb reduction and Pitx1 expression among threespine stickleback populations. Tinkering: the microevolution of development. Wiley, Chichester. Novartis Symposium 284, 225-244.
Londin, E.R., Niemiec, J. and Sirotkin, H.I., (2005). Chordin, FGF signaling, and mesodermal factors cooperate in zebrafish neural induction. Dev Biol. 279(1):1-19.
Gleason, M.R., Armisen, R., Verdecia, M.A., Sirotkin, H., Brehm, P., Mandel, G. (2004). A mutation in serca underlies motility dysfunction in accordion zebrafish. Dev Biol. 15;276(2):441-51.
Levkowitz, G., Zeller, J., Sirotkin, H.I., Schilbach, S., Hashimoto, H., Hibi, H., Talbot, W.S. and Rosenthal, A. (2003). Zinc finger protein too few controls the development of monoaminergic neurons. Nat Neurosci. 6:28-33.
Sirotkin, H.I., Gates, M.A., Kelly, P. A., Schier, A.F., and Talbot, W.S. (2000). fast1 is required for the development of dorsal axial structures in zebrafish. Current Biology 10, 1051-1054.
Sirotkin, H. I., Dougan, S.T., Schier, A.F. and Talbot, W.S. (2000). bozozok and squint act in parallel to specify dorsal mesoderm and anterior neuroectoderm. Development: 127:2583-2592.
Fekany, K., Yamanaka, Y., Leung, T., Sirotkin, H.I., Topczewski, J., Gates, M.A., Hibi, M., Renucci, A., Stemple, D., Radbill, A., Schier, A.F., Driever, W., Hirano, T., Talbot, W.S. and Solnica-Krezel, L. (1999). The zebrafish bozozok locus encodes the homeodomain protein Dharma and is sufficient in the extraembryonic yolk syncytial layer for gastrula organizer formation. Development 126:1427-38.
Feldman, B., Gates, M.A., Egan, E.S., Dougan, S.T., Rennebeck, G., Sirotkin, H.I., Schier, A.F., and Talbot, W.S. (1998). Zebrafish organizer development and germ-layer formation require nodal-related signals. Nature 395: 181-185
Laboratory Personnel
PhD Students:
Carly Gomes
Gina Rizzo
Stephanie Laderwager
MS Students:
Bharadwaj Ravi
Dani Shaji
David Smith
Technicians:
Rehman Basharat
Julia Dovi
Undergraduates:
Rebecca Bover
Ceania Rei Gonzales
Katherine Otavalo
Yash Patel