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ProteomicsImproving Genome Annotation of Enterotoxigenic Escherichia coli TW10598 by a Label-Free Quantitative MS/MS Approach
The most commonly used genome annotation processes are to a great extent based on computational methods. However, those can only predict genes that have been described earlier or that have sequence signatures indicative of a gene function. We reported a synonymous proteogenomic approach for experime...
ORGANISM(S): Escherichia coli 
2015-09-15 | PXD002473 | Pride
Synonymous proteogenomics Enterotoxigenic escherichia coli Label-free quantification Genome annotation 
GenomicsPCR-free Poecilia reticulata genome sequences
PCR-free high coverage whole-genome sequencing of the guppy (Poecilia reticulata)
PRJEB36450 | ENA
ProteomicsAssembly and cell-free expression of a partial genome for the synthetic cell
We designed and assembled a multicistronic DNA plasmid containing multiple genes that are relevant for a synthetic cell. This partial minimal synthetic genome was expressed in the recombinant PURE system. Cell-free biosynthesis of all encoded proteins was validated by liquid chromatography-mass spec...
ORGANISM(S): Anaplasma marginale Aequorea victoria Bacillus phage phi29 Escherichia coli 
2026-10-28 | PXD069407 | Pride
Partial genome Cell-free biosynthesis Label-free quantification Synthetic cell Lc-ms/ms 
GenomicsGenome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring
In many areas of oncology, we lack sensitive tools to track low burden disease. While cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low disease burden monitoring through the pr...
EGAS00001004406 | EGA
GenomicsGenome-wide cell-free DNA fragmentation in patients with cancer
Cell-free DNA (cfDNA) in the blood provides a noninvasive diagnostic avenue for patients with cancer. However, characteristics of the origins and molecular features of cfDNA are poorly understood. We developed an approach to evaluate fragmentation patterns of cfDNA across the genome and found that ...
EGAS00001003611 | EGA
TranscriptomicsWhole-Genome Transcriptome Profiling of Microvascular Free Flaps
Vascular compromise in microsurgical free flap transfers continues to present devastating outcomes in terms of flap failure and increased operating room costs. Current devices to detect early venous congestion have not become widely accepted because of insufficient sensitivity, incisiveness, or prac...
ORGANISM(S): Rattus norvegicus 
2016-07-24 | E-GEOD-35270 | biostudies-arrayexpress
TranscriptomicsBisulfite-free and Base-resolution Analysis of 5-formylcytosine at Whole-genome Scale
Active DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC). However, genome-wide detection of 5fC at single-base resolution remains challenging. Here we present a bisulfite-free ...
ORGANISM(S): Mus musculus 
2015-09-07 | E-GEOD-66144 | biostudies-arrayexpress
GenomicsSingle molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer
Somatic mutations are a hallmark of tumorigenesis and may be useful for non-invasive diagnosis of cancer. We analyzed whole-genome sequencing (WGS) data from 2,511 individuals in the Pan-Cancer Analysis of Whole Genomes (PCAWG) study as well as 489 individuals from four prospective cohorts and found...
EGAS00001007248 | EGA
GenomicsEfficient transgene-free multiplexed genome editing via viral delivery of an engineered TnpB
Efficient transgene-free multiplexed genome editing via viral delivery of an engineered TnpB
PRJNA1401771 | ENA
GenomicsGenome-wide cell-free DNA fragmentation in patients with cancer
Genome-wide cell-free DNA fragmentation in patients with cancer
PRJNA543358 | ENA
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