Genomics of Long noncoding RNA and Disease
Group
Group Leader
Rory Johnson
rory.johnson[at]ucd.ie
2020- Associate Professor, University College Dublin
2020- Adjunct Assistant Professor, University of Bern
2018 Visiting Fellow at Chinese Academy of Sciences (Guangzhou Institute of Biomedicine & Health)
2016-2021 Junior Group Leader, Swiss National Centre for Competence in Research in RNA & Disease
2014-2015 Diploma in Management for Scientists and Researchers (Instituto de Empresa, Madrid)
2010-2016 Ramón y Cajal Fellow / Staff Scientist, Centre for Genomic Regulation (with Roderic Guigó)
2007-2009 Postdoc, Genome Institute of Singapore (with Lawrence W. Stanton)
2002-2007 Wellcome Trust PhD, University of Leeds (with Noel J. Buckley)
1996-2000 MSci Physics, Imperial College (London)
Google Scholar
ORCID
Web of Science
UCD page
Group Members
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Michela Coan
DEVELOPMED Postdoctoral Fellow
BSc in Health Biotechnology (University of Udine)
MSc in Biotechnology (University of Trieste)
PhD (Italian National Cancer Institute, CRO and University of Verona)
michela.coan[at]ucd.ie
Sunandini Ramnarayanan
PhD student (Funded by SFI CRT Genomics Data Science & MSCA-Integrate)
Education: BS-MS in Biology (IISER, Mohali)
Field: Cancer driver analysis, CRISPR screen design, long non-coding RNAs
Project: Data-driven discovery of cancer driver long non-coding RNAs
Contact: sunandini.ramnarayanan@ucdconnect.ie
Ai Ming Tham
PhD student (Funded by Irish Research Council)
Education: BSc (Hons) Cell and Molecular Biology, University College Dublin
Field: CRISPR Prime Editing, driver mutations, long non-coding RNAs
Projects: Experimental modelling tumour mutations in long non-coding RNAs using CRISPR Prime Editing
Contact: ai.tham@ucdconnect.ie
Nivedha Balaji
PhD student (Funded by SBES, University College Dublin)
Education: B.Sc. in Microbiology, University of Madras
MS in Biological Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali)
Field: CRISPR Genome Editing, long non-coding RNAs, 3D spheroids
Project: Discovering long non-coding RNAs as novel therapeutic targets using 3D cancer cell models
Linkedin
Contact: nivedha.balaji@ucdconnect.ie
Roofiya Koya
PhD student (Funded by SFI's Centre for Research Training in Genomics Data Science)
Education: B.Tech in Electronics and Communication Engineering, Cochin University of Science and Technology, India
M.Sc in Data Science and Analytics, University College Cork, Ireland
Field: CRISPR-Cas9, Analysis of LncRNAs data
Project: Data analysis and CRISPR-Cas genome-editing for precision oncology
Contact: roofiya.koya@ucd.ie
Yifan Yu
PhD student (Funded by Chinese Scholarship Council)
Education: BSc Bioinformatics, Southern University of Science and Technology, China
Field: CRISPR screening, long non-coding RNAs
Project: Data-driven prioritization of targets for RNA therapeutics
Links: LinkedIn, Github
Contact: yifan.yu@ucdconnect.ie
Dylan Harvey
PhD student (Funded by Irish Research Council)
Education: BSc Biochemistry, University of Galway
MSc Biological and Biomolecular Science, University College Dublin
Field: lncRNA evolution
Project: Evolution of lncRNAs
LinkedIn
Contact: dylan.harvey@ucdconnect.ie
Ines Jover Bravo
Lab Manager & Research Associate
Education: Honours BSc in Biotechnology (University of Zaragoza, Spain)
MSc in Biological & Biomolecular Sciences (University College Dublin, Ireland)
Field: CRISPR-Cas9 and Genome Editing of LncRNAs, LncRNA Localisation
Project: The elements of long noncoding RNA function.
Contact: ines.joverbravo@ucd.ie
Sarang Bhutada
PhD student (Funded by SFI's Centre for Research Training in Genomics Data Science)
Education: B.Tech-M.Tech, Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, India
Project: Discovery and prediction of bioactive lncRNAs
Contact: sarang.bhutada@ucdconnect.ie
Bhavya Dhaka
PhD student (Funded by SFI CRT Genomics Data Science & MSCA-Integrate)
Education: M.Sc.in Bioinformatics and Applied Biotechnology (IBAB, Bangalore)
Field: Long non-coding RNA regulation in NSLC
Project: Single-cell genomics to accelerate the development of precision RNA therapeutics.
LinkedIn Github Google Scholar
Contact: bhavya.dhaka@ucdconnect.ie
Jack Roban
PhD student (Funded by SFI's Centre for Research Training in Genomics Data Science)
Education: BSc Genetics & Cell Biology, Dublin City University (Ireland)
MSc Bioinformatics & Computational Genomics, Queen's University Belfast (Northern Ireland, United Kingdom)
Field: Cancer genomics, long-non coding RNA's, analysis of lncRNA data
Project: Prioritization of targets for precision RNA therapeutics via cancer genomics data integration.
Contact: jack.roban@ucdconnect.ie
Zekiye Altan
Post-Doctoral Fellow (Funded by Irish Research Council)
Education: BSc in Molecular Biology and Genetics (Faculty of Science, Department of Molecular Biology and Genetics, University of Cumhuriyet, Turkey);
MSc in Medical Biology (Instute of Health Sciences, Department of Medical Biology, University of Gaziantep, Turkey);
PhD in Medical Biology and Genetics (Instute of Health Sciences, Department of Medical Biology and Genetics, University of Gaziantep, Turkey)
Contact: zekiye.altan[at]ucd.ie
Peiyi Chen
PhD student (Funded by Chinese Scholarship Council)
Education: MSc Japan Advanced Institute of Science and Technology, Japan
Field: Hepatocellular carcinoma, IncRNA, CRISPR screening, RNA therapy
Project: Advancing RNA Therapeutics for Hepatocellular Carcinoma through Enhanced Bioinformatics Strategies and CRISPR Technology
LinkedIn
Contact: peiyi.chen@ucdconnect.ie
Xingyu Guo
PhD student (Funded by Chinese Scholarship council)
Education: BSc in Chinese Traditional Medicine, Shihezi University
MSc in Drug Discovery and Pharmaceutical Science, University of Nottingham
Field: CRISPR Genome Editing, Long non-coding RNA, Antisense Oligonucleotide (ASO) therapy
Project: Non-protein coding RNA therapeutics in hepatocellular carcinoma powered by CRISPR-Cas9
Contact: Xingyu.Guo@ucdconnect.ie
Chengyang Ji
MSc student in Biological and Biomolecular Sciences
Education: BSc in Biological Sciences (Xi’an Jiaotong Liverpool University)
MSc in Bioinformatics and Systems Biology (The University of Manchester)
PhD in Biophysics (Peking Union Medical University)
Contact: chengyang.ji12@alumni.xjtlu.edu.cn
Wenjing Li
MSc student in Biological and Biomolecular Sciences
Education: BSc in Biological Science (University of Jinan)
Master project: Enhancing the role of lncRNA in cell proliferation
Contact: wenjing.li1@ucdconnect.ie
Amanda Piveta Schnepper
PhD student (Founded by São Paulo Research Foundation)
Education: BSc in Technological Chemistry with emphasis on Environmental Chemistry (State University of Ponta Grossa - Brazil)
MSc in Biotechnology (São Paulo State University - Brazil)
Field: Funcional analysis of lncRNAs Project: Discovery of lncRNAs associated with muscle-tumor communication
Contact: amanda.schnepper@unesp.br
Marwa Bekhet
PhD student (Funded by SFI's FutureNeuro)
Education: BSc (Hons) in Molecular and Genetics Engineering, Bahcesehir University, Turkey; MSc in Soft Biomechanics, Korea Advanced Institute of Science and Technology, South Korea
Field: IncRNA, CRISPR screening, RNA therapy, Neurodegenerative Diseases
Project: Development of RNA Therapies for Neurological Diseases
Contact: marwa.bekhet@ucdconnect.ie
Former Members
Panagiotis Chouvardas
Postdoc with SNF Sinergia Projects
Where is he now? Postdoc with Marianna Kruithof-de Julio group at Department for BioMedical Research at University of Bern
Sandra Zywssig
Research Assistant
Where is she now? Research Associate with Smart Surgical Instruments and Medical Devices Group at the University of Bern
Carlos Pulido-Quetglas
PhD student
Where is he now? Postdoc with Dirk Fasshauer, University of Lausanne
Núria Bosch
PhD student
Where is she now? Postdoc with Jolanda van Leeuwen, University of Lausanne
Roberta Esposito
Education: BSc in Biology (University Federico II, Italy); MSc in Molecular Diagnostics (University Federico II, Italy); PhD, Institute of Genetics and Biophysics - CNR of Naples.
Field: CRISPR-Cas9 and Genome Editing of lncRNAs
Project: CRISPR-Cas9 screening for identification of lncRNAs in drug resistance
Links: ResearchGate, Google Scholar
Contact: roberta.esposito[at]dbmr.unibe.ch
Where is she now? Senior Postdoc at Department for Biomedical Research, Bern
Taisia Polidori
MSc Biology for Molecular, Cellular and Pathophysiological Research (University of Roma Tre, Italy)
PhD (University of Bern)
taisia.polidor[at]dbmr.unibe.ch
Where is she now? Clinical trials manager, Bern
Adrienne Vancura
PhD student
BSc in Biology (University of Bern);
MSc in Biochemistry and Cancer Biology (University of Amsterdam)
adrienne.vancura@dbmr.unibe.ch
Where is she now? Postdoc at Whitehead Institute with Richard Young
Dominik Meise
Bioinformatician
BSc in Biology (University of Bern);
MSc in Bioinformatics and Computational Biology (University of Bern)
dominik.meise[at]dbmr.unibe.ch
Where is he now? Software engineer at Ender Diagnostics
Hugo Guillen-Ramirez
Marie Skłodowska-Curie Actions Postdoctoral Fellow
Education: BSc in Computer Systems Engineering (Instituto Tecnological de Tepic, Mexico); MSc in Computer Science (CICESE Research Centre, Mexico); PhD in Computer Science (CICESE Research Centre, Mexico).
Field: ncRNA annotation and machine learning applied to RNA.
Project: Annotation of lncRNA elements
Links: Google Scholar, LinkedIn, ORCID, ResearchGate
Contact: hugo.guillenramirez[at]ucd.ie
Where is he now? Senior Researcher at Department for BioMedical Research, Bern.
Tina Uroda
Marie Skłodowska-Curie Actions Postdoctoral Fellow
Education: BSc in Biotechnology and Pharmaceutical Research (Department of Biotechnology, University of Rijeka, Croatia); MSc in Pharmaceutical Research and Development (Department of Biotechnology, University of Rijeka, Croatia); PhD, European Molecular Biology Laboratory EMBL, Grenoble, and Universite Grenoble Alpes.
Field: CRISPR-Cas9 and Genome Editing of LncRNAs, LncRNA Localisation.
Projects: The elements of long noncoding RNA function.
Contact: tina.uroda[at]ucd.ie
Andrés Lanzós
Education: BSc in Biology (University of Vigo, Spain); MSc in Bioinformatics for Health Science (Pompeu Fabra University, Spain); PhD in Biomedical Sciences (University of Bern, Switzerland)
Field: Cancer genomics and LncRNA drivers identification
Projects: Bioinformatic analysis of lncRNAs implicated in cancer
Links: Google Scholar, LinkedIn, ORCID, Publons, ResearchGate, Twitter
Contact: andreslanzos@runbox.com
Where is he now? Bioinformatician at Biognosys
Alessandra Stuerchler
NCCR Predoc Programme
Education: BSc in Biology (University of Lausanne, Switzerland); MSc in Molecular Biology (ETH Zürich, Switzerland); NCCR RNA&Disease Predoc Program (University of Bern, Switzerland).
Field: Bioinformatics of lncRNA features and functional domains
Project: Relationship between exons and functional domains in lncRNAs.
Links: Linkedin
Contact: ale.stuerchler@gmail.com
Bernard Merlin
Education: BTech in Biotechnology (Anna University, India); MSc in Molecular Life Sciences (University of Bern, Switzerland)
Field: Bioinformatics of lncRNA features and functional domains
Project: Validation of cancer driver lncRNAs with CRISPRa
Contact: bernard.merlin@students.unibe.ch
Chantal Bachmann
MSc student
David Mas
MSc student
Kyriakos Schwarz
MSc student
Education: BSc in Computer Science (University of Applied Sciences FHNW, Switzerland); MSc in Bioinformatics and Computational Biology (University of Bern, Switzerland)
Field: Cancer genomics and LncRNA drivers identification
Projects: Bioinformatic analysis of lncRNAs implicated in cancer
Links: LinkedIn
Contact: kyriakos.schwarz@students.unibe.ch
Joana Carlevaro
PhD student and PostDoc
Education: BSc in Human Biology (Universitat Pompeu Fabra, Spain); MSc in Bioinformatics for Health Science (Pompeu Fabra University, Spain); PhD in Classification and Functional Prediction of LncRNAs (Graduate School for Cellular and Biomedical Sciences, University of Bern)
Field: Bioinformatics and genomics, lncRNA features, RNA expression
Projects: Characterisation and classification of lncRNAs
Links: ResearchGate, LinkedIn, ORCID
Contact: joana.carlevaro@dbmr.unibe.ch
Where is she now? Bioinformatician in Didier Trono's lab at EPFL.
Judith Bergadà
MSc student
Education: BSc in Industrial Technology Engineering (Polytechnic University of Catalonia, Spain); MSc in Bioinformatics and Computational Biology (University of Bern, Switzerland)
Field: Analysis of CRISPR-Cas9 screenings
Projects: Bioinformatic design of pipelines for CRISPR-Cas9 screening analysis
Contact: judith.bergadapijuan@students.unibe.ch
Mina Zamani
Visiting scientist
Education: BSc in Cellular and Molecular Biology-Genetics (University of Shahrekord, Iran); MSc in Genetics (Tarbiat Modares University, Iran)
Field: Study of the expression and function of lncRNAs implicated in cancer
Projects: Functional characterization of lncRNA using CRISPR-Cas system
Links: Google Scholar, ResearchGate
Contact: mina.zamani@dbmr.unibe.ch
Monalisa Das
Visiting scientist
Monica Torres
MSc student
Tatjana Zoller
MSc student
Education: BSc in Biochemestry (University of Bern, Switzerland); MSc in Molecular Life Science (University of Bern, Switzerland)
Field: lncRNA localization
Projects: Functional characterization of lncRNA based on localization
Contact: tatjana.zoller@students.unibe.ch
