List of major publications  

Cokol, M., Iossifov I., Weinreb, C. & Rzhetsky A. 2005. Emergent properties of growing knowledge about molecular interactions. Nature Biotech., 24, (10), 1243-1247.

Rzhetsky, A. & Fitch, W.M. 2005. Listening to viral tongues: comparing viral trees using a stochastic context-free grammar. Mol. Biol. Evol., 22, 905-913.

Krauthammer, M., Kaufmann, C.A., Gilliam, T.C. & Rzhetsky, A. 2004. Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc. Natl. Acad. Sci. U S A, 101, 15148-15153.

Chien, M., Morozova, I., Shi, S., Sheng, H., Chen, J., Gomez, S.M., Asamani, G., Hill, K., Nuara, J., Feder, M., Rineer, J., Greenberg, J.J., Steshenko, V., Park, S.H., Zhao, B., Teplitskaya, E., Edwards, J.R., Pampou, S., Georghiou, A., Chou, I.-C., Iannuccilli, W., Ulz, M.E., Kim, D.H., Goldsberry, C., Morozov, P., Fischer, S.G., Segal, G., Qu, X., Rzhetsky, A., Zhang, P., Cayanis, E., De Jong, P.J., Ju, J., Kalachikov, S., Shuman, H.A. & Russo, J.J. 2004. The Genomic Sequence of Legionella pneumophila. Science, 305, 1966-1968.

Iossifov, I., Krauthammer, M., Friedman, C., Hatzivassiloglou, V., Bader, J.S., White, K.P. & Rzhetsky, A. 2004. Probabilistic inference of molecular networks from noisy data sources. Bioinformatics, 20, 1205-1213. PDF 1,507Kb

Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P.A., Weng, W., Wilbur, W.J., Hatzivassiloglou, V. & Friedman, C. 2004. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform, 37, 43-53. PDF 578 Kb

Gomez, S.M., Noble, W.S. & Rzhetsky, A. 2003. Learning to predict protein-protein interactions from protein sequences. Bioinformatics, 19, 1875-1881. PDF 89 Kb

Roth, C.W., Holm, I., Graille, M., Dehoux, P., Rzhetsky, A., Wincker, P., Weissenbach, J. & Brey, P.T. 2003. Identification of the Anopheles gambiae ATP-binding cassette transporter superfamily genes. Molecules and Cells, 15, 150-158.

Karev, G. P., Wolf, Y. I., Rzhetsky, A., Berezovskaya, F. S., and Koonin, E. V. 2003. Mathematical Modeling of the Evolution of Domain Composition of Proteomes: A Birth-and-Death Process with Innovation. In Frontiers in Computational Genomics (M. Y. Galperin and E. V. Koonin, eds.).

Yu, H., Hatzivassiloglou, V., Friedman, C., Rzhetsky, A., and Wilbur, W. J. 2002. Automatic Extraction of Gene and Protein Synonyms from MEDLINE and Journal Articles. Proc AMIA Symp, 919-923.

Yu, H., Hatzivassiloglou, V., Rzhetsky, A. & Wilbur, W.J. 2002. Automatically identifying gene/protein terms in MEDLINE abstracts. J Biomed Inform, 35, 322-330. PDF 143 Kb

Karev, G. P., Wolf, Y. I., Rzhetsky, A. Y., Berezovskaya, F. S., and Koonin, E. V. 2002. Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evol Biol 2, 18. PDF 652 Kb

Friedman, C., Kra, P. & Rzhetsky, A. 2002. Two biomedical sublanguages: a description based on the theories of Zellig Harris. J Biomed Inform, 35, 222-235. PDF 196 Kb

Christophides, G. K., Zdobnov, E., Barillas-Mury, C., Birney, E., Blandin, S., Blass, C., Brey, P. T., Collins, F. H., Danielli, A., Dimopoulos, G., Hetru, C., Hoa, N. T., Hoffmann, J. A., Kanzok, S. M., Letunic, I., Levashina, E. A., Loukeris, T. G., Lycett, G., Meister, S., Michel, K., Moita, L. F., Muller, H. M., Osta, M. A., Paskewitz, S. M., Reichhart, J. M., Rzhetsky, A., Troxler, L., Vernick, K. D., Vlachou, D., Volz, J., Von Mering, C., Xu, J., Zheng, L., Bork, P., and Kafatos, F. C. 2002. Immunity-related genes and gene families in Anopheles gambiae. Science 298, 159-165.

Krauthammer, M., Kra, P., Iossifov, I., Gomez, S. M., Hripcsak, G., Hatzivassiloglou, V., Friedman, C., and Rzhetsky, A. 2002. Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics 18 Suppl 1, S249-S257.

Gomez, S.M. and A. Rzhetsky. 2002. Towards prediction of complete protein-protein interaction networks. Pac Symp Biocomput, p. 413-424.

Annilo, T., Tammur, J., Hutchinson, A., Rzhetsky, A., Dean, M., and Allikmets, R. 2001. Human and mouse orthologs of a new ATP-binding cassette gene, ABCG4. Cytogenet Cell Genet 94, 196-201.

Rzhetsky A., and S. M. Gomez. 2001. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics, 17, 988-996.

Gomez, S.M., S. H. Lo and A. Rzhetsky. 2001. Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics, 159, 1291-1298.

Dean M., Rzhetsky A., and Allikmets R. 2001. The human ATP-Binding cassette (ABC) transporter superfamily. Genome Res. 11,1156-1166. PDF file (205 K)

Tammur, J., C. Prades, I. Arnould, A. Rzhetsky, A. Hutchinson, M. Adachi, J. D. Schuetz, K. J., Swoboda, L. J. Ptacek, M. Rosier, M. Dean, and R. Allikmets. 2001. Two new genes from the human ATP-binding cassette transporter superfamily, ABCC11 and ABCC12, tandemly duplicated on chromosome 16q12. Gene 273: 89-96. PDF file (629 K)

Friedman, C., P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky. 2001. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17 Suppl 1: S74-82. PDF file (346 K)

Hatzivassiloglou, V., P. A. Duboue, and A. Rzhetsky. 2001. Disambiguating proteins, genes, and RNA in text: a machine learning approach. Bioinformatics 17 Suppl 1: S97-S106. PDF file (167 K)

Rzhetsky, A., and P. Morozov. 2001. Markov chain Monte Carlo computation of confidence intervals for substitution-rate variation in proteins. Pacific Symposium on Biocomputing 6: 203-214. PDF file (320K)

Scott K., Brady Jr. R., Cravchik A., Morozov P., Rzhetsky A., Zuker C., and Axel R. 2001. A chemosensory gene family encoding candidate gustatory and olfactory receptors in Drosophila. Cell, 104, 661-673. PDF file (1,525 K)

Rzhetsky, A., T. Koike, S. Kalachikov, S.M. Gomez, M. Krauthammer, S.H. Kaplan, P.Kra, J.J. Russo, and C. Friedman. 2000. A Knowledge Model for Analysis and Simulation of Regulatory Networks. Bioinformatics 16: 1120-1128. PDF file (253K)

Krauthammer, M., A. Rzhetsky, P.Morozov, and C. Friedman. 2000. Using BLAST for identifying gene and protein names in journal articles. Gene 259: 245-252. PDF file (>100K)

Koike, T., and A. Rzhetsky. 2000. A graphic editor for analyzing signal-transduction pathways.Gene 259: 235-244. PDF file (1,915 K)

Tilson, M.D., Rzhetsky, A. 2000. A novel hypothesis regarding the evolutionary origins of the immunoglobulin fold. Curr Med Res Opin. 16(2):88-93.

Morozov, P.S., T.L. Sitnikova, G. Churchill , F.J. Ayala , and A. Rzhetsky. 2000. A New Method for Characterizing Replacement Rate Variation in Molecular Sequences: Application of the Fourier and Wavelet Models to Drosophila and Mammalian Proteins. Genetics 154: 381–395. PDF file (524K)

Migliazza A., Cayanis E., Bosch-Albareda F., Komatsu H., Martinotti S., Toniato E., Kalachikov S., Bonaldo M. F., Jelene P., Ye X., Rzhetsky A., Qu X., Chien M., Inghirami G., Gaidano G., Vitolo U., Saglio G., Resegotti L., Zhang P., Soares M. B., Russo J., Fischer S. G., Edelman I. S., Efstratiadis A., and Dalla-Favera R. 2000. Molecular pathogenesis of B-cell chronic lymphocytic leukemia: analysis of 13q14 chromosomal deletions. Curr Top Microbiol Immunol, 252, 275-284.

Vosshall, L.B., H. Amrein, P.S. Morozov, A. Rzhetsky, and R. Axel. 1999. A spatial map of olfactory receptor expression in the Drosophila antenna. Cell 96: 725-736. PDF file (358K)

Rzhetsky, A., and F.J. Ayala. 1999. The enigma of intron origins. Cellular and Molecular Life Sciences 55: 3-6. PDF file (1,300K)

Ayala, F.J., A. Rzhetsky, and F.J. Ayala. 1999. Molecular Clocks and the Origin of Animals. In: S.P. Wasser (ed.), Evolutionary Theory and Processes: Modern Perspectives, Papers in Honour of Eviatar Nevo (Kluwer Academic Publishers, The Netherlands), pp. 1-19.

Qu, X.-Y., R.S. Hauptschein, A. Rzhetsky, L. Scotto, M.-H. Chien, X. Ye, F. Frigeri, P.H. Rao, L. Pasqualucci, B. Gamberi, L.L. Deaven, P. Zhang, R.S.K. Chaganti, R. Dalla-Favera, and J.J. Russo. 1998. Analysis of a 69-kb contiguous genomic sequence at a putative tumor suppressor gene locus on human chromosome 6q27. DNA Sequence 9: 1-16.

Rzhetsky, A., S. Kalachikov, X. Ye, P. Zhang, and J.J. Russo. 1998. Tools for visualization and integration of intermediate sequencing results in large disease discovery projects. Gene, 16: 31-35.

Ayala, F.J, A. Rzhetsky, and F.J. Ayala. 1998. Molecular clock and the divergence of metazoan phyla. Proc. Natl. Acad. Sci. USA 95: 606-611. PDF file (170K)

Comment by Stephen Jay Gould (PDF file, 31K)

Comment in Nature (PDF file, 237K)

Comment in Science (PDF file, 60K)

Rzhetsky, A., F.J. Ayala, L.C. Hsu, C. Chang, and A. Yoshida. 1997. Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory. Proc. Natl. Acad. Sci. USA 94: 6820-6825. PDF file (360K)

Yoshida, A., A. Rzhetsky, Chang, C., and L.C. Hsu. 1997. Human aldehyde dehydrogenase gene family. Eur. J. Biochemistry 251: 549-557.

Rzhetsky, A., F.J. Ayala, L.C. Hsu, C. Chang, and A. Yoshida. 1997. Fitting models of intron evolution to aldehyde dehydrogenase data. In B. Mirkin, F. McMorris, F. Roberts, and A. Rzhetsky (Eds.): Mathematical Hierarchies and Biology DIMACS Series in Discrete Mathematics and Theoretical Computer Science, AMS, Providence, p. 95-110. PDF file (160K)

Rzhetsky, A., J. Dopazo, E. Snyder, C.A. Dangler, and F.J. Ayala. 1996. Assessing dissimilarity of genes by comparing their RNAse A mismatch cleavage patterns. Genetics, 144: 1975-1983. PDF file (459K)

Rzhetsky, A., and T. Sitnikova. 1996. When is it safe to use a wrong model of nucleotide substitution in tree-making? Mol. Biol. Evol. 134: 1255-1265.

Kumar, S., and A. Rzhetsky. 1996. Evolutionary relationships among eukaryotic kingdoms. J. Mol. Evol. 42: 183-193.

Rzhetsky, A., and T. Sitnikova. 1995. Using a wrong model in tree-making. In: Proceeding of US-Japan Binational Workshop in Molecular Evolution. (M. Nei and N. Takahata, eds.). Pennsylvania State University.

Rzhetsky, A. 1995. On the models of nucleotide substitution applicable to ribosomal RNA genes. pp. 48-50 in: Proceedings of Phylogeny Workshop held in Princeton University, February 6-8, 1995. DIMACS Technical Report 95-48.

Rzhetsky, A, and T. Sitnikova. 1995. Using a wrong model in tree-making. Pp. 125-135 In: Current topics on Molecular Evolution. (Proceeding of US-Japan Binational Workshop in Molecular Evolution. (M. Nei and N. Takahata, eds.) Hayama, Japan.

Rzhetsky, A. 1995. Estimating substitution rates in ribosomal RNA genes. Genetics. 141: 771-783.

Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of molecular clock and linearized trees. Mol. Biol. Evol. 12: 823-833.

Rzhetsky, A., S. Kumar, and M. Nei. 1995. Four-cluster analysis: a simple method to test phylogenetic hypotheses. Mol. Biol. Evol. 12: 163-167.

Sitnikova, T., A. Rzhetsky, and M. Nei. 1995. Interior-branch and bootstrap tests of phylogenetic trees. Mol. Biol. Evol. 12: 319-333.

Rzhetsky, A., and M. Nei. 1995. Tests of applicability of several substitution models for DNA sequence data. Mol. Biol. Evol. 12: 131-151.

Rzhetsky, A. and M. Nei. 1994a. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J. Mol. Evol. 38: 295-299.

Rzhetsky, A., and M. Nei. 1994b. METREE: Program package for inferring and testing minimum-evolution trees. Comp. Appl. Biol. Scien. 10: 189-191.

Rzhetsky, A., and M. Nei. 1993. Theoretical foundation of the minimum evolution method of phylogenetic inference. Mol. Biol. Evol. 10: 1073-1095.

Zharkikh, A., and A. Rzhetsky. 1993. Quick assessment of similarity of two sequences by comparison of their L-tuple frequencies. BioSystems 30: 93-111. Elsevier Scientific Publishers Ireland, Ltd.

Rzhetsky, A., and M. Nei. 1992a. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9: 945-967.

Rzhetsky, A., and M. Nei. 1992b. Statistical properties of the ordinary least-squares, generalized least-squares and minimum-evolution methods of phylogenetic inference. J. Mol. Evol. 35: 367-475.

Zharkikh, A., A. Rzhetsky, P. Morozov, T. Sitnikova, and J. Krushkal. 1991. VOSTORG: a package of minicomputer programs for sequence analysis and phylogenetic trees construction. Gene. 101: 251-254.

Nei, M., and A. Rzhetsky. 1991. Reconstruction of phylogenetic trees and evolution of major histocompatibility complex genes. In: Evolution of MHC genes, eds. J.Klein and D.Klein, Springer-verlag, Heidelberg, 13-27.