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List of works by Dmitry Afonnikov

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

scientific article

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

scientific article published on January 1, 2002

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

article

Adult Opisthorchis felineus major protein fractions deduced from transcripts: Comparison with liver flukes Opisthorchis viverrini and Clonorchis sinensis ⬇️

scientific article published on July 25, 2013

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

scientific article

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

scientific article published on 14 April 2015

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

scientific article published in January 2011

Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.

scientific article

Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions ⬇️

scientific article published on November 1, 2001

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

scientific article published on 28 December 2017

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

scientific article published on 14 January 2016

Evaluation of heterosis through reciprocal crosses of inbred cucumber lines (Cucumis sativus L.)

scientific article published in 2022

Evaluation of the SeedCounter, A Mobile Application for Grain Phenotyping

scientific article

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

scientific article published on 19 September 2012

Haplotype analysis of APOE intragenic SNPs.

scientific article

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

scientific article

ICAnnoLncRNA: A Snakemake Pipeline for a Long Non-Coding-RNA Search and Annotation in Transcriptomic Sequences

scientific article published in 2023

Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain

scientific article published on 01 February 2020

Identification of microRNA genes in three opisthorchiids

scientific article published on 21 April 2015

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

scientific article

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

scientific article

Image-Based Wheat Fungi Diseases Identification by Deep Learning

scientific article

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

scientific article published on 01 May 2011

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

scientific article

Mechanical Behavior of Cells within a Cell-Based Model of Wheat Leaf Growth

scientific article published on 15 December 2016

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.

scientific article

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

scientific article

Molecular evolution of cyclin proteins in animals and fungi ⬇️

scientific article

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

scientific article

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

scientific article published on 22 May 2019

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

scientific article

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

scientific article published on 22 November 2019

Plant auxin biosynthesis did not originate in charophytes.

scientific article

Pluripotency gene network dynamics: System views from parametric analysis

scientific article published on 29 March 2018

QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing

scientific article published in 2022

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

scientific article published on 16 November 2018

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

scientific article published on 19 July 2018

The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family

scientific article published on 25 August 2020

The conserved characteristics of DNA-binding domains belonging to the homeodomain class that are associated with coadaptive substitutions of amino acid residues

scientific article published on 01 September 2001

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

scientific article

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

scientific article published on 15 February 2019

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

scientific article published on 01 January 2019

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