Accès ouvert
2026
article
OpenAlex
Özlem Muslu, Thomas Bukur, Pablo Riesgo-Ferreiro, Sameesh Kher et autres
BACKGROUND: Accurately identifying somatic variants from genomic sequencing is crucial for understanding and treating cancer. Previously, methods based on statistics and heuristics, as well as methods based on machine learning were proposed for somatic single nucleotide variant (SNV) calling from matched tumor-normal …
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Accès ouvert
2026
article
OpenAlex
Özlem Muslu, Thomas Bukur, Pablo Riesgo-Ferreiro, Sameesh Kher et autres
Additional file 2. Supplementary Figures (Fig. S1-S16).
de
(code pays fourni par la source)
Accès ouvert
2026
other
OpenAlex
Özlem Muslu, Thomas Bukur, Pablo Riesgo-Ferreiro, Sameesh Kher et autres
Abstract Background Accurately identifying somatic variants from genomic sequencing is crucial for understanding and treating cancer. Previously, methods based on statistics and heuristics, as well as methods based on machine learning were proposed for somatic single nucleotide variant (SNV) calling from matched …
de
(code pays fourni par la source)
Accès ouvert
2026
dataset
OpenAlex
Özlem Muslu, Thomas Bukur, Pablo Riesgo-Ferreiro, Sameesh Kher et autres
Additional file 1. Supplementary Tables (Table S1-S13).
de
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Accès ouvert
2026
dataset
OpenAlex
Özlem Muslu, Thomas Bukur, Pablo Riesgo-Ferreiro, Sameesh Kher et autres
Additional file 1. Supplementary Tables (Table S1-S13).
de
(code pays fourni par la source)
Accès ouvert
2026
other
OpenAlex
Özlem Muslu, Thomas Bukur, Pablo Riesgo-Ferreiro, Sameesh Kher et autres
Abstract Background Accurately identifying somatic variants from genomic sequencing is crucial for understanding and treating cancer. Previously, methods based on statistics and heuristics, as well as methods based on machine learning were proposed for somatic single nucleotide variant (SNV) calling from matched …
de
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Özlem Muslu, Thomas Bukur, Pablo Riesgo-Ferreiro, Sameesh Kher et autres
Additional file 2. Supplementary Figures (Fig. S1-S16).
de
(code pays fourni par la source)
Accès ouvert
2026
software
OpenAlex
Özlem Muslu, Pablo Riesgo-Ferreiro, Luis Kress
Changes: Upgrade the dependencies to latest versions that could be solved in conda environments/test environment Change samtools merge and index with sambamba merge and index, add an optional BAM sorting step if the BAM wasn't sorted before merge Move all params initializations …
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Accès ouvert
2026
software
OpenAlex
Pablo Riesgo-Ferreiro, Özlem Muslu, Luis Kress, Jonas Ibn-Salem
Upgrade Vafator to v3.0.0 There were breaking changes in this Vafator release.
in, de
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Accès ouvert
2026
software
OpenAlex
Pablo Riesgo-Ferreiro, Özlem Muslu, Luis Kress
vafator 3.0.0 Performance ~13x runtime improvement over v2 on a 292K variant VCF (SEQC2 WES WES_EA_1, 5.5 hours → 23 minutes with 4 cores). Streaming pileup iterator — replaced per-variant bam.pileup() calls with a single pileup iterator per chromosome per BAM. This …
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Accès ouvert
2025
article
OpenAlex
Robert Bentham, Thomas P. Jones, James R. Black, Carlos Martínez‐Ruiz et autres
Recognition and elimination of pathogens and cancer cells depend on the adaptive immune system. Thus, accurate quantification of immune subsets is vital for precision medicine. We present immune lymphocyte estimation from nucleotide sequencing (ImmuneLENS), which estimates T cell and B cell fractions, …
gb, us, jp, dk, sg
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Accès ouvert
2024
article
OpenAlex
Franziska Lang, Patrick Sorn, M Suchan, Alina Henrich et autres
Motivation: Neoantigens are promising targets for cancer immunotherapies and might arise from alternative splicing. However, detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumors also appear in healthy tissues. To increase tumor-specificity, we focused on splicing caused by …
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