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Bioinformatics Journal Club

Posted 08 November 2016 by In Bioinformatics Journal Club
Bioinformatics Journal Club

Tuesday 08/11/18, 14:00 @ Bioinformatics Lab

Ms. Andrea Kakouri

PhD student,

Bioinformatics Group and Neurogenetics Department, CING

“Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics alg”

Based on the paper by Seifi and Walter et al. 

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Tuesday 25/10/18, 14:00 @ Bioinformatics Lab

Mr. Evangelos Karatzas

PhD student

Department of Informatics, University of Athens and Visiting Student - Bioinformatics Group, CING

Network-based machine learning and graph theory algorithms for precision oncology

Based on the paper by Zhang et al. 

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Tuesday 05/06/18, 14:00 @ Bioinformatics Lab

Dr Kyriacos Felekkis

Associate Professor,

Head-Department of Life and Health Sciences, School of Science and Engineering, University of Nicosia

“Evolutionary and unique regulation of human genes by miRNAs”

Based on the papers by Dweep et al. (2013, 2015) and Felekkis et al.

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Tuesday 27/03/18, 12:00 @ Bioinformatics Lab

Dr. Vasileios Vavourakis

Assistant Professor,

Department of Mechanical and Manufacturing Engineering, University of Cyprus

“Cancer development, angiogenesis and cancer-drug delivery: An in-silico multiscale modelling approach”

Based on the paper by Vavourakis et al. 

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Thursday 15/03/18, 14:00 @ Bioinformatics Lab

Ms. Kyriaki Savva

PhD Student - Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“In silico drug repurposing”

Based on the papers by Vanhaelen et al. and Li et al.

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Thursday 22/02/18, 16:00 @ Bioinformatics Lab

Dr. Vasilis Promponas,  

Assistant Professor in Bioinformatics,

Head, Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus

“Exploring eukaryotic endomembrane systems with computational genomics tools”

Based on his recently published papers.

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Thursday 01/02/18, 14:00 @ Bioinformatics Lab

Ms. Chara Seitanidou,  

Postgraduate Erasmus Visitor at the Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“The Challenge and Promise of Glycomics”

Based on the homonymous paper by Cummings and Pierce 

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Thursday 30/11/17, 14:00 @ Bioinformatics Lab

Ms. Christiana Christodoulou

PhD Student - Bioinformatics Group and Neurology Clinic D, The Cyprus Institute of Neurology & Genetics

“HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington’s Disease”

Based on the homonymous paper by Kalathur et al.

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Thursday 16/11/17, 14:00 @ Bioinformatics Lab

Ms. Maria Zanti

PhD Student - Bioinformatics Group and Department of Electron Microscopy/Molecular Pathology

The Cyprus Institute of Neurology & Genetics

“Screening candidate microRNA-mRNA regulatory pairs for predicting the response to chemoradiotherapy in
rectal cancer by a bioinformatics approach”

Based on the homonymous paper by Peng et al.

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Thursday 2/11/17, 15:45 @ Bioinformatics Lab)

Dr Minas Karaolis

Department of Computer Science, University of Cyprus

“Computational data mining in Biomedicine”

Based on the paper “Assessment of the Risk Factors of Coronary Heart Events Based on Data Mining With Decision Trees”

by Karaolis et al.

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Thursday 19/10/17, 14:00 @ Bioinformatics Lab

Ms. Andrea Kakouri

PhD Student - Bioinformatics Group and Neurogenetics Dept., The Cyprus Institute of Neurology & Genetics

“A comparative study of techniques for Differential Expression Analysis on RNA-Seq Data”

Based on the paper “A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data”
by Zhang et al.

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Tue 04/07/17, 12:00, Room 104

Dr. Petros Kountouris

Molecular Genetics Thalassaemia Laboratory, The Cyprus Institute of Neurology & Genetics

“Predicting the impact of missense variants: an evaluation of existing methods”

Based on the paper “The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by
Two Types of Circularity” by Grimm et al.

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Tue 30/05/17, 12:00, Room 104

Dr. Athina Theodosiou,

Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology & Genetics

“Copy number variant detection in targeted NGS diagnostic services. Are we there yet?”

Based on the paper “Validation of copy number variation analysis for next-generation sequencing diagnostics”
by Ellingford et al.

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Tue 16/05/17, 12:00, Room 104

PhD Cand. Elena Loizidou

Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“Identification of driver genes in cancer through the integration of copy number variation with gene expression”

Based on the paper “Integrated DNA Copy Number and Gene Expression Regulatory Network Analysis of
Non-small Cell Lung Cancer Metastasis” by Iranmanesh and Guo

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Tue 02/05/17, 12:00, L10 Room

Dr. Christiana Demetriou

Neurology Clinic D, The Cyprus Institute of Neurology & Genetics

“Transcriptomic and metabolomic data integration”

Based on the paper “Transcriptomic and metabolomic data integration” by Cavill et al.

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Tue 21/03/17, 12:00, BI Lab

Dr. George Spyrou

Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“Network-based insight on expression data”

Based on the paper “Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from
gene co-expression network analysis on breast cancer data” by Bourdakou et al.

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Tue 07/03/17, 12:00, BI Lab

Dr. Kyriaki Michailidou

Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology & Genetics

“Genome-wide Association Studies in breast cancer”

Based on the papers “Large-scale genotyping identifies 41 new loci associated with breast cancer risk” and “Genome-wide
association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer”
by Michailidou et al.

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Tue 21/02/17, 12:00, BI Lab

Dr. Anastasis Oulas

Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“Machine Learning Approaches for Gene Expression, microRNAs and NGS Data”

Based on the papers “Prediction of novel microRNA genes in cancer associated genomic regions—a combined
computational and experimental approach” and “Improved Grading and Survival Prediction of human astrocytic
brain tumours by artificial neural network analysis of gene expression microarray data” by Oulas et al. and Petalidiset al.

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Tue 07/02/17, 12:00, BI Lab

Dr. Margarita Zachariou

Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“Modelling the Endocannabinoid System”

Based on the papers “Sensory gating and its modulation by cannabinoids: electrophysiological, computational and
mathematical analysis” and “A Biophysical Model of Endocannabinoid-Mediated Short Term Depression in
Hippocampal Inhibition” by Zachariou et al.

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Tue 24/01/17, 12:00, BI Lab

Dr. Kleitos Sokratous

Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“Targeting the Ubiquitin system”

Based on the paper “Drugging the undruggables: exploring the ubiquitin system for drug development”
by Huang and Dixit, Freely available at http://www.nature.com/cr/journal/v26/n4/full/cr201631a.html

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Tue 17/01/17, 12:00, BI Lab

Dr. George Minadakis

Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“The generation process of extreme events: epileptic seizures as quakes of the brain”

Based on the paper “Epileptic seizures: Quakes of the brain?” by Osorio et al.,

Freely available at http://chaos1.la.asu.edu/~yclai/papers/PRE_010_OFSML.pdf

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Tue 20/12/2016, 12:00, BI Lab

Dr. Petros Kountouris

Molecular Genetics Thalassaemia Laboratory, The Cyprus Institute of Neurology & Genetics

“Protein structure prediction”

Based on the paper “Prediction of backbone dihedral angles and protein secondary structure using support vector machines”
by Kountouris and Hirst,

Freely available at http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-437

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Tue 13/12/2016, 12:00, BI Lab

Dr. Athina Theodosiou,

Department of Cytogenetics and Genomics,
The Cyprus Institute of Neurology & Genetics

“Benchmarking bioinformatics pipelines for NGS using gold standard reference variant calls from GIAB”

Based on the papers “From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome
and Whole Exome Sequencing” of Laurie et al. and “Systematic comparison of variant calling pipelines using gold standard
personal exome variants” of Hwang et al.

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Tue 22/11/2016, 12:00, BI Lab

Ms. Elena Loizidou, 

PhD candidate at Imperial College, London,

Hosted by Neurogenetics Department and Bioinformatics Group, The Cyprus Institute of Neurology & Genetics

“Parkinson's disease and human variation”

Based on the paper “α-synuclein genetic variability: A biomarker for dementia in Parkinson disease”

of Guella et al.http://onlinelibrary.wiley.com/wol1/doi/10.1002/ana.24664/full

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Tue 8/11/2016, 12:00, BI Lab

Dr. Christiana Demetriou

Neurology Clinic D, The Cyprus Institute of Neurology & Genetics

“From Biological Embedding to the Diseasome”

Based on the paper “The human disease network” of Albert-László Barabási,

Freely available at http://www.pnas.org/content/104/21/8685.full

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