List of works - Svetlana A. Shabalina

A hierarchical approach to aligning collinear regions of genomes

scientific article published in December 2002

A periodic pattern of mRNA secondary structure created by the genetic code

scientific article

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

scientific article

A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions

scientific article

A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants

scientific article published on 01 October 2021

Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families

scientific article

Analysis of internal loops within the RNA secondary structure in almost quadratic time

scientific article published on 16 March 2006

Association of polymorphisms in odorant-binding protein genes with variation in olfactory response to benzaldehyde in Drosophila

scientific article

Calculation of contributions of individual monomeric units to biopolymer function.

scientific article published in October 1993

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals

scientific article published on 18 March 2004

Comparison of approaches for rational siRNA design leading to a new efficient and transparent method

scientific article published on 10 April 2007

Computational models with thermodynamic and composition features improve siRNA design

scientific article published on 12 February 2006

Connections between alternative transcription and alternative splicing in mammals

scientific article

Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes

scientific article published on 01 August 2003

Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements

scientific article

Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation

scientific article

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

scientific article

Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes

scientific article published on April 2010

Effect of Galleria mellonella larvae preparation and honeybee products on cell cultures

scientific article published on May 1, 1992

Evolution of alternative and constitutive regions of mammalian 5'UTRs.

scientific article

Expansion of the human mu-opioid receptor gene architecture: novel functional variants

scientific article

Expression patterns of protein kinases correlate with gene architecture and evolutionary rates

scientific article

Genetic architecture of human pain perception

scientific article

Genetic basis for individual variations in pain perception and the development of a chronic pain condition

article

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

scientific article published in December 2006

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

scientific article

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome

scientific article

Low enzymatic activity haplotypes of the human catechol-O-methyltransferase gene: enrichment for marker SNPs

scientific article

Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs

scientific article

OWEN: aligning long collinear regions of genomes

scientific article published in December 2002

Optimization of duplex stability and terminal asymmetry for shRNA design

scientific article

Optimized models for design of efficient miR30-based shRNAs

scientific article

Origins and evolution of eukaryotic RNA interference

scientific article

Pattern of selective constraint in C. elegans and C. briggsae genomes

scientific article published on 01 August 1999

Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs

scientific article

Persistence time of loss-of-function mutations at nonessential loci affecting eye color in Drosophila melanogaster

scientific article

Rapid decline of fitness in panmictic populations of Drosophila melanogaster maintained under relaxed natural selection.

scientific article published on November 1997

Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage

scientific article published on January 2012

Selective constraint in intergenic regions of human and mouse genomes.

scientific article

Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.

scientific article published on 21 June 2018

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

scientific article

The mammalian transcriptome and the function of non-coding DNA sequences

scientific article

The vast, conserved mammalian lincRNome

scientific article

Thermodynamic calculations and statistical correlations for oligo-probes design.

scientific article

Three major haplotypes of the beta2 adrenergic receptor define psychological profile, blood pressure, and the risk for development of a common musculoskeletal pain disorder

scientific article published on July 2006

Uncertainty-aware and interpretable evaluation of Cas9–gRNA and Cas12a–gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning

scientific article published on 12 November 2021

Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes

scientific article

Widespread positive selection in synonymous sites of mammalian genes

scientific article

List of works by Svetlana A. Shabalina

A hierarchical approach to aligning collinear regions of genomes

A periodic pattern of mRNA secondary structure created by the genetic code

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions

A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants

Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families

Analysis of internal loops within the RNA secondary structure in almost quadratic time

Association of polymorphisms in odorant-binding protein genes with variation in olfactory response to benzaldehyde in Drosophila

Calculation of contributions of individual monomeric units to biopolymer function.

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals

Comparison of approaches for rational siRNA design leading to a new efficient and transparent method

Computational models with thermodynamic and composition features improve siRNA design

Connections between alternative transcription and alternative splicing in mammals

Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes

Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements

Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes

Effect of Galleria mellonella larvae preparation and honeybee products on cell cultures

Evolution of alternative and constitutive regions of mammalian 5'UTRs.

Expansion of the human mu-opioid receptor gene architecture: novel functional variants

Expression patterns of protein kinases correlate with gene architecture and evolutionary rates

Genetic architecture of human pain perception

Genetic basis for individual variations in pain perception and the development of a chronic pain condition

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome

Low enzymatic activity haplotypes of the human catechol-O-methyltransferase gene: enrichment for marker SNPs

Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs

OWEN: aligning long collinear regions of genomes

Optimization of duplex stability and terminal asymmetry for shRNA design

Optimized models for design of efficient miR30-based shRNAs

Origins and evolution of eukaryotic RNA interference

Pattern of selective constraint in C. elegans and C. briggsae genomes

Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs

Persistence time of loss-of-function mutations at nonessential loci affecting eye color in Drosophila melanogaster

Rapid decline of fitness in panmictic populations of Drosophila melanogaster maintained under relaxed natural selection.

Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage

Selective constraint in intergenic regions of human and mouse genomes.

Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

The mammalian transcriptome and the function of non-coding DNA sequences

The vast, conserved mammalian lincRNome

Thermodynamic calculations and statistical correlations for oligo-probes design.

Three major haplotypes of the beta2 adrenergic receptor define psychological profile, blood pressure, and the risk for development of a common musculoskeletal pain disorder

Uncertainty-aware and interpretable evaluation of Cas9–gRNA and Cas12a–gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning

Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes

Widespread positive selection in synonymous sites of mammalian genes