Social signals and neuronal circuits that regulate development and aging
Aprison EZ, Dzitoyeva S, Ruvinsky I (2023) Serotonergic signaling plays a deeply conserved role in improving oocyte quality. Dev. Biol. 499: 24–30.
Burkhardt RN, Artyukhin AB, Aprison EZ, Curtis BJ, Fox BW, Ludewig AH, Palomino DF, Luo J, Chaturbedi A, Panda O, Wrobel CJJ, Baumann V, Portman DS, Lee SS, Ruvinsky I, Schroeder FC (2023) Sex-specificity of the C. elegans metabolome. Nat. Commun. 14: 320
Aprison EZ, Dzitoyeva S, Ruvinsky I (2022) The serotonin circuit that coordinates germline proliferation and egg laying with other reproductive functions in C. elegans. Proc. Biol. Sci. 289: 20220913.
Aprison EZ, Dzitoyeva S, Angeles-Albores D, Ruvinsky I (2022) A male pheromone that improves quality of the oogenic germline. Proc. Natl. Acad. Sci. USA 119: e2015576119.
Aprison EZ, Ruvinsky I (2022) The roles of several sensory neurons and the feedback from egg laying in regulating the germline response to a sex pheromone in C. elegans hermaphrodites. MicroPubl. Biol. 10.17912/micropub.biology.000523.
Aprison EZ, Ruvinsky I (2022) ODR-1 acts in AWB neurons to determine the sexual identity of C. elegans pheromone blends. MicroPubl. Biol. 10.17912/micropub.biology.000507.
Faerberg DF, Gurarie V, Ruvinsky I. (2021) Inferring temporal organization of postembryonic development from high-content behavioral tracking. Dev. Biol. 475: 54-64.
Aprison EZ, Ruvinsky I. (2019) Dynamic Regulation of Adult-Specific Functions of the Nervous System by Signaling from the Reproductive System. Curr Biol. 29(23):4116-4123.
Aprison EZ, Ruvinsky I. (2019) Coordinated Behavioral and Physiological Responses to a Social Signal Are Regulated by a Shared Neuronal Circuit. Curr Biol. 29(23):4108-4115.
Ludewig AH, Artyukhin AB, Aprison AZ, Rodrigues PR, Pulido DC, Burkhardt RN, Oishika P, Zhang YK, Gudibanda P, Ruvinsky I*, Schroeder FC* (2019) An excreted small-molecule signal promotes C. elegans reproductive development and aging. Nat. Chem. Biol. 15: 838-845.
McGrath PT, Ruvinsky I (2019) A primer on pheromone signaling in Caenorhabditis elegans for systems biologists. Curr. Opin. Sys. Biol. 13: 23–30.
Aprison EZ, Ruvinsky I (2017) Counteracting ascarosides act through distinct neurons to determine the sexual identity of C. elegans pheromones. Curr. Biol. 27: 2589–2599.
Aprison EZ, Ruvinsky I (2016) Sexually antagonistic male signals manipulate germline and soma of C. elegans hermaphrodites. Curr. Biol. 26: 2827-2833.
Aprison EZ, Ruvinsky I (2015) Sex pheromones of C. elegans males prime the female reproductive system and ameliorate the effects of heat stress. PLoS Genet. 11: e1005729.
Stress and the reproductive system
Gouvêa DY, Aprison EZ, Ruvinsky I (2015) Experience modulates the reproductive response to heat stress in C. elegans via multiple physiological processes. PLoS ONE 10: e0145925.
Aprison EZ, Ruvinsky I (2014) Balanced trade-offs between alternative strategies shape the response of C. elegans reproduction to chronic heat stress. PLoS ONE 9: e105513.
McMullen P, Aprison EZ, Winter P, Amaral L, Morimoto R, Ruvinsky I (2012) Macro-level modeling of the response of C. elegans reproduction to chronic heat stress. PLoS Comput. Biol. 8: e1002338.
Comparative studies of gene regulation
Gordon KL, Arthur RK, Ruvinsky I (2015) Phylum-level conservation of regulatory information in nematodes despite extensive non-coding sequence divergence. PLoS Genet. 11: e1005268.
Barrière A, Ruvinsky I. (2014) Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes. PLoS Genet. 10: e1004435.
Barrière A, Gordon KL, Ruvinsky I (2012) Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration. PLoS Genet. 8: e1002961.
Romero IG, Ruvinsky I, Gilad Y (2012) Evolution of gene expression: from comparative studies to emerging regulatory principles. Nat. Rev. Genet. 13: 505-516.
Gordon KL, Ruvinsky I (2012) Tempo and mode in evolution of transcriptional regulation. PLoS Genet. 8: e1002432.
Arthur R, Ruvinsky I (2011) Evidence that purifying selection acts on promoter sequences. Genetics 189: 1121-1126.
He Z, Eichel K, Ruvinsky I (2011) Functional conservation of cis-regulatory elements of heat-shock genes over long evolutionary distances. PLoS ONE 6: e22677.
Barrière A, Gordon KL, Ruvinsky I (2011) Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet. 7: e1002095.
Ruvinsky I, Ruvkun G (2003) Functional tests of enhancer conservation between distantly related species. Development 130: 5133-5142.
Comparative genomics
Wang PPS, Ruvinsky I (2012) Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes. Genome Biol. Evol. 4: 565–574.
Wang PPS, Ruvinsky I (2010) Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes. RNA 16: 290-298.
Barrière A, Yang SP, Pekarek E, Thomas CG, Haag ES, Ruvinsky I (2009) Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res. 19: 470-480.
Ruvinsky I, Ohler U, Burge CB, Ruvkun G (2007) Detection of broadly expressed neuronal genes in C. elegans. Dev. Biol. 302: 617-626.
T-box genes in vertebrate development and evolution
Horton AC, Mahadevan NR, Minguillon C, Osoegawa K, Rokhsar DS, Ruvinsky I, de Jong PJ, Logan MP, Gibson-Brown JJ (2008) Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Dev. Genes Evol. 218: 613-628.
Horton AC, Mahadevan NR, Ruvinsky I, Gibson-Brown JJ (2003) Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. J. Exp. Zool. (Mol. Dev. Evol.) 299B: 41-53.
Piotrowski T, Ahn D, Schilling TF, Nair S, Ruvinsky I, Geisler R, Rauch GJ, Haffter P, Zon LI, Zhou Y, Foott H, Dawid IB, Ho RK (2003) The zebrafish van gogh mutation disrupts tbx1, which is involved in the DiGeorge deletion syndrome in humans. Development 130: 5043-5052.
Ruvinsky I, Chertkov O, Borue XV, Agulnik SI, Gibson-Brown JJ, Lyle SR, Silver LM (2002) Genetic analysis of mouse mutations Abnormal feet and tail and rough coat, which cause developmental abnormalities and alopecia. Mamm. Genome 13: 675-679.
Ahn D, Ruvinsky I, Oates AC, Silver LM, Ho RK (2000) tbx20, a new vertebrate T-box gene expressed in the cranial motor neurons and developing cardiovascular structures in zebrafish. Mech. Dev. 95: 253-258.
Ruvinsky I, Gibson-Brown JJ (2000) Genetic and developmental bases of serial homology in vertebrate limb evolution. Development 127: 5233-5244.
Ruvinsky I, Oates AC, Silver LM, Ho RK (2000) The evolution of paired appendages in vertebrates: T-box genes in the zebrafish. Dev. Genes Evol. 210: 82-91.
Ruvinsky I, Silver LM, Gibson-Brown JJ (2000) Phylogenetic analysis of T-box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome. Genetics 156: 1249-1257.
Yelon D, Ticho B, Halpern ME, Ruvinsky I, Ho RK, Silver LM, Stainier DYR (2000) The bHLH transcription factor Hand2 plays parallel roles in zebrafish heart and pectoral fin development. Development 127: 2573-2582.
Yelon D, Ticho B, Halpern ME, Ruvinsky I, Ho RK, Silver LM, Stainier DYR (2000) The bHLH transcription factor Hand2 plays parallel roles in zebrafish heart and pectoral fin development. Development 127: 2573-2582.
Ruvinsky I, Silver LM, Ho RK (1998) Characterization of the zebrafish tbx16 gene and evolution of the vertebrate T-box family. Dev. Genes Evol. 208: 94-99.
Agulnik SI, Ruvinsky I, Silver LM (1997) Three novel T-box genes in Caenorhabditis elegans. Genome 40: 458-464.
Ruvinsky I, Silver LM (1997) Newly identified paralogous groups on mouse chromosomes 5 and 11 reveal the age of a T-box cluster duplication. Genomics 40: 262-266.
Agulnik SI, Garvey N, Hancock S, Ruvinsky I, Chapman DL, Agulnik I, Bollag R, Papaioannou V, Silver LM (1996) Evolution of the mouse T-box genes by tandem duplication and cluster dispersion. Genetics 144: 249-254.
Amphibian systematics
Ruvinsky I, Maxson LR (1996) Phylogenetic relationships among bufonoid frogs (Anura: Neobatrachia) inferred from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 5: 533-547.
Hay JM, Ruvinsky I, Hedges SB, Maxson LR (1995) Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Mol. Biol. Evol. 12: 928-937.