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MetabolomicsGenome-scale metabolic modelling of responses to polymyxins in Pseudomonas aeruginosa
Background: Pseudomonas aeruginosa often causes multidrug-resistant infections in immunocompromised patients and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics...
2018-02-28 | MTBLS630 | MetaboLights
ProteomicsREPARATION: Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes - PART 2
Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated techniques depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION ...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2017-08-03 | PXD005901 | Pride
Ribosome profiling : escherichia coli Genome (re-)annotation Shotgun N-terminal cofradic 
GenomicsGenome re-annotation of Aspergillus fumigatus
Genome re-sequencing and re-annotation of Aspergillus fumigatus
PRJEB33346 | ENA
ProteomicsREPARATION: Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes
Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated techniques depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION ...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 
2017-08-09 | PXD005844 | Pride
Shotgun Bacteria Salmonella typhimurium sl1344 
ProteomicsProteome driven re-evaluation and functional annotation of Streptococcus pyogenes SF370 genome.
Shotgun proteomic analysis for re-evaluation of genome S. pyogenes SF370, by using RP-HPLC ion trap MS/MS with six-frame database.
ORGANISM(S): Streptococcus pyogenes M1 GAS 
2011-11-18 | PRD000562 | Pride
ProteomicsProteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes aegypti
The incomplete genome annotation of non-model organisms hampers molecular and proteomic studies. Proteomics informed by transcriptomics (PIT) is suited to non-model organisms because peptides are identified using transcriptomic, not genomic, data. Aedes aegypti is the mosquito vector for the (re-)em...
ORGANISM(S): Aedes aegypti aegypti 
2017-02-15 | PXD003799 | Pride
Lc-ms/ms Pit Aedes aegypti Proteomics informed by transcriptomics 
UnknownRe-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence.
Not available
S-EPMC1899501 | biostudies-literature
ProteomicsTowards an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics.
The honey bee is a key pollinator in many agricultural operations as well as a model organism for studying the genetics and evolution of social behaviour. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant a...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Apis mellifera (Honeybee) Drosophila melanogaster (Fruit fly) Saccharomyces cerevisiae (Baker's yeast) Caenorhabditis elegans 
2016-01-18 | PXD002275 | Pride
Honey bees Proteogenomics Mass spectrometry Gene annotation Apis mellifera 
UnknownGenome-wide metabolic (re-) annotation of Kluyveromyces lactis.
Not available
S-EPMC3508617 | biostudies-literature
UnknownRe-annotation of the woodland strawberry (Fragaria vesca) genome.
Not available
S-EPMC4318131 | biostudies-literature
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