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GenomicsHIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort.
Distinct integration patterns of different retroviruses have puzzled virologists for over 20 years. The viral integrase (IN), as part of the intasome complex, docks onto the target DNA (tDNA) and catalyzes the insertion of the viral genome into the host chromatin. We identified retroviral IN amino a...
ORGANISM(S): Homo sapiens 
2015-01-26 | E-GEOD-61003 | biostudies-arrayexpress
MetabolomicsThe Toxoplasma monocarboxylate transporters are involved in the metabolism within the apicoplast and are linked to parasite survival

The apicoplast is a four-membrane plastid found in the apicomplexans, which harbors biosynthesis and organelle housekeeping activities in the matrix. However, the mechanism driving the flux of metabolites, in and out, remains unknown. Here we used TurboID and genome engineering to identify apicop...

2024-01-15 | MTBLS7060 | MetaboLights
TranscriptomicsIntertwining threshold settings, biological data and database knowledge to optimize the selection of differentially expressed genes
Background: Many tools used to analyze microarrays in different conditions have been described. However, the integration of the deregulated genes within coherent metabolic pathways is lacking. Currently no objective selection criterion, based on biological functions exists, to determine a threshold ...
ORGANISM(S): Homo sapiens 
2011-06-19 | E-GEOD-22858 | biostudies-arrayexpress
TranscriptomicseQTL mapping in Lake Whitefish Species Pairs.
Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied towards investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading...
ORGANISM(S): Coregonus clupeaformis 
2008-09-01 | E-GEOD-11378 | biostudies-arrayexpress
UnknownTransitions Into Freezing Environments Linked With Shifts in Phylogenetic Integration Between Vitaceae Leaf Traits.
Not available
S-EPMC11563691 | biostudies-literature
TranscriptomicsLentiviral shRNA library screen to identify growth-related genes in malignant melanoma
Little is known about genes that promote melanoma cell growth and proliferation. siRNAs may be used to address the role of individual genesin these processes. RNAi library screens were used in the past to gain a comprehensive overview of all genes involved in cell growth, proliferation, migration an...
ORGANISM(S): Homo sapiens 
2014-01-24 | E-GEOD-46675 | biostudies-arrayexpress
ProteomicsPlasmodium falciparum PfEMP1 DiQ-BioID data
PfEMP1 is the major virulence factor of Plasmodium falciparum parasites. PfEMP1 is expressed as an integral membrane protein on the surface of infected red blood cells. As a part of this project, the BioID system was utilized to biotinylate proximal proteins of a functional PfEMP1. In order to do th...
ORGANISM(S): Plasmodium falciparum 
2025-11-13 | PXD052297 | Pride
Var genes Virulence Protein export Malaria Pfemp1 Bira* Selection linked integration Bioid Plasmodium falciparum 
TranscriptomicsRapid activation of distinct member of multigene families in Plasmodium spp.
The objective of this study is to provide a novel method to study multigene proteins in Plasmodium spp. The method is based on selection linked integration (SLI), which allows positive selection of genomic integration events. By targeting specific members of multigene families, parasites are being s...
ORGANISM(S): Plasmodium falciparum 
2019-03-12 | GSE128123 | GEO
GenomicsHigh-throughput semi-quantitative analysis of insertional mutations in heterogeneous tumors
Exploiting the full potential of insertional mutagenesis screens with retroviruses and transposons requires methods for distinguishing clonal from subclonal insertion events within heterogeneous tumor cell populations. Current protocols, based on ligation mediated PCR, depend on endonuclease based f...
ORGANISM(S): Mus musculus 
2011-08-11 | E-GEOD-22657 | biostudies-arrayexpress
TranscriptomicsTranscriptional changes associated to resistance to the cell wall active bacteriocin Lcn972
Lcn972 is a non-modified bacteriocin that targets exclusively Lactococcus sp. Addition of Lcn972 inhibits cell wall biosynthesis at the septum by binding to the cell wall precursor lipid II. Resistance to Lcn972 develops upon selection with subinhibitory concentrations. The transcriptome of the high...
ORGANISM(S): Lactococcus lactis subsp. lactis 
2012-12-06 | E-GEOD-38349 | biostudies-arrayexpress
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