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Items: 38

1.

Web-Based Computational Tools for the Prediction and Analysis of Posttranslational Modifications of Proteins.

Ivanisenko VA, Ivanisenko TV, Saik OV, Demenkov PS, Afonnikov DA, Kolchanov NA.

Methods Mol Biol. 2019;1934:1-20. doi: 10.1007/978-1-4939-9055-9_1.

PMID:
31256369
2.

New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes.

Ershov NI, Mordvinov VA, Prokhortchouk EB, Pakharukova MY, Gunbin KV, Ustyantsev K, Genaev MA, Blinov AG, Mazur A, Boulygina E, Tsygankova S, Khrameeva E, Chekanov N, Fan G, Xiao A, Zhang H, Xu X, Yang H, Solovyev V, Lee SM, Liu X, Afonnikov DA, Skryabin KG.

BMC Genomics. 2019 May 22;20(1):399. doi: 10.1186/s12864-019-5752-8.

3.

The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development.

Doroshkov AV, Konstantinov DK, Afonnikov DA, Gunbin KV.

BMC Plant Biol. 2019 Feb 15;19(Suppl 1):53. doi: 10.1186/s12870-019-1640-2.

4.

Quantitative characteristics of pubescence in wheat (Triticum aestivum L.) are associated with photosynthetic parameters under conditions of normal and limited water supply.

Pshenichnikova TA, Doroshkov AV, Osipova SV, Permyakov AV, Permyakova MD, Efimov VM, Afonnikov DA.

Planta. 2019 Mar;249(3):839-847. doi: 10.1007/s00425-018-3049-9. Epub 2018 Nov 16.

PMID:
30446814
5.

Residue coevolution reveals functionally important intramolecular interactions in formamidopyrimidine-DNA glycosylase.

Endutkin AV, Koptelov SS, Popov AV, Torgasheva NA, Lomzov AA, Tsygankova AR, Skiba TV, Afonnikov DA, Zharkov DO.

DNA Repair (Amst). 2018 Sep;69:24-33. doi: 10.1016/j.dnarep.2018.07.004. Epub 2018 Jul 19.

PMID:
30032016
6.

Haplotype analysis of APOE intragenic SNPs.

Babenko VN, Afonnikov DA, Ignatieva EV, Klimov AV, Gusev FE, Rogaev EI.

BMC Neurosci. 2018 Apr 19;19(Suppl 1):16. doi: 10.1186/s12868-018-0413-4.

7.

Pluripotency gene network dynamics: System views from parametric analysis.

Akberdin IR, Omelyanchuk NA, Fadeev SI, Leskova NE, Oschepkova EA, Kazantsev FV, Matushkin YG, Afonnikov DA, Kolchanov NA.

PLoS One. 2018 Mar 29;13(3):e0194464. doi: 10.1371/journal.pone.0194464. eCollection 2018.

8.

Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis.

Kochetov AV, Glagoleva AY, Strygina KV, Khlestkina EK, Gerasimova SV, Ibragimova SM, Shatskaya NV, Vasilyev GV, Afonnikov DA, Shmakov NA, Antonova OY, Gavrilenko TA, Alpatyeva NV, Khiutti A, Afanasenko OS.

BMC Plant Biol. 2017 Dec 28;17(Suppl 2):251. doi: 10.1186/s12870-017-1193-1.

9.

Metabolic pathways and genes identified by RNA-seq analysis of barley near-isogenic lines differing by allelic state of the Black lemma and pericarp (Blp) gene.

Glagoleva AY, Shmakov NA, Shoeva OY, Vasiliev GV, Shatskaya NV, Börner A, Afonnikov DA, Khlestkina EK.

BMC Plant Biol. 2017 Nov 14;17(Suppl 1):182. doi: 10.1186/s12870-017-1124-1.

10.

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

Mustafin ZS, Lashin SA, Matushkin YG, Gunbin KV, Afonnikov DA.

BMC Bioinformatics. 2017 Jan 27;18(Suppl 1):1427. doi: 10.1186/s12859-016-1427-5.

11.

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq.

Shmakov NA, Vasiliev GV, Shatskaya NV, Doroshkov AV, Gordeeva EI, Afonnikov DA, Khlestkina EK.

BMC Plant Biol. 2016 Nov 16;16(Suppl 3):245. doi: 10.1186/s12870-016-0926-x.

12.

A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network.

Ignatieva EV, Afonnikov DA, Saik OV, Rogaev EI, Kolchanov NA.

BMC Genet. 2016 Dec 22;17(Suppl 3):158. doi: 10.1186/s12863-016-0466-2.

13.

High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations.

Medvedev KE, Kolchanov NA, Afonnikov DA.

J Biomol Struct Dyn. 2018 Jan;36(1):68-82. doi: 10.1080/07391102.2016.1268070. Epub 2017 Jan 4.

PMID:
27924686
14.

Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions.

Medvedev KE, Kolchanov NA, Afonnikov DA.

J Bioinform Comput Biol. 2017 Apr;15(2):1650036. doi: 10.1142/S0219720016500360. Epub 2016 Oct 14.

PMID:
27832721
15.

[Methods of high-throughput plant phenotyping for large-scale breeding and genetic experiments].

Afonnikov DA, Genaev MA, Doroshkov AV, Komyshev EG, Pshenichnikova TA.

Genetika. 2016 Jul;52(7):788-803. Review. Russian.

PMID:
29368867
16.

Erratum to: comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach.

Battulin N, Fishman VS, Mazur AM, Pomaznoy M, Khabarova AA, Afonnikov DA, Prokhortchouk EB, Serov OL.

Genome Biol. 2016 Jan 14;17:6. doi: 10.1186/s13059-016-0868-5. No abstract available.

17.

The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain.

Gunbin KV, Afonnikov DA, Kolchanov NA, Derevianko AP, Rogaev EI.

BMC Genomics. 2015;16 Suppl 13:S4. doi: 10.1186/1471-2164-16-S13-S4. Epub 2015 Dec 16.

18.

Plant auxin biosynthesis did not originate in charophytes.

Turnaev II, Gunbin KV, Afonnikov DA.

Trends Plant Sci. 2015 Aug;20(8):463-5. doi: 10.1016/j.tplants.2015.06.004. Epub 2015 Jul 15. No abstract available.

PMID:
26186977
19.

Identification of microRNA genes in three opisthorchiids.

Ovchinnikov VY, Afonnikov DA, Vasiliev GV, Kashina EV, Sripa B, Mordvinov VA, Katokhin AV.

PLoS Negl Trop Dis. 2015 Apr 21;9(4):e0003680. doi: 10.1371/journal.pntd.0003680. eCollection 2015 Apr.

20.

Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach.

Battulin N, Fishman VS, Mazur AM, Pomaznoy M, Khabarova AA, Afonnikov DA, Prokhortchouk EB, Serov OL.

Genome Biol. 2015 Apr 14;16:77. doi: 10.1186/s13059-015-0642-0. Erratum in: Genome Biol. 2016;17:6.

21.

[Genetic analysis of leaf pubescence in isogenic lines of conmmon wheat Novosibirsk 67].

Doroshkov AV, Afonnikov DA, Pshenichnikova TA.

Genetika. 2014 Feb;50(2):172-80. Russian.

PMID:
25711025
22.

Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species.

Medvedev KE, Alemasov NA, Vorobjev YN, Boldyreva EV, Kolchanov NA, Afonnikov DA.

BMC Struct Biol. 2014 Oct 15;14:23. doi: 10.1186/s12900-014-0023-z.

23.

Extraction of quantitative characteristics describing wheat leaf pubescence with a novel image-processing technique.

Genaev MA, Doroshkov AV, Pshenichnikova TA, Kolchanov NA, Afonnikov DA.

Planta. 2012 Dec;236(6):1943-54. doi: 10.1007/s00425-012-1751-6. Epub 2012 Sep 19.

PMID:
22990907
24.

[Morphological and genetic characteristics of leaf hairiness in wheat (Triticum aestivum L.) as analyzed by computer-aided phenotyping].

Doroshkov AV, Pshenichnikova TA, Afonnikov DA.

Genetika. 2011 Jun;47(6):836-41. Russian.

PMID:
21866865
25.

Molecular evolution of cyclin proteins in animals and fungi.

Gunbin KV, Suslov VV, Turnaev II, Afonnikov DA, Kolchanov NA.

BMC Evol Biol. 2011 Jul 28;11:224. doi: 10.1186/1471-2148-11-224.

26.

Important role of hydrophobic interactions in high-pressure adaptation of proteins.

Afonnikov DA, Medvedev KE, Gunbin KV, Kolchanov NA.

Dokl Biochem Biophys. 2011 May-Jun;438:113-6. doi: 10.1134/S160767291103001X. Epub 2011 Jul 3. No abstract available.

PMID:
21725885
27.

Computer System for Analysis of Molecular Evolution Modes (SAMEM): analysis of molecular evolution modes at deep inner branches of the phylogenetic tree.

Gunbin KV, Suslov VV, Genaev MA, Afonnikov DA.

In Silico Biol. 2011-2012;11(3-4):109-23. doi: 10.3233/ISB-2012-0446.

PMID:
22935965
28.

Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions.

Gunbin KV, Afonnikov DA, Kolchanov NA.

BMC Genomics. 2009 Dec 30;10:639. doi: 10.1186/1471-2164-10-639.

29.

Isolation and sequence analysis of the wheat B genome subtelomeric DNA.

Salina EA, Sergeeva EM, Adonina IG, Shcherban AB, Afonnikov DA, Belcram H, Huneau C, Chalhoub B.

BMC Genomics. 2009 Sep 5;10:414. doi: 10.1186/1471-2164-10-414.

30.

Adaptive evolution of genes of archaea belonging to the genus Pyrococcus associated with adaptation to life under high-pressure conditions.

Gunbin KV, Afonnikov DA, Boldyreva EV, Kolchanov NA.

Dokl Biochem Biophys. 2009 Mar-Apr;425:91-3. No abstract available.

PMID:
19496330
31.

The evolution of the Hh-signaling pathway genes: a computer-assisted study.

Gunbin KV, Afonnikov DA, Kolchanov NA.

In Silico Biol. 2007;7(3):333-54.

PMID:
18415981
32.

Web-based computational tools for the prediction and analysis of post-translational modifications of proteins.

Ivanisenko VA, Afonnikov DA, Kolchanov NA.

Methods Mol Biol. 2008;446:363-84. doi: 10.1007/978-1-60327-084-7_25.

PMID:
18373270
33.

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.

Afonnikov DA, Kolchanov NA.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W64-8.

34.

[Integrated computer system for regulating eukaryotic gene expression].

Kolchanov NA, Podkolodnaya OA, Ananko EA, Afonnikov DA, Vishnevsky OV, Vorobiev DG, Ignatieva EV, Levitskiĭ VG, Likhoshvaĭ VA, Omelyanchuk NA, Podkolodny NL, Ratushny AV, Suslov VV.

Mol Biol (Mosk). 2004 Jan-Feb;38(1):69-81. Review. Russian.

PMID:
15042837
35.

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro.

Valuev VP, Afonnikov DA, Ponomarenko MP, Milanesi L, Kolchanov NA.

Nucleic Acids Res. 2002 Jan 1;30(1):200-2.

36.
37.
38.

[Detection of correlating DNA-binding positions in CREB and AP-1 family transcription factors].

Afonnikov DA, Kondrakhin IuV, Titov II.

Mol Biol (Mosk). 1997 Jul-Aug;31(4):741-8. Russian. No abstract available.

PMID:
9340500

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