Ecosystem-specific microbiota and microbiome databases in the era of big data

V Lobanov, A Gobet, A Joyce - Environmental Microbiome, 2022 - Springer
The rapid development of sequencing methods over the past decades has accelerated both
the potential scope and depth of microbiota and microbiome studies. Recent developments …

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

P Giesselmann, B Brändl, E Raimondeau… - Nature …, 2019 - nature.com
Expansions of short tandem repeats are genetic variants that have been implicated in
several neuropsychiatric and other disorders, but their assessment remains challenging with …

TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers

J Charlton, EJ Jung, AL Mattei, N Bailly, J Liao… - Nature …, 2020 - nature.com
Mammalian cells stably maintain high levels of DNA methylation despite expressing both
positive (DNMT3A/B) and negative (TET1-3) regulators. Here, we analyzed the independent …

Dynamic antagonism between key repressive pathways maintains the placental epigenome

R Weigert, S Hetzel, N Bailly, C Haggerty, IA Ilik… - Nature Cell …, 2023 - nature.com
DNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and
operate within distinct genomic compartments. In mammals, the majority of the genome is …

T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation

A Landshammer, A Bolondi, H Kretzmer, C Much… - ELife, 2023 - elifesciences.org
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various
biological processes, including embryonic development and cellular differentiation. Despite …

Whole human genome 5'-mC methylation analysis using long read nanopore sequencing

C Silva, M Machado, J Ferrão… - Epigenetics, 2022 - Taylor & Francis
Methylation microarray and bisulphite sequencing are often used to study 5'-methylcytosine
(5'-mC) modification of CpG dinucleotides in the human genome. Although both …

Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation

A Landshammer, A Bolondi, H Kretzmer, C Much… - bioRxiv, 2022 - biorxiv.org
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various
biological processes, including embryonic development and cellular differentiation. Despite …

SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks

S Akbarinejad, M Hadadian Nejad Yousefi… - BMC …, 2021 - Springer
Background Once aligned, long-reads can be a useful source of information to identify the
type and position of structural variations. However, due to the high sequencing error of long …

T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation

L Alexandro, B Adriano, K Helene, C Much, B René… - eLife, 2023 - search.proquest.com
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various
biological processes, including embryonic development and cellular differentiation. Despite …

Pyro: A Comprehensive Pipeline for Eukaryotic Genome Assembly

D Southwood, RV Rane, SF Lee, JG Oakeshott… - bioRxiv, 2023 - biorxiv.org
The assembly of reference-quality, chromosome-level genomes for both model and novel
eukaryotic organisms is an increasingly achievable task for single research teams. However …