Arif Canakoglu
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View article: Elucidating the causal relationship of mechanical power and lung injury: a dynamic approach to ventilator management
Elucidating the causal relationship of mechanical power and lung injury: a dynamic approach to ventilator management Open
View article: Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles Open
View article: Correction: Processing genome-wide association studies within a repository of heterogeneous genomic datasets
Correction: Processing genome-wide association studies within a repository of heterogeneous genomic datasets Open
View article: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles Open
View article: Processing genome-wide association studies within a repository of heterogeneous genomic datasets
Processing genome-wide association studies within a repository of heterogeneous genomic datasets Open
Background Genome Wide Association Studies (GWAS) are based on the observation of genome-wide sets of genetic variants – typically single-nucleotide polymorphisms (SNPs) – in different individuals that are associated with phenotypic traits…
View article: VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants Open
With the progression of the COVID-19 pandemic, large datasets of SARS-CoV-2 genome sequences were collected to closely monitor the evolution of the virus and identify the novel variants/strains. By analyzing genome sequencing data, health …
View article: Association of COVID-19 Vaccinations With Intensive Care Unit Admissions and Outcome of Critically Ill Patients With COVID-19 Pneumonia in Lombardy, Italy
Association of COVID-19 Vaccinations With Intensive Care Unit Admissions and Outcome of Critically Ill Patients With COVID-19 Pneumonia in Lombardy, Italy Open
Importance Data on the association of COVID-19 vaccination with intensive care unit (ICU) admission and outcomes of patients with SARS-CoV-2–related pneumonia are scarce. Objective To evaluate whether COVID-19 vaccination is associated wit…
View article: Genomic data integration and user-defined sample-set extraction for population variant analysis
Genomic data integration and user-defined sample-set extraction for population variant analysis Open
View article: The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles
The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles Open
Functional genomics experiments are invaluable for understanding mechanisms of gene regulation. However, comprehensively performing all such experiments, even across a fixed set of sample and assay types, is often infeasible in practice. A…
View article: High Performance Integration Pipeline for Viral and Epitope Sequences
High Performance Integration Pipeline for Viral and Epitope Sequences Open
With the spread of COVID-19, sequencing laboratories started to share hundreds of sequences daily. However, the lack of a commonly agreed standard across deposition databases hindered the exploration and study of all the viral sequences co…
View article: Additional file 2 of Genomic data integration and user-defined sample-set extraction for population variant analysis
Additional file 2 of Genomic data integration and user-defined sample-set extraction for population variant analysis Open
Additional file 2. Example of transformed metadata: In this .xlsx (MS Excel) file, we list all the output metadata categories generated for each sample from the transformation of the 1KGP input datasets. The output metadata include informa…
View article: Additional file 1 of Genomic data integration and user-defined sample-set extraction for population variant analysis
Additional file 1 of Genomic data integration and user-defined sample-set extraction for population variant analysis Open
Additional file 1. Example of translation from VCF into GDM format for genomic region data: This .xlsx (MS Excel) spreadsheet exemplifies the transformation of the original 1KGP mutations—expressed in VCF format—into GDM genomic regions. A…
View article: GeCoAgent: A Conversational Agent for Empowering Genomic Data Extraction and Analysis
GeCoAgent: A Conversational Agent for Empowering Genomic Data Extraction and Analysis Open
With the availability of reliable and low-cost DNA sequencing, human genomics is relevant to a growing number of end-users, including biologists and clinicians. Typical interactions require applying comparative data analysis to huge reposi…
View article: EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species Open
EpiSurf is a Web application for selecting viral populations of interest and then analyzing how their amino acid changes are distributed along epitopes. Viral sequences are searched within ViruSurf, which stores curated metadata and amino …
View article: Mapping the human genetic architecture of COVID-19
Mapping the human genetic architecture of COVID-19 Open
View article: VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants
VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants Open
Variant visualization plays an important role in supporting the viral evolution analysis, extremely valuable during the COVID-19 pandemic. VirusViz is a web-based application for comparing variants of selected viral populations and their s…
View article: Automated Integration of Genomic Metadata with Sequence-to-Sequence Models
Automated Integration of Genomic Metadata with Sequence-to-Sequence Models Open
View article: Performance Prediction for Data-driven Workflows on Apache Spark
Performance Prediction for Data-driven Workflows on Apache Spark Open
Spark is an in-memory framework for implementing distributed applications of various types. Predicting the execution time of Spark applications is an important but challenging problem that has been tackled in the past few years by several …
View article: A review on viral data sources and search systems for perspective mitigation of COVID-19
A review on viral data sources and search systems for perspective mitigation of COVID-19 Open
With the outbreak of the COVID-19 disease, the research community is producing unprecedented efforts dedicated to better understand and mitigate the effects of the pandemic. In this context, we review the data integration efforts required …
View article: ViruSurf: an integrated database to investigate viral sequences
ViruSurf: an integrated database to investigate viral sequences Open
ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino…
View article: OpenGDC: Unifying, Modeling, Integrating Cancer Genomic Data and Clinical Metadata
OpenGDC: Unifying, Modeling, Integrating Cancer Genomic Data and Clinical Metadata Open
Next Generation Sequencing technologies have produced a substantial increase of publicly available genomic data and related clinical/biospecimen information. New models and methods to easily access, integrate and search them effectively ar…
View article: ViruSurf: an integrated database to investigate viral sequences
ViruSurf: an integrated database to investigate viral sequences Open
ViruSurf, available at http://gmql.eu/virusurf/ , is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid v…
View article: A Review on Viral Data Sources and Integration Methods for COVID-19 Mitigation
A Review on Viral Data Sources and Integration Methods for COVID-19 Mitigation Open
With the outbreak of the COVID-19 disease, the research community is producing unprecedented efforts dedicated to better understand and mitigate the affects of the pandemic. In this context, we review the data integration efforts required …
View article: META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration Open
The integration of genomic metadata is, at the same time, an important, difficult, and well-recognized challenge. It is important because a wealth of public data repositories is available to drive biological and clinical research; combinin…
View article: Empowering Virus Sequences Research through Conceptual Modeling
Empowering Virus Sequences Research through Conceptual Modeling Open
The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: bi…
View article: Federated sharing and processing of genomic datasets for tertiary data analysis
Federated sharing and processing of genomic datasets for tertiary data analysis Open
Motivation With the spreading of biological and clinical uses of next-generation sequencing (NGS) data, many laboratories and health organizations are facing the need of sharing NGS data resources and easily accessing and processing compre…
View article: The road towards data integration in human genomics: players, steps and interactions
The road towards data integration in human genomics: players, steps and interactions Open
Thousands of new experimental datasets are becoming available every day; in many cases, they are produced within the scope of large cooperative efforts, involving a variety of laboratories spread all over the world, and typically open for …
View article: Empowering Virus Sequence Research Through Conceptual Modeling
Empowering Virus Sequence Research Through Conceptual Modeling Open
View article: PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets
PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets Open
Background With the growth of available sequenced datasets, analysis of heterogeneous processed data can answer increasingly relevant biological and clinical questions. Scientists are challenged in performing efficient and reproducible dat…
View article: Genomic big data management, modeling and computing
Genomic big data management, modeling and computing Open