[HTML][HTML] Applications of single-cell and bulk RNA sequencing in onco-immunology

M Kuksin, D Morel, M Aglave, FX Danlos… - European journal of …, 2021 - Elsevier
The rising interest for precise characterization of the tumour immune contexture has recently
brought forward the high potential of RNA sequencing (RNA-seq) in identifying molecular …

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology

A Golebiewska, AC Hau, A Oudin, D Stieber… - Acta …, 2020 - Springer
Patient-based cancer models are essential tools for studying tumor biology and for the
assessment of drug responses in a translational context. We report the establishment a large …

[HTML][HTML] Integrative approaches for analysis of mRNA and microRNA high-throughput data

PV Nazarov, S Kreis - Computational and Structural Biotechnology Journal, 2021 - Elsevier
Advanced sequencing technologies such as RNASeq provide the means for production of
massive amounts of data, including transcriptome-wide expression levels of coding RNAs …

Extracellular Vesicle Secretion by Leukemia Cells In Vivo Promotes CLL Progression by Hampering Antitumor T-cell Responses

E Gargiulo, E Viry, PE Morande, A Largeot… - Blood cancer …, 2023 - aacrjournals.org
Small extracellular vesicle (sEV, or exosome) communication among cells in the tumor
microenvironment has been modeled mainly in cell culture, whereas their relevance in …

Early-life influenza A (H1N1) infection independently programs brain connectivity, HPA AXIS and tissue-specific gene expression profiles

MP Merz, SV Seal, N Grova, S Mériaux, P Guebels… - Scientific Reports, 2024 - nature.com
Early-life adversity covers a range of physical, social and environmental stressors. Acute
viral infections in early life are a major source of such adversity and have been associated …

iModulonMiner and PyModulon: software for unsupervised mining of gene expression compendia

AV Sastry, Y Yuan, S Poudel, K Rychel… - PLOS Computational …, 2024 - journals.plos.org
Public gene expression databases are a rapidly expanding resource of organism responses
to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics …

Multi-omics data integration and modeling unravels new mechanisms for pancreatic cancer and improves prognostic prediction

NA Fraunhoffer, AM Abuelafia, M Bigonnet… - NPJ precision …, 2022 - nature.com
Pancreatic ductal adenocarcinoma (PDAC), has recently been found to be a heterogeneous
disease, although the extension of its diversity remains to be fully understood. Here, we …

Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

AV Sastry, S Poudel, K Rychel, R Yoo, CR Lamoureux… - Biorxiv, 2021 - biorxiv.org
We are firmly in the era of biological big data. Millions of omics datasets are publicly
accessible and can be employed to support scientific research or build a holistic view of an …

Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz

M Scherer, PV Nazarov, R Toth, S Sahay, T Kaoma… - Nature …, 2020 - nature.com
DNA methylation profiling offers unique insights into human development and diseases.
Often the analysis of complex tissues and cell mixtures is the only feasible option to study …

Metabolic traits in cutaneous melanoma

M Neagu - Frontiers in oncology, 2020 - frontiersin.org
Tumor microenvironment is a network of complex cellular and molecular systems where
cells will gain specific phenotypes and specific functions that would drive tumorigenesis. In …