List of works - Esko Ukkonen

A global map of human gene expression

scientific article

Accurate self-correction of errors in long reads using de Bruijn graphs

scientific article published on 6 June 2016

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

scientific article

Computational methods for metabolic reconstruction

scientific article published on 18 February 2010

DNA-binding specificities of human transcription factors

scientific journal article

Efficient algorithms for the discovery of gapped factors

scientific article

Efficient construction of maximal and minimal representations of motifs of a string

Fast matching of transcription factor motifs using generalized position weight matrix models

scientific article published on 6 August 2013

Fast motif matching revisited: high-order PWMs, SNPs and indels

scientific article published on 22 December 2016

Fast profile matching algorithms — A survey

scholarly article by Cinzia Pizzi & Esko Ukkonen published May 2008 in Theoretical Computer Science

Fast scaffolding with small independent mixed integer programs

scientific article published on 13 October 2011

Finding significant matches of position weight matrices in linear time

scientific article published in January 2011

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

scientific article

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

scientific article

Integrating sequence, evolution and functional genomics in regulatory genomics

scientific article published on 30 January 2009

Locating potential enhancer elements by comparative genomics using the EEL software

scholarly article by Kimmo Palin et al published June 2006 in Nature Protocols

Longest common substrings with k mismatches ⬇️

scholarly article by Tomas Flouri et al published June 2015 in Information Processing Letters

MOODS: fast search for position weight matrix matches in DNA sequences

scientific article

Maximal and minimal representations of gapped and non-gapped motifs of a string

article published in 2009

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

scientific article published on 27 January 2018

Motif matching using gapped patterns

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

scientific article

On size reduction techniques for multitape automata

On the complexity of finding gapped motifs

On-line construction of suffix trees

article

Optimization of cDNA-AFLP experiments using genomic sequence data

scientific article

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes

scientific article published on 27 February 2006

Sequential and indexed two-dimensional combinatorial template matching allowing rotations

Systematic search for the best gene expression markers for melanoma micrometastasis detection

article

The BREW workshop series: a stimulating experience in PhD education

scientific article published on 23 January 2008

The Complexity of LALR(k) Testing

scientific article

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

scientific article

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling.

scientific article published on 28 June 2009

List of works by Esko Ukkonen

A global map of human gene expression

Accurate self-correction of errors in long reads using de Bruijn graphs

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

Computational methods for metabolic reconstruction

DNA-binding specificities of human transcription factors

Efficient algorithms for the discovery of gapped factors

Efficient construction of maximal and minimal representations of motifs of a string

Fast matching of transcription factor motifs using generalized position weight matrix models

Fast motif matching revisited: high-order PWMs, SNPs and indels

Fast profile matching algorithms — A survey

Fast scaffolding with small independent mixed integer programs

Finding significant matches of position weight matrices in linear time

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

Integrating sequence, evolution and functional genomics in regulatory genomics

Locating potential enhancer elements by comparative genomics using the EEL software

Longest common substrings with k mismatches ⬇️

MOODS: fast search for position weight matrix matches in DNA sequences

Maximal and minimal representations of gapped and non-gapped motifs of a string

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

Motif matching using gapped patterns

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

On size reduction techniques for multitape automata

On the complexity of finding gapped motifs

On-line construction of suffix trees

Optimization of cDNA-AFLP experiments using genomic sequence data

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes

Sequential and indexed two-dimensional combinatorial template matching allowing rotations

Systematic search for the best gene expression markers for melanoma micrometastasis detection

The BREW workshop series: a stimulating experience in PhD education

The Complexity of LALR(k) Testing

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling.

The complexity of maximum matroid–greedoid intersection and weighted greedoid maximization