Teaching
I used to teach topics like these:
Currently I am teaching Classical and Modern Algorithms
and Combinatorics at Budapest Semesters in
Mathematics, and Stochastic models in bioinformatics
at the Technical University of Budapest.
Some of my best 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:
- 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. Published paper:
Rearrangement of
ecological data matrices via Markov chain Monte Carlo simulation.
- Adrienn Szabó, PhD student, co-supervised with András Benczur, graduated
in 2015.
Working on bioinformatics. Published papers:
Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment,
Efficient representation of uncertainty in multiple
sequence alignments using directed acyclic
graphs
- From 2012 till today, I have had several undergraduate research projects at the BSM. The students who published peer-reviewed scientific papers with me so far are:
- Eliot Bixby, Toby Flint (2012 Fall)
- Mark Aksen, Kathleen Zhou (2015 Summer)
- Changshuo Liu (2016 Summer)
- Aravind Gollakota, William Hardt (2016 Fall)
- Zhangyang Wei (2017 Summer)
- Geneva Schlafly, Yuheng (Terry) Wang (2018 Summer)
- Letong Hong (2019 Summer)
- Aaron Li, Sohaib Nasir, Varun Srikanth (2020 Summer)
Publication list
- Erdős, E.L., Mezei, T.R., Miklós, I. (2023) Approximate Sampling of Graphs with Near-P-stable Degree Intervals
, Annals of Combinatorics, https://doi.org/10.1007/s00026-023-00678-8.
- Cibej, U., Li, A., Miklós, I., Nasir, S., Srikanth, V. (2023) Constructing bounded degree graphs with prescribed degree and neighbor degree sequences, Discrete Applied Mathematics, 332:47-61.
- Hong, L., Miklós, I. (2023) A Markov chain on the solution space of edge-colorings of bipartite graphs., Discrete Applied Mathematics, 332:7-22.
- Ecker, A., Bagi, B., Vértes, E., Steinbach-Németh, O., Karlócai, M. R., Papp, O. I., Miklós, I., Hájos, N., Freund, T. F., Gulyás, A. I., Káli, Sz. (2022) Hippocampal sharp wave-ripples and the associated sequence replay emerge from structured synaptic interactions in a network model of area CA3, eLife, 11:e71850.
- Erdős, E.L., Greenhill, C., Mezei, T. R., Miklós, I., Soltész, D., Soukup, L. (2022) The mixing time of the switch Markov chains: a unified approach, Eur. J. Comb., 99:103421.
- Lőrincz, O., Tóth, J., Molnár, L., Miklós, I., Pántya, K., Megyesi, M., Somogyi,E., Csiszovszki, Zs., Tőke, E.R. (2021) In Silico Model Estimates the Clinical Trial Outcome of Cancer Vaccines, Cells, 11(10):3048.
- Erdős, E.L., Győri, E., Mezei, T. R., Miklós, I., Soltész, D. (2021) Half-graphs, other non-stable degree sequences, and the switch Markov chain, Electronic Journal of Combinatorics, 28:3 #P3.7.
- Miklós, I., Schlafly, G., Wang, Y., Wei, Z. (2021) Edge Disjoint Caterpillar Realizations, Discrete Applied Mathematics, 289:327-344.
- Gollakota, A., Hardt, W., Miklós, I. (2020) Packing tree degree sequences Graphs and Combinatorics, 36:779-801.
- Erdős, E.L., Greenhill, C.S., Mezei, T. R., Miklós, I., Soltész, D., Soukup, L. (2019) Mixing time of the swap Markov chain and P-stability. Acta Math. Univ. Comenianae, 88(3):659-665.
- Bérczi, K., Király, Z., Liu, C. Miklós, I. (2019) Packing tree degree sequences. Informatica, 43(1):11-17.
- Miklós, I., Smith, H. (2019) The computational complexity of calculating partition functions of optimal medians with Hamming distance Advances in Applied Mathematics102:18-82.
- Miklós, I. (2019) Computational Complexity of Counting and Sampling, Chapman and Hall/CRC, ISBN 9781138035577 - CAT# K31733
- Gáspári, Z., Mészáros, B., Miklós, I., Simon, I. (2018) Bioinformatika (in Hungarian: Bioinformatics). Chapter 13 in the book Ezerarcú fehérjék (in Hungarian: 1000 faces of proteins), eds: Buday, L., Nyitrai, L. Percel, A. ISBN: 9789633314586, Semmelweis Kiadó
- Erdős, E.L. Mezei, T., Miklós, I., Soltész, D. (2018) Efficiently
sampling the realizations of bounded, irregular degree sequences of
bipartite and directed graphs. PLoS ONE, 13(8): e0201995.
- Erdős, E.L., Miklós, I. (2018)
Not all simple looking degree sequence problems are easy, Journal of Combinatorics, 9(3):553-566.
- Erdős, L.P., Miklós, I., Toroczkai, Z. (2018) New classes of degree sequences with fast mixing swap Markov chain sampling Combinatorics, Probability and Computing, 27(2):186-207.
- Erdős, E.L., Hartke, S.G., van Iersel, L., Miklós, I. (2017)
Graph Realizations Constrained by Skeleton Graphs, Electronic Journal of Combinatorics, #P2.47
- Aksen, M. Miklós, I., Zhou, K. (2017) Half-regular factorizations of the complete bipartite graph Discrete Applied Mathematics, 230:21-33.
- Bixby, E, Flint, T, Miklós, I., (2016)
Proving the
Pressing Game Conjecture on Linear Graphs
Involve, 9(1):41-56.
- Miklós, I., Smith, H (2015) Sampling and counting genome rearrangement
scenarios, BMC Bioinformatics, 16(Suppl 14): S6.
- Bassler, K.E., Del Genio, C.I., Erdős, E.L., Miklós, I., Toroczkai, Z. (2015) Exact sampling of graphs with prescribed degree correlations New Journal of Physics, 17:083052
- Erdős, L.P., Kiss, S.Z., Miklós, I., Soukup, L. (2015) Approximate Counting of Graphical Realizations PLoS ONE, 10(7): e0131300
- Herman, J.L., Novák, Á., Lyngsoe, R.,
Szabó, A., Miklós, I.,
and Hein, J. (2015)
Efficient representation of uncertainty in multiple
sequence alignments using directed acyclic
graphs
BMC Bioinformatics, 16:108
- Erdős, L.P., Miklós, I., Toroczkai, Z. (2015)
A
decomposition based proof for fast mixing of a
Markov chain over balanced realizations of a
joint degree matrix. SIAM
J. Discr. Math. 29, 481-499
- Czabarka, É, Dutle, A, Erdős, L.P.,
Miklós, I., (2014) On
Realizations of a Joint Degree Matrix
Discrete Applied Mathematics, 181(30):283-288.
- Miklós, I., Tannier, E., Kiss,
Z.S. (2014) On
sampling SCJ rearrangement scenarios
Theoretical Computer Science, 552:83-98
- Apostolico, A., Erdős, P.,Miklós, I., Siemons, J. (2013) Modulated String Searching, Theoretical Computer Science, 525:23-29.
- Erdős, P., Király, Z., Miklós, I. (2013)
On the swap-distances of different realizations of a graphical degree sequence
Combinatorics, Probability and Computing 22(3):366-383.
- 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, L.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,
2nd 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,
3rd 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,
1st 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,
30th 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.
3rd 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.
45th 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
|