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Offline Website BuilderBorn in Izmir, Turkey on November 12th 1992
e-mail: oguzhanbegik@gmail.com
Currently living in Barcelona , Spain
Molecular Biology and Genetics
Molecular Biology and Genetics
Medicine
January 2022 - Current
Centre for Genomic Regulation (CRG) - Barcelona, Spain
Epitranscriptomics and RNA Dynamics Lab, Supervisor : Dr. Eva Maria Novoa
Research focus : Exploring RNA dynamics using nanopore sequencing technologies from both bench and computer perspective
August 2017 - January 2022
Garvan Institute of Medical Research - Sydney, Australia
Centre for Genomic Regulation (CRG) - Barcelona, Spain
RNA and Plasticity Lab, Supervisor: Prof. Dr. John S. Mattick
Epitranscriptomics and RNA Dynamics Lab, Supervisor: Dr. Eva Maria Novoa
PhD Thesis title: "Characterizing the RNA modification and polyadenylation landscape at single molecule resolution using third-generation sequencing Technologies"
January 2015 - June 2017
Middle East Technical University (METU) - Ankara, Turkey
Cancer Genetics Lab, Supervisor : Prof. Dr. Elif Erson Bensan
MSc Thesis title: "Role of alternative polyadenylation in cancer and differentiation"
September 2014 - January 2015
Middle East Technical University (METU) - Ankara, Turkey
Cancer Genetics Lab, Supervisor : Prof. Dr. Sreeparna Banerjee
Research focus : Effects of AKR1B10 gene on proliferation of colorectal cancer cells
June 2014 - September 2014
Centre for Genomic Regulation (CRG) - Barcelona, Spain
Genomic Architecture Lab, Supervisor : Dr. Guillaume Filion
Research focus : Epigenetic Mechanisms and Reactivation of Latent HIV Reservoirs
August 2012 - June 2013
Middle East Technical University (METU) - Ankara, Turkey
Nanotechnology Lab, Supervisor : Prof. Dr. Irem Erel
Research focus : Hydrogen-bonded Multilayers with Contrallable pH-induced Disintegration Kinetics for Controlled Release Applications from Surfaces
• Beğik O, Diensthuber G, Liu H, Delgado-Tejedor A, Kontur C, Niazi AM, Valen E, Giraldez AJ, Beaudoin JD, Mattick JS, Novoa EM. “Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing” accepted in Nature Methods, 2022
• Beğik O, Mattick JS, Novoa EM. “Diving into the epitranscriptome: challenges and opportunities of native RNA nanopore sequencing”. RNA, 2022
• Liu H*, Beğik O*, Novoa EM. “EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing” RNA Modifications, Methods in Molecular Biology, vol 2298, 2021
• Beğik O*, Lucas MC*, Pryszcz LP, Ramirez JM, Medina R, Milenkovic I, Cruciani S, Liu H, Vieira HGS, Sas-Chen A, Mattick JS, Schwartz S, Novoa EM. “Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing”. Nature Biotechnology, 2021
• Smith MA*, Ersavas T*, Ferguson JM*, Liu H, Lucas MC, Beğik O, Bojarski L, Barton K, Novoa EM. “Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning”. Genome Research, 2020
• Beğik O, Lucas MC, Liu H, Ramirez JM, Mattick JS, Novoa EM. “Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures”. Genome Biology, 21, 97, 2020.
• Liu H*, Beğik O*, Lucas MC, Ramirez JM, Mason C, Wiener D, Schwartz S, Mattick JS, Smith M, Novoa EM. “Accurate detection of m6A RNA modifications in native RNA sequences”. Nature Communications, 2019
• Beğik O, Oyken M, Cinkilli Alican T, Can T, Erson Bensan AE. “Alternative Polyadenylation patterns for novel gene discovery and classification in cancer”. Neoplasia, 2017
• Erson Bensan AE, Beğik O, “m6A Modification and Implications for microRNAs” MicroRNA, 2017
• Bag E, Beğik O, Yusan P, Erel-Goktepe I. “Hydrogen-bonded Multilayers with Contrallable pH-induced Disintegration Kinetics for Controlled Release Applications from Surfaces”. Journal of Macromolecular Science, Part A: Pure and Applied Chemistry, 2015, 52, 286.
* Co-first authors
• RNA Society Meeting 2022 (RNA 2022), “Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing”. Boulder-USA, May 2022 (RNA Society Eclipse Award)
• RNA Society Meeting 2021 (RNA 2021), “Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing”. Virtual Conference, June 2021
• Cambridge RNA Club, “Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing”. Virtual Talk, April 2021
• RNA Institute Mini Symposium, “Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing”. Virtual Symposium, March 2021
• XIII. PhD Symposium of Centre for Genomic Regulation, “Identifying the molecular fingerprints of rRNA modifications using paired direct RNA and cDNA sequencing”. Barcelona-Spain, November 2019
• EMBL Symposium: Complex life of RNA, “Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics
using end-capture nanopore cDNA sequencing”. Heidelberg-Germany, October 2022
• RNA Editing Gordon Research Conference, “Accurate detection of m6A RNA modifications in native RNA sequences”. Lucca- Italy, March 2019 (Poster Prize Winner)
• XII. PhD Symposium of Centre for Genomic Regulation, “Deciphering m3C Modifications on mRNA”. Barcelona-Spain, November 2018
• EMBL Post-Graduate Symposium, “Deciphering m3C Modifications on mRNA”. Sydney-Australia, November 2017
• RNA Society Meeting 2017 (RNA 2017), ““Alternative Polyadenylation patterns for novel gene discovery and classification in cancer””, Prague-Czechia, June 2017
• EMBO Conference: From Functional Genomics to Systems Biology, . “Identification of a potential cancer related lncRNA”. Heidelberg-Germany, November 2016
• FEBS 2016 41st Congress, “3’UTR length isoform generation profile in a differentiation model.”. Kusadasi-Turkey, September 2016
• IV. International Congress of the Molecular Biology Association of Turkey, “Alternative Polyadenylation in a Differentiation Model: Caco-2 Cells”. Ankara-Turkey, November 2015
• EMBL Symposium: Complex life of RNA (October 2022, Heidelberg-Germany)
• RNA Society Meeting 2022 (May 2022, Boulder-USA)
• XIII. PhD Symposium of Centre for Genomic Regulation (November 2019, Barcelona-Spain)
• RNA Editing Gordon Research Conference (March 24-29 2019, Lucca-Italy)
• EMBL Course: Advanced Training with Oxford Nanopore Technologies (January 2019, Heidelberg-Germany)
• XII. PhD Symposium of Centre for Genomic Regulation (November 2018, Barcelona-Spain)
• EMBL Post-Graduate Symposium, Garvan Institute of Medical Research (November 2017, Sydney-Australia)
• Australian National Computational Infrastructure (NCI) Autumn Training Session (April 2018, Canberra-Australia)
• AMSI Bioinfosummer Course 2017 (December 2017, Melbourne-Australia)
• 22nd Annual Meeting of the RNA Society (June 2017- Prague-Czechia)
• EMBO Conference: From Functional Genomics to Systems Biology (November 2016, Heidelberg-Germany)
• EMBO Course: Regulatory small and long ncRNAs: Durat et lucet (11-17 June 2016, Trento-Italy)
• Molecular Biology Association of Turkey Congress (November 2015, Ankara-Turkey)
• UNSW School of Clinical Medicine St Vincent’s Healthcare Clinical Campus HDR Thesis Award, 2022
• Garvan Institute of Medical Research PhD Thesis Award, 2022
• RNA Society Eclipse Award for Innovation in High Throughput Biology, January 2022
• Poster Prize Winner at GRC RNA Editing Conference, March 2019
• Boehringer Ingelheim Travel Grant for EMBL Course, January 2019
• University International Postgraduate Award (UIPA) at UNSW, Semester 2 2017
• Travel Grant for 22nd Annual Meeting of the RNA Society, June 2017
• Travel Grant for EMBO Course: Regulatory small and long ncRNAs: Durat et lucet, June 2016
• The Scientific and Technological Research Council of Turkey Project Scholar (09/2015- 02/2016)
• Middle East Technical University High Honor List (2014) /Honor List (2011, 2012, 2013, 2015)
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