I primarily develop in (object oriented) Perl and use R for heavier statistics and plotting. I have been heavily involved in the development of a Perl object oriented framework that facilitates sequencing analyses (see GenOO here). This framework has been extended to a suite of tools that can be applied to CLIP-Seq analyses by users of different levels – from complete novice to experienced user (see CLIPSeqTools here).
During my Undergraduate degree in Genetics and especially during my 1-year Industrial Placement practice in a Molecular Endocrinology laboratory I was formally and practically trained in laboratory techniques and basic cell and animal work. However, by the end of my Undergraduate degree I had decided to shift my focus towards Bioinformatics. My Undergraduate thesis was an (extremely basic) Regulatory Region prediction for a set of genes of interest. For the first time I used tools to predict Transcription Factor Binding Sites, Enhancers, Conserved Regions etc.
My MSc in Bioinformatics gave me much more formal training in basic algorithms and programming. I learned basic Perl formally and worked mainly with MatLab. My MSc degree involved three semesters of embedded lab work during which time I worked in MatLab to expand a method of Analysis of Variation and Principal Component Regression for Metabolomics Data. The method was then extended and applied to Proteomic Data.
For my PhD research, I joined a (mostly) microRNA focused bioinformatics laboratory (DIANA Lab in Athens, Greece). During the microRNA ‘boom’, I was involved in developing one of the most sensitive microRNA prediction programs (and web-server), a web-server with information about microRNA genes and their TF regulation, a method for the identification of deregulated microRNAs from the changes in levels of their targets, and several collaborations for practical applications of this research.
After obtaining my PhD, I joined the Zissimos Mourelatos Lab at the University of Pennsylvania School of Medicine. The lab expertise is in Biochemical and genetic studies of Ribonucleoproteins (RNPs) with emphasis on small regulatory RNPs such as microRNAs (miRNAs) and piRNAs (Piwi-associated RNAs) and RNA dysregulation in the pathogenesis of neurodegeneration. I have been involved in studies of microRNA biogenesis, piRNA biogenesis and function and neurodegeneration associated RNA binding proteins. Colleagues in the laboratory have expertise in CLIP-Seq techniques and much of the analysis for these projects has involved tens of CLIP-Seq datasets produced and analyzed in the lab. To simplify such analyses I have been heavily involved in the development of the Perl object oriented framework called GenOO and the CLIPSeqTools analysis suite.
High Throughput Sequencing analysis
RNA binding proteins
RNA mediated targeting
State of the Art Sequencing Technologies
RNA Conservation / Structure
Multiple HTS Sample Data Analysis