Information for existing EBI predocs - Predoc training

I obtained 5-years-degrees in Medical Biology and Biochemistry at the University of Navarra, Spain, where I also completed a Diploma in Bioinformatics. Therefore, I have computational (using R and Matlab) and molecular biology background and both wet and dry laboratory experience.

During the last year of my studies, I moved to Switzerland as a part of a ERASMUS exchange program with the University of Geneva, where I had subjects of MSc in Proteomics and Bioinformatics. As for my research projects, I focused on proteomics and genomics analysis (using R and Perl). Concretely, I studied genome wide eQTLs variation in different human tissues and also analysed effect of glycation PTM in proteins from several human fluids.

My scientific interests include dynamics aspect related to genome regulation. Epigenomic networks, novel histone modifications and functional transcriptomics integration are among my main interests.

At the moment I am improving my computational skills in R, Python and Java. I am enthusiastic to clarify some of those curiosities and make them fit in the whole picture of biology.

My first degree was in Biochemistry at the University of Sheffield. Afterwards I took a Master's in Computational Biology at the University of York. Having first been more interested in structural biology I was surprised to find that my focus was shifting towards phylogenetics and evolution as my Master's progressed. I've learned a little programming in Python and C++, a bit of R, and brushed up on my stats, and now I plan to study methods of making phylogenetic inferences from large amounts of multi-locus sequence data.

I began my studeis in BioEngineering at Imperial College, where I obtained an MEng in 2011. My course focused on applying principles from electrical and software engineering to biollogical or medical problems- for example, I spent a year working on a real-time image processing device to aid vision for sufferes of retinitis pigmentosa; after that, I applied signal processing techniques to ECoG data to automatically detect "after-shock" waves occurring in 24-48 hours post-stroke.

This kind of degree focused on providing tools and applying these, alongside a range of 'primer' courses into anatomy, chemistry, maths etc. I am confident in Matlab, C/C++ and am finding my way in Perl.

My interests now are to apply these skills to bigger and more exciting problems- I am particularly interested in neurological disease and complex traits and how machine learning algorithms may be used to interpret this data in new ways.

I have limited background knowledge with regards to biology- I am building on this by reading papers and attending journal clubs etc.

I graduated from University of California Berkeley in December 2010 with a degree in Integrative Biology. As an undergrad I completed coursework in biochemistry, systems biology, and evolutionary and population genetics. At the same time, I did research on the phylogenetics of Hawaiian Drosophila; cryptic speciation in wild populations of the tropical passerine bird Corapipo altera; and the telomeric depletion of cultured B cells in response to the stress hormones cortisol and epinephrine, in labs at both UC Berkeley and UCSF.

Despite my varied background, at Sanger I plan on combining my interest in evolutionary biology with genetics and bioinformatics, focusing on computational-heavy, high-throughput sequencing approaches to the study of vector-pathogen interactions between the malaria parasite and the mosquito vector. I am mainly interested in data mining of whole genome short-read sequence data, with the objective of detecting potential loci under selection in the genome of the malaria parasite. I look forward to strengthen my computational biology skills and expand my knowledge of programming, which at the moment is limited to a very basic knowledge of MATLAB.

I did my Bachelor's degree on Genomic Sciences at the National Autonomous University of Mexico, where I learned both biological and computational sciences. I had courses on biology and chemistry, as well as genetics and evolution, but also on mathematics, basic statistics, programming and bioinformatics. I can program in Perl and C, and the basics of R. I have knowledge on several bioinformatic analysis tools, mainly working with DNA sequences but also a little bit on modelling macromolecules structure. I have also worked with data from microarrays and next-generation sequencing.

I am interested in Neurobiology and my main goal is to be able to study any type of question with a global approach, trying to integrate data from the different layers of organization that operate in cells and combine into regulatory networks to achieve higher levels of complexity. I find Systems Biology really appealing and no matter the project I'm working on, I want to combine both experimental and bioinformatic approaches.

I completed my undergraduate and master's studies at Yonsei University in South Korea focusing on pathogens and the human immune system. My work on the immune system was mainly on the innate immune pathways and aimed to engineer and permeabilize specific transcription factors in order to modulate early response to intracellular pathogens. However, the more I learned about this complex system, the more I struggled to understand it. The numerous dynamic interactions between different components were highly context dependent which made it impossible to understand the system as a whole. These thoughts eventually led me to the field of systems biology and networks.

During my master's studies I initially started with a focus on the relatively simpler single-celled pathogen side of the host-pathogen interaction. I've constructed a genome-scale probabilistic functional gene network of a bacterial pathogen and showed that the predictions were accurate through biological experiments.

Here, I wish to elaborate on this holistic view of biological systems and expand my research from a gene-centered point of view to a whole genomic analysis of the host-pathogen interaction. Starting from the pathogen's view and the host's perspective, then to their relationships with each other, and ultimately to validating the results on model organisms and population studies.

I began my career in the British army as a combat engineer and electrician. After four years and a few deployments overseas, I decided a life in science would be a safer bet. I then went on to study biology at the University of Nottingham. During my studies I took part in a number of internships covering a wide range of topics including fungal biology, microbiology and bioinformatics. Having been a computer and electronics enthusiast for years I decided bioinformatics is clearly the future!

My undergraduate thesis was focused on understanding the genetic components of the regulation of lateral root development in Arabidopsis thaliana. Transcription factors identified using a temporal transcriptomics data set were characterised by generating knock-out lines and subsequent genetics analysis. I also completed an internship based on analysing different rates of respiration using Biolog phenotype arrays. Models for respiratory growth were fitted to time course reduction-dye based data using a MCMC scheme to accurately compare different microbial samples.

During my time at the EBI I intend to focus on developing my computational skills while investigating interesting biological problems. Broadly stated, my research interests are genetic regulation and the mechanisms of cellular control. One such problem is the derivation and differentiation of cancer and neural stem cells.

I studied copy number variation and bioinformatics at the National Institutes of Health as a medical student intern at the National Institutes of Health, USA. My main project was to help develop a copy number variation detection program for exome sequence data. I'm fascinated by the complexity of the human genome, and am especially interested in large-scale structural changes to the genome. Mainly I've programmed in perl and R, but am excited to hone my coding abilities.

Before coming to EBI I studied Bioinformatics and Computational Biology at Jacobs University in Bremen, Germany. As you can tell by the name this was a pretty interdisciplinary major, so I actually have a background in both computer science and biology. I also got to work in the wet lab for a while, so I have some general knowledge on lab methods too. Nevertheless, my focus so far has been mostly on the computational side of things, since I have been interested in computers since long before I even started my studies. Thanks to that, I am familiar with a lot of programming languages and tools, which should come in handy during my time in Hinxton.

My projects so far were on experimental pattern formation and dynamics on graphs (with some sociology and psychology mixed in) and on the evolution of robust networks, with applications both in biology in logistics. Both of them involved a lot of software development, but I was also responsible for designing the experiments and analyzing the results.

So I hope at EBI I will get the chance to apply my programming knowledge to cool new projects and also learn some interesting new biology as well!

I studied for my bachelor¹s and master¹s degree in University of Helsinki with genetics as my major. During my studies I worked in a cancer genetics group, studying germ-line and somatic genetic variants implicated in cancer. I spend my first years in the lab working with SNP and gene expression microarray data, and during the last year transitioned to analysing next-generation sequencing data. My master¹s thesis project was about finding somatic rearrangements from tumor genomic sequencing data.

I have used R, MatLab and Perl for my scripting purposes, but have not really done any real programming. Data analysis and studying biological phenomena are my primary interests. Currently, I am interested in cancer genetics, and what and how genetic alterations in cancer contribute to the disease.

I studied Bioinformatics at the University of Applied Sciences Weihenstephan-Triesdorf in Germany (2006-2011). During my studies I was involved in an undergraduate research project at the EBI (Proteomics Service Team) in cooperation with the University of Cambridge (FlyMine Group), where I applied and developed tools for established advanced biological data warehouses (InterMine & BioMart). During another semester I was also employed as Visiting Research Scientist at Harvard Medical School (Sorger Lab) in the Department for Systems Biology. There I took responsibility to model a hyper dimensional data standard to store the meta-data of high-throughput images. I did my diploma thesis at the Technical University of Munich (Rost Lab) and developed a novel method to predict DNA-binding residues from protein sequence data.

I am interested in systems biology, molecular medicine, and biological challenges, which could be solved with computational simulation.

My background is mainly computer science. I did a computer science bachelor with a minor in life sciences (chemistry and biology) at the EPFL in Lausanne (SWI). I then studied for my master in computer science at the University of Oxford (UK). I attended an introductory course to bioinformatics that gave me a broad insight to the field. During my master's project, I worked within the Computational Biology Group of Oxford. This project involved contributing to a simulation environment for cell models.

To me, bioinformatics is the perfect field to apply computer science tools and techniques, solve "real world" issues and answer fundamental questions about the inner workings of life.

My background implies that I am familiar with a fair amount of programming languages, algorithms and other specific topics. After having improved my biological skills in the predoc course, I hope to apply my dry-lab experience and contribute to the fascinating field of bioinformatics.

I am a programmer. Well, technically I did an MSc in bioinformatics in Berlin but so far, all my bioinformatics projects required designing and writing software more than anything else. I have also contributed to a few non-bioinformatics software projects over the years. As a consequence, I am reasonably well-versed in most common programming languages as well as a few uncommon ones.

My main work at University was in the context of the SeqAn project, which mainly is a high-performance sequence analysis library in C++. In the course of this work I did an internship at Illumina and also implemented a method of executing existing algorithms in parallel to improve their performance. This culminated in my master thesis. The common thread of my work so far has been the difficulty of dealing with the huge amount of data that modern sequencing methods produces.

At the EBI, I am hoping to apply a different approach to the problem: Rather than tackling the problem with sheer machine power and highly optimised, parallel algorithms, I am interested to see whether we can reduce the amount of data to something more manageable by somehow finding interesting features and ignoring the rest, thus reducing the signal-to-noise ratio. This, of course, requires massive amounts of statistics.

I studied Natural Sciences at Cambridge, and though I came intending to do Physics I ended up specialising in Genetics in my last year. My main wet lab experience was during the summer of 2010 - I was a member of the iGEM team for Cambridge, designing a genetically engineered bacterium.

My undergraduate course did not have very much bioinformatics but I have spent a lot of my life around computers and so have acquired by osmosis knowledge of Python, Perl, PHP, and some C and Java. This allowed me to do a dry project, which involved analyzing and annotating the genome of a bdelloid rotifer. These multicellular creatures are very interesting as more than 10% of their genes have been horizontally acquired from as far afield as bacteria, fungi and plants. It is believed that their proficiency for homologous recombination has allowed them to survive as a clade for a very long time despite their asexuality. Usually asexual clades are shortlived. It involved setting up the MAKER pipeline for annotation, and analysing this data with Perl scripts. BLAST homologues of each gene were processed into phylogenies with Phylip and also categorised based on their Gene Ontology terms, using R to test the significance of patterns.

I'm doing a rotational PhD at Sanger and am still struggling to work out what I want to specialize in. I would ideally like to combine wet and dry work. My current rotation is in Pentao Liu's lab working on induced pluripotent stem cells.