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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.
This article was published in Frontiers in Immunology, with a pre-print on bioRxiv.
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}
}
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}
}
make
make frontiers
Will create a file ~/frontiers.zip
with all files for a Frontiers submission.
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.
See https://github.com/richelbilderbeek/bbbq_article_issue_157.
See https://github.com/richelbilderbeek/bbbq_1_smart.
See https://github.com/richelbilderbeek/ncbi_peregrine for the scripts.
See https://github.com/richelbilderbeek/ncbi_results to see how the results are processed.
| Repository | |
|---|---|
bbbq |
 |
bbbq_1_smart |
 |
bbbq_article_issue_157 |
 |
ncbi_peregrine |
 |
ncbi_results |
 |
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:
| 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.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