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View article: Efficient identification of de novo mutations in family trios: a consensus-based informatic approach
Efficient identification of de novo mutations in family trios: a consensus-based informatic approach Open
Accurate identification of de novo variants (DNVs) remains challenging despite advances in sequencing technologies, often requiring ad hoc filters and manual inspection. Here, we explored a purely informatic, consensus-based approach for i…
View article: PANGENOMES AID ACCURATE DETECTION OF LARGE INSERTION AND DELETIONS FROM GENE PANEL DATA: THE CASE OF CARDIOMYOPATHIES
PANGENOMES AID ACCURATE DETECTION OF LARGE INSERTION AND DELETIONS FROM GENE PANEL DATA: THE CASE OF CARDIOMYOPATHIES Open
Gene panels represent a widely used strategy for genetic testing in a vast range of Mendelian disorders. While this approach aids reliable bioinformatic detection of short coding variants, it fails to detect most larger variants. Recent st…
View article: Pangenome References Improve Biomarker Estimation from Tumor Sequencing Data
Pangenome References Improve Biomarker Estimation from Tumor Sequencing Data Open
It has recently been shown that patients from non-European ancestries are at a higher risk of inappropriate clinical intervention because of inaccurate biomarker estimation, arising from the reference bias inherent in standard methods for …
View article: Automated Identification of Germline<i>de novo</i>Mutations in Family Trios: A Consensus-Based Informatic Approach
Automated Identification of Germline<i>de novo</i>Mutations in Family Trios: A Consensus-Based Informatic Approach Open
Accurate identification of germline de novo variants (DNVs) remains a challenging problem despite rapid advances in sequencing technologies as well as methods for the analysis of the data they generate, with putative solutions often involv…
View article: Whole genome sequencing for metastatic mutational burden in extraskeletal myxoid chondrosarcoma
Whole genome sequencing for metastatic mutational burden in extraskeletal myxoid chondrosarcoma Open
Extraskeletal myxoid chondrosarcoma (EMC) is an ultra-rare cancer that makes up less than 3% of all soft tissue sarcomas. It most often arises in the soft tissues of the proximal limbs and has a higher incidence in males. Though EMC has a …
View article: Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis
Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis Open
View article: PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions Open
View article: Population-specific genome graphs improve high-throughput sequencing data analysis: A case study on the Pan-African genome
Population-specific genome graphs improve high-throughput sequencing data analysis: A case study on the Pan-African genome Open
Graph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference to represent the diverse genetic information from different human populations and its inabili…
View article: precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions Open
Summary The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied th…
View article: Inferring causal molecular networks: empirical assessment through a community-based effort
Inferring causal molecular networks: empirical assessment through a community-based effort Open
Inferring molecular networks is a central challenge in computational biology. However, it has remained unclear whether causal, rather than merely correlational, relationships can be effectively inferred in complex biological settings. Here…
View article: Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues
Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues Open
View article: Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations
Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations Open
View article: Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles
Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles Open
RNA-binding proteins (RBPs) control the regulation of gene expression at posttranscriptional level. Several CLIP (crosslinking and immunoprecipitation) protocols are available to study RBPs; however, there are very few tools to understand …
View article: Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles
Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles Open
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols …
View article: ExSurv: A Web Resource for Prognostic Analyses of Exons Across Human Cancers Using Clinical Transcriptomes
ExSurv: A Web Resource for Prognostic Analyses of Exons Across Human Cancers Using Clinical Transcriptomes Open
Survival analysis in biomedical sciences is generally performed by correlating the levels of cellular components with patients' clinical features as a common practice in prognostic biomarker discovery. While the common and primary focus of…
View article: ExSurv: A Web Resource for Prognostic Analyses of Exons across Human Cancers Using Clinical Transcriptomes
ExSurv: A Web Resource for Prognostic Analyses of Exons across Human Cancers Using Clinical Transcriptomes Open
Survival analysis in biomedical sciences is generally performed by correlating the levels of cellular components with patients’ clinical features as a common practice in prognostic biomarker discovery. While the common and primary focus of…
View article: Seten: a tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles
Seten: a tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles Open
View article: Reconstruction of the temporal signaling network in Salmonella-infected human cells
Reconstruction of the temporal signaling network in Salmonella-infected human cells Open
Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the pathogen proteins into the host cells leads to changes in the signaling mechanism either by activating or inhibiting the h…
View article: Reconstruction of the temporal signaling network in <i>Salmonella</i>-infected human cells
Reconstruction of the temporal signaling network in <i>Salmonella</i>-infected human cells Open
Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the pathogen proteins into the host cells leads to changes in the signaling mechanism either by activating or inhibiting the h…