Stenzel A, Mumme-Monheit A, Sucharov J, Walker M, Mitchell JM, Appel B, Nichols JT. Distinct and redundant roles for zebrafish her genes during mineralization and craniofacial patterning. Front Endocrinology. 2022 Dec 12;13:1033843. doi: 10.3389/fendo.2022.1033843
Raisa Bailon-Zambrano, Juliana Sucharov, Abigail Mumme-Monheit, Matthew Murry, Amanda Stenzel, Anthony T Pulvino, Jennyfer M Mitchell, Kathryn L Colborn, James T Nichols (2022) Variable paralog expression underlies phenotype variation eLife 11:e79247 https://doi.org/10.7554/eLife.79247
Thomas Desvignes, Amy E. Robbins, Andrew Z. Carey, Raisa Bailon-Zambrano, James T. Nichols, John H. Postlethwait, Kryn Stankunas. Coordinated patterning of zebrafish caudal fin symmetry by a central and two peripheral organizers. Developmental Dynamics 2022. DOI: doi.org10.1002/dvdy.475
Jennyfer M. Mitchell, Juliana Sucharov, Anthony T. Pulvino, Elliott P. Brooks, Austin E. Gillen, James T. Nichols; The alx3 gene shapes the zebrafish neurocranium by regulating frontonasal neural crest cell differentiation timing. Development 1 April 2021; 148 (7): dev197483. DOI: https://doi.org/10.1242/dev.197483
Tessadori, F., de Bakker, D.E.M., Barske, L..., Nichols J.T., et al. Zebrafish prrx1a mutants have normal hearts. Nature 585, E14–E16 (2020).
Kimmel, C. B., Wind, A. L., Oliva, W., Ahlquist, S. D., Walker, C., Dowd, J., ... & Nichols J.T. Transgene‐mediated skeletal phenotypic variation in zebrafish. Journal of Fish Biology (2020).
Juliana Sucharov, Kuval Ray, Elliot P. Brooks,and James T. Nichols. Selective breeding modifies mef2ca mutant incomplete penetrance by tuning the opposing Notch pathway. PLoS Genetics, (2019).
Elliott P. Brooks, and James T. Nichols. Shifting Zebrafish Lethal Skeletal Mutant Penetrance by Progeny Testing. Journal of visualized experiments: JoVE 127 (2017).
James T. Nichols, Bernardo Blanco-Sanchez, Elliott P. Brooks, Raghuveer Parthasarathy, John Dowd, Arul Subramanian, Greg Nachtrab, Kenneth D. Poss, Thomas F. Schilling, Charles B. Kimmel. Ligament versus bone cell identity in the zebrafish hyoid skeleton is regulated by mef2ca. Development, (2016).
Talbot, Jared Coffin, James T. Nichols, Yi-Lin Yan, Isaac F. Leonard, Ruth A. BreMiller, Sharon L. Amacher, John H. Postlethwait, and Charles B. Kimmel. "Pharyngeal morphogenesis requires fras1-itga8-dependent epithelial-mesenchymal interaction." Developmental biology (2016).
Lindsey Barske, Amjad Askary, Elizabeth Zuniga, Bartosz Balczerski, Paul Bump, James T. Nichols, and J. Gage Crump. "Competition between Jagged-Notch and Endothelin1 Signaling Selectively Restricts Cartilage Formation in the Zebrafish Upper Face." PLoS Genet 12, no. 4 (2016): e1005967.
Aniket V. Gore, Brett Athans, James R. Iben, Kristin Johnson, Valya Russanova, Daniel Castranova, Van N. Pham, Matthew G Butler, Lisa Williams-Simons, James T. Nichols, Erica Bresciani, Bejamin Feldman, Charles B. Kimmel, Paul P. Liu, Brant M. Weinstein. "Epigenetic regulation of hematopoiesis by DNA methylation." eLife 5 (2016): e11813.
Charles B. Kimmel, Sawyer Watson, Ryan B. Couture, Natasha S. McKibben, James T. Nichols, Shannon E. Richardson, and David LG Noakes. "Patterns of variation and covariation in the shapes of mandibular bones of juvenile salmonids in the genus Oncorhynchus." Evolution & development 17, no. 5 (2015): 302-314.
April DeLaurier, Tyler R. Huycke, James T. Nichols, Mary E. Swartz, Ashlin Larsen, Charline Walker, John Dowd, Luyuan Pan, Cecilia B. Moens, and Charles B. Kimmel. "Role of mef2ca in developmental buffering of the zebrafish larval hyoid dermal skeleton." Developmental biology 385, no. 2 (2014): 189-199.
B. Frank Eames, April DeLaurier, Bonnie Ullmann, Tyler R. Huycke, James T. Nichols, John Dowd, Marcie McFadden, Mark M. Sasaki, and Charles B. Kimmel. "FishFace: interactive atlas of zebrafish craniofacial development at cellular resolution." BMC developmental biology 13, no. 1 (2013): 1.
Mark M. Sasaki*, James T. Nichols*, and Charles B. Kimmel. "edn1 and hand2 Interact in early regulation of pharyngeal arch outgrowth during zebrafish development." PLoS One 8, no. 6 (2013): e67522.
*Equal contribution
James T. Nichols, Luyuan Pan, Cecilia B. Moens, and Charles B. Kimmel. "barx1 represses joints and promotes cartilage in the craniofacial skeleton." Development 140, no. 13 (2013): 2765-2775.
James T. Nichols, Gerry Weinmaster. Proteolytic activation of Notch signaling: Roles for ligand endocytosis and mechanotransduction. In Handbook of Cell Signaling, Second Edition, Ed. Bradshaw RA and Dennis EA. 2008.
James T. Nichols, Alison Miyamoto, and Gerry Weinmaster. "Notch signaling–constantly on the move." Traffic 8, no. 8 (2007): 959-969. Review
James T. Nichols, Alison Miyamoto, Samantha L. Olsen, Brendan D'Souza, Christine Yao, and Gerry Weinmaster. "DSL ligand endocytosis physically dissociates Notch1 heterodimers before activating proteolysis can occur." The Journal of cell biology 176, no. 4 (2007): 445-458.
Ena Ladi, James T. Nichols, Weihong Ge, Alison Miyamoto, Christine Yao, Liang-Tung Yang, Jim Boulter, Yi E. Sun, Chris Kintner, and Gerry Weinmaster. "The divergent DSL ligand Dll3 does not activate Notch signaling but cell autonomously attenuates signaling induced by other DSL ligands." The Journal of cell biology 170, no. 6 (2005): 983-992.
Haritunians, T., T. Chow, R. P. J. De Lange, James T. Nichols, D. Ghavimi, N. Dorrani, D. M. St Clair, G. Weinmaster, and C. Schanen. "Functional analysis of a recurrent missense mutation in Notch3 in CADASIL." Journal of Neurology, Neurosurgery & Psychiatry 76, no. 9 (2005): 1242-1248.
Liang-Tung Yang, James T. Nichols, Christine Yao, Jennifer O. Manilay, Ellen A. Robey, and Gerry Weinmaster. "Fringe glycosyltransferases differentially modulate Notch1 proteolysis induced by Delta1 and Jagged1." Molecular biology of the cell 16, no. 2 (2005): 927-942.
Raisa Bailon-Zambrano, Juliana Sucharov, Abigail Mumme-Monheit, Matthew Murry, Amanda Stenzel, Anthony T Pulvino, Jennyfer M Mitchell, Kathryn L Colborn, James T Nichols (2022) Variable paralog expression underlies phenotype variation eLife 11:e79247 https://doi.org/10.7554/eLife.79247
Thomas Desvignes, Amy E. Robbins, Andrew Z. Carey, Raisa Bailon-Zambrano, James T. Nichols, John H. Postlethwait, Kryn Stankunas. Coordinated patterning of zebrafish caudal fin symmetry by a central and two peripheral organizers. Developmental Dynamics 2022. DOI: doi.org10.1002/dvdy.475
Jennyfer M. Mitchell, Juliana Sucharov, Anthony T. Pulvino, Elliott P. Brooks, Austin E. Gillen, James T. Nichols; The alx3 gene shapes the zebrafish neurocranium by regulating frontonasal neural crest cell differentiation timing. Development 1 April 2021; 148 (7): dev197483. DOI: https://doi.org/10.1242/dev.197483
Tessadori, F., de Bakker, D.E.M., Barske, L..., Nichols J.T., et al. Zebrafish prrx1a mutants have normal hearts. Nature 585, E14–E16 (2020).
Kimmel, C. B., Wind, A. L., Oliva, W., Ahlquist, S. D., Walker, C., Dowd, J., ... & Nichols J.T. Transgene‐mediated skeletal phenotypic variation in zebrafish. Journal of Fish Biology (2020).
Juliana Sucharov, Kuval Ray, Elliot P. Brooks,and James T. Nichols. Selective breeding modifies mef2ca mutant incomplete penetrance by tuning the opposing Notch pathway. PLoS Genetics, (2019).
Elliott P. Brooks, and James T. Nichols. Shifting Zebrafish Lethal Skeletal Mutant Penetrance by Progeny Testing. Journal of visualized experiments: JoVE 127 (2017).
James T. Nichols, Bernardo Blanco-Sanchez, Elliott P. Brooks, Raghuveer Parthasarathy, John Dowd, Arul Subramanian, Greg Nachtrab, Kenneth D. Poss, Thomas F. Schilling, Charles B. Kimmel. Ligament versus bone cell identity in the zebrafish hyoid skeleton is regulated by mef2ca. Development, (2016).
Talbot, Jared Coffin, James T. Nichols, Yi-Lin Yan, Isaac F. Leonard, Ruth A. BreMiller, Sharon L. Amacher, John H. Postlethwait, and Charles B. Kimmel. "Pharyngeal morphogenesis requires fras1-itga8-dependent epithelial-mesenchymal interaction." Developmental biology (2016).
Lindsey Barske, Amjad Askary, Elizabeth Zuniga, Bartosz Balczerski, Paul Bump, James T. Nichols, and J. Gage Crump. "Competition between Jagged-Notch and Endothelin1 Signaling Selectively Restricts Cartilage Formation in the Zebrafish Upper Face." PLoS Genet 12, no. 4 (2016): e1005967.
Aniket V. Gore, Brett Athans, James R. Iben, Kristin Johnson, Valya Russanova, Daniel Castranova, Van N. Pham, Matthew G Butler, Lisa Williams-Simons, James T. Nichols, Erica Bresciani, Bejamin Feldman, Charles B. Kimmel, Paul P. Liu, Brant M. Weinstein. "Epigenetic regulation of hematopoiesis by DNA methylation." eLife 5 (2016): e11813.
Charles B. Kimmel, Sawyer Watson, Ryan B. Couture, Natasha S. McKibben, James T. Nichols, Shannon E. Richardson, and David LG Noakes. "Patterns of variation and covariation in the shapes of mandibular bones of juvenile salmonids in the genus Oncorhynchus." Evolution & development 17, no. 5 (2015): 302-314.
April DeLaurier, Tyler R. Huycke, James T. Nichols, Mary E. Swartz, Ashlin Larsen, Charline Walker, John Dowd, Luyuan Pan, Cecilia B. Moens, and Charles B. Kimmel. "Role of mef2ca in developmental buffering of the zebrafish larval hyoid dermal skeleton." Developmental biology 385, no. 2 (2014): 189-199.
B. Frank Eames, April DeLaurier, Bonnie Ullmann, Tyler R. Huycke, James T. Nichols, John Dowd, Marcie McFadden, Mark M. Sasaki, and Charles B. Kimmel. "FishFace: interactive atlas of zebrafish craniofacial development at cellular resolution." BMC developmental biology 13, no. 1 (2013): 1.
Mark M. Sasaki*, James T. Nichols*, and Charles B. Kimmel. "edn1 and hand2 Interact in early regulation of pharyngeal arch outgrowth during zebrafish development." PLoS One 8, no. 6 (2013): e67522.
*Equal contribution
James T. Nichols, Luyuan Pan, Cecilia B. Moens, and Charles B. Kimmel. "barx1 represses joints and promotes cartilage in the craniofacial skeleton." Development 140, no. 13 (2013): 2765-2775.
James T. Nichols, Gerry Weinmaster. Proteolytic activation of Notch signaling: Roles for ligand endocytosis and mechanotransduction. In Handbook of Cell Signaling, Second Edition, Ed. Bradshaw RA and Dennis EA. 2008.
James T. Nichols, Alison Miyamoto, and Gerry Weinmaster. "Notch signaling–constantly on the move." Traffic 8, no. 8 (2007): 959-969. Review
James T. Nichols, Alison Miyamoto, Samantha L. Olsen, Brendan D'Souza, Christine Yao, and Gerry Weinmaster. "DSL ligand endocytosis physically dissociates Notch1 heterodimers before activating proteolysis can occur." The Journal of cell biology 176, no. 4 (2007): 445-458.
Ena Ladi, James T. Nichols, Weihong Ge, Alison Miyamoto, Christine Yao, Liang-Tung Yang, Jim Boulter, Yi E. Sun, Chris Kintner, and Gerry Weinmaster. "The divergent DSL ligand Dll3 does not activate Notch signaling but cell autonomously attenuates signaling induced by other DSL ligands." The Journal of cell biology 170, no. 6 (2005): 983-992.
Haritunians, T., T. Chow, R. P. J. De Lange, James T. Nichols, D. Ghavimi, N. Dorrani, D. M. St Clair, G. Weinmaster, and C. Schanen. "Functional analysis of a recurrent missense mutation in Notch3 in CADASIL." Journal of Neurology, Neurosurgery & Psychiatry 76, no. 9 (2005): 1242-1248.
Liang-Tung Yang, James T. Nichols, Christine Yao, Jennifer O. Manilay, Ellen A. Robey, and Gerry Weinmaster. "Fringe glycosyltransferases differentially modulate Notch1 proteolysis induced by Delta1 and Jagged1." Molecular biology of the cell 16, no. 2 (2005): 927-942.