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Katharine (Kate) Lewis

Katharine (Kate) Lewis

Katharine (Kate) Lewis



262 Life Sciences Complex
Office: 315.443.5902




  • Postdoc, University of Oregon (1999-2003)
  • Ph.D., University College London (1994-1998)
  • Kennedy Memorial Scholar, Harvard University (1993-1994)
  • B.A. (Honors), Cambridge University (1990-1993)

Social/Academic Links

Research Interests

Specification and patterning of spinal cord interneurons; Formation of functional neuronal circuitry; Evolution of spinal cord patterning and function; Dorsal-ventral neural tube patterning; zebrafish development; effects of environmental contaminants on seizure susceptibility .

Research Spotlight

three photo montage related to fish

The Lewis Lab explores multiple areas of biology, including specification and patterning of spinal cord interneurons, formation of functional neuronal circuitry, evolution of spinal cord patterning and function, dorsal-ventral neural tube patterning, and zebrafish development. The team predominantly uses zebrafish as a model system, as its relatively simple nervous system facilitates easy study of neural circuitry and function, as well as cell fate specification of single and multiple cells. The knowledge they gain from this research can be used to develop more effective treatments for nervous system diseases, disorders, and tumors and to facilitate the repair of particular nerves after injury or neurodegeneration. For example, understanding the roles different genes play in particular neurons should help researchers to grow specific types of neurons from stem cells to treat neural diseases, stroke, and spinal cord injuries.

Previous Academic Positions

Royal Society University Research Fellow, University of Cambridge 2004-2010

Teaching Philosophy and Interests

I teach undergraduate and graduate courses in the general fields of genetics, developmental biology, developmental neuroscience, and biological research. I use inclusive, evidence-based teaching practices and my main goals when working with students are to help them develop their critical thinking, analysis, and scientific communication skills, as well as their metacognition, confidence and agency.

Undergraduate Research Opportunities

The Lewis Lab has space for a limited number of undergraduate students to participate in cutting-edge research using zebrafish to examine either effects of environmental contaminants on seizure susceptibility (predisposition to epilepsy) or the development of the nervous system. We ask for a commitment of at least two years and at least one full-time summer research period (which would be funded). For more information, please see the lab website and contact Dr. Lewis.


Professor Lewis and her lab are committed to sharing the excitement of science with the wider community and particularly K-12 students. In recent years, we have worked with Syracuse City School District and Solvay schools and teachers as well as the Westcott Community Center and the MOST to help young people experience hands-on experiments using zebrafish.

Selected Publications

S. England, A. Rusnock, A. Mujcic, A. Kowalchuk, S. de Jager, W. C. Hilinski, J. L. Juárez-Morales, M. Smith, G. Grieb, S. Banerjee, K. E. Lewis (2023) Molecular Analyses of Zebrafish V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in these Cells. Neural Development. 18:8. PMCID:PMC10683209

W. Haws, S. England, G. Grieb, G. Susana, S. Hernandez, H. Mirer, and K. E. Lewis (2023) Analyses of binding partners and functional domains for the developmentally essential protein Hmx3a/HMX3. Scientific Reports 13:1151 PMCID: PMC9859826

Juárez-Morales, J. L., Weierud, F., England, S. J., Demby, C., Santos, N., Grieb, G., Mazan, S., & Lewis, K. E. (2021). Evolution of lbx spinal cord expression and function. Evolution & Development, 23, 404– 422.

S. J. England, G. A. Cerda, A. Kowalchuk, T. Sorice, G. Grieb, and K. E. Lewis (2020) Hmx3a has essential functions in zebrafish spinal cord, ear and lateral line development. Genetics 216: 1153-1185. DOI: PMCID: PMC7768253

K. L. Duggan, M. Morris, S. K. Bhatia, M. M. Khachan, K. E. Lewis (2019). Effects of Cationic Polyacrylamide and Cationic Starch on Aquatic Life. Journal of Hazardous, Toxic, and Radioactive Waste 23 (4).

R. Hartwell, S. England, N. Monk, N. van Hateren, S. Baxendale, M. Marzo, K. E. Lewis and T. Whitfield (2019). Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation of hmx3a expression. PLoS genetics 15 (4), e1008051.

D. R. Johnson, M. M. Blum, K. E. Lewis, and S. W. Alestalo (2019) Intersectionality as Praxis for Equity in STEM: A WiSE Women of Color Program. Chapter 19 in "Intersectionality & Higher Education: Theory, Research and Praxis". Second Edition. Peter Lang. [Peer-reviewed chapter].

R. Wilk, N. Ali, S. J. England, K. E. Lewis (2018) Using Zebrafish to Bring Hands-On Laboratory Experiences to Urban Classrooms. Zebrafish 15: 2

Andrzejczuk LA, Banerjee S, England SJ, Voufo C, Kamara K and Lewis KE (2018) Tal1, Gata2a, and Gata3 Have Distinct Functions in the Development of V2b and Cerebrospinal Fluid-Contacting KA Spinal Neurons. Front. Neurosci. 12:170. doi: 10.3389/fnins.2018.00170

J. L. Juárez-Morales, R. I. Martinez-De Luna, M. E. Zuber, A. Roberts and K. E. Lewis (2017) Zebrafish transgenic constructs label specific neurons in Xenopus laevis spinal cord and identify frog V0v spinal neurons. Devel. Neurobio. DOI: 10.1002/dneu.22490

S. England, P. Campbell, S. Banerjee, A. Swanson, K. E. Lewis (2017) Identification and expression analysis of the complete family of zebrafish pkd genes.Frontiers in Cell and Developmental Biology 5:5 doi: 10.3389/fcell.2017.00005

G.M.W Cook., K. E. Lewis, R. J. Keynes (2017) Neural Patterning: Spinal Cord Segmentation and Somite Patterning. In Reference Module in Neuroscience and Biobehavioral Psychology, Elsevier. ISBN 9780128093245

W. C. Hilinski; J. R. Bostrom; S. J. England; J. L. Juárez-Morales; S. de Jager; O. Armant; J. Legradi; U. Strähle; B. A. Link; K. E. Lewis (2016) Lmx1b is required for the glutamatergic fates of a subset of spinal cord neurons. Neural Development. 11:16 doi: 10.1186/s13064-016-0059-9

J. L. Juarez-Morales, C. Schulte, S. A. Pezoa, G. K. Vallejo, W. Hilinski, S. England, S. de Jager and K. E. Lewis (2016) Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2 independent mechanism. Neural Development. 11: 5 doi: 10.1186/s13064-016-0059-9

A.Thélie, S. Desiderio, J. Hanotel, I. Quigley, B. Van Driessche, A. Rodari, M. D. Borromeo, S. Kricha, F. Lahaye, J. Croce, G. Cerda-Moya, J. O. Fernandez, B. Bolle, K. E. Lewis, M. Sander, A. Pierani, M. Schubert, J. E. Johnson, C. R. Kintner, T. Pieler, C. Van Lint, K. A. Henningfeld, E. J. Bellefroid, and C. V. Campenhout (2015) Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus. Development:142:3416-3428

S. England, Hilinski, W., de Jager, S., Andrzejczuk, L. , Campbell, P., Chowdhury, T. , Demby, C. , Fancher, W. , Gong, Y. , Lin, C. , Machikas, A., Rodriguez-Larrain, G. , Roman Rivera, V. and Lewis, K. E. (2014) Identifying Transcription Factors expressed by Ventral Spinal Cord Interneurons. ZFIN on-line publication.

S. England, M. F. Batista, J. K. Mich, J. K. Chen and K. E. Lewis (2011) Roles of Hedgehog Pathway Components and Retinoic Acid Signalling in Specifying Zebrafish Ventral Spinal Cord Neurons. Development 138: 5121-5134.

D. K Goode, H. A. Callaway, G. A. Cerda, K. E. Lewis, and G. Elgar (2011) Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events. Development 138: 879-884.

C. J. Schulte, C. Allen, S. England, J. Juárez-Morales, K. E. Lewis (2011) Evx1 is required for joint formation in zebrafish fin dermoskeleton. Developmental Dynamics 240: 1240-1248.

K. Wotton, F. Weierud J. L. Juarez Morales, L. E. Alvares, S. Dietrich, K. E Lewis (2010) Conservation of gene linkage in dispersed vertebrate NK homeobox clusters. Development, Genes and Evolution 219:481-496

M. Hargrave, G. Cerda-Moya, K.E. Lewis (2009) RNA-profiling a specific class of zebrafish interneurons. Dev. Dyn. 238(1):150-161

G. Cooke, K.E. Lewis and R. Keynes (2009) Segmentation: Spinal cord segmentation - A-P somite patterning. The New Encyclopedia of Neuroscience 8: 537-544. Edited by Larry Squire et al. Oxford: Academic Press.

M.F. Batista and K.E. Lewis (2008) Pax2/8 act redundantly to specify glycinergic and GABAergic fates of multiple spinal interneurons. Developmental Biology. 323: 88–97. doi:10.1016/j.ydbio.2008.08.009 . doi:10.1016/j.ydbio.2008.08.009.

M.F. Batista, J. Jacobstein and K.E. Lewis (2008) Zebrafish V2 cells develop into excitatory CiD and Notch signaling dependent inhibitory VeLD interneurons. Developmental Biology. 322: 263-275. doi:10.1016/j.ydbio.2008.07.015 . doi:10.1016/j.ydbio.2008.07.015. (Plus cover image).

K. Wotton, F. Weierud, S.Dietrich, and K.E. Lewis (2008) Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates. BMC Evolutionary Biology 8:171.

G. Lupo, W.A. Harris, K.E. Lewis (2006) Mechanisms of ventral patterning in the vertebrate nervous system. Nature Reviews Neuroscience 7:103-114.

K.E. Lewis (2006) How do genes regulate simple behaviours? Understanding how different neurons in the vertebrate spinal cord are genetically specified. Philosophical Transactions of the Royal Society B: Biological Sciences 361(1465): 45-66.

K.E. Lewis, J. Bates & J.S. Eisen (2005) Regulation of iro3 expression in the zebrafish spinal cord. Developmental Dynamics 232:140-148.

C. Wolff, S. Roy, K.E. Lewis, H. Schauerte, G. Joerg-Rauch, A. Kirn, C. Weiler, R. Geisler, P. Haffter & P. W. Ingham (2004) iguana encodes a novel zinc finger protein with coiled-coil domains essential for Hedgehog signal transduction in the vertebrate embryo. Genes and Development 18: 1565-1576.

K.E. Lewis & J.S. Eisen (2004) Paraxial Mesoderm Specifies Zebrafish Primary Motoneuron Subtype Identity. Development 131: 891-902.

K.E. Lewis & J.S. Eisen (2003) From Cells to Circuits: Development of the Zebrafish Spinal Cord. Progress in Neurobiology 69 (6): 419-449.

K.E. Lewis & J.S. Eisen (2001) Hedgehog signaling is required for primary motoneuron induction in zebrafish. Development 128: 3485-3495.

Z.M. Varga, A. Amores, K.E. Lewis, Y.-L. Yan, J.H. Postlethwait, J.S. Eisen, M. Westerfield (2001) Zebrafish smoothened functions in ventral neural tube specification and axon tract formation. Development 128: 3497-3509.

G. Drossopoulou, K.E. Lewis, J.J. Sanz-Ezquerro, C. Hofmann, A.P. McMahon and C. Tickle (2000) A new model for antero-posterior patterning of the limb involving sequential long and short range Shh signalling and Bmp signalling. Development 127: 1337-1348.

K.E. Lewis, J.P. Concordet and P.W. Ingham (1999) Characterisation of a second patched gene in the zebrafish Danio rerio and the differential response of patched genes to Hedgehog signalling. Developmental Biology 208: 14-29.

K.E. Lewis, P.D. Currie, S. Roy, H. Schauerte, P. Haffter, and P.W. Ingham (1999) Control of muscle cell-type specification in the zebrafish embryo by hedgehog signalling. Developmental Biology 216: 469-480.

K.E. Lewis, G. Drossopoulou, I.R. Paton, D.R. Morrice, K.E. Robertson, D.W. Burt, P.W. Ingham and C. Tickle (1999) Expression of ptc and gli genes in talpid3;suggests bifurcation in Shh Pathway. Development 126: 2297-2407.

J.P. Concordet, K.E. Lewis, L. Goodrich, R. Johnson, M. Scott and P. Ingham (1996) Spatial Regulation of a Zebrafish Patched Homologue Reflects the Roles of Sonic Hedgehog and Protein Kinase A in Neural Tube and Somite Patterning. Development 122: 2835-2846.

J.D. Morrison, J.D. Corcoran and K.E. Lewis (1992) The Determination of Particle Size Distributions in Small-Angle Scattering using the Maximum-Entropy Method. J. Appl. Cryst. 25: 504-513.