Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes.
The 1 match
- [1] § Materials and methods › HLA typing, mutation detection ↔ src/FunctionalTester.py, lines 214–234 · score 0.61 · Mutation pipeline, reference genome, Variant Call, STAR, bam, VCF
Paper
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The authors' code
Python · 372 lines · 18 KB · BSD-3-Clause · 1 match
- __author__ = "Timothy Tickle"
- __copyright__ = "Copyright 2015"
- __credits__ = ["Timothy Tickle", "Brian Haas"]
- __license__ = "MIT"
- __maintainer__ = "Timothy Tickle"
- __email__ = "[email hidden]"
- __status__ = "Development"
- import Commandline
- import os
- import ParentPipelineTester
- import unittest
- class FunctionalTester(ParentPipelineTester.ParentPipelineTester):
- """
- Functional testing for scripts, these are focused on making sure the script can be called in different ways and complete without error.
- """
- # Testing environment
- str_script_dir = "/ahg/regev/users/ttickle/dev/Trinity_CTAT/mutation/src"
- str_test_data = "/seq/RNASEQ/public_ftp/CTAT/mutation/demo_data"
- str_testing_area = "/broad/hptmp/ttickle/active_testing_script_tester"
- os.environ['PATH'] = ":".join([str_script_dir,os.getenv('PATH',None)])
- str_input_index = os.path.join(str_test_data, "Hg19_11")
- str_input_test_bam = os.path.join(str_test_data, "Aligned.sortedByCoord.out.bam")
- str_left_file = os.path.join(str_test_data, "FLI1.left.fq")
- str_right_file = os.path.join(str_test_data, "FLI1.right.fq")
- str_reference_vcf = os.path.join(str_test_data, "dbsnp_FLI1.vcf")
- str_reference_genome = os.path.join(str_test_data, "Hg19_11.fa")
- str_update_command = "".join(["--update AddOrReplaceReadGroups.jar",
- ":/seq/regev_genome_portal/SOFTWARE/Picard/current,",
- "MarkDuplicates.jar",
- ":/seq/regev_genome_portal/SOFTWARE/Picard/current,",
- "SortSam.jar",
- ":/seq/regev_genome_portal/SOFTWARE/Picard/current,",
- "snpEff.jar",
- ":/seq/regev_genome_portal/SOFTWARE/snpEff,",
- "GenomeAnalysisTK.jar",
- ":/humgen/gsa-hpprojects/GATK/bin/GenomeAnalysisTK-3.1-1-g07a4bf8"])
- def test_rnaseq_mutation_pipeline_for_no_args(self):
- """
- Tests rnaseq_mutation_pipeline.py for no args call.
- """
- # Create test environment
- str_command = "python rnaseq_mutation_pipeline.py"
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertFalse(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_args_short(self):
- """
- Tests rnaseq_mutation_pipeline.py for help args call short.
- """
- # Create test environment
- str_command = "python rnaseq_mutation_pipeline.py -h"
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_args_long(self):
- """
- Tests rnaseq_mutation_pipeline.py for help args call short.
- """
- # Create test environment
- str_command = "python rnaseq_mutation_pipeline.py --help"
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_test(self):
- """
- Tests rnaseq_mutation_pipeline.py for test mode.
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--test",
- "--out_dir", "_".join([self.str_testing_area,"vanilla_test"]),
- "--vcf",self.str_reference_vcf,
- self.str_update_command])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_gatk_call(self):
- """
- Tests rnaseq_mutation_pipeline.py for gatk call.
- """
- str_output_dir = os.path.join(self.str_testing_area,"vanilla_gatk")
- self.func_make_dummy_dirs([self.str_testing_area, str_output_dir])
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--variant_filtering_mode GATK",
- "--out_dir",
- str_output_dir,
- "--vcf", self.str_reference_vcf,
- self.str_update_command])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_compression(self):
- """
- Tests rnaseq_mutation_pipeline.py for compression.
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right",self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_compression"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--compress","archive"])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_clean(self):
- """
- Tests rnaseq_mutation_pipeline.py for clean.
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_clean"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--clean"])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_archive(self):
- """
- Tests rnaseq_mutation_pipeline.py for archive.
- """
- # Create test environment
- str_copy_dir = os.path.join(self.str_testing_area, "copy_test_runs")
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_archive"]),
- "--vcf",self.str_reference_vcf, self.str_update_command,
- "--copy", str_copy_dir])
- # Run command
- if not os.path.exists(str_copy_dir):
- os.mkdir(str_copy_dir)
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_realign(self):
- """
- Tests rnaseq_mutation_pipeline.py for realignment.
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_realign"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--realign"])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_starting_with_bam(self):
- """
- Tests rnaseq_mutation_pipeline.py for starting with a bam.
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right",self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_bam"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--bam", self.str_input_test_bam])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_star_limited(self):
- """
- Tests rnaseq_mutation_pipeline.py for starting with start limited mode
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode LIMITED",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_limited"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_named_log_file(self):
- """
- Tests rnaseq_mutation_pipeline.py for starting with a named log file.
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_samtools"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--log", os.path.join("_".join([self.str_testing_area,"vanilla_log"]),"run.log")])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_starting_with_premade_index(self):
- """
- Tests rnaseq_mutation_pipeline.py for starting with a premade index
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_premade_index"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--index", self.str_input_index])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_no_recalibration(self):
- """
- Tests rnaseq_mutation_pipeline.py for no recalibration
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_no_recal"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--recalibrate_sam"])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_move(self):
- """
- Tests rnaseq_mutation_pipeline.py for moving files
- """
- # Create test environment
- str_move_dir = os.path.join(self.str_testing_area, "move_test_runs")
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--out_dir", "_".join([self.str_testing_area,"vanilla_no_move"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command,
- "--move", str_move_dir])
- # Run command
- if not os.path.exists(str_move_dir):
- os.mkdir(str_move_dir)
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- def test_rnaseq_mutation_pipeline_for_no_filtering(self):
- """
- Tests rnaseq_mutation_pipeline.py for a run with no filtering.
- """
- # Create test environment
- str_command = " ".join(["python rnaseq_mutation_pipeline.py",
- "--alignment_mode STAR",
- "--variant_call_mode GATK",
- "--threads 8",
- "--plot",
- "--reference", self.str_reference_genome,
- "--left", self.str_left_file,
- "--right", self.str_right_file,
- "--variant_filtering_mode NONE",
- "--out_dir", "_".join([self.str_testing_area,"vanilla_samtools"]),
- "--vcf", self.str_reference_vcf,
- self.str_update_command])
- # Run command
- f_success = Commandline.Commandline().func_CMD(str_command)
- # Test error
- self.assertTrue(f_success, str_command)
- # Creates a suite of tests
- def suite():
- return unittest.TestLoader().loadTestsFromTestCase(FunctionalTester)
FunctionalTester.py at commit 42855af, under BSD-3-Clause · at the source
Overview
Abstract
Glioblastoma (GBM) is an aggressive brain tumour with limited responsiveness to current immunotherapeutic approaches, partly due to its low mutational burden and intra-tumour heterogeneity. A systematic understanding of the tumour antigen landscape is therefore essential for advancing tumour immunology and supporting rational development of immunotherapeutic strategies. In this study, we performed whole-transcriptome sequencing of RNA extracted from 79 formalin-fixed paraffin-embedded (FFPE) IDH-wildtype GBM samples to systematically identify and prioritise candidate tumour antigens derived from three sources: single-nucleotide variants (SNVs), overexpressed tumour-associated antigens (TAAs), and gene fusion events. Candidate peptides were evaluated using integrated computational criteria, including transcript expression, predicted antigen processing features, peptide–HLA binding affinity and stability. Across the cohort, mutation-derived tumor-specific antigens (TSAs) were largely private to individual samples, whereas TAAs constituted a larger and more recurrent candidate pool. Despite comparable predicted binding characteristics across antigen classes, recurrence patterns differed substantially, reflecting their distinct biological origins. Fusion-derived candidates were rare and sample-specific. Predicted peptide presentation was disproportionately associated with a limited subset of HLA class I alleles. Collectively, this study provides a systematically prioritized catalogue of transcriptionally expressed GBM antigen candidates and offers a comparative evaluation of mutation-, expression-, and fusion-derived antigen sources within a unified transcriptome-based framework.
Supplementary Information: The online version contains supplementary material available at 10.1007/
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.
NCIP/ctat-mutations
42855afcc771db09819388ef71fb91f3a83a8415, 13 January 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
64 files
- Docker/
build_docker.sh , Shell, 10 lines - Docker/
install_R_packages.R , R, 24 lines - Docker/
make_simg.sh , Shell, 12 lines - Docker/
push_docker.latest.sh , Shell, 7 lines - Docker/
push_docker.sh , Shell, 9 lines - PyLib/
Pipeliner.py , Python, 256 lines - PyLib/
ctat_util.py , Python, 11 lines - WDL/
terra_data_prep/ , Python, 134 linesterra_data_prep.py - download_cromwell.sh, Shell, 5 lines
- mutation_lib_prep/
cosmic_integrator.py , Python, 122 lines - mutation_lib_prep/
ctat-mutation-lib-integr , Python, 154 linesation.py - mutation_lib_prep/
gencode_gtf_to_bed.pl , Perl, 46 lines - mutation_lib_prep/
gencode_gtf_to_splice_ad , Perl, 83 linesjacent_regions.pl - mutation_lib_prep/
make_CTAT_rnaediting_vcf , Perl, 110 liness.pl - src/
FunctionalTester.py , Python, 372 lines, 1 match - src/
ScriptTester.py , Python, 819 lines - src/
SingleCells/ , Perl, 39 linesadd_fake_quals_to_sam.pl - src/
SingleCells/ , Python, 67 linesvariant_cell_UMI_count_r eport.py - src/
Tester.py , Python, 23 lines - src/
VariantBoosting/ , Python, 738 linesApply_ML.py - src/
VariantBoosting/ , Python, 272 linesrun_boosting_methods.py - src/
annotate_DJ.py , Python, 160 lines - src/
annotate_ED.py , Python, 246 lines - src/
annotate_PASS_reads.extr , Python, 688 linesact_sc_info.py - src/
annotate_PASS_reads.py , Python, 532 lines - src/
annotate_boosted_vcf.py , Python, 90 lines - src/
annotate_entropy_n_homop , Python, 214 linesolymers.py - src/
annotate_exon_splice_pro , Python, 138 linesximity.py - src/
annotate_repeats.py , Python, 90 lines - src/
annotate_with_cravat.py , Python, 63 lines - src/
annotated_vcf_to_feature , Python, 226 lines_matrix.py - src/
cigar_N_splitter.py , Python, 191 lines - src/
combine_vchk.py , Python, 104 lines - src/
confirm_maf_mutations.py , Python, 311 lines - src/
ctat_util.py , Python, 10 lines - src/
filter_snps_rna_editing. , Python, 146 linespy - src/
filter_variant_clusters. , Python, 143 linespy - src/
filter_vcf_for_cancer_pr , Python, 137 linesediction_report.py - src/
groom_cravat_annotation. , Python, 117 linespy - src/
groom_vcf.py , Python, 156 lines - src/
hold/ , Python, 147 linessummarize_annotate_vcf.p y - src/
hold/ , Python, 316 linestabs_to_percent_mutation s.py - src/
jaccard_distance.R , R, 30 lines - src/
jaccard_distance_restric , R, 45 linested.R - src/
make_dendrogram_generic. , R, 28 linesR - src/
make_inspector_json.py , Python, 180 lines - src/
make_mutation_inspector_ , Python, 47 linesjson.py - src/
make_paired_to_unpaired_ , Perl, 75 linesbam.pl - src/
normalize_bam_by_strand. , Python, 84 linespy - src/
plot_vcf_sizes.py , Python, 47 lines - src/
reduce_vcf_to_snps.py , Python, 101 lines - src/
separate_bam_by_strand.p , Python, 79 linesy - src/
separate_snps_indels.py , Python, 158 lines - src/
update_snpeff_annotation , Python, 68 liness.py - src/
vcf_attribute_counter.py , Python, 88 lines - src/
vcfs_to_genotype_matrix. , Python, 103 linespy - src/
vcfs_to_snp_calls_tab.py , Python, 237 lines - src/
visualize_mutation_depth , R, 559 lines_tab_files.R - testing/
__init__.py , Python, 1 line - testing/
conftest.py , Python, 12 lines - testing/
test.sh , Shell, 11 lines - testing/
test_ctat_mutations.py , Python, 63 lines - LICENSE.txt, License, 16 lines
- README.md, Text, 19 lines
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 62 scripts, each with its path and the digest of its content;
- 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability
The data presented in this study are available on request from the corresponding author. The normal tissue dataset analysed in this study was obtained from: [https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 29 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 5 keywords, 8 MeSH terms, 1 funder, 48 references.
Cite
This paper
Kert, Š., Pižem, J., Petrin, S., Bošnjak, M., Jerala, M., Matjašič, A., & Zupan, A. (2026). Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes. Cancer immunology, immunotherapy : CII, 75(5), 149. https://
BibTeX
@article{kert2026identif
author = {Kert, Špela and Pižem, Jože and Petrin, Sara and Bošnjak, Matic and Jerala, Miha and Matjašič, Alenka and Zupan, Andrej},
title = {{Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes}},
journal = {Cancer immunology, immunotherapy : CII},
year = {2026},
month = apr,
volume = {75},
number = {5},
pages = {149},
publisher = {Springer},
issn = {0340-7004},
doi = {10.1007/
url = {https://
pmid = {42012534},
pmcid = {PMC13100171}
}
RIS
TY - JOUR
AU - Kert, Špela
AU - Pižem, Jože
AU - Petrin, Sara
AU - Bošnjak, Matic
AU - Jerala, Miha
AU - Matjašič, Alenka
AU - Zupan, Andrej
TI - Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes
T2 - Cancer immunology, immunotherapy : CII
J2 - Cancer Immunol Immunother
PY - 2026
DA - 2026/
VL - 75
IS - 5
SP - 149
SN - 0340-7004
PB - Springer
DO - 10.1007/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1007/
"type": "article-journal",
"title": "Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes",
"container-title": "Cancer immunology, immunotherapy : CII",
"author": [
{
"family": "Kert",
"given": "Špela"
},
{
"family": "Pižem",
"given": "Jože"
},
{
"family": "Petrin",
"given": "Sara"
},
{
"family": "Bošnjak",
"given": "Matic"
},
{
"family": "Jerala",
"given": "Miha"
},
{
"family": "Matjašič",
"given": "Alenka"
},
{
"family": "Zupan",
"given": "Andrej"
}
],
"container-title-short":
"volume": "75",
"issue": "5",
"page": "149",
"DOI": "10.1007/
"PMID": "42012534",
"PMCID": "PMC13100171",
"ISSN": "0340-7004",
"publisher": "Springer",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
21
]
]
}
}
The tracing map gets a citation of its own once an author has validated it and it has a DOI.
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The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.
- [1] doi:10.1038/s41592-026-03211-w [code]
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Journal: Nature methodsIn common: pysam, BEDTools, XGBoost, 10 other tools, genetics / omics, 1 reference
- [2] doi:10.21203/rs.3.rs-9927928/v1 [code]
- Genome-wide and allele-resolved maps of the radial architecture of the mouse genomeJournal: Research Square (preprint)In common: BCFtools, pysam, BEDTools, 8 other tools, genetics / omics, 2 references
- [3] doi:10.1038/s41467-026-76675-1 [code]
- Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.Journal: Nature communicationsIn common: pysam, BEDTools, SAMtools, 8 other tools, genetics / omics, 3 references
- [4] doi:10.1038/s41467-026-72598-z [code]
- Functional impact of genetic background on variable expressivity in neurodevelopmental disorders.Journal: Nature communicationsIn common: BCFtools, BEDTools, SAMtools, 7 other tools, other condition, 3 references
- [5] doi:10.1038/s41467-026-71790-5 [code]
- Recurrent DNA break clusters drive replication-stress-induc
ed copy number variants and genome diversification. Journal: Nature communicationsIn common: BCFtools, pysam, BEDTools, 8 other tools, genetics / omics, cellular / molecular - [6] doi:10.1093/bioinformatics/btag592 [code]
- Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.Journal: Bioinformatics (Oxford, England)In common: BCFtools, SAMtools, reshape2, 7 other tools, genetics / omics, other condition, 3 references
- [7] doi:10.1002/alz.71271 [code]
- Intracellular protein GBF1 displays significant associations with amyloid pathology in Alzheimer's disease.Journal: Alzheimer's & dementia : the journal of the Alzheimer's AssociationIn common: BCFtools, pysam, BEDTools, 8 other tools, cellular / molecular
- [8] doi:10.1038/s42003-026-10957-8 [code]
- Brain defence by the extracellular matrix protein Cochlin.Journal: Communications biologyIn common: BCFtools, XGBoost, SAMtools, 9 other tools, cellular / molecular
- [9] doi:10.1038/s41467-026-69944-6 [code]
- Multi-modal dissection of cell-type specific TDP-43 pathology in the motor cortex.Journal: Nature communicationsIn common: pysam, BEDTools, SAMtools, 7 other tools, genetics / omics, other condition, 2 references
- [10] doi:10.1038/s41598-026-53415-5 [code]
- Computational design and immunoinformatics validation of a T cell multi-epitope vaccine targeting glioblastoma stem cells.Journal: Scientific reportsIn common: scikit-learn, pandas, SciPy, 2 other tools, other condition, cellular / molecular, 6 references
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