Adam Novak
Postdoctoral Researcher
novak at stats.ox.ac.uk
+44 (0) 1 865 272860 (Department)
+44 (0) 1 865 285366 (Direct)
+44 (0) 1 865 272595 (Fax)
Biographical sketch
I graduated from Eotvos Lorand University, Budapest with an MSc degree in Computer Science. I also have a background in Biology and Mathematics. Through employment at various software development companies I gained valuable IT industrial experience. Their target field ranges from computer-aided manufacturing to 3-tiered CRM systems to expert systems in sport physiology. Since 2007, I have been working in Jotun Hein's group at University of Oxford.
Research interests
MCMC methods, statistical alignment, protein secondary structure prediction, TFBS prediction, genome research.
About my research
My research is focused around applying Markov chain Monte Carlo and other algorithmic techniques to various challenging problems that arise in Bioinformatics. We have developed a method for high-quality multiple alignment of protein and nucleotide sequences. The advantage of our approach is the coherent statistical model that allows reliable phylogenetic tree reconstruction and measurement of the accuracy of the results, We worked on a number of extensions of the model and successfully applied it to a few diverse problems such as the secondary structure prediction of proteins through homology modelling and locating transcription factor binding sites via recognition of slowly evolving regions in a set of homologous sequences.
Selected publications
Szabó, A., Novák, Á., Miklós, I. and Hein, J. (2010) Reticular alignment: A progressive corner-cutting method for multiple sequence alignment. BMC Bioinformatics 11:570 doi:10.1186/1471-2105-11-570
Satija, R., Novák, Á., Miklós, I., Lyngsoe, R., Hein, J. (2009) BigFoot: Bayesian Alignment and Phylogenetic Footprinting for Multiple Sequences with MCMC. BMC Evolutionary Biology 9, 217 doi: 10.1186/1471-2148-9-217
Miklós, I., Novák, Á., Satija, R., Lyngsoe, R., Hein, J. (2009) Stochastic Models of Sequence Evolution including Insertion-Deletion events. Statistical Methods in Medical Research 18(5), 453-485 doi: 10.1177/0962280208099500
Novák, Á., Miklós, I., Lyngsoe, R., Hein, J. (2008) StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. Bioinformatics 24(20), 2403-2404 doi:10.1093/bioinformatics/btn457
Miklós, I., Novák, Á., Dombai, B., Hein, J. (2008) How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics 9,137
and link to fuller list of publications
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