- Comprehensive survey and geometric classification of base triples in RNA structures. NAR
- WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs. NAR
- A Three-Dimensional RNA Motif in Potato spindle tuber viroid Mediates Trafficking from Palisade Mesophyll to Spongy Mesophyll in Nicotiana benthamiana. PMC
- Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? Pubmed
- Understanding Sequence Variability of RNA Motifs Using Geometric Search and IsoDiscrepancy Matrices. Abstract and pdf
- Bowling Green State UniversityBioinformatics, 2007 - 2012
- St.Petersburg State UniversityBiology, 2003 - 2007
- European Bioinformatics InstituteBioinformatician/Web Developer, 2013 - present
- Bowling Green State UniversityPostdoc, 2012 - 2013
- Bowling Green State UniversityGraduate Assistant (Teaching & Research), 2007 - 2012
iPfam: a database of protein family and domain interactions found in the...
Abstract The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found
ArchDB 2014: structural classification of loops in proteins
Abstract The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helice
The non-nuclear genome: including a mitochondrial genome in GRCh38
The GRC maintains and improves the reference nuclear assembly only. The MITOMAP (http://www.mitomap.org/MITOMAP) group has served a similar
Install and Configure wget on OS X Mavericks 10.9 and fix SSL GNUTLS error
how to install download the source code for wget and compile to run on OS X 10.9 Mavericks using the GCC compiler from xcode and fix the SSL
RNA–DNA differences in human mitochondria restore ancestral form of 16S ...
Abstract RNA transcripts are generally identical to the underlying DNA sequences. Nevertheless, RNA–DNA differences (RDDs) were found in the
RNA secondary structure diagrams for very large molecules: RNAfdl
Abstract Summary: There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that c
Analysis of base-pairing probabilities of RNA molecules involved in prot...
Abstract Motivation: Understanding the details of protein–RNA interactions is important to reveal the functions of both the RNAs and the pro
Automated identification of RNA 3D modules with discriminative power in ...
Abstract Recent progress in predicting RNA structure is moving towards filling the ‘gap’ in 2D RNA structure prediction where, for example,
RNA nanotechnology for computer design and in vivo computation
Abstract Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computa
Astrogenomics: big data, old problems, old solutions?
Comment. Astrogenomics: big data, old problems, old solutions? Aaron Golden , S George Djorgovski and John M Greally. Genome Biology 2013, 1
The mcrypt extension is missing | PHP OS X Lion How to Install mcrypt
installing and configuring mcrypt to work in a Mac OS X 10.8 Mountain Lion and 10.7 development environment using php 5.3.13 and libmcrypyt
BMC Bioinformatics | Full text | The Enzyme Portal: A case study in appl...
User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of
BMC Bioinformatics | Abstract | PFClust: a novel parameter free clusteri...
We present the algorithm PFClust (Parameter Free Clustering), which is able automatically to cluster data and identify a suitable number of
Conservation of mRNA secondary structures may filter out mutations in Es...
Abstract Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt
RNAlyzer—novel approach for quality analysis of RNA structural models
Abstract The continuously increasing amount of RNA sequence and experimentally determined 3D structure data drives the development of comput
BMC Bioinformatics | Abstract | bioWeb3D: an online webGL 3D data visual...
Data visualization is critical for interpreting biological data. However, in practice it can prove to
Structure-based whole-genome realignment reveals many novel noncoding RNAs
Abstract Recent genome-wide computational screens that search for conservation of RNA secondary structure in whole-genome alignments (WGAs)