Husen M. Umer
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View article: Proteogenomics analysis of human tissues using pangenomes
Proteogenomics analysis of human tissues using pangenomes Open
The genomics landscape is evolving with the emergence of pangenomes, challenging the conventional single-reference genome model. The new human pangenome reference provides an extra dimension by incorporating variations observed in differen…
View article: Glioblastoma stem cells express non‐canonical proteins and exclusive mesenchymal‐like or non‐mesenchymal‐like protein signatures
Glioblastoma stem cells express non‐canonical proteins and exclusive mesenchymal‐like or non‐mesenchymal‐like protein signatures Open
Glioblastoma (GBM) cancer stem cells (GSCs) contribute to GBM's origin, recurrence, and resistance to treatment. However, the understanding of how mRNA expression patterns of GBM subtypes are reflected at global proteome level in GSCs is l…
View article: Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia Open
Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications rem…
View article: Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia Open
Summary Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic based diagnostics. The relevance of proteomics for disease classificat…
View article: Glioblastoma stem cells express non-canonical proteins and exclusive mesenchymal-like or non-mesenchymal-like protein signatures
Glioblastoma stem cells express non-canonical proteins and exclusive mesenchymal-like or non-mesenchymal-like protein signatures Open
Glioblastoma’s (GBM) origin, recurrence and resistance to treatment are driven by GBM cancer stem cells (GSCs). Existing transcriptomic characterisations of GBM classify the tumours to three subtypes: classical, proneural, and mesenchymal.…
View article: Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides Open
Summary We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a …
View article: Bioinformatics analysis of NSCLC multi-omics data
Bioinformatics analysis of NSCLC multi-omics data Open
The associated publication reports proteogenomic analysis of non-small cell lung cancer (NSCLC), where we identified molecular subtypes with distinct immune evasion mechanisms and therapeutic targets, and validated our classification metho…
View article: Mass spectrometry-based proteomic analysis of NSCLC tumor and biopsy samples
Mass spectrometry-based proteomic analysis of NSCLC tumor and biopsy samples Open
The associated publication reports proteogenomic analysis of non-small cell lung cancer, where we identified molecular subtypes with distinct immune evasion mechanisms and therapeutic targets, and validated our classification method in sep…
View article: Immune landscape evaluation of NSCLC clinical samples
Immune landscape evaluation of NSCLC clinical samples Open
The associated publication reports proteogenomic analysis of non-small cell lung cancer, where we identified molecular subtypes with distinct immune evasion mechanisms and therapeutic targets, and validated our classification method in sep…
View article: STK11 pathway in vitro validation
STK11 pathway in vitro validation Open
The associated publication reports proteogenomic analysis of non-small cell lung cancer (NSCLC), where we identified molecular subtypes with distinct immune evasion mechanisms and therapeutic targets, and validated our classification metho…
View article: Functional annotation of noncoding mutations in cancer
Functional annotation of noncoding mutations in cancer Open
In a cancer genome, the noncoding sequence contains the vast majority of somatic mutations. While very few are expected to be cancer drivers, those affecting regulatory elements have the potential to have downstream effects on gene regulat…
View article: Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy
Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy Open
Knowledge of clinically targetable tumor antigens is becoming vital for broader design and utility of therapeutic cancer vaccines. This information is obtained reliably by directly interrogating the MHC-I presented peptide ligands, the imm…
View article: Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides Open
Summary We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a …
View article: funMotifs: Tissue-specific transcription factor motifs
funMotifs: Tissue-specific transcription factor motifs Open
Transcription factors (TF) regulate gene expression by binding to specific sequences known as motifs. A bottleneck in our knowledge of gene regulation is the lack of functional characterization of TF motifs, which is mainly due to the larg…
View article: Supplementary Tables for funMotifs: Tissue-specific transcription factor motifs
Supplementary Tables for funMotifs: Tissue-specific transcription factor motifs Open
funMotifs is developed to annotate transcription factor motifs using functional annotations.
View article: Computational Modelling of Gene Regulation in Cancer : Coding the noncoding genome
Computational Modelling of Gene Regulation in Cancer : Coding the noncoding genome Open
Technological advancements have enabled quantification of processes within and around us. The information stored within our body converts into petabytes of data. Processing and learning from such data requires comprehensive computational p…
View article: Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes Open
Discovery of cancer drivers has traditionally focused on the identification of protein-coding genes. Here we present a comprehensive analysis of putative cancer driver mutations in both protein-coding and non-coding genomic regions across …
View article: Maps of context-dependent putative regulatory regions and genomic signal interactions
Maps of context-dependent putative regulatory regions and genomic signal interactions Open
Gene transcription is regulated mainly by transcription factors (TFs). ENCODE and Roadmap Epigenomics provide global binding profiles of TFs, which can be used to identify regulatory regions. To this end we implemented a method to systemat…