1. Ponomarenko J.V., Ponomarenko M.P., Frolov A.S., Vorobyev D.G., Overton G.C., Kolchanov N.A. (1999) Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, 15, 7/8, 654-668.
  2. Kolchanov N.A., Ponomarenko M.P., Frolov A.S., Ananko E.A., Kolpakov F.A., E., Ignatieva E.V., Podkolodnaya O.A., Goryachkovskaya T.N., Stepanenko I.L., Merkulova T.I., Babenko V.V., Ponomarenko Yu.V., Kochetov A.V., Podkolodny N.L., Vorobiev D.V., Lavryushev S.V., Grigorovich D.A., Kondrakhin Yu.V., Milanesi L., Wingender E., Solovyev V. and Overton G.C. (1999) Integrated databases and computer systems for studying eukaryotic gene expression. Bioinformatics, 15, 7/8, 669-686.
  3. Kolchanov N. A., Ponomarenko M. P., Kel A. E., Kondrakhin Yu. V., Frolov A. S., Kolpakov F. A., Kel O. V., Ananko E. A., Ignatieva E.V., Podkolodnaya O. A., Stepanenko I. L., Merkulova T. I., Babenko V. N., Vorobiev D.G, Lavryushev S.V., Ponomarenko Yu. V., Kochetov A. V., Kolesov G.B., Podkolodny N. L., Milanesi L., Wingender E., Heinemeyer T., Solovyev V.V. (1998) GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences of the eukaryotic genome. Proceedings of The Sixth International Conference on Intelligent Systems for Molecular Biology, ISMB-98. Ed.: Glasgow J. et al. June 28 - July 1, 1998, Montreal, Canada, AAAI Press, P. 95-104. Full Text (html)
  4. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Vorobiev D.G., Levitsky V.G., Podkolodnaya O.A., Overton G.C., Kolchanov N.A. (1998) B-DNA-VIDEO: an active database for the significant B-DNA features of transcription factor binding sites. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 66-70. Full Text (html)

  5. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A., Karas H., Wingender E., Sklenar H. (1997) Computer analysis of conformational features of the eukaryotic TATA-box DNA promotors. Mol Biol (Mosk). V. 31(4), P. 733-740. (Russ)
  6. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A. (1997) Search for DNA conformational features for functional sites. Investigation of the TATA box. In: “Biocomputing: proceedings of the 1997 Pacific Symposium” (Altman, R., et al., eds.), Word Sci. Publ., Singapore, 1997, P. 340-351.

  7. Suslov V.V., Ponomarenko P.M., Efimov V.M., Savinkova L.K., Ponomarenko M.P., Kolchanov N.A. (2010) SNPs in the HIV-1 TATA box and the AIDS pandemic. J. Bioinform. Comput. Biol. V. 8(3). P. 607-625 (pdf)

  8. Ponomarenko M.P., Savinkova L.K., Ponomarenko Yu.V., Kel A.E., Titov I.I., Kolchanov N.A. (1997) Simulation of TATA box sequences in eukaryotes. Mol Biol (Mosc), V. 31(4), P. 616-622. (pdf)

  9. Ponomarenko M.P., Ponomarenko Yu.V., Kel A.E., Kolchanov N.A., Karas H., Wingender E., Sklenar H. Computer conformation analysis of TATA-box sequences in eukaryotic Promoters. (1997) Mol Biol (Mosc), V. 31(4), P. 623-630. (pdf)

  10. Ponomarenko MP, Ponomarenko IuV, Titov II, Kolchanov NA, Mazin AV, Kowalczykowski SC. (1998) Preference of RecA-filament to the DNA sequences correlates with genetic code. Dokl. Akad. Nauk. V. 363(1). P. 179-182. (pdf)

  11. Kel AE, Ponomarenko MP, Likhachev EA, Orlov YuL, Ischenko IV, Milanesi L, Kolchanov NA. (1993) SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. CABIOS. V. 9. P. 617-627. (pdf)

  12. Kolchanov NA, Ponomarenko MP, Ponomarenko IuV, Podkolodny NL, Frolov AS. (1998) Functional sites in pro- and eukaryotic genomes: computer models for predicting activity. Mol. Biol. (Mosc). V. 32. P. 220-232. (pdf)

  13. Ponomarenko MP, Ponomarenko IuV, Podkolodnaia OA, Frolov AS, Vorob'ev DV, Kolchanov NA, Overton GC. (1999) Averaging results of site recognition can increase the accuracy of annotating the human genome. Biophysics (Mosc). V. 44. P. 631-635. (pdf)

  14. Ponomarenko MP, Ponomarenko IuV, Kolchanov NA. (1999) Contribution of signals and antisignals in the mutational spectrum of the td-intron insertion site. Biophysics (Mosc). V. 44. P. 636-643. (pdf)

  15. Kolpakov FA, Podkolodnyi NL, Lavryushev SV, Grigorovich DA, Ponomarenko MP, Kolchanov NA (2000) Methods for integration of heterogeneous information resources in molecular biology in the digital library GeneExpress. Programming Comput Soft (Mosc). V. 26. P. 170-176. (pdf)

  16. Ponomarenko JV, Merkulova TI, Orlova GV, Fokin ON, Gorshkova EV, Ponomarenko MP, (2002) Mining DNA sequences to predict sites which mutations cause genetic diseases. Knowledge-Based Systems J. V. 15. P. 225-233. (pdf)