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bbbq_article

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The article 'Transmembrane helices are an overlooked and evolutionarily conserved source of major histocompatibility complex class I and II epitopes', by Bilderbeek, Baranov, van den Bogaart and Bianchi.

Article download and citation

This article was published in Frontiers in Immunology, with a pre-print on bioRxiv.

Frontiers in Immunology

This article on Frontiers in Immunology

Bilderbeek, Richèl JC, et al. "Transmembrane Helices Are an Over-Presented and Evolutionarily Conserved Source of Major Histocompatibility Complex Class I and II Epitopes." Frontiers in immunology 12 (2021).

@article{bilderbeek2021transmembrane,
  title={Transmembrane Helices Are an Over-Presented and Evolutionarily Conserved Source of Major Histocompatibility Complex Class I and II Epitopes},
  author={Bilderbeek, Rich{\`e}l JC and Baranov, Maksim V and Van Den Bogaart, Geert and Bianchi, Frans},
  journal={Frontiers in immunology},
  volume={12},
  year={2021},
  publisher={Frontiers Media SA}
}

bioRxiv

This article on biorxiv

Bilderbeek, Richèl JC, et al. "Transmembrane helices are an overlooked and evolutionarily conserved source of major histocompatibility complex class I and II epitopes." bioRxiv (2021).

@article{bilderbeek2021transmembrane,
  title={Transmembrane helices are an overlooked and evolutionarily conserved source of major histocompatibility complex class {I} and {II} epitopes},
  author={Bilderbeek, Richèl JC and Baranov, Maxim and van den Bogaart, Geert and Bianchi, Frans},
  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

Build the article

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Zip the article for Frontiers

make frontiers

Will create a file ~/frontiers.zip with all files for a Frontiers submission.

Figure sources

See numbered_figure_files.csv where the numbered figures (figure_1a.tiff, etc) originally come from.

The subfigures (e.g. figure 1a, figure 1b), were put into TIFF figure files (e.g. figure 1, figure 2) by @fransbianchi.

The figure TIFF files (e.g. figure_1.tiff, figure_2.tiff) were converted to EPS files (e.g. figure_1.eps, figure_2.eps) using https://www.freeconvert.com/tiff-to-eps.

Re-do the analysis

Dependencies

Repository
`bbbq`
`bbbq_1_smart`
`bbbq_article_issue_157`
`ncbi_peregrine`
`ncbi_results`

How did you make the comparison figure?

I made the comparison figure using:

compare bbbq_1_smart_results/fig_f_tmh_2_panel.png bbbq_1_smart_2aa_results/fig_f_tmh_2_panel.png compare_fig_f_tmh_2_panel.png

The comparison figure:

Labels

Fig	Label
1A	`fig:bbbq_1_smart_results`
1B	`fig:hydrophobicity_1`
1C	`fig:hydrophobicity_2`
2	`fig:elution`
2A	`fig:2a`
2B	`fig:2b`
3A	`fig:f_snps_found_and_expected`
3B	`fig:f_tmh_ncbi`
3C	`fig:conservation`
4A	`fig:f_snps_found_and_expected_per_spanner`
4B	`fig:conservation_per_spanner`
4C	`fig:f_tmh_ncbi_per_spanner`
S1	`fig:bianch_et_al_2017_1a`
S2	`fig:bilderbeek_et_al_2021_1a`
S3	`fig:snp_rel_pos`
S4	`fig:thm_presentation_correlation`
S5	`fig:t_cells_present_tmh_derived_epitopes`
S6	`fig:f_tmh_mhc1_normalized`
S7	`fig:f_tmh_mhc2_normalized`
S8	`fig:rel_presentation_per_haplotype`
S9	`fig:rel_presentation`
S10	`fig:snps_per_gene_name_ncbi`
S11	`fig:snps_per_gene_name_processed`
S12	`fig:n_proteins_per_gene_name`
S13	`fig:fig_n_snps_per_tmp`
S14	`fig:fig_n_tmhs_per_protein`
S15	`fig:bbbq_1_smart_results_2aas`

Tab	Label
ST1	`tab:ic50_binders_mhc1`
ST2	`tab:ic50_binders_mhc2`
ST3	`tab:ncbi_counts_1`
ST4	`tab:ncbi_counts_2`
ST5	`tab:tmh_binders_mhc2`
ST6	`tab:elution`
ST7	`tab:tmh_binders_mhc1`
ST8	`tab:haplotype_abbreviations`
ST9	`table:software_used`
ST10	`tab:f_tmh`
ST11	`tab:snp_stats`
ST12	`tab:snp_stats_per_spanner_single`
ST13	`tab:snp_stats_per_spanner_multi`
ST14	`tab:tmh_binders_mhc2_2aas`
ST15	`tab:tmh_binders_mhc1_2aas`

Frontiers files

frontiers.aux
frontiersFPHY.cls
frontiersHLTH.cls
frontiersinHLTH&FPHY.bst
frontiersinSCNS_ENG_HUMS.bst
frontiers.log
frontiers.out
frontiers.pdf
frontiersSCNS.cls
frontiers_SupplementaryMaterial.tex
frontiers_suppmat.cls
frontiers.tex
logo1.eps
logo1-eps-converted-to.pdf
logo2.eps
logos.eps
logos-eps-converted-to.pdf
PDF examples
stfloats.sty
test.bib
YM-logo.eps