Prediction of functional sites by analysis of sequence and structure conservation
A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.

Bioinformatical assay of human gene morbidity
F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.

A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications
F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.

Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs
A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.

Role of Arabidopsis ARGONAUT in RNA-directed DNA methylation triggered by inverted repeats
D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220.

Genetic and functional diversification of small RNA pathways in plants
Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.

Silencing of transposons in plant genomes: kick them when they're down
D. Zilberman, S. Henikoff, Genome Biology 5 (2004).

A limit shape theorem for periodic stochastic dispersion
D. Dolgopyat, V. Kaloshin, L. Koralov, Communications on Pure and Applied Mathematics 57 (2004) 1127–1158.

Sample path properties of the stochastic flows
L. Koralov, V. Kaloshin, D. Dolgopyat, The Annals of Probability 32 (2004) 1–27.

Positive selection at sites of multiple amino acid replacements since rat-mouse divergence
G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562.

The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811.

RNA silencing genes control de novo DNA methylation
S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.

A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides
Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.

Multicolour micropatterning of thin films of dry gels
R. Klajn, M. Fialkowski, I.T. Bensemann, A. Bitner, C.J. Campbell, K. Bishop, S. Smoukov, B.A. Grzybowski, Nature Materials 3 (2004) 729–735.

Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts
C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski, Advanced Materials 16 (2004) 1912–1917.

Stress-dependent regulation of FOXO transcription factors by the SIR deacetylase
A. Brunet, L.B. Sweeney, J.F. Sturgill, K. Chua, P. Greer, Y. Lin, H. Tran, S. Ross, R. Mostoslavsky, H. Cohen, L. Hu, H.-L. Chen, M. Jedrychowski, S. Gygi, D. Sinclair, F. Alt, M. Greenberg, Science 303 (2004) 2011–2015.