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We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…
Trans-splicing of leader sequences onto the 59ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 59splice sites and analyze the…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
The revelation of the supreme authority of nucleic acids in the cellular landscape has precipitated the recognition of the versatility of RNAs in cells. The subsequent discovery of non-coding RNAs was a major breakthrough that revealed…
Strategies for in-liquid micro-organism detection are crucial for the clinical and pharmaceutical industries. While Raman spectroscopy is a promising label-free technique for micro-organism detection, it remains challenging due to the weak…
Rapid identification of bacterial species is crucial in medicine and food hygiene. In order to achieve rapid and label-free identification of bacterial species at the single bacterium level, we propose and experimentally demonstrate an…
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including…
Cancer is one of the leading causes of human death. Many efforts have made to understand its mechanism and have further identified many proteins and DNA sequence variations as suspected targets for therapy. However, drugs targeting these…
RNA editing by members of the double-stranded RNA-specific ADAR family leads to site-specific conversion of adenosine to inosine (A-to-I) in precursor messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is essential…
This study evaluates the concordance between RNA sequencing (RNA-Seq) and NanoString technologies for gene expression analysis in non-human primates (NHPs) infected with Ebola virus (EBOV). We performed a detailed comparison of both…
The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
Understanding how 5' untranslated regions (5'UTRs) regulate mRNA translation is critical for controlling protein expression and designing effective therapeutic mRNAs. While recent deep learning models have shown promise in predicting…
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
Background: Microbiota have evolved to acclimate themselves to many environments. Humanity is become ever increasingly medicated and many of those medications are antibiotics. Sadly, Microbiota are adapting to medication and with each…
Insertion Sequences (ISs) are small DNA segments that have the ability of moving themselves into genomes. These types of mobile genetic elements (MGEs) seem to play an essential role in genomes rearrangements and evolution of prokaryotic…
Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…
In bacteria such as $\textit{Escherichia coli}$, DNA is compacted into a nucleoid near the cell center, while ribosomes$-$molecular complexes that translate messenger RNAs (mRNAs) into proteins$-$are mainly localized at the poles. We study…
We developed a simple way to generate binary patterns based on spectral slopes in different frequency ranges at fluctuation-enhanced sensing. Such patterns can be considered as binary "fingerprints" of odors. The method has experimentally…