Istvan_Miklos

Beyond Next Generation Sequencing workshop, 2011 July 20-23, Renyi Institute, Budapest, Hungary

Contact
	e-mail address:
	Phone:	+36-1-4838304
	Phone (at home):	+36-1-275-9115
	Regular mail:	Department of Stochastics Rényi Institute, Hungarian Academy of Sciences Reáltanoda u. 13-15. H-1053, Budapest HUNGARY
Background I started studying biology and chemistry at Eötvös Loránd University, Faculty of Science in 1992. After I have decided to be an applied mathematician, I picked up mathematics in 1993. I graduated in 1998 and started a PhD course at the Department of Plant Taxonomy and Ecology Dissertations Enzymatic reaction networks (supervisor: Eörs Szathmáry) String processing algorithms (supervisor: Lajos Rónyai) PhD thesis Statistical Sequence Alignment (supervisor János Podani) In pdf format (in Hungarian, sorry): PhD1.pdf, PhD2.pdf, PhD3.pdf, PhD4.pdf, PhD5.pdf, I've spent 18 months at the Genom Analysis and Bioinformatics group, University of Oxford between 2002 August and 2004 January, and returned twice for 7-9 months between 2007 September and 2009 August. I was a postdoc at the Theoretical Biology and Ecology Modelling Group. I was also a poject leader at the eScience Regional Knowledge Centre. Now I'm a member of the Bioinformatics group in the Rényi Institute. Currently, I am a work package leader in an EU FP7 project. The project is in collaboration with ClcBio and other SMEs and RTDs and is about finding transcription factor binding sites in Vertebrate genomes.
Research interest I have been working on modelling molecular evolution. My research focuses on insertion-deletion process (statistical alignment), on genome rearrangement and RNA folding. I am partly involved in a project on multivariate biological data analysis, such as horseshoe effect in PCoA and statistical properties of presence-absence matrices. I am interested in possible MCMC applications in bioinformatics (mainly Bayesian phylogenetic inferring) and ecology (generating null-distributions). My current love is the intersection of complexity classes #P-complete and FPRAS.
Teaching I used to teach tons of topics like these: Algorithms in bioinformatics (in Hungarian) Stochastic models in bioinformatics (in Hungarian) (in English) Monte Carlo methods in biostatistics (in Hungarian) The bioinformatics of RNA sequences (in Hungarian) Statistics for MSc in biology students (in Hungarian) Bioinformatics and Genomics in medical research (in Hungarian) Currently I am teaching Introduction to Computer Science at the Central European University, Bioinformatics at Budapest Semesters in Mathematics, and Stochastic models in bioinformatics at the Technical University of Budapest Note for my student: TÉTELSOR!!! Students Timothy Brooks Paige, summer student, 2005. Worked on genome rearrangement, published paper: Efficient Sampling of transpositions and inverted transpositions for Bayesian MCMC Bence Mélykúti, MSc student, graduated in 2006. Thesis: The Mixing Rate of Markov Chain Monte Carlo Methods and some Applications of MCMC Simulation in Bioinformatics Published paper: The Metropolized Partial Importance Sampling MCMC mixes slowly on minimum reversal rearrangement paths Ádám Novák, MSc student, graduated in 2007. Thesis : Sampling evolutionary trees and multiple alignments in a Bayesian MCMC framework (in Hungarian) Published papers: Stochastic Models of Sequence Evolution including Insertion-Deletion events StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. How reliably can we predict the reliability of protein structure predictions? Márton Münz, MSc student, graduated in 2007. Thesis: Stochastic biclusrtering of DNA chip data (in Hungarian) part1 part2 Imelda Somodi, PhD student, co-supervised with János Podani, graduated in 2007. Working on spatial models in ecology. Paper: Rearrangement of ecological data matrices via Markov chain Monte Carlo simulation. Publication list Erdős, P., Király, Z., Miklós, I. (2013) On the swap-distances of different realizations of a graphical degree sequence Combinatorics, Probability and Computing accepted. Miklós, I., Erdős, P., Soukup, L. (2013) Towards random uniform sampling of bipartite graphs with given degree sequence Electronic Journal of Combinatorics 20(1):P16 Miklós, I., Tannier, E. (2012) Approximating the number of Double Cut-and-Join scenarios, Theoretical Computer Science 439:30-40, doi: 10.1016/j.tcs.2012.03.006 Miklós, I., Zádori, Z. (2012) Positive Evolutionary Selection of an HD Motif on Alzheimer Precursor Protein Orthologues Suggests a Functional Role PLoS Comp.Biol., 8(2): e1002356. Miklós, I. (2011) Sztochasztikus modellek a bioinformatikában (in Hungarian: Stochastic models in bioinformatics), electronic notes. Somodi, I., Miklós, I., Virág, K. (2011) A Bayesian MCMC approach to reconstruct spatial vegetation dynamics from sparse vegetation maps. Landscape Ecology, 26(6):805-822. Miklós, I. (2010) Introduction to Algorithms in Bioinformatics. Electronic notes. Szabó, A., Novák, Á., Miklós, I., Hein, J. (2010) Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment BMC Bioinformatics, 11:570. Miklós, I., Tannier, E. (2010) Bayesian Sampling of Genomic Rearrangement Scenarios via Double Cut and Join Bioinformatics, 26: 3012-3019 Miklós, I. (2010) RNA Structure Prediction. in: David Fenyö (ed.), Compiutational Biology, Methods in Molecular Biology 673:19-36 Friedman, E., Miklós, I., Hein, J. (2010) MCMC Network: Graphical Interface for Bayesian Analysis of Metabolic Networks ERCIM News, 82:31-32 Miklós, I., Mélykúti, B., Swenson, K. (2010) The Metropolized Partial Importance Sampling MCMC mixes slowly on minimum reversal rearrangement paths ACM/IEEE Transactions on Computational Biology and Bioinformatics, 4(7):763-767. Erdős, P., Miklós, I.,, Toroczkai, Z. (2010) A simple Havel-Hakimi type algorithm to realize graphical degree sequences of directed graphs Elec. J. Combinatorics 17(1):R66 Kim, H., Toroczkai, Z., Erdős, P., Miklós, I., Székely, L. (2009) Degree-based graph construction. J. Phys. A., 42(39): 392001.1-392001.10. Satija, R., Novák, Á., Miklós, I., Lyngsoe, R., Hein, J. (2009) BigFoot: Bayesian Alignment and Phylogenetic Footprinting with MCMC BMC Evolutionary Biology, 9:217 Miklós, I., Darling, A. (2009) Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia Genome Biology and Evolution, 1(1):153-164 Csürös, M., Miklós, I. (2009) Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model Mol. Biol. Evol. 26(9):2087-2095 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, 18:453-485. 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 Darling, A., Miklós, I., Ragan, M. (2008) Dynamics of genome rearrangement in bacterial populations. PLoS Genetics, 4(7): e1000128 Miklós, I., Novák, Á., Dombai, B., Hein, J. (2008) How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics 9:137. Miklós, I. (2008) Statistical multiple alignment chapter in Encyclopedia of Algorithms (ed. M. Kao), New York: Springer, pp. 892-894. Meyer, I.M. Miklós, I. (2007) SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework PLoS Computational Biology, 3(8):e149. Miklós, I. (2007) Algorithms of Bioinformatics chapter in Algorithms of Informatics (ed.: Antal Iványi), pp. 973--1011. Mondat Kiado Miklós, I., Paige, T.B., Ligeti, P. (2006) Efficient Sampling of transpositions and inverted transpositions for Bayesian MCMC Proceedings of WABI2006, LNBI 4175: 174-185. Csürös, M. & Miklós, I. (2006) A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer Proceedings of RECOMB2006, LNBI 3909:206-220. Meyer, I.M. & Miklós, I. (2005) Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Research, 33(19)6338-6348. Miklós, I. &Meyer, I.M. (2005) A linear memory algorithm for Baum-Welch training. BMC Bioinformatics 6:231. Csürös, M. & Miklós, I. (2005) Statistical alignment of retropseudogenes and their functional paralogs. Mol. Biol. Evol., 22(12): 2457-2471. Csürös, M. & Miklós, I. (2005) Statistical alignment of retropseudogenes and their functional paralogs via a common ancestor. FEBS JOURNAL, 272: 110-110 Suppl. 1. Miklós, I. Somodi, I. & Podani, J. (2005) Rearrangement of ecological data matrices via Markov chain Monte Carlo simulation. Ecology, 86(12):3398-3410. Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L., & Hein, J. (2005) Bayesian Coestimation of Phylogeny and Sequence Alignment BMC Bioinformatics, 6:83. Podani, J., Csontos, P., Tamás, J. & Miklós, I. (2005) A new multivariate approach to studying temporal changes of vegetation. Plant Ecology, 181:1-16. Miklós, I., Ittzés, P. & Hein, J. (2005) ParIS Genome Rearrangement Server Bioinformatics, 21(6):817-820. Miklós, I. & Hein, J. (2005) Genome rearrangement in mitochondria and its computational biology Lecture Notes in Bioinformatics 3388:85-96. Miklós, I., Meyer, I.M. & Nagy, B. (2005) Moments of the Boltzmann distribution for RNA secondary structures Bul. Math. Biol., 67(5):1031-1047. Meyer, I.M. & Miklós, I. (2004) Co-transcriptional folding is encoded within RNA genes. BMC Molecular Biology, 5:10 Miklós, I. (2004) Bioinformatikai algoritmusok(Algorithms in bioinformatics, in Hungarian) In: Informatikai algoritmusok (Algorithms of Computer Science), (ed.: Antal Iványi), Eötvös Kiadó Budapest. pp. 538-579. Lunter, G.A., Drummond, A., Miklós, I., & Hein, J. (2004) Statistical aligment: recent progress, new applications and challenges In: Nielsen, R. (ed): Statistical methods in molecular evolution Springer-Verlag, New-York, in press. Miklós, I., Lunter, G. A. & Holmes, I. (2004) A 'long indel' model for evolutionary sequence alignment. Mol. Biol. Evol., 21(3):529-540. Miklós, I. & Podani, J. (2004) Randomization of presence/absence matrices: comments and new algorithms Ecology, 85:86-92. Lunter G.A., Miklós, I. , Song, Y.S. & Hein, J. (2003) An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees J. Comp. Biol. 10(6):869-889. Miklós, I. (2003) MCMC Genome Rearrangement Bioinformatics, special issue for ECCB2003 19(Suppl.2):ii130-ii137. Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L., & Hein, J. (2003) Bayesian phylogenetic inference under a statistical indel model, ps pdf Lecture Notes in Bioinformatics, Proceedings of WABI'03, 2812:228-244. Miklós, I. (2003) Algorithm for statistical alignment of sequences derived from a Poisson sequence length distribution. Disc. Appl. Math. 127(1):79-84. Podani, J. & Miklós, I. (2002) Resemblance coefficients and the horseshoe effect in principal coordinates analysis. Ecology, 84(12):3331-3343. Miklós, I. (2002) An improved algorithm for statistical alignment of sequences related by a star tree. Bul Math. Biol. 64(4):771-779. Miklós, I. & Toroczkai, Z. (2001) An improved model for statistical alignment, in: WABI2001, Lecture Notes in Computer Science, (O.Gascuel & B.M.E.Moret, eds.) 2149:1-10. Springer, Berlin Pál C. & Miklós, I.(1999) Epigenetic inheritance, genetic assimilation and speciation. J. theor. Biol. 200:19-37. Conferences Miklós, I. (2007) Computational challanges in multiple genome rearrangement MCMC 5th Bertinoro Computational Biology workshop, 12-17 May, 2007. Bertinoro, Italy http://www.mcb.mcgill.ca/research/bertinoro/ Miklós, I., Paige, T.B., Ligeti, P. (2006) Efficient Sampling of transpositions and inverted transpositions for Bayesian MCMC 6th Workshop on Algorithms in Bioinformatics, September 11/13, 2006. Zürich, Switzerland http://algo06.inf.ethz.ch/wabi Csürös, M. Miklós, I. (2006) A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. RECOMB 2006, April 2-5, 2006. Venice Convention at The Cinema Palace, Venice Lido - Italy http://recomb06.dei.unipd.it/ Miklós, I., Somodi, I. & Podani, J. (2005) Ökológiai adatmátrixok átrendezése Markov Lánc Monte Carlo szimuláció segítségével (In Hungarian: Rearranging ecological data matrices using MCMC) VII. Magyar Biometriai és Biomatematikai Konferencia 2005. July 5-6., Budapest Miklós, I. (2005) Fast algorithm for calculating the likelihood of a tree in a gene gain-loss-duplication model SBC-WCN workshop on protein structure/function prediction and comparative genomics 2005. May 28-29, Stockholm, Sweden http://www.sbc.su.se/seminars/sbc_wcn_05/ Miklós, I., Somodi, I. & Podani, J. (2004) Új statisztikai módszer hasonlósági hálózatok felderítésére cönológiai adatmátrixok alapján (In Hungarian, New statistical methods for inferring similarity networks from ecological data matrices) Szegedi Ökológiai Napok, 2004. Nov. 25-26. Miklós, I. & Hein, J. (2004) Genome rearrangement in mitochondria and its computational biology. 2nd RECOMB Comparative Genomics Satellite Workshop, 2004. Oct. 16-19. Bertinoro, Italy http://www.nada.kth.se/~jensl/recombcg2004.html Miklós, I. (2004) Two applications of Metropolised partial importance sampler in bioinformatics, Karlsruher Stochastik-Tage 2004. Mar. 23-26, Germany http://www.stoch2004.uni-karlsruhe.de/stoch2004/index_en.html Miklós, I. (2003) MCMC Genome rearrangement, 2^nd European Conference on Computational Biology 2003. Sep. 27-30, Paris, France. http://www.inra.fr/eccb2003/ Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L.,& Hein, J. (2003) Bayesian phylogenetic inference under a statistical indel model, 3^rd Workshop on Algorithms in Bioinformatics, 2003 Sep. 15-20, Budapest, Hungary http://www.conferences.hu/ALGO2003/algo_2003.htm Miklós, I. & Toroczkai, Z. (2001) An improved model for statistical alignment, 1^st Worksop on Algorithms in Bioinformatics 2001. Aug. 28-31, Aarhus, Denmark. http://www.brics.dk/wabi2001/index.html Miklós, I. (2001b) An improved algorithm for statistical alignment of sequences evolved by a star tree. Phylogenetics Combinatorics, 2001. Jun. 10-16, Bielefeld Germany http://www.mathematik.uni-bielefeld.de/~fspm_gk/Veranstaltungen/Workshops/Abstracts/phylogenetics1.html Miklós, I. (2001a) Irreversible likelihood models. European Mathematical Genetics Meeting, 2001. Apr. 20-21, Lille, France. Posters Münz, M. Mikl&oacuta;s, I (2006) Finding biclusters in microarray data with Bayesian Markov chain Monte Carlo BCII2006, 2006, October 8-12, Budapest, Hungary, http://www.diamond-congress.hu/bcii2006/ Paige, T.B.,Miklós, I. (2006) Efficient Sampling of transpositions and inverted transpositions for Bayesian MCMC RECOMB 2006, April 2-5, 2006. Venice Convention at The Cinema Palace, Venice Lido - Italy http://recomb06.dei.unipd.it/ Novák, Á., Miklós, I. (2006) Structure Projector: protein structure prediction from Bayesian distribution of multiple alignments. RECOMB 2006, April 2-5, 2006. Venice Convention at The Cinema Palace, Venice Lido - Italy http://recomb06.dei.unipd.it/ Lunter, G.A., Miklós, I., Csürös, M. (2006) ReticularAlignment: a new heuristic for multiple sequence alignment using transducers and suboptimal alignments. RECOMB 2006, April 2-5, 2006. Venice Convention at The Cinema Palace, Venice Lido - Italy http://recomb06.dei.unipd.it/ Csürös, M., Miklós, I. (2005) Statistical alignment of retropseudogenes and their functional paralogs via a common ancestor, 30^th FEBS Congress, 2005 Jul. 2-7, Budapest, Hungary http://www.febs-iubmb-2005.com/ Miklós, I.,, Drummond, A., Lunter, G.A., Hein, J. (2003) Cosamling alignments and evolutionary trees in a Bayesian framework. 3^rd Workshop on Algorithms in Bioinformatics, 2003 Sep. 15-20, Budapest, Hungary http://www.conferences.hu/ALGO2003/algo_2003.htm Podani, J., & Miklós, I. (2002) On the horseshoe effect in ecological ordinations. 45^th Symposium of the International Association for Vegetation Science, March 3-8, 2002, Porto Alegre, Brazil Podani, J., & Miklós, I. (2001) Resemblance coefficients and the horseshoe effect in principal co-ordinates analysis. AbuDiv2001, August 28-September 2, 2001, Balatonfüred, Hungary Szathmáry E.,Miklós, I. (1999) Epistasis of deleterious mutations affecting biochemical networks. NATO Advanced Research Workshop on Technological and Medical Implications of Metabolic Control Analysis, April 10-16, 1999, Visegrád, Hungary http://bip.cnrs-mrs.fr/bip10/meet99.htm Other Talks Random walk on random walks Mathematical Genetics Seminar, 2006 Dec 5, OCGF, Oxford, UK Genomátrendeződések Rényi Intézet, 2006 március 13. Genomátrendeződés és genom architektúra humán tumor genomokban (Genome rearrangement and genome architecture in human tumor genomes, in Hungarian) Bioinformatika konferencia, 2005 május 21-22, Balatonfüred Can we distinguish RNA genes from random sequences? Collegium Budapest, 2004-11-24 Összehasonlító bioinformatika (Comparative bioinformatics, in Hungarian) Bioinformatics seminar, Renyi Institute 2004 October 1. http://www.renyi.hu/~bioinf/ MCMC methods for inferring genome rearrangement Mathematical Genetics seminar, 20 January 2004, OCGF, Oxford Algorithmic challenges in MCMC. Oxford-BiRC meeting, 2003 June 24-26, Sandbjerg, Denmark Trees sequences and the molecular evolution Fellow seminar, 30 May 2002, Collegium Budapest