BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC (2009)
Satija, Rahul, Novák, Ádám, Miklós, István, Lyngsø, Rune, Hein, Jotun
Abstract Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a...
Degree-based graph construction (2009)
Kim, Hyunju, Toroczkai, Zoltan, Erdős, Péter L., Miklós, István, Székely, László Á.
Degree-based graph construction is an ubiquitous problem in network modeling, ranging from social sciences to chemical compounds and biochemical reaction networks in the cell. This problem includes...
A simple Havel-Hakimi type algorithm to realize graphical degree sequences of directed graphs (2009)
Erdős, Péter L., Miklós, István, Toroczkai, Zoltán
One of the simplest ways to decide whether a given finite sequence of positive integers can arise as the degree sequence of a simple graph is the greedy algorithm of Havel and Hakimi. This note...
Mathematical Framework for Phylogenetic Birth-And-Death Models (2009)
Csűrös, Miklós, Miklós, István
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a...
Csurös, Miklós, Miklós, István
Homologous genes originate from a common ancestor through vertical inheritance, duplication, or horizontal gene transfer. Entire homolog families spawned by a single ancestral gene can be identified...
statistical insertion–deletion (2008)
Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Jotun Hein
phylogenetic inference under a
Efficient sampling of transpositions and inverted transpositions for Bayesian MCMC (2008)
István Miklós, Timothy Brooks Paige, Péter Ligeti
Abstract. The evolutionary distance between two organisms can be determined by comparing the order of appearance of orthologous genes in their genomes. Above the numerous parsimony approaches that...
How reliably can we predict the reliability of protein structure predictions? (2008)
Miklós, István, Novák ', Ádám, Dombai, Balázs, Hein, Jotun
Abstract Background Comparative methods have been the standard techniques for in silico protein structure prediction. The prediction is based on a multiple alignment that contains both reference...
Novák, Ádám, Miklós, István, Lyngsø, Rune, Hein, Jotun
Motivation: Bayesian analysis is one of the most popular methods in phylogenetic inference. The most commonly used methods fix a single multiple alignment and consider only substitutions as...
Irmtraud M. Meyer, István Miklós
Computational methods for predicting evolutionarily conserved rather than thermodynamic RNA structures have recently attracted increased interest. These methods are indispensable not only for...
Miklos Csuros And, Miklós Csűrös, István Miklós
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition...
Csűrös, Miklós, Miklós, István
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition...
A linear memory algorithm for Baum-Welch training (2005)
Miklós, István, Meyer, Irmtraud M
Abstract Background: Baum-Welch training is an expectation-maximisation algorithm for training the emission and transition probabilities of hidden Markov models in a fully automated way. It can be...
Bayesian coestimation of phylogeny and sequence alignment (2005)
Lunter, Gerton, Miklós, István, Drummond, Alexei, Jensen, Jens, Hein, Jotun
Abstract Background Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to...
Statistical Alignment of Retropseudogenes: (2005)
Supplementary Material Miklos, Miklós Csűrös, István Miklós
Budapest, Pazmany Peter Setany 1/c, Hungary. E-mail: miklosi@ramet.elte.hu 1 SH1(i, j) = A(i 1)#HH# p(g SE1(i, j) = A(i 1, j)#Hp(g EH1(i, j) = A(i, j 1)#H# p # (h EE1(i, j) = A(i, j)# EN1(i.j) =...
Research article A linear memory algorithm for Baum-Welch training (2005)
Bmc Bioinformatics, István Miklós, Irmtraud M Meyer
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: Baum-Welch training is an expectation-maximisation algorithm...
Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Alexei Drummond, Jens Ledet Jensen, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Statistical Alignment of Retropseudogenes and Their Functional Paralogs (2005)
We describe a model for the sequence evolution of a processed pseudogene and its paralog from a common protein-coding ancestor. The model accounts for substitutions, insertions and deletions, and...
Statistical Alignment of Retropseudogenes and Their Functional Paralogs (2005)
We describe a model for the sequence evolution of a processed pseudogene and its paralog from a common protein-coding ancestor. The model accounts for substitutions, insertions and deletions, and...
Statistical Alignment of Retropseudogenes and Their Functional Paralogs (2005)
Csurös, Miklós, Miklós, István
We describe a model for the sequence evolution of a processed pseudogene and its paralog from a common protein-coding ancestor. The model accounts for substitutions, insertions, and deletions and...
Meyer, Irmtraud M., Miklós, István
Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes...
Statistical Alignment of Retropseudogenes and Their Functional Paralogs (2005)
We describe a model for the sequence evolution of a processed pseudogene and its paralog from a common protein-coding ancestor. The model accounts for substitutions, insertions and deletions, and...
Co-transcriptional folding is encoded within RNA genes (2004)
Meyer, Irmtraud M, Miklós, István
Abstract Background Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed...
Co-transcriptional folding is encoded within rna genes (2004)
Irmtraud M Meyer, István Miklós, Irmtraud M Meyer, István Miklós
© 2004 Meyer and Miklós; licensee BioMed Central Ltd. This is an open-access article distributed under the terms of the Creative Commons Attribution License
MCMC genome rearrangement (2003)
Motivation: As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions...
BIOINFORMATICS MCMC genome rearrangement (2003)
Motivation: As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions...
MCMC genome rearrangement (2003)
Motivation: As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions...
Bayesian coestimation of phylogeny and sequence alignment
Lunter, Gerton, Miklós, István, Drummond, Alexei, Jensen, Jens Ledet, Hein, Jotun
Meyer, Irmtraud M., Miklós, István
Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes...
Bayesian coestimation of phylogeny and sequence alignment
Lunter, Gerton, Miklós, István, Drummond, Alexei, Jensen, Jens Ledet, Hein, Jotun
Meyer, Irmtraud M., Miklós, István
Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes...
Meyer, Irmtraud M, Miklós, István
Computational methods for predicting evolutionarily conserved rather than thermodynamic RNA structures have recently attracted increased interest. These methods are indispensable not only for...
Dynamics of Genome Rearrangement in Bacterial Populations
Darling, Aaron E., Miklós, István, Ragan, Mark A.
Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic...
Csűrös, Miklós, Miklós, István
Homologous genes originate from a common ancestor through vertical inheritance, duplication, or horizontal gene transfer. Entire homolog families spawned by a single ancestral gene can be identified...