Integrating Molecular Biology and Bioinformatics Education

Pucker, Boas; Schilbert, Hanna Marie; Schumacher, Sina Franziska

doi:10.1515/jib-2019-0005

Cited by 25 publications

(11 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We postulate that adopting Open Reviews and complete transparency in the reviewing process, in addition to all the already highlighted benefits identified in the literature [17][18][19]77], would have helped in detecting potential mistakes in manuscripts or frauds and saved precious research time during the pandemic. Furthermore, it would make analyses of peer-review processes and their quality easier to conduct [78] and would accelerate the training of Early Career Researchers [78,79] whose help might be critical during a public health crisis…”

Section: Open Reviewmentioning

confidence: 99%

Open science saves lives: lessons from the COVID-19 pandemic

Besançon

Peiffer-Smadja

Ségalas

et al. 2021

BMC Med Res Methodol

184

132

View full text Add to dashboard Cite

In the last decade Open Science principles have been successfully advocated for and are being slowly adopted in different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. We provide all data and scripts at https://osf.io/renxy/.

show abstract

Section: Open Reviewmentioning

confidence: 99%

Open science saves lives: lessons from the COVID-19 pandemic

Besançon

Peiffer-Smadja

Ségalas

et al. 2021

BMC Med Res Methodol

184

132

View full text Add to dashboard Cite

show abstract

“…Sequences around the CHS loci of interest were retrieved from the respective genome sequence using the Python script seqex3.py v0.5 [25]. Sequence similarity between the different domains predicted in the inspected sequences was analyzed by constructing dot plots with dotplotter v0.1 [26] using a k-mer size of 31.…”

Section: Methodsmentioning

confidence: 99%

Identification of annotation artifacts concerning theCHALCONE SYNTHASE(CHS)

Bartas

Volná

Červeň

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Objective: Chalcone synthase (CHS) catalyzes the initial step of the flavonoid biosynthesis. The CHS encoding gene is well studied in numerous plant species. Rapidly growing sequence databases contain hundreds of CHS entries that are the result of automatic annotation. In this study, we evaluated apparent multiplication of CHS domains in CHS gene models of four plant species. Main findings: CHS genes with an apparent triplication of the CHS domain encoding part were discovered through database searches. Such genes were found in Macadamia integrifolia, Musa balbisiana, Musa troglodytarum, and Nymphaea colorata. A manual inspection of the CHS gene models in these four species with massive RNA-seq data suggests that these gene models are the result of artificial fusions in the annotation process. While there are hundreds of apparently correct CHS records in the databases, it is not clear why these annotation artifacts appeared.

show abstract

“…The approach is separated into two parts: Molecular and Bioinformatic methods [59]. Environmental community genomes (metagenomes) are the focus of metagenomic research in recent days.…”

Section: Metagenomic Methodologiesmentioning

confidence: 99%

Diversity of Endophytic Mycobiota through Metagenomic Approach and Bioprospecting the Phytoconstituent

Thangavel

Mani

Surendrababu

et al. 2022

Advanced Chemicobiology Research

View full text Add to dashboard Cite

Endophytic fungi are important organisms that live and thrive in the intercellular or intracellular regions of host tissues of plants without causing immediate or adverse effects on the host plant. Endophytes constitute a large diversity of microbial adaptations that have been developed to survive adverse environments. Plant endophytic fungi play an important role to enhance the uptake and transfer of nutrients from the soil to plants simultaneously influencing the physical and chemical properties of soil. The discovery of fungal endophytes in their natural habitat is quite difficult due to few of its non-sporulating and non-culture-dependent endophytes by the traditional methods. The molecular characterization of isolated fungal endophytes can be carried out by isolation of genomic deoxyribonucleic acid (DNA), polymerase chain reaction (PCR) amplification of internal transcribed spacer (ITS) regions, DNA sequencing and analysis. One of the culture-independent approaches known as ‟metagenomics” is capable of reading the variety of ambient microbes that do not include cultivation from the environmental sample. Several researches on fungal endophytes in plants are in progress and have been under exploitation. Several secondary metabolites with diverse biological activities have been discovered in these fungi, suggesting that they have the ability to create a vast selection of secondary metabolites. In the hunt for new medications such as bioactive properties or innovative drug-like compounds, their variety and specialized habituation make them an attractive subject of research. The review highlights the biology of fungal endophytes, their discovery, isolation and identification by molecular methods.

show abstract

Integrating Molecular Biology and Bioinformatics Education

Cited by 25 publications

References 32 publications

Open science saves lives: lessons from the COVID-19 pandemic

Open science saves lives: lessons from the COVID-19 pandemic

Identification of annotation artifacts concerning theCHALCONE SYNTHASE(CHS)

Diversity of Endophytic Mycobiota through Metagenomic Approach and Bioprospecting the Phytoconstituent

Contact Info

Product

Resources

About