An overview of duplicated gene detection methods: Why the duplication mechanism has to be accounted for in their choice

T Lallemand, M Leduc, C Landès, C Rizzon, E Lerat - Genes, 2020 - mdpi.com
Gene duplication is an important evolutionary mechanism allowing to provide new genetic
material and thus opportunities to acquire new gene functions for an organism, with major …

Tuning in to the signals: noncoding sequence conservation in vertebrate genomes

G Elgar, T Vavouri - Trends in genetics, 2008 - cell.com
Aligning and comparing genomic sequences enables the identification of conserved
sequence signatures and can enrich for coding and noncoding functional regions. In …

NFATc1 in mice represses osteoprotegerin during osteoclastogenesis and dissociates systemic osteopenia from inflammation in cherubism

AO Aliprantis, Y Ueki, R Sulyanto… - The Journal of …, 2008 - Am Soc Clin Investig
Osteoporosis results from an imbalance in skeletal remodeling that favors bone resorption
over bone formation. Bone matrix is degraded by osteoclasts, which differentiate from …

Genomics meets glycomics—the first GWAS study of human N-glycome identifies HNF1α as a master regulator of plasma protein fucosylation

G Lauc, A Essafi, JE Huffman, C Hayward… - PLoS …, 2010 - journals.plos.org
Over half of all proteins are glycosylated, and alterations in glycosylation have been
observed in numerous physiological and pathological processes. Attached glycans …

Site-specific programming of the host epithelial transcriptome by the gut microbiota

F Sommer, I Nookaew, N Sommer, P Fogelstrand… - Genome biology, 2015 - Springer
Background The intestinal epithelium separates us from the microbiota but also interacts
with it and thus affects host immune status and physiology. Previous studies investigated …

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

RA Chodroff, L Goodstadt, TM Sirey, PL Oliver… - Genome biology, 2010 - Springer
Background Long considered to be the building block of life, it is now apparent that protein is
only one of many functional products generated by the eukaryotic genome. Indeed, more of …

The mononuclear phagocyte system of the pig as a model for understanding human innate immunity and disease

L Fairbairn, R Kapetanovic, DP Sester… - Journal of leukocyte …, 2011 - academic.oup.com
The biology of cells of the mononuclear phagocyte system has been studied extensively in
the mouse. Studies of the pig as an experimental model have commonly been consigned to …

PPD: a manually curated database for experimentally verified prokaryotic promoters

W Su, ML Liu, YH Yang, JS Wang, SH Li, H Lv… - Journal of Molecular …, 2021 - Elsevier
As a key region, promoter plays a key role in transcription regulation. A eukaryotic promoter
database called EPD has been constructed to store eukaryotic POL II promoters. Although …

Identifying regulatory elements in eukaryotic genomes

L Narlikar, I Ovcharenko - Briefings in functional genomics and …, 2009 - academic.oup.com
Proper development and functioning of an organism depends on precise spatial and
temporal expression of all its genes. These coordinated expression-patterns are maintained …

MAGIA2: from miRNA and genes expression data integrative analysis to microRNA–transcription factor mixed regulatory circuits (2012 update)

A Bisognin, G Sales, A Coppe, S Bortoluzzi… - Nucleic acids …, 2012 - academic.oup.com
Abstract MAGIA2 (http://gencomp. bio. unipd. it/magia2) is an update, extension and
evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target …