Esko Ukkonen | Academic Influence

Esko Ukkonen's AcademicInfluence.com Rankings

Esko Ukkonen

Computer Science

#1545

World Rank

#1599

Historical Rank

Algorithms

#49

World Rank

#49

Historical Rank

Database

#4262

World Rank

#4432

Historical Rank

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Computer Science

Esko Ukkonen's Degrees

PhD Computer Science University of Helsinki

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Why Is Esko Ukkonen Influential?

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According to Wikipedia, Esko Juhani Ukkonen is a Finnish theoretical computer scientist known for his contributions to string algorithms, and particularly for Ukkonen's algorithm for suffix tree construction. He is a professor emeritus of the University of Helsinki.

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Esko Ukkonen's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

On-line construction of suffix trees (1995) (1222)
DNA-Binding Specificities of Human Transcription Factors (2013) (1065)
Algorithms for Approximate String Matching (1985) (671)
Approximate String Matching with q-grams and Maximal Matches (1992) (668)
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling (2009) (520)
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo (2010) (509)
Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity (2006) (502)
Finding Approximate Patterns in Strings (1985) (441)
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. (2010) (414)
Predicting gene regulatory elements in silico on a genomic scale. (1998) (387)
A global map of human gene expression (2010) (376)
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera (2014) (197)
Two Algorithms for Approximate String Matching in Static Texts (1991) (190)
Approximate String-Matching over Suffix Trees (1993) (168)
A Greedy Approximation Algorithm for Constructing Shortest Common Superstrings (1988) (163)
From gene networks to gene function. (2003) (162)
Constructing Suffix Trees On-Line in Linear Time (1992) (154)
The Shortest Common Supersequence Problem over Binary Alphabet is NP-Complete (1981) (148)
MOODS: fast search for position weight matrix matches in DNA sequences (2009) (142)
A Comparison of Approximate String Matching Algorithms (1996) (125)
Local average intensity-based method for identifying spherical particles in electron micrographs. (2000) (125)
Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data (2000) (119)
SEQAID: a DNA sequence assembling program based on a mathematical model (1984) (115)
Approximate Boyer-Moore String Matching (1993) (109)
Lempel-Ziv parsing and sublinear-size index structures for string matching (1996) (102)
Pattern Discovery in Biosequences (1998) (97)
On Approximate String Matching (1983) (94)
Geometric algorithms for transposition invariant content based music retrieval (2003) (93)
Accurate self-correction of errors in long reads using de Bruijn graphs (2016) (89)
Fast scaffolding with small independent mixed integer programs (2011) (83)
An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries (2002) (82)
Including Interval Encoding into Edit Distance Based Music Comparison and Retrieval (2003) (69)
Autumn temperature and carbon balance of a boreal Scots pine forest in Southern Finland. (2010) (66)
Switch to an invasive growth phase in melanoma is associated with tenascin‐C, fibronectin, and procollagen‐I forming specific channel structures for invasion (2006) (65)
Algorithms for Some String Matching Problems Arising in Molecular Genetics (1983) (64)
Approximate Matching of Run-Length Compressed Strings (2001) (60)
Discovering Patterns and Subfamilies in Biosequences (1996) (57)
Reasoning about strings in databases (1994) (55)
Flow Analysis of Prolog Programs (1987) (54)
Transposition invariant string matching (2005) (52)
On{line Construction of Suux Trees 1 (1995) (52)
An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments (2008) (48)
Computational methods for metabolic reconstruction. (2010) (48)
Finding Founder Sequences from a Set of Recombinants (2002) (46)
A Rotation Invariant Filter for Two-Dimensional String Matching (1998) (45)
Locating potential enhancer elements by comparative genomics using the EEL software (2006) (45)
A Simple Linear-Time Algorithm for in Situ Merging (1984) (44)
Optimal Exact and Fast Approximate Two Dimensional Pattern Matching Allowing Rotations (2002) (40)
Systematic search for the best gene expression markers for melanoma micrometastasis detection (2007) (40)
Approximate String Matching over Ziv-Lempel Compressed Text (2000) (39)
Boyer-Moore Approach to Approximate String Matching (Extended Abstract) (1990) (39)
Data Mining for Regulatory Elements in Yeast Genome (1997) (39)
Longest common substrings with k mismatches (2014) (38)
A linear-time algorithm for finding approximate shortest common superstrings (1990) (37)
Maximal and minimal representations of gapped and non-gapped motifs of a string (2009) (37)
Two and higher dimensional pattern matching in optimal expected time (1994) (36)
Finding Significant Matches of Position Weight Matrices in Linear Time (2011) (35)
A Hidden Markov Technique for Haplotype Reconstruction (2005) (35)
The Exact Path Length Problem (2002) (35)
Approximate string matching on Ziv-Lempel compressed text (2003) (34)
Approximate string matching with suffix automata (1993) (33)
Sweepline the Music! (2003) (31)
Learning rules with local exceptions (1994) (31)
Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes (2006) (29)
MDL learning of unions of simple pattern languages from positive examples (1995) (28)
Algorithms for the search of amino acid patterns in nucleic acid sequences (1986) (28)
The Set Union Problem with Backtracking (1986) (27)
Fast motif matching revisited: high‐order PWMs, SNPs and indels (2016) (27)
Assigning probes into a small number of pools separable by electrophoresis (2002) (26)
Optimization of selectivity in high-performance liquid chromatography using desirability functions and mixture designs according to PRISMA. (1998) (26)
Integrating sequence, evolution and functional genomics in regulatory genomics (2009) (26)
Two Results on Polynomial Time Truth-Table Reductions to Sparse Sets (1983) (25)
Algorithms for Transposition Invariant String Matching (2003) (24)
On the Equivalence Problem for E-Pattern Languages (1996) (24)
Optimization of cDNA-AFLP experiments using genomic sequence data (2005) (23)
Finding Lowest Common Ancestors in Arbitrarily Directed Trees (1994) (23)
Accurate selfcorrection of errors in long reads using de Bruijn graphs (2016) (23)
Mining the UKIDSS Galactic Plane Survey: star formation and embedded clusters (2012) (23)
The C-BRAHMS project (2003) (21)
Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries. (2003) (21)
A Geometric Approach to Feature Selection (1994) (21)
Haplotype Inference Via Hierarchical Genotype Parsing (2007) (20)
Mining the VVV: star formation and embedded clusters (2013) (18)
Combinatorial methods for approximate image matching under translations and rotations (1999) (18)
On the Complexity of Unification Sequences (1986) (18)
Combinatorial methods for approximate pattern matching under rotations and translations in 3D arrays (2000) (18)
Learning hierarchical rule sets (1992) (18)
Correlating gene promoters and expression in gene disruption experiments (2002) (18)
Faster template matching without FFT (2001) (18)
Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract) (1996) (17)
ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis (2008) (17)
Fast Search Algorithms for Position Specific Scoring Matrices (2007) (17)
Fast profile matching algorithms - A survey (2008) (16)
An Index for Two Dimensional String Matching Allowing Rotations (2000) (15)
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information (2003) (15)
Bideterministic automata and minimal representations of regular languages (2003) (14)
A Characterization of LL(k) Languages (1976) (14)
The equivalence problem for some non-real-time deterministic pushdown automata (1982) (13)
Efficient algorithms for the discovery of gapped factors (2011) (13)
Online timestamped text indexing (2002) (13)
Implementing a Declarative String Query Language with String Restructuring (1999) (13)
Retrieving Music --- To Index or not to Index (1998) (13)
Lower Bounds on the Size of Deterministic Parsers (1983) (13)
A Computational Method for Reconstructing Gapless Metabolic Networks (2008) (12)
Phasing genotypes using a hidden Markov model (2008) (12)
Time Parameter and Arbitrary Deunions in the Set Union Problem (1988) (12)
On the complexity of finding gapped motifs (2008) (11)
Minimizing the Number of Evaluation Passes for Attribute Grammars (1981) (11)
Finding transcription factor binding site combinations in the yeast genome (1997) (11)
Mining the UKIDSS GPS: Star Formation and Embedded Clusters (2012) (11)
Design and implementation of a string database query language (2003) (11)
Sequential and indexed two-dimensional combinatorial template matching allowing rotations (2005) (11)
Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets (2018) (10)
Finding Feasible Pathways in Metabolic Networks (2005) (10)
Local Similarity Based Point-Pattern Matching (2002) (10)
A method for transforming grammars into LL(k) form (1979) (9)
Probabilistic modeling and machine learning in structural and systems biology (2007) (9)
Structural Analysis of Gapped Motifs of a String (2007) (9)
Finding Paths with the Right Cost (1999) (9)
Timestamped Term Representation for Implementing Prolog (1986) (8)
Exploring long DNA sequences by information content (2006) (8)
Autumn warming and carbon balance of a boreal Scots pine forest in Southern Finland (2009) (8)
A Greedy Algorithm for Constructing Shortest Common Superstrings (1986) (7)
Hidden Markov Modelling Techniques for Haplotype Analysis (2004) (7)
A Modification of the LR(k) Method for Constructing Compact Bottom-Up Parsers (1979) (7)
Tranformations to Produce Certain Covering Grammars (1978) (7)
A voting margin approach for the detection of retinal microaneurysms (2005) (6)
AQL: an Alignment Based Language for Querying String Databases (1998) (6)
Exponential lower bounds for some NP-complete problems in a restricted linear decision tree model (1983) (6)
Algorithm Theory — SWAT '92 (1992) (6)
Proceedings of the 22nd international conference on Algorithmic learning theory (1995) (6)
Motif Matching Using Gapped Patterns (2013) (6)
Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models (2013) (6)
The Complexity of LALR(k) Testing (1983) (5)
The Nonexistence of Some Covering Context-Free Grammars (1979) (5)
Upper Bounds on the Size of LR(k) Parsers (1985) (5)
Approximate string-matching and the q-gram distance (1993) (5)
Point Pattern Matching (2016) (5)
LALR(k) testing is PSPACE-complete (1981) (4)
On the calculation of the effects of roundoff errors (1981) (4)
Finding Temporary Terms in Prolog Programs (1984) (4)
On the Optimal Assignment of Attributes to Passes in Multi-Pass Attribute Evaluators (1980) (4)
An analytic and systematic framework for estimating metabolic flux ratios from ¹³C tracer experiments: methodology article (2008) (4)
Neural Networks in the Ice-Correction of Discharge Observations (1997) (4)
A decision method for the equivalence of some non-real-time deterministic pushdown automata (1980) (4)
The Computational Complexity of Orientation Search in Cryo-Electron Microscopy (2004) (4)
Algorithms For 2 – D Hamming Distance Under Rotations ( extended abstract ) 1 (1999) (4)
Combinatorial Pattern Matching, 20th Annual Symposium, CPM 2009, Lille, France, June 22-24, 2009, Proceedings (2009) (3)
The Complexity of Maximum Matroid-Greedoid Intersection and Weighted Greedoid Maximization (2004) (3)
Searching for General Documents (1998) (3)
18th International Workshop on Algorithms in Bioinformatics (WABI 2018) (2018) (3)
Flow analysis of metabolite fragments for ux estimation (2005) (3)
Recombination Systems (2004) (3)
Sweepline and Recursive Geometric Algorithms for Melodic Similarity (2005) (3)
MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs (2020) (3)
Pathway assistant: a web portal for metabolic modelling (2006) (3)
On Size Bounds for Deterministic Parsers (1981) (3)
Relation Patterns and their Automatic Discovery in Biosequences (1997) (3)
Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation (2006) (2)
Matching Numeric Strings under Noise (2003) (2)
Discovery of putative transcription factor binding sites from microarray-based gene expression profiles (1999) (2)
Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way (2010) (2)
The Computational Complexity of Orientation Search Problems in Cryo-Electron Microscopy (2004) (2)
Predicting gene regulatory elements from their expression data in the complete yeast genome (1998) (2)
On size reduction techniques for multitape automata (2006) (2)
Algorithmic Learning Theory (2011) (2)
Remarks on the Nonexistence of some Covering Grammars (1979) (2)
Size Reduction of Multitape Automata (2004) (2)
An analysis of the effect of rounding errors on the flow of control in numerical processes (1979) (2)
Sequential and indexed two-dimensional pattern matching allowing rotations (2003) (2)
Algorithms for Transposition Invariant StringMat hing ( Extended Abstra t ) ? (2002) (2)
Balancing Syntactic and Semantic Power in Compiler Specification (1980) (1)
Efficient construction of maximal and minimal representations of motifs of a string (2009) (1)
The Complexity of Maximum Matroid-Greedoid Intersection (2001) (1)
The BREW workshop series: a stimulating experience in PhD education (2008) (1)
An ALgorithm for Learning Hierarchical Classifiers (1994) (1)
Common subsequences and supersequences and their expected length (1995) (1)
Proceedings of the Third Scandinavian Workshop on Algorithm Theory (1992) (1)
Seed-driven Learning of Position Probability Matrices from Large Sequence Sets (2017) (1)
Term Weighting in Query-Based Document Clustering (Extended Abstract) (1998) (1)
Planning isotopomer measurements for estimation of metabolic fluxes (2005) (0)
A reason for investigating the effect of rounding errors on the flow of control is that the effect decreases the reliability of the automatic techniques for rounding (0)
FASTER THAN FFT : ROTATION INVARIANTCOMBINATORIAL TEMPLATE MATCHINGKimmo Fredriksson (2002) (0)
How to Reconstruct a Genome (2012) (0)
VizieR Online Data Catalog: Stellar clusters from UKIDSS Galactic Plane Survey (Solin+, 2012) (2012) (0)
VizieR Online Data Catalog: VVV: star formation and embedded clusters (Solin+, 2014) (2014) (0)
University of Helsinki Department of Computer Science Annual Report 1998 (1999) (0)
Using Trainable Computing Networks in the Optimization of Lake Regulation (1997) (0)
Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching (2009) (0)
An Experiment in Learning the Language of Sequence Motifs: Sequence Logos vs. Finite-State Machines (2017) (0)
Editorial (2016) (0)
Algorithm Theory--Swat '92: Third Scandinavian Workshop on Algorithm Theory, Helsinki, Finland, July 8-10, 1992 : Proceedings (1992) (0)
Combinatorial Pattern Matching: 6th Annual Symposium, CPM 95, Espoo, Finland, July 5 - 7, 1995. Proceedings (1995) (0)
Fast Filters for Two Dimensional String Matching AllowingRotationsKimmo Fredriksson (2000) (0)
Local approximate 3D matching of proteins in viral cryo-EM density maps (2004) (0)
HIIT Annual Report 2006 (2007) (0)
Discovery of Regulatory Motifs in DNA (2018) (0)
Toward Complete Genome Data Mining in Computational Biology (2000) (0)
Identification of the best molecular markers for early detection of melanoma metastases (2008) (0)
Finding a Good Collection of Patterns Covering a Set of Sequences Finding a Good Collection of Patterns Covering a Set of Sequences (1995) (0)
The switch to an invasive growth phase in melanoma is associated with TN-C, FN, and PCOL-I forming special channel structures for invasion (2006) (0)
vator receptor (uPAR). In melanocytic tumors, uPAR is overexpressed in late-stage melanomas and one incidence of melanoma was observed in a family carrying the germline translocation in chromosome (2006) (0)
Motif Construction from High-Throughput SELEX Data (2009) (0)
Editor's foreword (1989) (0)
A Geometr ic Approach to Feature Select ion (2005) (0)
A framework for direct metabolic flux estimation (2006) (0)
Editors' Introduction (2011) (0)
Structure Preserving Elimination of Null Productions from Context-Free Grammars (1982) (0)
Term Frequency-Based Identification of FAQ-Articles (1999) (0)
Unifications, deunifications, and their complexity (1990) (0)
From gene expression profiling to gene regulation (2008) (0)
Exact and Approximate Two Dimensional Pattern Matchingallowing RotationsKimmo Fredriksson (2001) (0)

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What Schools Are Affiliated With Esko Ukkonen?

Esko Ukkonen is affiliated with the following schools:

University of Helsinki