Related papers: Approaches to link RNA secondary structures with s…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short…
Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer…
MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs, which suppress gene expression by selectively binding to the 3-noncoding region of specific message RNAs through base-pairing. Given the diversity and abundance of miRNA targets, miRNAs…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching --…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
Often in bacterial regulatory networks, small noncoding RNAs (sRNA) interact with several mRNA species. The competition among mRNAs for binding to the same pool of sRNA might lead to crosstalk between the mRNAs. This is similar to the…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Genetic oscillators are present in the cells of many organisms and control several biological processes. The common feature of such oscillators is the presence of a protein which represses the transcription of its own gene. Recently, it has…