Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure [PDF]
, 2012 The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper
Abate, Francesco +5 more
core
Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors. [PDF]
, 2017 Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability.
Jeddi, Iman, Saiz, Leonor
core +2 more sources
FEBS Letters, EarlyView.Glutaredoxin (Grx) 3 proteins contain a thioredoxin domain and one to three class II Grx domains. These proteins play a crucial role in iron homeostasis in eukaryotic cells. In human Grx3, at least one of the two Grx domains, together with the thioredoxin domain, is essential for its function in iron metabolism.
Laura Magdalena Jordt +4 more
wiley +1 more source
Transcriptomic and ChIP-sequence interrogation of EGFR signaling in HER2+ breast cancer cells reveals a dynamic chromatin landscape and S100 genes as targets. [PDF]
, 2019 BACKGROUND:The Human Epidermal Growth Factor Receptor (EGFR/HER1) can be activated by several ligands including Transforming Growth Factor alpha (TGF-α) and Epidermal Growth Factor (EGF).
Dutta, Pranabananda +5 more
core +5 more sources
FEBS Letters, EarlyView.To explore the impact of the overexpression of the multidrug‐transporter P‐glycoprotein (ABCB1) on membrane fluidity, we compared the transversal gradient of mobility and microviscosity in plasma membranes of drug‐sensitive Chinese hamster ovary cells (AuxB1) and their multidrug‐resistant derivatives (B30) using the fluorescent n‐(9‐anthroyloxy) fatty ...
Roger Busche +2 more
wiley +1 more source
High-throughput detection of RNA processing in bacteria
BMC Genomics, 2018 Background Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically ...
Erin E. Gill +12 more
doaj +1 more source
Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues. [PDF]
, 2016 Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a
Britton, Monica +3 more
core +2 more sources
Evolutionary interplay between viruses and R‐loops
FEBS Letters, EarlyView.Viruses interact with specialized nucleic acid structures called R‐loops to influence host transcription, epigenetic states, latency, and immune evasion. This Perspective examines the roles of R‐loops in viral replication, integration, and silencing, and how viruses co‐opt or avoid these structures.
Zsolt Karányi +4 more
wiley +1 more source
Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. [PDF]
, 2017 In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation.
Aviran, Sharon +5 more
core +2 more sources
Purification tags markedly affect self‐aggregation of CPEB3
FEBS Letters, EarlyView.Although recombinant proteins are used to study protein aggregation in vitro, uncleaved tags can interfere with accurate interpretation. Our findings demonstrate that His₆‐GFP and His₁₂ tags significantly affect liquid droplet and amyloid fibril formation in the intrinsically disordered region (IDR) of mouse cytoplasmic polyadenylation element‐binding ...
Harunobu Saito +6 more
wiley +1 more source