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Qasim-Hussain-Code/README.md

Qasim Hussain. PhD Aspirant | Virologist | Immunologist | Bioinformatician

Viral replication. Animated diagram of the replication cycle of an enveloped virus in a host cell, in seven numbered steps: 1 attachment: a viral glycoprotein binds a receptor on the cell surface; 2 entry: the virion is taken up by endocytosis, or its envelope fuses directly with the plasma membrane; 3 uncoating: membrane fusion releases the capsid into the cytoplasm, and the capsid opens to free the genome; 4 genome replication: the genome is copied and viral genes are expressed as mRNA, in the nucleus or the cytoplasm depending on the virus family; 5 protein synthesis: host ribosomes translate the viral mRNA, and envelope glycoproteins are made at the endoplasmic reticulum and pass through the Golgi; 6 assembly: new genomes are packaged into capsids, which gather at membrane that carries the viral glycoproteins; 7 release: new virions bud from the membrane and take their envelope from it. A highlight moves from step to step. Viral proteins in orange, host structures in grey. A simplified, general scheme; details differ between virus families.

An enveloped virus binds a receptor, enters the cell and frees its genome, which is copied and expressed so that the host's ribosomes make new viral proteins, and new particles assemble and bud from a cell membrane; the scheme is simplified and general, and its details differ between virus families.


Antigen presentation. Animated diagram of the MHC class I pathway, in six numbered steps. A viral protein in the cytosol of an infected cell is degraded by the proteasome into peptides. TAP carries one peptide into the endoplasmic reticulum, where the peptide-loading complex (tapasin, calreticulin and ERp57) loads it onto MHC class I with beta-2-microglobulin. The loaded molecule passes through the Golgi apparatus to the cell surface, where the T cell receptor and CD8 of a CD8 T cell recognise it. The viral protein and peptide in orange, MHC class I in blue, the T cell receptor and CD8 in grey.

In the same infected cell, the proteasome cuts viral protein into peptides, TAP carries them into the endoplasmic reticulum, a peptide is loaded onto MHC class I with beta-2-microglobulin, and the complex travels to the cell surface, where the T cell receptor of a CD8 T cell recognises peptide and MHC together.


Horizontal gene transfer. Animated diagram of bacterial conjugation in four steps: 1 contact, the donor's pilus attaches to a recipient cell; 2 mating bridge, the pilus retracts, drawing the cells together, and a pore forms; 3 transfer, one strand of the plasmid is nicked at its origin of transfer and passes into the recipient; 4 each cell makes the complementary strand, completing the plasmid, so both carry the resistance gene. The plasmid and resistance gene in orange, the cells in grey. A simplified, general scheme; details differ between plasmids and bacterial species.

In bacteria, a plasmid carrying a resistance gene can pass from one cell to another by conjugation, one of the ways antimicrobial resistance and accessory genes spread between strains; the scheme is simplified and general.


The spike glycoprotein trimer of SARS-CoV-2 in its closed state, PDB 6VXX, turning slowly, each of its three chains in its own colour (green, orange and purple), drawn as spheres for every atom.      Influenza H5 haemagglutinin trimer with Fab fragments of the antibody CR9114 bound to its stem, PDB 4FQI, turning slowly, each chain in its own colour as in the RCSB Protein Data Bank's image of the entry.

SARS-CoV-2 spike glycoprotein, PDB 6VXX   ·   Influenza haemagglutinin with antibody CR9114, PDB 4FQI


qasim-hussain-code.github.io  ·  ORCID  ·  Google Scholar  ·  LinkedIn  ·  Hugging Face

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  1. nf-core-viralrecon-influenza nf-core-viralrecon-influenza Public

    Reference-guided genomic variant mapping pipeline and intrahost variome atlas for the segmented Influenza A virus (H1N1pdm09), characterizing within-host quasispecies diversity and mutational burde…

    Python 1

  2. neoantigen_immunogenicity_prediction neoantigen_immunogenicity_prediction Public

    Chapter 6 of Machine Learning for Biology. Sequence-only immunogenicity prediction on 1,200 HLA-A*02:01 IEDB binders, cluster-split and pre-registered. Network 0.610 AUPRC, binding-only baseline 0.…

    Python

  3. HCV_Riboseq HCV_Riboseq Public

    A multi-omic bioinformatics pipeline interrogating viral translational hijacking in HCV-infected hepatoma cells. By integrating Ribosome Profiling and RNA-seq, it quantifies translational efficienc…

    Python

  4. immune_cell_subtype_discovery immune_cell_subtype_discovery Public

    Test of whether k-means, never shown a label, recovers ten immune cell populations from 94,655 single-cell RNA-seq profiles.

    Python

  5. colabfold_boltz_structure_confidence_pipeline colabfold_boltz_structure_confidence_pipeline Public

    A measured benchmark of structure prediction confidence, reporting pLDDT calibration against lDDT, the physical validity of predicted structures, and what docking into a predicted receptor costs ag…

    Python

  6. bakta_prokka_disagreement_prediction bakta_prokka_disagreement_prediction Public

    Bakta and Prokka call the same 87,859 CDS regions in 25 complete bacterial genomes, then give 51.7% of them different product names. Both wrap Prodigal, so they agree on gene boundaries and diverge…

    Python