Results 61 to 70 of about 15,621,385 (284)

Ten simple rules for managing high-throughput nucleotide sequencing data [PDF]

, 2016
Abstract The challenges posed by large data volumes produced by high-throughput nucleotide sequencing technologies are well known. This document establishes ten simple rules for coping with these challenges. At the level of master data management, (1) data triage reduces data volumes; (2) some lossless data representations are much more
openaire   +1 more source

Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies

PeerJ, 2023
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area.
Rollin, Johan, Bester, Rachelle, Brostaux, Yves, Caglayan, Kadriye, De Jonghe, Kris, Eichmeier, Ales, Foucart, Yoika, Haegeman, Annelies, Koloniuk, Igor, Kominek, Petr, Maree, Hans, Onder, Serkan, Posada Céspedes, Susana, Roumi, Vahid, Šafářová, Dana, Schumpp, Olivier, Ulubas Serce, Cigdem, Sõmera, Merike, Tamisier, Lucie, Vainio, Eeva, van der Vlugt, Rene AA, Massart, Sebastien   +22 more
openaire   +12 more sources

Peripheral lysosomes recruit PLEKHG3 to focal adhesions and restrain protrusion dynamics

FEBS Letters, EarlyView.
Proximity‐dependent labeling at the LAMTOR complex revealed the Rho GEF PLEKHG3 as a lysosome‐proximal protein directing the study toward the influence of lysosome positioning on actin dynamics and cell motility. We show that PLEKHG3 colocalizes with lysosomes at focal adhesion sites and observe that forced peripheral dispersion of lysosomes hinders ...
Rainer Ettelt, Ana‐Maria Sandru, Georg Vucak, Sebastian Didusch, Biljana Riemelmoser, Karin Ehrenreiter, Markus Hartl, Lukas A. Huber, Manuela Baccarini   +8 more
wiley   +1 more source

Multidimensional analysis of the host response reveals prognostic and pathogen-driven immune subtypes among adults with sepsis in Uganda

Critical Care, 2022
Background The global burden of sepsis is concentrated in sub-Saharan Africa, where severe infections disproportionately affect young, HIV-infected adults and high-burden pathogens are unique. In this context, poor understanding of sepsis immunopathology
Matthew J. Cummings, Barnabas Bakamutumaho, Adam Price, Nicholas Owor, John Kayiwa, Joyce Namulondo, Timothy Byaruhanga, Moses Muwanga, Christopher Nsereko, Stephen Sameroff, Rafal Tokarz, Wai Wong, Shivang S. Shah, Michelle H. Larsen, W. Ian Lipkin, Julius J. Lutwama, Max R. O’Donnell   +16 more
doaj   +1 more source

A single-nucleotide-polymorphism real-time PCR assay for genotyping of mycobacterium tuberculosis complex in peri-urban Kampala [PDF]

, 2015
Accurate and high-throughput genotyping of Mycobacterium tuberculosis complex (MTBC) may be important for understanding the epidemiology and pathogenesis of tuberculosis (TB).
Eddie M. Wampande, Kathleen Eisenach, Mary Nsereko, Stavroula K. Hatzios, Wampande, Eddie M., Hatzios, Stavroula K., Mayanja, Harriet K., Mupere, Ezekiel, Gagneux, Sebastien, Eisenach, Kathleen, Joloba, Moses L., Moses L. Joloba, Achan, Beatrice, Ezekiel Mupere, Nsereko, Mary, Sebastien Gagneux, Harriet K. Mayanja, null null, Boom, W Henry, Boom, W. Henry, W Henry Boom, Tuberculosis Research Unit,, Beatrice Achan   +22 more
core   +2 more sources

The Shewanella oneidensis Fic enzyme SoFic targets the switch‐I region of EF‐Tu for AMPylation

FEBS Letters, EarlyView.
Fic enzymes mediate diverse post‐translational modifications across all domains of life, including AMPylation. Prokaryotic EF‐Tu can be AMPylated and deAMPylated by the conserved Fic enzyme SoFic. Structural and biochemical approaches were used to characterize the effect of AMPylation on EF‐Tu, SoFic's enzymatic activities, and the enzyme‐target ...
Svenja Runge, Vivian Pogenberg, Alexander Baumgart, Bente Siebels, Hartmut Schlüter, Michael Hecht‐Bucher, Aymelt Itzen   +6 more
wiley   +1 more source

Bioinformatics' approaches to detect genetic variation in whole genome sequencing data [PDF]

, 2010
Current genetic marker repositories are not sufficient or even are completely lacking for most farm animals. However, genetic markers are essential for the development of a research tool facilitating discovery of genetic factors that contribute to ...
Kerstens, H.H.D.
core  

Transcriptional profiling of circulating extracellular vesicles from prebiopsy prostate cancer patients

Molecular Oncology, EarlyView.
RNA profiling of circulating extracellular vesicles (EVs) from blood samples of men undergoing prostate biopsy identifies transcripts associated with clinically significant prostate cancer. Integrative analysis with public tumor datasets links EV‐derived gene signatures to tumor stage and progression‐free survival, highlighting CASP3, XRCC2, and RIT1 ...
Stefan Werner, Pierre Tennstedt, Randi C. Pose, Christian Müller, Katharina Besler, Svenja Schneegans, Malik Alawi, Marie C. Roesch, Sven Peine, Desiree Bonci, Joanna Budna‐Tukan, Evi Lianidou, Catherine Alix‐Panabières, Derya Tilki, Klaus Pantel   +14 more
wiley   +1 more source

High-Throughput Sequencing Reveals Bacterial Diversity in Raw Milk Production Environment and Production Chain in Tangshan City of China

Food Science of Animal Resources, 2021
Raw milk is a nature media of microbiota that access milk from various sources, which constitutes a challenge in dairy production. This study characterizes the relationship between the raw milk quality and the bacteria diversity at different sampling ...
Huihui Cao, Yanhua Yan, Lei Wang, Lixue Dong, Xueliang Pang, Sining Tang, Aijun Li, Aili Xiang, Litian Zhang, Baiqin Zheng   +9 more
doaj   +1 more source

Targeting transcription factors associated with hemoglobinopathies: Lessons from successful interventions and implications for cancer

Molecular Oncology, EarlyView.
This review summarizes the transcription factors, repressive chromatin‐modifying complexes, and epigenetic mechanisms that control fetal hemoglobin repression. Notably, many regulators of γ‐globin silencing also function in transcriptional and epigenetic networks that drive cancer, highlighting opportunities to translate advances in hemoglobinopathy ...
Meigen Yu, Puspa Das, Xing Zhang, Xiaodong Cheng   +3 more
wiley   +1 more source