image taken from the Darwin archive


Aprison E.Z. and Ruvinsky I. (2014). Balanced Trade-Offs between Alternative Strategies Shape the Response of C. elegans Reproduction to Chronic Heat Stress. PLoS One. 9(8): e105513.

Barrière A. and Ruvinsky I. (2014). Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes. PLoS Genet. 10: e1004435.

Barrière A., Gordon K. L. and Ruvinsky I. (2012). Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration. PLoS Genet. 8: e1002961.

Romero I. G., Ruvinsky I. and Gilad Y. (2012) Evolution of gene expression: from comparative studies to emerging regulatory principles. Nat. Rev. Genet. 13: 505-516.

Wang, P. P.-S. and 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.

McMullen P., Aprison E. Z., Winter P., Amaral L., Morimoto R. and Ruvinsky I. (2012). Macro-level modeling of the response of C. elegans reproduction to chronic heat stress. PLoS Comput. Biol. 8: e1002338.

Gordon K. L. and Ruvinsky I. (2012). Tempo and mode in evolution of transcriptional regulation. PLoS Genet. 8: e1002432.

Arthur R. and Ruvinsky I. (2011). Evidence that purifying selection acts on promoter sequences. Genetics 189: 1121-1126.

He Z., Eichel K. and Ruvinsky I. (2011). Functional conservation of cis-regulatory elements of heat-shock genes over long evolutionary distances. PLoS One 6: e22677.

Barrière A., Gordon K. L. and Ruvinsky I. (2011). Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet. 7: e1002095.

Wang P. P.-S. and 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 S.-P., Pekarek E., Thomas C. G., Haag E. S. and Ruvinsky I. (2009). Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res. 19: 470-480.

Must Read

Pre-University of Chicago Era (nematode genomics and evolution)

Ruvinsky I., Ohler U., Burge C. B. and Ruvkun G. (2007). Detection of broadly expressed neuronal genes in C. elegans. Dev. Biol. 302: 617-626.

Ruvinsky I. and Ruvkun G. (2003). Functional tests of enhancer conservation between distantly related species. Development 130: 5133-5142.

Pre-University of Chicago Era (genome evolution, Evo-Devo, phylogenetics, etc.)

Horton A. C., Mahadevan N. R., Minguillon C., Osoegawa K., Rokhsar D. S., Ruvinsky I., de Jong P. J., Logan M. P. and Gibson-Brown J. J. (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 A. C., Mahadevan N. R., Ruvinsky I. and Gibson-Brown J. J. (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 T. F., Nair S., Ruvinsky I., Geisler R., Rauch G. J., Haffter P., Zon L. I., Zhou Y., Foott H., Dawid I. B. and Ho R. K. (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 X. V., Agulnik S. I., Gibson-Brown J. J., Lyle S. R. and Silver L. M. (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 A. C., Silver L. M. and Ho R. K. (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. and Gibson-Brown J. J. (2000). Genetic and developmental bases of serial homology in vertebrate limb evolution. Development 127: 5233-5244.

Ruvinsky I., Oates A. C., Silver L. M. and Ho R. K. (2000). The evolution of paired appendages in vertebrates: T-box genes in the zebrafish. Dev. Genes Evol. 210: 82-91.

Ruvinsky I., Silver L. M. and Gibson-Brown J. J. (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 M. E., Ruvinsky I., Ho R. K., Silver L. M. and Stainier D. Y. R. (2000). The bHLH transcription factor Hand2 plays parallel roles in zebrafish heart and pectoral fin development. Development 127: 2573-2582.

Ruvinsky I., Silver L. M. and Ho R. K. (1998). Characterization of the zebrafish tbx16 gene and evolution of the vertebrate T-box family. Dev. Genes Evol. 208: 94-99.

Agulnik S. I., Ruvinsky I. and Silver L. M. (1997). Three novel T-box genes in Caenorhabditis elegans. Genome 40: 458-464.

Ruvinsky I. and Silver L. M. (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 S. I., Garvey N., Hancock S., Ruvinsky I., Chapman D. L., Agulnik I., Bollag R., Papaioannou V. and Silver L. M. (1996). Evolution of the mouse T-box genes by tandem duplication and cluster dispersion. Genetics 144: 249-254.

Ruvinsky I. and Maxson L. R. (1996). Phylogenetic relationships among bufonoid frogs (Anura: Neobatrachia) inferred from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 5: 533-547.

Hay J. M., Ruvinsky I., Hedges S. B. and Maxson L. R. (1995). Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Mol. Biol. Evol. 12: 928-937.

(c) The University of Chicago, 2009. Designed and maintained by Paul Wang