From trash to treasure: detecting unexpected contamination in unmapped NGS data

M Sangiovanni, I Granata, AS Thind, MR Guarracino - BMC bioinformatics, 2019 - Springer
Abstract Background Next Generation Sequencing (NGS) experiments produce millions of
short sequences that, mapped to a reference genome, provide biological insights at …

The gut, vaginal, and urine microbiome in overactive bladder: a systematic review

C Sze, M Pressler, JR Lee, B Chughtai - International Urogynecology …, 2022 - Springer
Introduction and hypothesis The objective was to systemically review the current literature
on the association of gut, vaginal, and urinary dysbiosis in female patients with overactive …

Establishing the architecture of plant gene regulatory networks

F Yang, WZ Ouma, W Li, AI Doseff, E Grotewold - Methods in enzymology, 2016 - Elsevier
Gene regulatory grids (GRGs) encompass the space of all the possible transcription factor
(TF)–target gene interactions that regulate gene expression, with gene regulatory networks …

[HTML][HTML] Identification of sugar responsive transcription factors in silico

K Kokki - 2022 - helda.helsinki.fi
In order to survive, all organism require sugars, amino acids and lipids, which are used for
energy and growth. The nutritional needs of an organism vary tremendously between …

Design of knowledge bases for plant gene regulatory networks

E Mukundi, F Gomez-Cano, WZ Ouma… - Plant Gene Regulatory …, 2017 - Springer
Developing a knowledge base that contains all the information necessary for the researcher
studying gene regulation in a particular organism can be accomplished in four stages. This …

DecontaMiner: a pipeline for the detection and analysis of contaminating sequences in human NGS sequencing data

I Granata, M Sangiovanni, M Guarracino - Dynamics of Mathematical …, 2016 - Springer
Reads alignment is an essential step of next generation sequencing) data analyses. One
challenging issue is represented by unmapped reads that are usually discarded and …

[PDF][PDF] Transcriptional and epigenetic regulation of differentially activated macrophages

W Krebs - 2016 - core.ac.uk
Furthermore, I want to thank all Postdocs in the Schultze group for their constant attendance
to give competent support no matter if it was day or night, especially Dr. Susanne V. Schmidt …

Functional analysis of the osteoarthritis susceptibility loci marked by the polymorphisms rs10492367 and rs9350591

K Johnson - 2016 - theses.ncl.ac.uk
Approximately 8.5 million people in the UK are affected by osteoarthritis (OA), a
multifactorial, polygenic disease characterised by articular cartilage loss. In 2012, the …

[引用][C] Genetic adaptations in Microbacteriaceae species inhabiting a salinity gradient

MG Ram - 2024 - University of Auckland