scholarly journals In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

2016 ◽  
Vol 26 (9) ◽  
pp. 1257-1267 ◽  
Author(s):  
Igor Rodrigues Costa ◽  
Francisco Prosdocimi ◽  
W. Bryan Jennings
Keyword(s):  
In Silico ◽  
Complete Genomes

scholarly journals How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b

2021 ◽  
Author(s):  
Yorick Bernardus Cornelis van de Grift ◽  
Nika Heijmans ◽  
Renée van Amerongen
Keyword(s):  
Mammary Gland ◽  
In Silico ◽  
Online Tools ◽  
Mammary Gland Biology ◽  
User Friendly ◽  
In Silico Analyses ◽  
Biology Research ◽  
Selection Of

AbstractAn increasing number of ‘-omics’ datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Fortunately, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach. Using regulation of Wnt7b expression as an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used for in silico analyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific ‘-omics’ datasets and thereby expand the in silico toolbox.

A case study on the in silico absorption simulations of levothyroxine sodium immediate-release tablets

2012 ◽  
Vol 33 (3) ◽  
pp. 146-159 ◽  
Author(s):  
Ivana Kocic ◽  
Irena Homsek ◽  
Mirjana Dacevic ◽  
Sandra Grbic ◽  
Jelena Parojcic ◽  
...  
Keyword(s):  
In Silico ◽  
Immediate Release ◽  
Levothyroxine Sodium

scholarly journals Application of In Silico and HTS Approaches to Identify Nuclear Import Inhibitors for Venezuelan Equine Encephalitis Virus Capsid Protein: A Case Study

2020 ◽  
Vol 8 ◽  
Author(s):  
Sharon Shechter ◽  
David R. Thomas ◽  
David A. Jans
Keyword(s):  
Drug Design ◽  
Nuclear Import ◽  
In Silico ◽  
Venezuelan Equine Encephalitis Virus ◽  
Encephalitis Virus ◽  
Venezuelan Equine Encephalitis ◽  
Nuclear Targeting ◽  
Equine Encephalitis Virus ◽  
Screening Approaches

The development of new drugs is costly and time-consuming, with estimates of over $US1 billion and 15 years for a product to reach the market. As understanding of the molecular basis of disease improves, various approaches have been used to target specific molecular interactions in the search for effective drugs. These include high-throughput screening (HTS) for novel drug identification and computer-aided drug design (CADD) to assess the properties of putative drugs before experimental work begins. We have applied conventional HTS and CADD approaches to the problem of identifying antiviral compounds to limit infection by Venezuelan equine encephalitis virus (VEEV). Nuclear targeting of the VEEV capsid (CP) protein through interaction with the host nuclear import machinery has been shown to be essential for viral pathogenicity, with viruses incapable of this interaction being greatly attenuated. Our previous conventional HTS and in silico structure-based drug design (SBDD) screens were successful in identifying novel inhibitors of CP interaction with the host nuclear import machinery, thus providing a unique opportunity to assess the relative value of the two screening approaches directly. This focused review compares and contrasts the two screening approaches, together with the properties of the inhibitors identified, as a case study for parallel use of the two approaches to identify antivirals. The utility of SBDD screens, especially when used in parallel with traditional HTS, in identifying agents of interest to target the host–pathogen interface is highlighted.

scholarly journals Analysis of the Similarity between in Silico Ideotypes and Phenotypic Profiles to Support Cultivar Recommendation—A Case Study on Phaseolus vulgaris L.

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1733
Author(s):  
Livia Paleari ◽  
Fosco M. Vesely ◽  
Riccardo A. Ravasi ◽  
Ermes Movedi ◽  
Sofia Tartarini ◽  
...  
Keyword(s):  
Functional Traits ◽  
In Silico ◽  
Cropping System ◽  
Time Factors ◽  
Functional Trait ◽  
Light Extinction ◽  
Sowing Time ◽  
Light Extinction Coefficient ◽  
Context Specific

Cultivar recommendation is a key factor in cropping system management. Classical approaches based on comparative multi-environmental trials can hardly explore the agro-climatic and management heterogeneity farmers may have to face. Moreover, they struggle to keep up with the number of genotypes commercially released each year. We propose a new approach based on the integration of in silico ideotyping and functional trait profiling, with the common bean (Phaseoulus vulgaris L.) in Northern Italy as a case study. Statistical distributions for six functional traits (light extinction coefficient, radiation use efficiency, thermal time to first pod and maturity, seed weight, plant height) were derived for 24 bean varieties. The analysis of soil, climate and management in the study area led us to define 21 homogeneous contexts, for which ideotypes were identified using the crop model STICS (Simulateur mulTIdisciplinaire pour les Cultures Standard), the E-FAST (Extended Fourier Amplitude Sensitivity Test) sensitivity analysis method, and the distributions of functional traits. For each context, the 24 cultivars were ranked according to the similarity (weighted Euclidean distance) with the ideotype. Context-specific ideotypes mainly differed for phenological adaptation to specific combinations of climate and management (sowing time) factors, and this reflected in the cultivar recommendation for the different contexts. Feedbacks from bean technicians in the study area confirmed the reliability of the results and, in turn, of the proposed methodology.

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