Andrey Grigoriev

Small RNA

Karaiskos, S., Grigoriev, A. (2016) Dynamics of tRNA fragments and their targets in aging mammalian brain. F1000Research, 5(ISCB Comm J):2758.

Karaiskos, S., Naqvi, A., Swanson, K., Grigoriev, A. (2015) Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. Biology Direct, 10:51. (voted best student paper for 2015 by CCIB)

Grigoriev, A., & Bonini, N. M. (2014) Age-dependent patterns of microRNA RISC loading Aging, 6(9), 705-706.

Abe, M., Naqvi, A., Hendriks, G. J., Feltzin, V., Zhu, Y., Grigoriev, A.*, & Bonini, N. M.* (2014). Impact of age-associated increase in 2'-O-methylation of miRNAs on aging and neurodegeneration in Drosophila. Genes & Development, 28(1), 44-57. *Corresponding co-authors

Naqvi. A, Cui, T., Grigoriev, A. (2014) Visualization of nucleotide substitutions in the (micro) transcriptome. BMC Genomics, 15(4), 1-8.

Proteomics and Systems biology

Liu, M., Walch, H., Wu, S., and Grigoriev, A. (2005) Significant expansion of exon-bordering protein domains during animal proteome evolution. Nucleic Acids Research 33, 95-105.

Liu, M., Wu, S., Walch, H., and Grigoriev, A. (2005) Exon-domain correlation and its corollaries. Bioinformatics 21, 3213-3216.

Grigoriev, A. (2004) Understanding the yeast proteome: a bioinformatics perspective. Expert Reviews in Proteomics 1, 133-145.

Grigoriev, A. (2003) On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Research, 31, 4157-4161.

Grigoriev, A. (2001) On relationships between protein-protein interactions, gene expression, mutation and composition in complete genomes. 2001 Meeting on Genome Sequencing and Biology, Cold Spring Harbor, New York. Selected as Oral presentation, could not attend due to 9/11 terrorism.

Grigoriev, A. (2001) A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Research, 29, 3513-3519.

Virus genomics and evolution

Grigoriev, A. (2004) Mutational patterns correlate with genome organization in SARS and other coronaviruses. Trends in Genetics, 20, 131-135.

Berkhout B, Grigoriev A, Bakker M, Lukashov VV. (2002) Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure. AIDS Res Hum Retroviruses, 18, 133-141.

Beletskii, A., Grigoriev, A., Joyce ,S. and Bhagwat, A. S. (2000) Mutations induced by bacteriophage T7 RNA polymerase and their effects on the composition of the T7 genome. J Mol Biol, 300, 1057-1065.

Grigoriev, A. (1999) Strand-specific compositional asymmetries in dsDNA viruses. Virus Research, 60, 1-19.

Genome/metagenome analysis

Smith, S., Kawash, J., Grigoriev, A. (2017) Lightning-fast genome variant detection with GROM. GigaScience 6: 1-7.

Smith, S., Kawash, J., Karaiskos, S., Biluck, I., Grigoriev, A. (2017) Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants. DNA Research 24(4): 359-369.

Choudhari, S., Grigoriev, A. (2017) Phylogenetic Heatmaps Highlight Composition Biases in Sequenced Reads. Microorganisms, 5(1), 4.

Smith, S., Kawash, J., Grigoriev, A. (2015) GROM-RD: resolving genomic biases to improve read depth detection of copy number variants. PeerJ, 3:e836.

Choudhari S, Lohia R, Grigoriev A. (2014) Comparative Metagenome Analysis of an Alaskan Glacier. J. Bioinform. Comput. Biol. 12(02)

Shadrin, A. A., Grigoriev, A., and Parkhomchuk, D. V. (2013). Positional information storage in sequence patterns. Comput. Mol. Biosci., 3(2), 18-26.

Choudhari, S., Smith, S., Owens, S., Gilbert, J.A., Shain, D.H., Dial, R.J., Grigoriev, A. (2013) Metagenome sequencing of prokaryotic microbiota collected from Byron Glacier, Alaska. GenomeA 1(2):e00099-13.

Liu, M. and Grigoriev, A. (2004) Protein domains correlate strongly with exons in multiple eukaryotic genomes - evidence of exon shuffling? Trends in Genetics, 20, 399-403.

Contursi P, Pisani FM, Grigoriev A, Cannio R, Bartolucci S, Rossi M. (2004) Identification and autonomous replication capability of a chromosomal replication origin from the archaeon Sulfolobus solfataricus. Extremophiles 8, 385-391.

Grigoriev, A. (2000) Graphical genome comparison: rearrangements and replication origin of Helicobacter pylori. Trends in Genetics, 16, 376-378.

Grigoriev, A. (1999) Nucleotide composition analysis of complete genomes 1999 Meeting on Genome Sequencing and Biology, Cold Spring Harbor, New York.

Grigoriev, A. (1998) Genome Arithmetic. Science, 281, 1923.

Grigoriev, A. (1998) Analyzing genomes with cumulative skew diagrams. Nucleic Acids Research, 26, 2286-2290.

Grigoriev, A. (1998) Genome Navigator. Trends in Microbiology, 6, 184.

Grigoriev, A. (1997) Genomes with a view. Trends in Genetics, 13, 499.

Online databases and analysis tools

Liu, M. and Grigoriev, A. (2005) Fast parsers for Entrez Gene. Bioinformatics 21, 3189-3190.

Grigoriev, A., Levin, A., and Lehrach, H. (1998) A distributed environment for physical map construction. Bioinformatics, 14, 252-258.

Leser, U., Wagner, R., Grigoriev, A., Lehrach, H., and Roest Crollius, H. (1998) IXDB, An Integrated X Chromosome Database. Nucleic Acids Research, 26, 108-111.

Mironov, A.A., Alexandrov, N.N., Bogodarova, N.Yu., Grigorjev, A., Lebedev, V.F., Lunovskaya, L.V., Truchan, M.E., and Pevzner, P.A. (1995) DNASUN: a package of computer programs for the biotechnology laboratory. CABIOS, 11(3), 331-335.

Grigoriev, A., Levin, A., and Lehrach, H. (1997) Distributed Computing in Genomic Mapping: Building Contigs on the Web. In "Computer Science and Biology" (proceedings of the German Conference on Bioinformatics, GCB'97), Kloster Irsee, Germany.

Physical mapping (large-scale projects and analysis algorithms)

Crollius, H.R., Ross, M.T., Grigoriev, A., Knights, C.J., Holloway, E., Misfud, J., Li, K., Playford, M., Gregory, S.G., Humphray, S.J., Coffey, A., J., See, C.G., Marsh, S., Vatcheva, R., Kumlien, J., Labella, T., Lam, V., Rak, K.H., Todd, K., Mott, R., Graeser, D., Rappold, G., Zehetner, G., Poustka, A., Bentley, D.R., Monaco, A.P., Lehrach, H. (1996) An integrated yac map of the human X chromosome. Genome Research 6 (10), 943-955.

Kumlien, J., Grigoriev, A., Roest Crollius, H., Ross, M., Goodfellow, P.N., and Lehrach, H. (1996) A radiation hybrid map spanning the entire human X chromosome integrating YACs, genes, and STS markers. Mammalian Genome, 7 (10), 758-766

Grigoriev, A., Mott, R., and Lehrach, H. (1994) An algorithm to detect chimeric clones and random noise in genomic mapping. Genomics 22, 482-486.

Nizetic, D., Gellen, L., Hamvas, R. M. J., Mott, R., Grigoriev, A., Vatcheva, R., Zehetner, G., Yaspo, M.-L., Dutriaux, A., Lopes, C., Delabar, J.-M., Van Broeckhoven, C., Potier, M.-C., Lehrach, H. (1994) An integrated YAC-overlap and 'cosmid-pocket' map of the human chromosome 21. Human Molecular Genetics 3, 759-770.

Hoheisel, J. D., Maier, E., Mott, R. F., McCarthy, L., Grigoriev, A. V., Schalkwyk, L. C., Nizetic, D., Francis, F. and Lehrach, H. (1993) High resolution cosmid and P1 maps spanning the 14Mb genome of the fission yeast Schizosaccharomyces pombe. Cell 73, 109-120.

Mott, R. F., Grigoriev, A. V., Maier, E., Hoheisel, J. D., and Lehrach, H. (1993) Algorithms and software tools for ordering clone libraries: appplication to the mapping of the genome of Schizosaccharomyces pombe, Nucleic Acids Research 21, 1965-1974.

Grigoriev, A. V. (1993) Theoretical predictions and experimental observations of genomic mapping by anchoring random clones. Genomics, 15, 311-316.

Maier, E., Hoheisel, J. D., McCarthy, L., Mott, R. F., Grigoriev, A. V., Monaco, A. P., Larin, Z. and Lehrach, H. (1992) Complete coverage of the Schizosaccharomyces pombe genome in yeast artificial chromosomes. Nature Genetics 1, 273-277.

Algorithms for restriction mapping

Grigorjev, A. V. and Mironov, A. A. (1991) Mapping DNA by stochastic relaxation: schedule for optimal annealing. DNA Sequence, 1, 221-226.

Grigorjev, A. V. and Mironov, A. A. (1990) Mapping DNA by stochastic relaxation: a new approach to fragment sizes. CABIOS, 6, 107-111.


Grigoriev, A. (2011) How do replication and transcription change genomes? In Pevzner, P., Shamir, R., (Eds.) Bioinformatics for Biologists. Cambridge University Press.

Uetz, P., and Grigoriev, A. (2005) The yeast proteome. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons.

Mott, R. F., Grigoriev, A., and Lehrach, H. (1998) Long range physical map construction and the integration of genetic and physical maps. In Spurr, N.K, Young, B.D., and Bryant, S.P. (Eds) ICRF Handbook of Genome Analysis, pp. 421-440, Blackwell Science, Oxford.

Grigoriev, A. (1998) Reusable graphical interface to genome information resources. In Altman, R.B. et al. (Eds.), Pacific Symposium on Biocomputing '98, pp. 130-141, World Scientific, Singapore.

Grigoriev, A., Lehrach, H., and Kumlien, J. (1997) Integrating heterogenous datasets in genomic mapping: radiation hybrids, YACs, genes and STS markers over the entire human chromosome X. In Hofestaedt, R., Lengauer, T., Koeffler, M. and Schomburg, D. (Eds.) "Lecture Notes in Computer Science, Bioinformatics", Vol. 1278, pp. 106-114, Springer-Verlag, Berlin-Heidelberg.

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