You can find my publications on my Google Scholar page.
My GitHub page contains some of the code I’m working on. I recently wrote a post about CorrMapper which constitutes about 75% of PhD. I intend to open-source the whole project once it is published, so if you’re interested in this research please check back in a few months time.
Also here’s a poster I’ve done about my recent work for a conference.
PhD in Data Integration and Visualisation
I’m currently a PhD student in the STRATiGRAD PhD program, at Imperial College London. My project is entitled: Integration and visualization of clinical-metabolic datasets for medical-decision making.
To get a picture about what I’ve spent my previous years on it’s probably easiest if you read this post.
Initially I was analyzing the NMR profiles and gut-bacterial communities (16S rRNA pyrosequencing) of a hundred morbidly obese patients, who have undergone Roux-en-Y Gastric Bypass bariatric surgery. The aim of this project was to develop novel ways of integrating the various high-throughput biological data types, as this could provide a more comprehensive snapshot of living systems (obese humans in this case), which might facilitate the mechanistic understanding of the disease and the stratification of patients.
Essentially we wanted to know which metabolites and bacterial groups change after this intervention, and how these changes relate to the biochemical pathways and metabolism of the patients. The hope (as usual) was that this integrative high-throughput approach might provide us with new drugable targets on the long run, which would not only lower the cost of the care, but also make it more accessible to less obese individuals.
Although we managed to confirm previous hypotheses and learned a lot from it, the project did not bear fruit as we had hoped (we still don’t fully understand what’s going on in these patients after bariatric intervention) but CorrMapper grew out of my grappling with this dataset, so it’s been definitely useful and eye-opening.
MSc in Bioinformatics and Theoretical System Biology
I graduated with distinction from Imperial College London, in September 2012.
In my final project, I developed a novel tool for the normalisation of 16S rRNA gene copy numbers by utilizing various evolutionary models and phylogenetic reconstruction techniques. The software also provides advanced visualisation of OTU (Operational Taxonomic Unit) tables combined with phylogenetic tree and patient metadata. This work is in preparation for publication: “Tool development for 16S rRNA gene copy number normalisation and visualization“.
While working at the National Heart & Lung Institute, Imperial College London, my code was used in the analysis of patients suffering from Chronic Obstructive Pulmonary Disease.
Molyneaux PL, Mallia P, Cox MJ, Footitt J, Willis-Owen S, Homola D et al. (2013). Outgrowth of the Bacterial Airway Microbiome after Rhinovirus Exacerbation of Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine. doi: 10.1164/rccm.201302-0341OC, Pubmed
BSc in Biology
I graduated with an excellent degree in Biology in 2010 at Eötvös Lóránd Science University’s Natural Sciences Faculty. I wrote my final thesis on “Universal laws in the construction of protein and gene networks”.
I worked as a graduate research student for 2 years at the Hungarian Academy of Sciences’ Institute of Enzimology, in the research group of Peter Tompa. My first finished project was “Structural disorder brings order to crystal growth in biomineralization”. It is discussing the universal utilization of disordered proteins as biomineralization initiators, inhibitors and related transporters in surprisingly diverse forms of life, ranging from marine diatoms, through mollusks to mammalian bones and teeth.We managed to give quite a complete explanation of this strange phenomenon and relatedness. The work has been published in Bone.
Kalmar, L., Homola, D., Varga, G., & Tompa, P. (2012). Structural disorder in proteins brings order to crystal growth in biomineralization. Bone. doi:10.1016/j.bone.2012.05.009, Pubmed