Osorio-Vasquez, V., Zhu, J., Lumibao, J.C., Lande, K., Peck, K.L., Stamp, M.K., Okhovat, S.R., Song, H., Ogawa, S., Kubota, C., Pantazopoulou, V., Dai, Y., Rock, A., Bottomley, C., Thomas, E., Hsu, J., Morales, A.H., Fowler, A., McGriff, T., Evensen, K.G., Larsen, S., Abdulla, M., Greer, P., Gibson, J., Downes, M., Evans, R., Lowy, A.M., Whitcomb, D.C., Zou, J., Molinolo, A., Oh, T.G., White, R., Bellin, M., Tiriac, H., Engle, D.D. Chronic pancreatitis patient-derived organoids reveal new paths to precision therapeutics. (2025) bioRxiv. DOI: 10.1101/2024.10.30.620903

Dondi, C., Vogler, G., Gupta, A., Walls, S.M., Kervadec, A., Marchant, J., Romero, M.R., Diop, S., Goode, J., Thomas, J.B., Colas, A.R., Bodmer, R., Montminy, M., Ocorr, K. The nutrient sensor CRTC and Sarcalumenin/thinman represent an alternate pathway in cardiac hypertrophy. (2024) Cell Reports. 43(8):114549. DOI: 10.1016/j.celrep.2024.114549

Thomas, S.T., Shin, Y., La Clair, J.J., Noel, J.P. Plant-based CO drawdown and storage as SiC. (2021) RSC Adv. 11(26):15512-15518. DOI: 10.1039/d1ra00954k

Wang, T., Wiater, E., Zhang, X., Thomas, J.B., Montminy, M. Crtc modulates fasting programs associated with 1-C metabolism and inhibition of insulin signaling. (2021) Proceedings of the National Academy of Sciences of the United States of America. 118(12). DOI: 10.1073/pnas.2024865118

Babski, H., Jovanic, T., Surel, C., Yoshikawa, S., Zwart, M.F., Valmier, J., Thomas, J.B., Enriquez, J., Carroll, P., Garcès, A. A GABAergic Maf-expressing interneuron subset regulates the speed of locomotion in Drosophila. (2019) Nature Communications. 10(1):4796. DOI: 10.1038/s41467-019-12693-6

Shen, R., Wang, B., Giribaldi, M.G., Ayres, J., Thomas, J.B., Montminy, M. Neuronal energy-sensing pathway promotes energy balance by modulating disease tolerance. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(23):E3307-14. DOI: 10.1073/pnas.1606106113

Long, H., Yoshikawa, S., Thomas, J.B. Equivalent Activities of Repulsive Axon Guidance Receptors. (2016) Journal of Neuroscience. 36(4):1140-1150. DOI: 10.1523/JNEUROSCI.3406-15.2016

Yoshikawa, S., Long, H., Thomas, J.B. A subset of interneurons required for Drosophila larval locomotion. (2016) Molecular and Cellular Neurosciences. 70:22-29. DOI: 10.1016/j.mcn.2015.11.008

Read, R.D., Fenton, T.R., Gomez, G.G., Wykosky, J., Vandenberg, S.R., Babic, I., Iwanami, A., Yang, H., Cavenee, W.K., Mischel, P.S., Furnari, F.B., Thomas, J.B. A kinome-wide RNAi screen in Drosophila Glia reveals that the RIO kinases mediate cell proliferation and survival through TORC2-Akt signaling in glioblastoma. (2013) PLOS Genetics. 9(2). DOI: 10.1371/journal.pgen.1003253

Wang, B., Moya, N., Niessen, S., Hoover, H., Mihaylova, M.M., Shaw, R.J., Yates, J.R., Fischer, W.H., Thomas, J.B., Montminy, M. A hormone-dependent module regulating energy balance. (2011) Cell. 145(4):596-606. DOI: 10.1016/j.cell.2011.04.013

Sakurai, M., Aoki, T., Yoshikawa, S., Santschi, L.A., Saito, H., Endo, K., Ishikawa, K., Kimura, K., Ito, K., Thomas, J.B., Hama, C. Differentially expressed Drl and Drl-2 play opposing roles in Wnt5 signaling during Drosophila olfactory system development. (2009) Journal of Neuroscience. 29(15):4972-4980. DOI: 10.1523/JNEUROSCI.2821-08.2009

Read, R.D., Cavenee, W.K., Furnari, F.B., Thomas, J.B. A drosophila model for EGFR-Ras and PI3K-dependent human glioma. (2009) PLOS Genetics. 5(2). DOI: 10.1371/journal.pgen.1000374

Wang, B., Goode, J., Best, J., Meltzer, J., Schilman, P.E., Chen, J., Garza, D., Thomas, J.B., Montminy, M. The insulin-regulated CREB coactivator TORC promotes stress resistance in Drosophila. (2008) Zellstoffwechsel. 7(5):434-44. DOI: 10.1016/j.cmet.2008.02.010

Inaki, M., Yoshikawa, S., Thomas, J.B., Aburatani, H., Nose, A. Wnt4 is a local repulsive cue that determines synaptic target specificity. (2007) Current Biology. 17(18):1574-9. DOI: 10.1016/j.cub.2007.08.013

Hughes, C.L., Thomas, J.B. A sensory feedback circuit coordinates muscle activity in Drosophila. (2007) Molecular and Cellular Neurosciences. 35(2):383-396. DOI: 10.1016/j.mcn.2007.04.001

Boyle, M., Nighorn, A., Thomas, J.B. Drosophila Eph receptor guides specific axon branches of mushroom body neurons. (2006) Development. 133(9):1845-1854. DOI: 10.1242/dev.02353

Fradkin, L.G., Garriga, G., Salinas, P.C., Thomas, J.B., Yu, X., Zou, Y. Wnt signaling in neural circuit development. (2005) Journal of Neuroscience. 25(45):10376-10378. DOI: 10.1523/JNEUROSCI.3429-05.2005

Labrador, J.P., O'keefe, D., Yoshikawa, S., McKinnon, R.D., Thomas, J.B., Bashaw, G.J. The homeobox transcription factor even-skipped regulates netrin-receptor expression to control dorsal motor-axon projections in Drosophila. (2005) Current Biology. 15(15):1413-1419. DOI: 10.1016/j.cub.2005.06.058

Yoshikawa, S., Thomas, J.B. Secreted cell signaling molecules in axon guidance. (2004) Current Opinion in Neurobiology. 14(1):45-50. DOI: 10.1016/j.conb.2004.01.005

Imondi, R., Thomas, J.B. Neuroscience. The ups and downs of Wnt signaling. (2003) Wissenschaft. 302(5652):1903-1904. DOI: 10.1126/science.1092976

van Meyel, D.J., Thomas, J.B., Agulnick, A.D. Ssdp proteins bind to LIM-interacting co-factors and regulate the activity of LIM-homeodomain protein complexes in vivo. (2003) Development. 130(9):1915-1925.

Yoshikawa, S., McKinnon, R.D., Kokel, M., Thomas, J.B. Wnt-mediated axon guidance via the Drosophila Derailed receptor. (2003) Natur. 422(6932):583-588. DOI: 10.1038/nature01522

Thor, S., Thomas, J.B. Motor neuron specification in worms, flies and mice: conserved and 'lost' mechanisms. (2002) Current Opinion in Genetics & Development. 12(5):558-564.

Diagana, T.T., Thomas, U., Prokopenko, S.N., Xiao, B., Worley, P.F., Thomas, J.B. Mutation of Drosophila homer disrupts control of locomotor activity and behavioral plasticity. (2002) Journal of Neuroscience. 22(2):428-436.

Herzig, M.C., Thor, S., Thomas, J.B., Reichert, H., Hirth, F. Expression and function of the LIM homeodomain protein Apterous during embryonic brain development of Drosophila. (2001) Dev. Genes Evol. 211(11):545-554. DOI: 10.1007/s00427-001-0195-y

O'Keefe, D.D., Thomas, J.B. Drosophila wing development in the absence of dorsal identity. (2001) Development. 128(5):703-710.

Yoshikawa, S., Bonkowsky, J.L., Kokel, M., Shyn, S., Thomas, J.B. The derailed guidance receptor does not require kinase activity in vivo. (2001) Journal of Neuroscience. 21(1):RC119.

van Meyel, D.J., O'Keefe, D.D., Thor, S., Jurata, L.W., Gill, G.N., Thomas, J.B. Chip is an essential cofactor for apterous in the regulation of axon guidance in Drosophila. (2000) Development. 127(9):1823-1831.

Jurata, L.W., Thomas, J.B., Pfaff, S.L. Transcriptional mechanisms in the development of motor control. (2000) Current Opinion in Neurobiology. 10(1):72-9.

Bonkowsky, J.L., Yoshikawa, S., O'Keefe, D.D., Scully, A.L., Thomas, J.B. Axon routing across the midline controlled by the Drosophila Derailed receptor. (1999) Natur. 402(6761):540-544. DOI: 10.1038/990122

Lilly, B., O'Keefe, D.D., Thomas, J.B., Botas, J. The LIM homeodomain protein dLim1 defines a subclass of neurons within the embryonic ventral nerve cord of Drosophila. (1999) Mech. Dev. 88(2):195-205.

van Meyel, D.J., O'Keefe, D.D., Jurata, L.W., Thor, S., Gill, G.N., Thomas, J.B. Chip and apterous physically interact to form a functional complex during Drosophila development. (1999) Molecular Cell. 4(2):259-265.

Scully, A.L., McKeown, M., Thomas, J.B. Isolation and characterization of Dek, a Drosophila eph receptor protein tyrosine kinase. (1999) Molecular and Cellular Neurosciences. 13(5):337-347. DOI: 10.1006/mcne.1999.0752

Bonkowsky, J.L., Thomas, J.B. Cell-type specific modular regulation of derailed in the Drosophila nervous system. (1999) Mech. Dev. 82(1-2):181-184.

Thor, S., Andersson, S.G., Tomlinson, A., Thomas, J.B. A LIM-homeodomain combinatorial code for motor-neuron pathway selection. (1999) Natur. 397(6714):76-80. DOI: 10.1038/16275

Benveniste, R.J., Thor, S., Thomas, J.B., Taghert, P.H. Cell type-specific regulation of the Drosophila FMRF-NH2 neuropeptide gene by Apterous, a LIM homeodomain transcription factor. (1998) Development. 125(23):4757-4765.

Oates, A.C., Bonkovsky, J.L., Irvine, D.V., Kelly, L.E., Thomas, J.B., Wilks, A.F. Embryonic expression and activity of doughnut, a second RYK homolog in Drosophila. (1998) Mech. Dev. 78(1-2):165-169.

Callahan, C.A., Yoshikawa, S., Thomas, J.B. Tracing axons. (1998) Current Opinion in Neurobiology. 8(5):582-586.

O'Keefe, D.D., Thor, S., Thomas, J.B. Function and specificity of LIM domains in Drosophila nervous system and wing development. (1998) Development. 125(19):3915-3923.

Thomas, J.B. Axon guidance: crossing the midline. (1998) Current Biology. 8(3):R102-R104.

Thor, S., Thomas, J.B. The Drosophila islet gene governs axon pathfinding and neurotransmitter identity. (1997) Neuron. 18(3):397-409.

Callahan, C.A., Bonkovsky, J.L., Scully, A.L., Thomas, J.B. derailed is required for muscle attachment site selection in Drosophila. (1996) Development. 122(9):2761-2767.

Callahan, C.A., Muralidhar, M.G., Lundgren, S.E., Scully, A.L., Thomas, J.B. Control of neuronal pathway selection by a Drosophila receptor protein-tyrosine kinase family member. (1995) Natur. 376(6536):171-174. DOI: 10.1038/376171a0

Lundgren, S.E., Callahan, C.A., Thor, S., Thomas, J.B. Control of neuronal pathway selection by the Drosophila LIM homeodomain gene apterous. (1995) Development. 121(6):1769-1773.

Blair, S.S., Brower, D.L., Thomas, J.B., Zavortink, M. The role of apterous in the control of dorsoventral compartmentalization and PS integrin gene expression in the developing wing of Drosophila. (1994) Development. 120(7):1805-1815.

Callahan, C.A., Thomas, J.B. Tau-beta-galactosidase, an axon-targeted fusion protein. (1994) Proceedings of the National Academy of Sciences of the United States of America. 91(13):5972-5976.

Muralidhar, M.G., Thomas, J.B. The Drosophila bendless gene encodes a neural protein related to ubiquitin-conjugating enzymes. (1993) Neuron. 11(2):253-266.

Muralidhar, M.G., Callahan, C.A., Thomas, J.B. Single-minded regulation of genes in the embryonic midline of the Drosophila central nervous system. (1993) Mech. Dev. 41(2-3):129-138.

Bourgouin, C., Lundgren, S.E., Thomas, J.B. Apterous is a Drosophila LIM domain gene required for the development of a subset of embryonic muscles. (1992) Neuron. 9(3):549-561.

Thomas, J.B., Crews, S.T. Molecular genetics of neuronal development in the Drosophila embryo. (1990) FASEB Journal. 4(8):2476-2482.

Crews, S.T., Thomas, J.B., Goodman, C.S. The Drosophila single-minded gene encodes a nuclear protein with sequence similarity to the per gene product. (1988) Cell. 52(1):143-151.

Thomas, J.B., Crews, S.T., Goodman, C.S. Molecular genetics of the single-minded locus: a gene involved in the development of the Drosophila nervous system. (1988) Cell. 52(1):133-141.

Goodman, C.S., Bastiani, M.J., Doe, C.Q., du Lac, S., Helfand, S.L., Kuwada, J.Y., Thomas, J.B. Cell recognition during neuronal development. (1984) Wissenschaft. 225(4668):1271-1279.

Thomas, J.B., Bastiani, M.J., Bate, M., Goodman, C.S. From grasshopper to Drosophila: a common plan for neuronal development. (1984) Natur. 310(5974):203-207.

Thomas, J.B., Wyman, R.J. Duplicated neural structure in bithorax mutant Drosophila. (1984) Developmental Biology. 102(2):531-3.

Thomas, J.B., Wyman, R.J. Mutations altering synaptic connectivity between identified neurons in Drosophila. (1984) Journal of Neuroscience. 4(2):530-538.

Wyman, R.J., Thomas, J.B. What genes are necessary to make an identified synapse? (1983) Cold Spring Harbor Symposia on Quantitative Biology. 48 Pt 2:641-652.

Thomas, J.B., Wyman, R.J. A mutation in Drosophila alters normal connectivity between two identified neurones. (1982) Natur. 298(5875):650-651.

Wyman, R.J., Thomas, J.B. The mathematics of mosaic analysis. I: The relationship between sturts and distance. (1982) Genetics. 100(4):659-676.

Koto, M., Tanouye, M.A., Ferrus, A., Thomas, J.B., Wyman, R.J. The morphology of the cervical giant fiber neuron of Drosophila. (1981) Brain Research. 221(2):213-217.