Στα πλαίσια των ανοιχτών σεμιναρίων που διοργανώνει η Ομάδα Υπολογιστής Βιολογίας και Βιοπληροφορικής του Τμήματος Μηχανικών Η/Υ και Πληροφορικής, την Δευτέρα 18/01 και ώρα 13.00, στην Αίθουσα Συνεδριάσεων στο ισόγειο του κτιρίου Β’, θα δοθεί ομιλία από τον Δημήτρη Κλεφτογιάννη.
Title: Identification of enhancers in human: Advances in computational studies
Abstract
Transcription regulation in multicellular eukaryotes is orchestrated by a number of DNA regulatory elements (e.g., enhancers, promoters). Identification of enhancers is a challenging problem for the current Computational Biology. We present recent advances in computational studies aiming at identifying enhancers and analysing their properties.
First, we present a general computational framework for identifying enhancers called DEEP. DEEP develops many cell-specific classification models that are combined to classify DNA regions as enhancers or non-enhancers. DEEP uses as input features derived from histone modification marks (ChIP-seq) and DNA sequence characteristics. Experimental results indicate that DEEP achieves high recognition performance on enhancer data coming from ENCODE, FANTOM5 and VISTA.
Next DENdb, the Database of Integrated Human Enhancers, is presented. DENdb archives enhancer data from 16 ENCODE cell-lines and offers a number of utilities that facilitate downstream analysis on enhancers. Examples are: overlap of enhancers with DNase I hypersensitivity sites; information about TFs binding sites from ChIP-seq experiments and binding motifs from Position Weight Matrices (PWM); and connection of enhancers with candidate target genes based on chromatin conformation data (5C or ChIA-PET). Finally, a new annotation for enhancers based on different computational methods is proposed.
Finally, recent findings stemming from Cap Analysis of Gene Expression (CAGE) on a MCF-7 time-course are discussed.
Short Bio
Dimitrios Kleftogiannis obtained a Diploma in Computer Science and Engineering and a Master Degree in Informatics for Life Sciences from University of Patras, in 2009 and 2011 respectively. Currently he is a PhD candidate at King Abdullah University of Science and Technology (KAUST) under the supervision of Professors Vladimir Bajic and Panos Kalnis. Dimitrios research interest is in facilitating biological discoveries using bioinformatics systems and machine learning algorithms. His work has been published in different journals including Nucleic Acids Research, Bioinformatics, Oxford Database and Briefings in Bioinformatics.
Εκ μέρους της Ομάδας Υπολογιστής Βιολογίας και Βιοπληροφορικής
Σεφερίνα Μαυρουδή