In silico identification

Identifying expressed somatic mutations from single-cell RNA sequencing data de novo is challenging but highly valuable. We propose RESA – Recurrently Expressed SNV Analysis, a computational framework to identify expressed somatic mutations from scRNA-seq data. RESA achieves an average precision of 0.77 on three in silico spike-in datasets.

18p vicwell 29-02-2024 3 2   Download

Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies.

24p vinarcissa 21-03-2023 3 1   Download

Master's thesis of Science "Investigation into the modulation of circadian clock proteins by dietary compounds and small molecules" is structured as follows: Chapter 1 Introduction; Chapter 2 Identification of novel bioactive compounds from Olea europaea by evaluation of chemical compounds in the OliveNetTM library: in silico bioactivity and molecular modelling, and in vitro validation of hERG activity; Chapter 3 Modulation of circadian core clock proteins by dietary compounds; Chapter 4 Molecular mechanisms of action of selected olive phenolics against epigenetic modifiers and the structur...

235p runthenight04 02-02-2023 2 2   Download

Cyclic nucleotide-gated channels (CNGCs) are ligand-gated calcium signaling channels, play vital biological functions. Nonetheless, the CNGC gene families have not been well studied in Brassicaceae which includes commercially important and evolutionary model crops. Here, using in silico approaches, we recognized 414 CNGC genes in sixteen sequenced genomes of Brassicaceae species, which represent 10 genera of 8 tribes, ranging between 10‒51 genes.

53p lyhuyenthu 31-01-2023 8 2   Download

In this study, the complete chloroplast (cp) genome sequences from eight Aquilaria species were analyzed in silico. For identification of the simple sequence repeats (SSRs), MISA PERL script which had a repeat length of 12 for mononucleotides (mono-), 6 for dinucleotides (di-), 4 for trinucleotides (tri-), 3 for tetranucleotides (tetra-), pentanucleotides (penta-), and hexanucleotides (hexa-), respectively, along with frequency were utilized.

11p lyhuyenthu 31-01-2023 4 2   Download

Physical molecular interactions are the basis of intracellular signaling and gene regulatory networks, and comprehensive, accessible databases are needed for their discovery. Highly correlated transcripts may reflect important functional associations, but identification of such associations from primary data are cumbersome.

6p vihagrid 30-01-2023 8 3   Download

Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can predict the locations of enhancers with a high degree of accuracy, the mechanisms underpinning the activity of enhancers are often unclear.

23p viarchimedes 26-01-2022 8 0   Download

Saintpaulia ionantha H. Wendl (synonym Streptocarpus ionanthus) has been considered an ornamental plant. The PHANTASTICA (PHAN) gene has a significant role in the formation of plant organs adaxial–abaxial polarity. In the present study the PHAN gene was identified in Saintpaulia for the first time using PCR. To determine the expression pattern of the PHAN gene, gene expression was compared at 3 developmental stages using real time PCR.

14p tudichquannguyet 29-11-2021 3 0   Download

The leishmaniasis are parasitic diseases caused by protozoans of the genus Leishmania, highly divergent eukaryotes, characterized by unique biological features. To survive in both the mammalian hosts and insect vectors, these pathogens make use of a number of mechanisms, many of which are associated with parasite specific proteases.

17p vigiselle2711 30-08-2021 12 1   Download

The small hive beetle, Aethina tumida, is a rapidly emerging global pest of honey bee colonies. Small hive beetle infestation can be extremely destructive, which may cause honey bees to abscond and render colony infrastructure unusable.

12p vijeeni2711 24-07-2021 11 0   Download

The common cutworm, Spodoptera litura Fabricius is a leaf and fruit feeding generalist insect of the order Lepidoptera and a destructive agriculture pest. The broad host range of the herbivore is due to its ability to downregulate plant defense across different plants.

16p vijeeni2711 30-06-2021 8 1   Download

Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea.

17p vijeeni2711 30-06-2021 10 1   Download

Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog.

12p vijeeni2711 30-06-2021 10 1   Download

Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. βgalactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear.

13p vilichoo2711 23-06-2021 12 1   Download

Research objective: Establish the genetic variants database of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Identification of genotype and allele frequencies of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Perform in silico functional analysis of novel variants.

27p extraenglish 24-05-2021 23 4   Download

The present study makes use of in silico subtractive approach based on the criteria of essentiality and selectivity to discover potential drug targets in P. fluorescens, followed by in silico virtual screening of drug targets against natural ligands to discover potential drug candidates.

15p trinhthamhodang1218 26-02-2021 7 1   Download

Establish the genetic variants database of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Identification of genotype and allele frequencies of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Perform in silico functional analysis of novel variants.

27p capheviahe27 23-02-2021 4 3   Download

NipahVirus (NiV) is a zoonotic Virus which infects several animals and humans worldwide. Currently, there is no specific drug or vaccine to treat or control NiV infections. The present study is aimed to identify novel inhibitors of NiV from Indian medicinal plants. Glycoprotein was taken as target protein. Around 600 phytocompounds were taken from 10 Indian medicinal plants and subjected to Virtual Screening by using Libdock module from Discovery Studio 4.0. From these, the best 20 compounds were screened and evaluated for their Pharmacokinetic properties by using ADMETSAR and pKCSM tools.

14p trinhthamhodang9 16-12-2020 9 2   Download

Keeping in view above considerations, the present study was framed for isolation, biochemical characterization and molecular identification of iron nanoparticles synthesizing bacteria by use of 16S rRNA technology to determine evolutionary rates of different bacterial isolates and close synteny between them by using various bioinformatics tools.

12p angicungduoc8 07-11-2020 26 3   Download

Drug-target networks are receiving a lot of attention in late years, given its relevance for pharmaceutical innovation and drug lead discovery. Different in silico approaches have been proposed for the identification of new drug-target interactions, many of which are based on kernel methods.

16p vioklahoma2711 19-11-2020 9 2   Download