Publications by authors named "Arif Canakoglu"

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The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Jacob Matthew Schreiber, Carles A Boix, Jin Wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert

Genome Biol· April 2023

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Jacob Matthew Schreiber, Carles A Boix, Jin Wook Lee, Hongyang Li, Yuanfang Guan, Arif Canakoglu

Genome Biol· February 2025

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Elucidating the causal relationship of mechanical power and lung injury: a dynamic approach to ventilator management.
ChaoPing Wu, Arif Canakoglu, Jacob Vine, Anya Mathur, Ronit Nath

Intensive Care Med Exp· February 2025

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Impact of Positive End-Expiratory Pressure and FiO on Lung Mechanics and Intrapulmonary Shunt in Mechanically Ventilated Patients with ARDS Due to COVID-19 Pneumonia.
Gaetano Florio, Alberto Zanella, Douglas Slobod, Amedeo Guzzardella, Ilaria Protti, Arif Canakoglu

J Intensive Care Med· May 2024

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VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants.
Pietro Pinoli, Arif Canakoglu, Stefano Ceri, Matteo Chiara, Erika Ferrandi

Database (Oxford)· July 2023

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Correction: Processing genome-wide association studies within a repository of heterogeneous genomic datasets.
Anna Bernasconi, Arif Canakoglu, Federico Comolli

BMC Genom Data· June 2023

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Processing genome-wide association studies within a repository of heterogeneous genomic datasets.
Anna Bernasconi, Arif Canakoglu, Federico Comolli

BMC Genom Data· March 2023

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Association of COVID-19 Vaccinations With Intensive Care Unit Admissions and Outcome of Critically Ill Patients With COVID-19 Pneumonia in Lombardy, Italy.
Giacomo Grasselli, Alberto Zanella, Eleonora Carlesso, Gaetano Florio, Arif Canakoglu

JAMA Netw Open· October 2022

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Genomic data integration and user-defined sample-set extraction for population variant analysis.
Tommaso Alfonsi, Anna Bernasconi, Arif Canakoglu, Marco Masseroli

BMC Bioinformatics· September 2022

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ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time.
Luca Cilibrasi, Pietro Pinoli, Anna Bernasconi, Arif Canakoglu, Matteo Chiara

Bioinformatics· March 2022

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High Performance Integration Pipeline for Viral and Epitope Sequences.
Tommaso Alfonsi, Pietro Pinoli, Arif Canakoglu

BioTech (Basel)· March 2022

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META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration.
Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri

IEEE/ACM Trans Comput Biol Bioinform· February 2022

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Investigating Deep Learning Based Breast Cancer Subtyping Using Pan-Cancer and Multi-Omic Data.
Francisco Cristovao, Silvia Cascianelli, Arif Canakoglu, Mark Carman, Luca Nanni

IEEE/ACM Trans Comput Biol Bioinform· February 2022

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VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants.
Anna Bernasconi, Andrea Gulino, Tommaso Alfonsi, Arif Canakoglu, Pietro Pinoli

Nucleic Acids Res· September 2021

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EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species.
Anna Bernasconi, Luca Cilibrasi, Ruba Al Khalaf, Tommaso Alfonsi, Stefano Ceri, Arif Canakoglu

Database (Oxford)· September 2021

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Federated sharing and processing of genomic datasets for tertiary data analysis.
Arif Canakoglu, Pietro Pinoli, Andrea Gulino, Luca Nanni, Marco Masseroli

Brief Bioinform· May 2021

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A review on viral data sources and search systems for perspective mitigation of COVID-19.
Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Pietro Pinoli, Stefano Ceri

Brief Bioinform· March 2021

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The road towards data integration in human genomics: players, steps and interactions.
Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri

Brief Bioinform· January 2021

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ViruSurf: an integrated database to investigate viral sequences.
Arif Canakoglu, Pietro Pinoli, Anna Bernasconi, Tommaso Alfonsi, Damianos P Melidis

Nucleic Acids Res· January 2021

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PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets.
Luca Nanni, Pietro Pinoli, Arif Canakoglu, Stefano Ceri

BMC Bioinformatics· November 2019

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Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language.
Stefano Perna, Arif Canakoglu, Pietro Pinoli, Stefano Ceri, Limsoon Wong

Methods Mol Biol· March 2019

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Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data.
Marco Masseroli, Arif Canakoglu, Pietro Pinoli, Abdulrahman Kaitoua, Andrea Gulino

Bioinformatics· March 2019

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GenoSurf: metadata driven semantic search system for integrated genomic datasets.
Arif Canakoglu, Anna Bernasconi, Andrea Colombo, Marco Masseroli, Stefano Ceri

Database (Oxford)· January 2019

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Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction.
Marco Masseroli, Arif Canakoglu, Stefano Ceri

IEEE/ACM Trans Comput Biol Bioinform· January 2017

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Detection of gene annotations and protein-protein interaction associated disorders through transitive relationships between integrated annotations.
Marco Masseroli, Arif Canakoglu, Massimiliano Quigliatti

BMC Genomics· February 2016

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