Zachary R. Lewis

Senior Scientist | Product Owner | Manager | Data analyst

What I Do

I am fascinated by morphology and evolution. In particular, my work has focused on the genomic and developmental mechanisms by which morphology and physiology evolve.

Spatial biology. Developing new spatial -omic technologies for high-plex visualization of proteins and DNA loci.

Comparative genomics. Utilization of long read sequencing and genome scaffolding approaches to understand animal evolution and the evolution of genomes.

Lungless respiration. Studying the molecular adaptations that facilitate respiration in salamanders without lungs.

Lung development in lungless salamanders. What are the developmental and genetic mechanisms that account for lunglessness in salamanders? Most salamanders have undergone an evolutionary loss of lungs. There is little known about how such a loss is genetically or developmentally achieved.

Pleiotropic interactions between the lungs and heart in the development of the cardio-pulmonary system. Does lung loss have pleiotropic effects on the development of the heart? Despite clear circulatory changes that must accompany lung loss, there is little information on the associated changes to the heart and how these changes may be developmentally patterned.

resume available here

Positions

Allen Institute for Brain Science, Senior Scientist. Oct. 2024 - present

Allen Institute for Brain Science, Scientist 3. Jan. 2024 - Oct. 2024

NanoString Technologies, Senior Scientist. Dec. 2022 - Oct. 2023

NanoString Technologies, Scientist 2. Aug. 2020 - Nov. 2022

Yale University, Lecturer in Ecology and Evolutionary Biology. Aug. 2019 - Jul. 2020

Yale University, Postdoctoral Associate. Advisor: Casey Dunn. Jul. 2017 - Jul. 2020

Brown University, Postdoctoral Associate. Advisors: Casey Dunn and Erika Edwards. Jul. 2016 - Jun. 2017

Harvard University, Postdoctoral Associate. Advisor: James Hanken. Jan. 2016 - Jun. 2016

Education

Harvard University, PhD, 2009 - 2015

Reed College, BA, 2002-2006

Publications

Church S, et al. 2024. Global genomics of the man-o'-war (Physalia) reveals biodiversity at the ocean surface. https://www.biorxiv.org/content/10.1101/2024.07.10.602499v2 Preprint

Dezem F, et al. 2023. A machine learning one-class logistic regression model to predict stemness for single cell transcriptomics and spatial omics. BMC Genomics. 24:717. https://doi.org/10.1186/s12864-023-09722-6 Preprint

He S, et al. 2022. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nature Biotechnology. https://doi.org/10.1038/s41587-022-01483-z Preprint

Lewis ZR, Kerney R, Hanken J. 2022. Developmental basis of evolutionary lung loss in plethodontid salamanders. Science Advances: 8, eabo6108. https://www.science.org/doi/10.1126/sciadv.abo6108.

Gilman IS, Moreno-Villena JJ, Lewis ZR, Goolsby EW, Edwards EJ. 2022. Gene co-expression reveals the modularity and integration of C4 and CAM in Portulaca. Plant Physiology: kiac116. https://doi.org/10.1093/plphys/kiac116 [preprint]

Lewis ZR, Mathewson B, Hanken J. 2019. Nesting notes on an indicator amphibian on the verge of losing a foundation overstory tree. In revision.

Lewis ZR, Dorantes JA, Hanken J. Expression of a novel surfactant protein gene is associated with sites of extrapulmonary respiration in a lungless salamander. Proceedings of the Royal Society, B. 285: 20181589 http://dx.doi.org/10.1098/rspb.2018.1589 [supplement] [preprint]

Lewis ZR, Dunn CW. 2018. Genome evolution: We are not so special. eLife 2018;7:e38726. https://doi.org/10.7554/eLife.38726

Lewis ZR, Hanken J. 2017. Convergent evolutionary reduction of atrial septation in lungless salamanders. Journal of Anatomy 230: 16-29. [Cover Article] doi:10.1111/joa.12535 [supplement]

Lewis ZR. 2016. Causes and Consequences of Lung Loss in Salamanders. PhD Dissertation, Harvard University. [link]

McCarroll MN, Lewis ZR, Culbertson MD, Martin BL, Kimelman D, Nechiporuk AV. 2012. Graded levels of Pax2a and Pax8 regulate cell differentiation during sensory placode formation. Development 139: 2740-2750. [link] [supplement] [pdf]

Culbertson MA, Lewis ZR, Nechiporuk AV. 2011. Chondrogenic and Gliogenic Subpopulations of Neural Crest Play Distinct Roles During the Assembly of Epibranchial Ganglia. PLoS ONE 6(9): e24443. doi:10.1371/journal.pone.0024443 [pdf]

Lewis ZR, McClellan MC, Postlethwait JH, Cresko WA, Kaplan RH. 2008. Female-Specific Increase in Primordial Germ Cells Marks Sex Differentiation in Threespine Stickleback (Gasterosteus aculeatus). Journal of Morphology 269(8): 909-921. [Cover Article] [pdf]

Lewis ZR. 2006. Proliferation of Primordial Germ Cells and Sex Differentiation in Threespine Stickleback (Gasterosteus aculeatus). Baccalaureate thesis.

Selected Grants and Awards

Honorable Mention, Brian K. Hall Award (Canadian Society of Zoologists); 2015

Harvard University Certificate of Distinction in Teaching; 2014

E.E. Williams Award (Society for the Study of Amphibians and Reptiles); 2014

Barbour Award (Museum of Comparative Zoology); 2014

Robert G. Goelet research award (Museum of Comparative Zoology); 2013

First prize, Harvard Integrated Life Sciences Gallery Night; 2013

Sigma Xi Grant-in-Aid of Research; 2013

Kenneth Miyata Award (Museum of Comparative Zoology); 2012

NSF Graduate Research Fellowship; 2011

William F. Milton Fund Award (to Jim Hanken and ZRL); 2011

RIKEN Center for Developmental Biology (CDB) Travel Fellowship; 2010

Phi Beta Kappa; 2007

Class of '21 Award (Reed College); 2007

Betty C. Liu Memorial Biology Research Fellowship (Reed College); 2007

NAS Reed College Summer Research Fellowship; 2006

Selected Posters and Oral Presentations

Lewis ZR, et al., 2023. "Single cell spatial molecular imaging of 76-plex proteins in clinical cancer samples in response to personalized treatment." American Association of Cancer Research (AACR) Annual Meeting, Orlando, FL, Apr. 2023.

Lewis ZR, et al., 2022. "CosMx Spatial Molecular Imager: Breaking the 100-plex protein spatial single-cell imaging barrier in FFPE tissues." Advances in Genome Biology and Technology (AGBT), Orlando, FL, Jun. 2022.

Lewis ZR, et al., 2022. "Subcellular characterization of over 100 proteins in FFPE tumor biopsies with CosMx Spatial Molecular Imager." AACR Annual Meeting, New Orleans, LA, Apr. 2022.

Lewis ZR, Dunn CW. "UV tolerance in the Portuguese man of war (Physalia physalis).” Society for Integrative and Comparative Biology annual meeting, Austin, TX, Jan. 2020.

Lewis ZR, Munro C, Dunn CW. "The genome of the Portuguese man of war (Physalia physalis).” International Plants and Animal Genomes, San Diego, CA, Jan. 2019.

Lewis ZR, Dorantes JA, Hanken J. "Neofunctionalization of a lung gene paralog may facilitate respiration in lungless salamanders.” Society for Integrative and Comparative Biology annual meeting, Portland, OR, Jan. 2016.

Lewis ZR, Hanken J. “A transcriptional and morphological investigation of lung loss in salamanders.” Invited talk. Canadian Society of Zoologists annual meeting, Calgary, AB. May 2015.

Lewis ZR, Hanken J. “A salamander model for atrial septal defects and cardiopulmonary evolution.” American Association of Anatomists annual meeting, Boston, MA. Mar. 2015.

Lewis ZR, Hanken J. "Take Another Little Piece of My Heart: Convergent heart evolution in independent lineages of lungless salamanders." Oral presentation, 6th Conference on the Biology of Plethodontid Salamanders, Tulsa, OK. Mar. 2014.

Lewis ZR, Hanken J. “Co-evolution of heart and lung development in lungless salamanders.” Poster presentation, Society for Integrative and Comparative Biology annual meeting, Austin, TX. Jan. 2014.

Lewis ZR, Kerney RK, Dorantes JA, Hanken J. "Lung Loss: Molecular and Morphological Consequences" Oral presentation, International Congress of Vertebrate Morphology, Barcelona, Spain, July 2013.

Lewis ZR, Kerney RK, Dorantes JA, Hanken J. “Extrapulmonary Expression of Surfactant Proteins in Lungless Salamanders.” Poster, Keystone Lung Development, Cancer and Disease Symposium, Taos, NM. Feb. 2013.

Lewis ZR, Kerney RK, Dorantes JA, Hanken J. “Genetic and Morphological Vestiges of Lost Lungs in Plethodontid Salamanders.” Oral presentation, Society for Integrative and Comparative Biology annual meeting, San Francisco, CA. Jan. 2013.

Lewis ZR, Kerney RK, Dorantes JA, Hanken J. “Pulmonary surfactant proteins are expressed in lungless salamanders.” Oral presentation, Society for Integrative and Comparative Biology annual meeting, Charleston, SC. January 2012.

Lewis ZR, Kerney RK, Hanken J. “Lung Development in Lungless Salamanders!” Poster, Society for Developmental Biology annual meeting, Chicago, IL. July 2011. doi:10.1016/j.ydbio.2011.05.560

Lewis ZR, Kerney RK, Hanken J. “Lung Development in Lungless Salamanders!” Poster, Keystone Lung Development and Repair Symposium, Santa Fe, NM. February 2011.

Lewis ZR, Nechiporuk AV. “Origins of the Epibranchial Placodes and Ganglia in Zebrafish.” Poster, RIKEN CDB Symposium 2010 “Frontiers in Organogenesis,” Kobe, Japan. March 2010.