Tximeta: Reference sequence checksums for provenance identification in RNA-seq

MI Love, C Soneson, PF Hickey… - PLoS computational …, 2020 - journals.plos.org
Correct annotation metadata is critical for reproducible and accurate RNA-seq analysis.
When files are shared publicly or among collaborators with incorrect or missing annotation …

[HTML][HTML] Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

D Rosati, M Palmieri, G Brunelli, A Morrione… - Computational and …, 2024 - Elsevier
In recent years, the role of bioinformatics and computational biology together with omics
techniques and transcriptomics has gained tremendous importance in biomedicine and …

Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS

S Sahadevan, KM Hembach, E Tantardini… - Nature …, 2021 - nature.com
Mutations disrupting the nuclear localization of the RNA-binding protein FUS characterize a
subset of amyotrophic lateral sclerosis patients (ALS-FUS). FUS regulates nuclear RNAs …

Cytoplasmic FUS triggers early behavioral alterations linked to cortical neuronal hyperactivity and inhibitory synaptic defects

J Scekic-Zahirovic, I Sanjuan-Ruiz, V Kan… - Nature …, 2021 - nature.com
Gene mutations causing cytoplasmic mislocalization of the RNA-binding protein FUS lead to
severe forms of amyotrophic lateral sclerosis (ALS). Cytoplasmic accumulation of FUS is …

Cortical hyperexcitability in mouse models and patients with amyotrophic lateral sclerosis is linked to noradrenaline deficiency

J Scekic-Zahirovic, C Benetton, A Brunet… - Science Translational …, 2024 - science.org
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease,
characterized by the death of upper (UMN) and lower motor neurons (LMN) in the motor …

[HTML][HTML] A model of human neural networks reveals NPTX2 pathology in ALS and FTLD

M Hruska-Plochan, VI Wiersma, KM Betz, I Mallona… - Nature, 2024 - nature.com
Human cellular models of neurodegeneration require reproducibility and longevity, which is
necessary for simulating age-dependent diseases. Such systems are particularly needed for …

RASflow: an RNA-Seq analysis workflow with Snakemake

X Zhang, I Jonassen - BMC bioinformatics, 2020 - Springer
Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq
data are being generated giving novel insight into gene expression and regulation. Prior to …

AMPKα1 deletion in myofibroblasts exacerbates post-myocardial infarction fibrosis by a connexin 43 mechanism

C Dufeys, EP Daskalopoulos… - Basic research in …, 2021 - Springer
We have previously demonstrated that systemic AMP-activated protein kinase α1 (AMPKα1)
invalidation enhanced adverse LV remodelling by increasing fibroblast proliferation, while …

Meta-analysis of two human RNA-seq datasets to determine periodontitis diagnostic biomarkers and drug target candidates

C Moreno, E Bybee, CM Tellez Freitas… - International Journal of …, 2022 - mdpi.com
Periodontitis is a chronic inflammatory oral disease that affects approximately 42% of adults
30 years of age or older in the United States. In response to microbial dysbiosis within the …

Seq2science: an end-to-end workflow for functional genomics analysis

M van der Sande, S Frölich, T Schäfers, JGA Smits… - PeerJ, 2023 - peerj.com
Sequencing databases contain enormous amounts of functional genomics data, making
them an extensive resource for genome-scale analysis. Reanalyzing publicly available data …