BioBam Supported Project – with OmicsBox. Researchers: Richard Lathe – Division of Infection Medicine, University of Edinburgh Medical School, Edinburgh, UK Project: In managing the COVID-19 pandemic there is an urgent need to understand why some people develop severe infection leading to hospitalization and mortality, whereas others are relatively unaffected.
BioBam Supported Project – with OmicsBox. Researchers: Pr. Sami Aifa from the Laboratory of Molecular and Cellular Screening Processes (LPCMC) from the Centre of Biotechnology of Sfax, Tunisia Dr. Amor Mosbah from the Laboratory of Biotechnology and Valorization of Bio-Geo-Ressources (LBVBGR) from the Superior Institute of Biotechnology of Sidi Thabet, Tunisia Dr. Salma Abdeljalil and Pr. Ali Gargouri from the
BioBam Supported Project – with OmicsBox. Researchers: Luis Fernando Saraiva Macedo Timmers – Coordinator – Univates, Brazil Rafael Andrade Caceres – UFCSPA, Brazil Leandro de Mattos Pereira, UFRJ, Brazil Fernando Ruggiero Bachega – UFCSPA, Brazil Marcia Ines Goettert – Univates, Brazil Luiz Augusto Basso – PUCRS, Brazil Project: Currently, a large amount of data is available regarding the new SARS-CoV-2
Identification and Expression analysis of genes involved in endodormancy break in potato (Solanum tuberosum L.)
BioBam Scholarship Supported Project – with OmicsBox. Researchers: Madhuri Gupta Dr. Pushpender Kumar Project and Overview At harvest, potato (Solanum tuberosum L.) tubers, one of the most important crops among vegetables, are dormant and will not sprout. Tubers contain shoot apical meristems on their surface with the ability to differenciate and grow into a new clone of the parent plant.
In this use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes show high levels of sodium
Any annotation of metagenomic sequences, whether it involves pathways, clusters of orthologous genes, species or any other taxonomic or functional classification can be compared across samples. These analyses are encompassed within the Differential Abundance Analysis, and they require robust statistical approaches to achieve reliable results because metagenomics datasets often show under-sampling and low signal-to-noise ratios. All differential abundance analyses can
This project reproduces the study carried out by Hittalmani S. et al. in 2016 about the S. oryzae fungus, which causes sheath rot of rice. We used OmicsBox for all necessary steps till functional analysis in order to predict pathogenic functions. (Original research paper: https://doi.org/10.1186/s12864-016-2599-0)
BioBam Scholarship Supported Project – with OmicsBox. Researchers: Mr. Arun Arumugaperumal Mr. Sayan Paul and Miss Saranya Lathakumari, PhD students Dr. Sudhakar Sivasubramaniam Abstract The earthworm Eisenia fetida has a symbiotic bacteria named Verminephrobacter eiseniae in its nephridia. A new strain of V. eiseniae msu was found out and the genome of the bacteria was found hidden in the genome
De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. Once the assembly is complete, researchers need to know how good it is or compare the quality of similar assemblies generated by different parameters. There are several ways to characterize the quality of transcriptome assemblies. A good metric of assembly
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