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bacterial-pathogenesis

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Qasim-Hussain-Code / s-pneumo-pan-secretome

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Pangenomic structural analysis of bacterial secretion machineries across Streptococcus pneumoniae isolates using optimized TXSScan hidden Markov models.

computational-biology bioinformatics-pipeline proteomics comparative-genomics hidden-markov-models pangenomics virulence-factors streptococcus-pneumoniae protein-translocation macsyfinder secretion-systems pan-secretome bacterial-pathogenesis txsscan
  • Updated Apr 12, 2026
  • Python

Qasim-Hussain-Code / msqrob2_lfq_proteomics_pipeline

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Label-free DDA proteomics differential abundance analysis, benchmarked against a spike-in study with known ground truth and applied to an arginine transporter knockout in Francisella tularensis.

bioinformatics r computational-biology bioconductor proteomics dda mass-spectrometry maxquant false-discovery-rate label-free-quantification mixed-models robust-regression qfeatures lfq differential-abundance bacterial-pathogenesis msqrob2 spike-in-benchmark pseudo-replication francisella-tularensis
  • Updated Sep 18, 2026
  • R

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