Refereed papers

Stinchfield, M.J., Weasner, B.P., Zhitomersky, D., Weasner, B.M., Kumar, J., O’Connor, M.B., Newfeld, S.J. (2023) Drosophila fourth chromosome resource project: a comprehensive resource for genetic analysis that includes humanized strains. Genetics (invited revision).

Maizels, R., Newfeld, S.J. (2023) A path less traveled: convergent evolution in an intestinal parasite rapidly created a new family of molecular mimics capable of suppressing the mammalian immune response. Genome Biol Evol (invited revision).

Goldsmith, S.L., Newfeld, S.J. (2023) dSmad2 differentially regulates dILP2 and dILP5 in insulin producing and circadian pacemaker cells in unmated adult females. PLoS One 18:e0280529.

Goldsmith, S.L., Shimell, M.J., Tauscher, P., Daly S.M., Shimmi, O., O'Connor, M.B., Newfeld, S.J. (2022) New resources for the Drosophila 4th chromosome: FRT101F enabled mitotic clones and Bloom syndrome helicase enabled meiotic recombination. G3: Genes, Genomes, Genetics 12(4):jkac019.

Newfeld, S.J., O'Connor, M.B. (2022) New aspects of TGF-β superfamily signaling in development and disease (2022 FASEB meeting review). Faculty Reviews 11(36).

Daly, S.M., Peraza, A., Newfeld, S.J. (2022) Computational analysis of prodomain cysteines in human TGF-β proteins reveals frequent loss of disulfide dependent regulation in tumors. G3: Genes, Genomes, Genetics 12(12):jkac271.

Nguyen, T., Han, T., Newfeld, S.J, Serpe, M. (2020) Selective disruption of synaptic BMP signaling by a Smad mutation adjacent to the highly conserved H2 helix. Genetics 216:159-175.

Dimitriadou, A., Chatzianastasi, N., Zacharaki, P., O'Connor, M.J., Goldsmith, S., O'Connor, M.B. Consoulas, C., Newfeld, S.J. (2020) Adult movement defects associated with a CORL mutation in Drosophila display behavioral plasticity. G3: Genes, Genomes, Genetics 10:1697-1706.

Wisotzkey, R.G., Newfeld, S.J. (2020) TGF-β prodomain alignments reveal unexpected cysteine conservation consistent with phylogenetic predictions of cross-subfamily heterodimerization. Genetics 214:447-465.

Stinchfield, M.J., Miyazawa, K., Newfeld, S.J. (2019) Transgenic analyses in Drosophila reveal that mCORL1 is functionally distinct from mCORL2 and dCORL. G3: Genes, Genomes, Genetics 9:3781-3789.

Tran, N., Goldsmith S.L., Dimitriadou, A., Takaesu, N., Consoulas, C., and Newfeld S.J. (2018) CORL Expression and Function in Insulin Producing Neurons Reversibly Influences Adult Longevity in Drosophila. G3: Genes, Genomes, Genetics 8:2979-2990.

Tran, N., Takaesu, N., Cornell, E. and Newfeld S.J. (2018) CORL expression in the Drosophila central nervous system is regulated by stage specific interactions of intertwined activators and repressors. G3: Genes, Genomes, Genetics 8:2527-2536.

Kumar, S., Konikoff, C., Sanderford, M., Liu, L., Newfeld, S., Ye, J., and Kulathinal, R.J. (2017) FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Using in Situ Hybridization Images in Drosophila. G3: Genes, Genomes, Genetics 7:2791-2797.

Quijano, J., Wisotzkey, R., Tran, N.L., Huang, Y., Stinchfield, M. Haerry, T., Shimmi, O. and Newfeld, S.J. (2016) lolal is an evolutionarily new epigenetic regulator of dpp transcription during dorsal-ventral axis formation. Molecular Biology and Evolution 33:2621–2632. [Recommended by Faculty 1000].

Wisotzkey, Robert G., Quijano, Janine C., Stinchfield, Michael J., & Newfeld, Stuart J. (2014) New Gene Evolution in the Bonus-TIF1-γ/TRIM33 Family Impacted the Architecture of the Vertebrate Dorsal–Ventral Patterning Network. Molecular Biology and Evolution, 31(9):2309-2321. [Recommended by Faculty 1000].

Yuan, L., Pan, C., Ji, S., McCutchan, M., Zhou, Z., Newfeld, S.J., Kumar, S. & Ye, J. (2014) Automated annotation of developmental stages of Drosophila embryos in images with spatial patterns of expression. Bioinformatics 30:266-273.

Zhang, W., Feng, D., Li. R., Chernikov, A., Chrisochoides, N., Osgood, C., Konikoff, C., Newfeld, S.J., Kumar, S. & Ji, S. (2013) A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis. BMC Bioinformatics 14:372.

Zhang, Y., & Newfeld, S.J. (2013) Meeting Report - TGF-β Superfamily: Signaling in Development and Disease. J Cell Science 126:4809-4813.

Sun, Q., Muckatira, S., Yuan, L., Ji, S., Newfeld, S.J., Kumar, S. & Ye, J. (2013) Image-level and group-level models for Drosophila gene expression pattern annotation. BMC Bioinformatics 14:350.

Shimmi, O. & Newfeld, S.J. (2013) New insights into extracellular and post-translational regulation of TGF-β signaling pathways. J Biochem 154:11-19. Invited review.

Quijano, J. & Newfeld, S.J. (2013) Ski/Sno Proto-Oncogene Family. Brenner's Encyclopedia of Genetics Second Edition, Eds. S. Maloy & K. Hughes, Elsevier, New York, vol. 6 pp. 472-474. Invited review.

Wisotzkey, R. Konikoff, C., & Newfeld, S.J. (2012) Hippo pathway phylogenetics predicts monoubiquitylation of Salvador and Merlin/Nf2. PLoS One 7:e51599.

Wisotzkey, R. & Newfeld, S.J. (2012) Review of Methods in Molecular Biology772: Molecular Methods for Evolutionary Genetics. ChemBioChem 13:2456-2457. Invited book review.

Takaesu, N., Stinchfield, M., Shimizu, K., Arase, M., Quijano, J., Watabe, T., Miyazono, K. & Newfeld, S.J. (2012) Drosophila CORL is required for Smad2-mediated activation of Ecdysone Receptor expression in the mushroom body. Development 139:3392-3401.

Stinchfield, M., Takaesu, N., Quijano, J., Castillo, A., Tiusanen, N., Shimmi, O., Dupont, S. Piccolo, S. & Newfeld, S.J. (2012) Fat facets deubiquitylation of Medea/Smad4 modulates interpretation of a Dpp morphogen gradient. Development 139:2721-2729.

Dupont, S., Inui, M., & Neweld, S. (2012) Regulation of TGF-β signal transduction by mono- and deubiquitylation of Smads. FEBS Letters 586:1913-1920.

Konikoff, C., Karr, T., McCutchan, M., Newfeld, S.J. & Kumar, S. (2012) Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence. Dev Dynamics 241:150-160.

Kumar, S. Konikoff, C., Van Emden, B., Busick, C., Davis, K., Ji, S., Wu, L., Ramos, H., Brody, T., Panchanathan, S., Ye, J., Karr, T., Gerold, K., McCutchan, M. & Newfeld, S.J. (2011) FlyExpress: Visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinformatics 27:3319-3320.

Quijano, J., Stinchfield, M. & Newfeld, S.J. (2011) Wg signaling via Zw3 and Mad restricts self-renewal of sensory organ precursor cells in Drosophila. Genetics 189:809-824.

Quijano JC, Stinchfield MJ, Zerlanko B, Gibbens YY, Takaesu NT,Hyman-Walsh, C., Wotton, D. & Newfeld, S.J. (2010) The Sno Oncogene Antagonizes Wingless Signaling during Wing Development in Drosophila. PLoS ONE 5(7): e11619. doi:10.1371/journal.pone.0011619

Konikoff, C., Wisotzkey, R., Stinchfield, M. & Newfeld, S.J. (2010) Distinct molecular evolutionary mechanisms underlie the functional diversification of the Wnt and TGFbeta pathways. J Mol Evol 70:303-312. Cover.

Kahlem, P. & Newfeld, S.J. (2009) Informatics approaches to understanding TGF-beta pathway regulation. Development 136:3729-3740.

Dupont, S., Mamidi, A., Cordenonsi, M., Montagner, M., Zacchigna, L., Adorno, M., Martello, G., Stinchfield, M., Soligo, S., Morsut, L., Inui, M., Moro, S., Argenton, F., Newfeld, S.J. & Piccolo, S. (2009) FAM/USP9x, a deubiquitinating enzyme essential for TGFb signaling, controls Smad4 monoubiquitination. Cell 136:123-135. Cover.

Newfeld, S.J. (2008) An unabridged view of The TGFbeta Family. Development 135:3976-3977. Invited book review.

Konikoff, C., Wisotzkey, R. & Newfeld, S.J. (2008) Lysine conservation and context in TGFbeta and Wnt signaling suggests new targets and general themes for post-translational modification. J Mol Evol 67:323-333. Cover.

Frandsen, J., Gunn, B., Muratoglu, S., Fossett, N. & Newfeld, S.J. (2008) Salmonella pathogenesis reveals that BMP signaling regulates blood cell homeostasis and immune responses in Drosophila. Proc Natl Acad Sci USA 105:14952-14957.

Campbell, G. & Newfeld, S.J. (2008) Current topics in organogenesis and gametogenesis. Fly 2:125-128. Invited meeting review.

Takaesu, N.T, Bulanin, D., Orenic, T. & Newfeld, S.J. (2008) A combinatorial enhancer recognized by Mad, TCF and Brinker first activates then represses dpp expression in the posterior spiracles of Drosophila. Dev Biol 313:829-843.

Drosophila Comparative Genome Sequencing and Analysis Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.

Hudson, S.G., Garrett, M., Carlson, J., Micklem, G., Celniker, S., Goldstein, E.S. & Newfeld, S.J. (2007) Phylogenetic and genome-wide analyses suggest a functional relationship between kayak the Drosophila Fos homolog and fig a predicted PP2C phosphatase nested within a kayak intron. Genetics 177:1349-1361.

Johnson, A.N., Burnett, L., Sellin, J. Paululat, A. & Newfeld, S.J. (2007) Defective Dpp signaling results in heart overgrowth and reduced cardiac output in Drosophila. Genetics 176:1609-1624.

Takaesu, N.T., Hyman-Walsh, C.A., Ye, S., Wisotzkey, R.G., Stinchfield, M.J., O'Connor, M.B., Wotton, D.& Newfeld, S.J.(2006) dSno facilitates Baboon signaling in the Drosophila brain by switching the affinity of Medea away from Mad and toward dSmad2. Genetics (174:1299-1313).

Newfeld, S. J. & Wisotzkey, R.G. (2006) Molecular Evolution of Smad Proteins. In Smad Signal Transduction, Eds. C. Heldin, & P. ten Dijke, Springer, Netherlands, pp. 15-35.
-- Invited Chapter One and the Cover Illustration for the first book on the Smad Family.

Takaesu, N.T., Herbig, E.J., Zhitomersky, D., O'Connor, M.B. & Newfeld, S.J. (2005) DNA-binding domain mutations in Smad genes yield dominant negative proteins or a neomorphic protein that can activate Wg target genes in Drosophila. Development 132:4883-4894.

Hyman, C.A., Bartholin, B., Newfeld, S.J. & Wotton, D. (2003) Drosophila TGIF proteins are transcriptional activators. Molecular and Cellular Biology 23:9262-9274.

Johnson, A.N. Bergman, C., Kreitman, M. & Newfeld, S.J. (2003) Embryonic enhancers in the dpp disk region regulate a second round of Dpp signaling from the dorsal ectoderm to the mesoderm that represses Zfh-1 expression in a subset of pericardial cells. Developmental Biology 262:137-151.

Wisotzkey, R., Johnson, A., Takaesu, N.T. & Newfeld, S.J. (2003) α / β hydrolase2, a predicted gene adjacent to Mad in Drosophila melanogaster, belongs to a new global multigene family and is associated with obesity. Journal of Molecular Evolution 56:351-361.

Kumar, S., Jayaraman, K., Panchanathan, S., Gurunathan, R., Marti-Subirana, A., & Newfeld, S.J. (2002) BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics 162:2037-2047.

Takaesu, N.T., Johnson, A.N. & Newfeld, S.J. (2002) Posterior spiracle specific GAL4 lines: New reagents for developmental biology and respiratory physiology. genesis: the Journal of Genetics and Development 34:16-18.

Takaesu, N.T., Johnson, A.N., Sultani, O. & Newfeld, S.J. (2002) Combinatorial signaling by an unconventional Wg pathway and the Dpp pathway requires Nejire (CBP/p300) to regulate dpp expression in posterior tracheal branches. Developmental Biology 247:225-236.

Newfeld, S.J. & Takaesu, N.T. (2002) An analysis using the hobo genetic system reveals that combinatorial signaling by the Dpp and Wg pathways regulates dpp expression in leading edge cells of the dorsal ectoderm in Drosophila. Genetics 161:685-692

Johnson, A.N. & Newfeld, S.J. (2002) The TGF-β family: Signaling pathways, developmental roles and tumor suppressor activities. The Scientific World Journal 2:892-925. Invited research review (Editor - Norbert Perrimon, Harvard Medical School).

Marquez, R.M., Singer, M.A., Takaesu, N.T., Waldrip, W.R., Kraytsberg, Y. & Newfeld, S.J. (2001) Transgenic analysis of the Smad family of TGF-β signal transducers in Drosophila melanogaster suggests new roles and new interactions between family members. Genetics 157:1639 -1648.

Su, M.A., Wisotzkey, R.G. & Newfeld, S.J. (2001) A screen for modifiers of dpp mutant phenotypes identifies lilliputian, the only member of the Fragile-X/Burkitt’s Lymphoma family of transcription factors in Drosophila melanogaster. Genetics 157:717-725.

Jockush, E., Nulsen, C., Newfeld, S.J. & Nagy, L. (2000) Leg development in flies versus grasshoppers: Differences in dpp expression do not lead to differences in the expression of downstream components of the leg patterning pathway. Development 127:1617-1626.

Newfeld, S.J., Wisotzkey, R.G. & Kumar, S. (1999) Molecular evolution of a developmental pathway: Phylogenetic analyses of TGF-β family ligands, receptors and Smad signal transducers. Genetics 152:783-795.

Newfeld, S.J. & Takaesu, N.T. (1999) Local transposition of a hobo element within the decapentaplegic locus of Drosophila. Genetics 151:177-187.

Newfeld, S.J., Mehra, A., Singer, M.A., Wrana, J.L., Attisano, L. & Gelbart, W.M. (1997) Mothers against dpp participates in a dpp/TGF-β responsive serine-threonine kinase signal transduction cascade. Development 124:3167-3176.

Newfeld, S.J., Padgett, R.W., Findley, S.D., Richter, B.G., Sanicola, M., de Cuevas, M. & Gelbart, W.M. (1997) Molecular evolution at the decapentaplegic locus in Drosophila. Genetics 145:297-309.

Newfeld, S.J., Chartoff, E.H., Graff, J.M., Melton, D.A. & Gelbart, W.M. (1996) Mothers against dpp encodes a conserved cytoplasmic protein required in dpp/TGF-β responsive cells. Development 122:2099-2108.

Schmid, A., Newfeld, S.J. & Yedvobnick, B. (1996) Interspecific RNA in situ hybridization reveals perinuclear mastermind transcripts in Drosophila virilis. Molecular Biology & Evolution 13:280-282.

Sekelsky, J.J., Newfeld, S.J., Raftery, L.A., Chartoff, E.H. & Gelbart, W.M. (1995) Genetic characterization and cloning of Mothers against dpp: A gene required for decapentaplegic function in Drosophila. Genetics 139:1347-1358.

Newfeld, S.J. & Gelbart, W. (1995) Identification of two Drosophila TGF-β family members in the grasshopper Schistocerca americana. Journal of Molecular Evolution 141:155-160.

Brummel, T., Twombly, V., Marques, G., Wrana, J., Newfeld, S.J., Attisano, L., Massagué, J., O'Connor, M. & Gelbart, W.M. (1994) Characterization and relationship of dpp receptors encoded by the Sax and Tkv genes in Drosophila. Cell 78:251-262.

Newfeld, S.J., Tachida, H. & Yedvobnick, B. (1994) Drive-selection equilibrium: Homopolymer evolution in Drosophila gene mastermind. Journal of Molecular Evolution 38:637-641.

Newfeld, S.J., Schmid, A.T. & Yedvobnick, B. (1993) Homopolymer length variation in the Drosophila gene mastermind. Journal of Molecular Evolution 37:483-495.

Takaesu, N.T., Newfeld, S.J. & Hassold, T.J. (1992) Characterization of three VNTR systems at D21S112. Genomics 14:816-817.

Newfeld, S.J., Smoller, D. & Yedvobnick, B. (1991) Interspecific comparison of the unusually repetitive Drosophila locus mastermind. Journal of Molecular Evolution 32:415-420.

Non-refereed papers

Kumar, S. & Newfeld, S.J. (2002) Review of Modern Genetic Analysis by Griffiths, Gelbart, Lewontin & Miller. Quarterly Review of Biology 77:456-457. Invited textbook review.

Waldrip, W.R., Takaesu, N.T. & Newfeld, S.J. (2001) Identification of blue balancers and mutant collections compatible with hobo element transgenes. Drosophila Information Service 84:169-172. Technical note.