Esko Ukkonen

PhD, Professor of Computer Science
Head of the Department of Computer Science
Address: PO Box 68 (Gustaf Hällströmin katu 2b), FIN-00014 University of Helsinki, Finland
Phone: +358-9-191 51280 (office), +358-9-4128524 (home)
Fax: +358-9-191 51120
Email: ukkonen [at] cs.Helsinki.FI
Office hour/vastaanotto, by appointment, room D240b Exactum

Research interests

Combinatorial pattern matching
Design and analysis of algorithms
Machine learning
Computational biology

Projects and activities

Algorithmic Data Analysis (ALGODAN), a center of excellence of the Academy of Finland
Pattern matching and data mining (PMDM)
- Combinatorial pattern matching and algorithms on strings (CPM)
- Machine learning (ML)
Graduate School in Computational Biology, Bioinformatics, and Biometry (ComBi)
Nordic Journal of Computing (NJC)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Presentations

Mature writings

Essays originally printed in Kymenlaakson Osakunta's bulletin 'Kypsä':

CV

Adventures

Seoul June 2005

Selected publications

E. Soisalon-Soininen & E. Ukkonen: A characterization of LL(k) languages. Proc. ICALP 76, Edinburgh University Press 1976, pp. 20-30.
E. Ukkonen: An analysis of the effect of rounding errors on the flow of control in numerical processes. BIT 19 (1979), 116-133.
E. Ukkonen: The non-existence of some covering context-free grammars. Information Processing Letters 8 (1979), 187-192.
E. Soisalon--Soininen & E. Ukkonen: A method for transforming grammars into LL(k) form. Acta Informatica 12 (1979), 339-369.
E. Ukkonen: A modification of the LR(k) method for constructing compact bottom-up parsers. Proc. ICALP 79, Lecture Notes in Computer Science 71, 646-658, Springer 1979.
E. Ukkonen: A decision method for the equivalence of some non-real-time deterministic pushdown automata. Proc. 12th Ann. ACM Symposium on Theory of Computing, 29-38, ACM 1980.
K.-J. Räihä & E. Ukkonen: On the optimal assignment of attributes to passes in multi-pass attribute evaluators. Proc. ICALP 80, Lecture Notes in Computer Science 85, 500-511, Springer 1980.
K.-J. Räihä & E. Ukkonen: Balancing syntactic and semantic power in compiler specification. Proc. IFIP Congress 80, 65-70, North-Holland 1980.
E. Ukkonen: On the calculation of the effects of roundoff errors. ACM Transactions on Mathematical Software 7 (1981), 259-271.
K.-J. Räihä & E. Ukkonen: The shortest common supersequence problem over binary alphabet is NP-complete. Theoretical Computer Science 16 (1981), 187-198.
K.-J. Räihä & E. Ukkonen: Minimizing the number of evaluation passes for attribute grammars. SIAM J. on Computing 10 (1981), 772-786.
E. Ukkonen & E. Soisalon-Soininen: LALR(k) testing is PSPACE--complete. Proc. 13th Ann. ACM Symposium on Theory of Computing, 202-206, ACM 1981.
E. Ukkonen: On size bounds for deterministic parsers. Proc. ICALP 81, Lecture Notes in Computer Science 115, 218-228, Springer 1981.
E. Ukkonen: Structure preserving elimination of null productions from context-free grammars. Theoretical Computer Science 17 (1982), 43-54.
E. Ukkonen: The equivalence problem for some non-real-time deterministic pushdown automata. Journal of the ACM 29 (1982), 1166-1181.
S. Sippu, E. Soisalon-Soininen & E. Ukkonen: The complexity of LALR(k) testing. Journal of the ACM 30 (1983), 259-270.
E. Ukkonen: Two results on polynomial time truth--table reductions to sparse sets. SIAM J. on Computing 12 (1983), 580-587.
E. Ukkonen: Lower bounds on the size of deterministic parsers. Journal of Computer and System Sciences 26 (1983), 153-170.
E. Ukkonen: Exponential lower bounds for some NP--complete problems in restricted linear decision tree model. BIT 23 (1983), 181-192.
H. Peltola, H. Söderlund, J. Tarhio & E. Ukkonen: Algorithms for some string matching problems arising in molecular genetics. Proc. IFIP Congress 83, 59-64, Elsevier 1983.
H. Mannila & E. Ukkonen: A simple linear-time algorithm for in situ merging. Information Processing Letters 18 (1984), 203-208.
H. Peltola, H. Söderlund & E. Ukkonen: SEQAID: A DNA sequence assembling program based on a mathematical model. Nucleic Acids Research 12 (1984), 307-321.
P. Vataja & E. Ukkonen: Finding temporary terms in Prolog programs. Proc. Int. Conf. on Fifth Generation Computer Systems 1984}, 275-282, ICOT (Tokyo) 1984.
E. Ukkonen: Finding approximate patterns in strings. J. Algorithms 6 (1985), 132-137. [PDF]
E. Ukkonen: Upper bounds on the size of deterministic parsers. Information Processing Letters 20 (1985), 99-103.
E. Ukkonen: Algorithms for approximate string matching. Information and Control 64 (1985), 100-118. [PDF]
H. Peltola, H. Söderlund & E. Ukkonen: Algorithms for the search of amino acid patterns in nucleic acid sequences. Nucleic Acids Research 14 (1986), 99-107.
H. Mannila & E. Ukkonen: On the complexity of unification sequences. Proc. Third Int. Conf. on Logic Programming, Lecture Notes in Computer Science 225, 122-133, Springer 1986.
H. Mannila & E. Ukkonen: The set union problem with backtracking. Proc. ICALP 86, Lecture Notes in Computer Science 226, 236-243, Springer 1986.
H. Mannila & E. Ukkonen: Timestamped term representation for implementing Prolog. Proc. IEEE Symp. on Logic Programming 1986, 159-167.
H. Mannila & E. Ukkonen: Flow analysis of Prolog programs. Proc. IEEE Symp. on Logic Programming 1987, 205-214.
J. Tarhio & E. Ukkonen: A greedy approximation algorithm for constructing shortest common superstrings. Theoretical Computer Science 57 (1988), 131-145.
H. Mannila & E. Ukkonen: Time parameter and arbitrary deunions in the set union problem. Proc. SWAT 88, Lecture Notes in Computer Science 318, 34-42, Springer 1988.
E. Ukkonen: A linear time algorithm for finding approximate shortest common superstrings. Algorithmica 5 (1990), 313-323.
H. Mannila & E. Ukkonen: Unifications, deunifications, and their complexity. BIT 30 (1990), 599-619.
P. Jokinen & E. Ukkonen: Two algorithms for approximate string matching in static texts. Proc. MFCS 91. Lecture Notes in Computer Science 520, 240-248, Springer 1991. [PDF]
E. Ukkonen: Approximate string-matching with q-grams and maximal matches. Theoretical Computer Science 92 (1992), 191-211. [PDF]
J. Kivinen, H. Mannila & E. Ukkonen: Learning hierarchical rule sets. Proc. Fifth Annual ACM Workshop on Computational Learning Theory, 37-44, ACM Press 1992.
E. Ukkonen: Constructing suffix trees on-line in linear time. Proc. Information Processing 92, Vol. 1, IFIP Transactions A-12, 484-492, Elsevier 1992.
J. Tarhio & E. Ukkonen: Approximate Boyer--Moore string matching. SIAM J. Computing 22 (1993), 243-260.
E. Ukkonen & D. Wood: Fast approximate string matching with suffix automata. Algorithmica 10 (1993), 353-364.
E. Ukkonen: Approximate string-matching over suffix trees. Proc. CPM 93. Lecture Notes in Computer Science 684, pp. 228-242, Springer 1993. [PS] [PDF]
J. Kivinen, H. Mannila & E. Ukkonen: Learning rules with local exceptions. Proc. EuroCOLT'93, pp. 35-46, Clarendon Press, Oxford 1994.
M. Nykänen & E. Ukkonen: Finding lowest common ancestors in arbitrarily directed trees. Information Processing Letters 50 (1994), 307-310.
J. Kärkkäinen & E. Ukkonen: Two and higher dimensional pattern matching in optimal expected time. Proc. Fifth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 94), 1994, pp. 715-723.
T. Elomaa & E. Ukkonen: A geometric approach to feature selection. Proc. Machine Learning: ECML-94, Lecture Notes in Artificial Intelligence 784, pp. 351-354, Springer 1994.
J. Kivinen, H. Mannila, E. Ukkonen & J. Vilo: An algorithm for learning hierarchical classifiers. Proc. Machine Learning: ECML-94, Lecture Notes in Artificial Intelligence 784, pp. 375-378, Springer 1994.
G. Grahne, M. Nykänen & E. Ukkonen: Reasoning about strings in databases. Proc. Thirteenth ACM Symp. on Principles of Database Systems (PODS'94)}, 303-312, ACM 1994.
E. Ukkonen: On-line construction of suffix-trees. Algorithmica 14 (1995), 249-260. [PDF]
P. Kilpeläinen, H. Mannila & E. Ukkonen: MDL learning of unions of simple pattern languages from positive examples. Proc. EuroCOLT'95, Lecture Notes in Artificial Intelligence 904, pp. 252-260, Springer 1995.
J. Kärkkäinen & E. Ukkonen: Sparse suffix trees. Proc. COCOON'96, Lecture Notes in Computer Science 1090, pp. 219-230, Springer 1996.
A. Brazma, I. Jonassen, E. Ukkonen & J. Vilo: Discovering patterns and subfamilies in biosequences. Proc. Fourth International Conference on Intelligent Systems for Molecular Biology (ISMB'96), pp. 34-43, AAAI Press (Menlo Park) 1996.
P. Jokinen, J. Tarhio & E. Ukkonen: A comparison of approximate string matching algorithms. Software - Practice and Experience 26 (1996), 1439-1458.
J. Kärkkäinen & E. Ukkonen: Lempel-Ziv parsing and sublinear-size index structures for string matching. Proc. Third South American Workshop on String Processing (WSP'96), International Informatics Series 4, pp. 141-155, Carleton University Press 1996.
A. Brazma, E. Ukkonen & J. Vilo: Discovering unbounded unions of regular pattern languages from positive examples. Proc. Seventh International Symposium on Algorithms and Computation (ISAAC'96), Lecture Notes in Computer Science} 1178, pp. 95-104, Springer 1996.
M. Huttunen, B. Vehviläinen & E. Ukkonen: Coding a conceptual model into a neural network in modeling ice--correction. Proc. of the Artificial Neural Networks in Engineering (ANNIE'96) Conference. Intelligent Engineering Systems Through Artificial Neural Networks, Vol. 6, pp. 1001-1006, ASME Press, New York 1996.
A. Brazma, E. Ukkonen, J. Vilo & K. Valtonen: Data mining for regulatory elements in yeast genome. Proc. Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB'97), pp. 65-74, AAAI Press (Menlo Park) 1997.
E. Ohlebusch & E. Ukkonen: On the equivalence problem for E-pattern languages. Theoretical Computer Science 186 (1997), 231-248.
M. Huttunen, B. Vehviläinen & E. Ukkonen: Neural networks in the ice-correction of discharge observations. Nordic Hydrology 28 (1997), 283-296.
M. Huttunen, E. Ukkonen & B. Vehviläinen: Using trainable computing networks in the optimization of lake regulation. Proc. Fourth International Conference on Neural Information Processing and Intelligent Information Systems (ICONIP'97), pp. 975-978, Springer 1997.
K. Fredriksson & E. Ukkonen: A rotation invariant filter for two--dimensional string matching. Proc. Combinatorial Pattern Matching (CPM'98), Lecture Notes in Computer Science 1448, pp. 118-125, Springer 1998.
K. Korpimies & E. Ukkonen: Term weighting in query--based document clustering (extended abstract). Proc. Advances in Databases and Information Systems (ADBIS'98), Lecture Notes in Computer Science 1475, pp. 151-153, Springer 1998.
K. Korpimies & E. Ukkonen: Searching for general documents. Proc. International Conf. on Flexible Query Answering Systems (FQAS'98). Lecture Notes in Computer Science 1495, pp. 203-214, Springer 1998.
G. Grahne, R. Hakli, M. Nykänen & E. Ukkonen: AQL: An alignment based language for querying string databases. Proc. Ninth Int. Conf. on Management of Data (COMAD'98), pp. 235-251, McGraw-Hill 1998.
H. Haario, P. Vuorela, M. Nyman, E. Ukkonen, H. J. Vuorela & K. Outinen: Optimization of selectivity in high--performance liquid chromatography using desiderability functions and mixture designs according to PRISMA. European Journal of Pharmaceutical Sciences 6 (1998), 197-205.
A. Brazma, I. Jonassen, J. Vilo & E. Ukkonen: Predicting gene regulatory elements in silico on a genomic scale. Genome Research 8 (1998), 1202-1215.
R. Hakli, M. Nykänen, H. Tamm & E. Ukkonen: Implementing a declarative string query language with string restructuring. Proc. Practical Aspects of Declarative Languages (PADL'99), Lecture Notes in Computer Science 1551, pp. 179-195, Springer 1999.
G. Grahne, M. Nykänen & E. Ukkonen: Reasoning about strings in databases. Journal of Computer and System Sciences 59 (1999), 116-162.
K. Fredriksson & E. Ukkonen: Combinatorial methods for approximate image matching under translations and rotations. Pattern Recognition Letters 20 (1999), 1249-1258.
J. Kärkkäinen & E. Ukkonen: Two- and higher-dimensional pattern matching in optimal expected time. SIAM J. on Computing 29 (1999), 571-589.
K. Lemström & E. Ukkonen: Including interval encoding into edit distance based music comparison and retrieval. Proc. of the AISB'2000 Symposium on Creative & Cultural Aspects and Applications of AI & Cognitive Science, pp. 53-60, University of Birmingham, 2000. [PS]
M. Huttunen, E. Ukkonen & B. Vehviläinen: Using trainable computing networks in the control of a physical system. Preprints of the Second AMS Conference on Artificial Intelligence, pp. 60-64, American Meteorological Society 2000.
J. Kärkkäinen, G. Navarro & E. Ukkonen: Approximate string matching over Ziv-Lempel compressed text. Proc. Combinatorial Pattern Matching (CPM'00), Lecture Notes in Computer Science 1848, pp. 195-209, Springer 2000.
K. Fredriksson, G. Navarro & E. Ukkonen: An index for two dimensional string matching allowing rotations. In: Theoretical Computer Science (IFIP TCS 2000), Lecture Notes in Computer Science 1872, pp. 59-75, Springer 2000.
J. Vilo, A. Brazma, I. Jonassen, A. Robinson & E. Ukkonen: Mining for putative regulatory elements in the yeast genome using gene expression data. Proc. Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB-2000), pp. 384-394, AAAI Press 2000. [PS]
T. Kivioja, J. Ravantti, A. Verkhovsky, E. Ukkonen & D. Bamford: Local average intensity--based method for identifying spherical particles in electron micrographs. J. Structural Biology 131 (2000), 126-134.
K. Fredriksson & E. Ukkonen: Combinatorial methods for approximate pattern matching under rotations and translations in 3D arrays. Proc. 7th International Symposium on String Processing and Information Retrieval (SPIRE 2000), pp. 96-104, IEEE Computer Society 2000.
E. Ukkonen: Toward complete genome data mining in computational biology. Proc. 7th Scandinavian Workshop on Algorithm Theory (SWAT 2000), Lecture Notes in Computer Science 1851, pp. 20-21, Springer 2000.
V. Mäkinen, G. Navarro & E. Ukkonen: Approximate matching of run--length compressed strings. Proc. 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001), Lecture Notes in Computer Science 2089, pp. 31-49, Springer 2001.
K. Fredriksson & E. Ukkonen: Faster template matching without FFT. Proc. 2001 International Conference on Image Processing (ICIP 2001), pp. 678-681, IEEE Signal Processing Society 2001.
T. Mielikäinen & E. Ukkonen: The complexity of matroid-greedoid intersection. Proc. Fundamentals of Computation Theory (subsection Efficient Algorithms WEA 2001), Lecture Notes in Computer Science 2138, pp. 535-539, Springer 2001. (Full version to appear in Discrete Applied Mathematics.)
K. Fredriksson, G. Navarro & E. Ukkonen: Faster than FFT: Rotation invariant combinatorial template matching. In: S.G. Pandalai (ed), Recent Research Developments in Pattern Recognition, Vol. 3 (2002), pp. 75-112, Transworld Research Network 2002.
M. Nykänen & E. Ukkonen: The exact path length problem. Journal of Algorithms 42 (2002), 41-53.
A. Amir, G. M. Landau & E. Ukkonen: Online time stamped text indexing. Information Processing Letters 82 (2002), 253-259.
K. Fredriksson, G. Navarro & E. Ukkonen: Optimal exact and fast approximate two dimensional pattern matching allowing rotations. Proc. 13th Annual Symposium on Combinatorial Pattern Matching (CPM 2002), Lecture Notes in Computer Science 2373, pp. 235-248, Springer 2002.
V. Mäkinen & E. Ukkonen: Local similarity based point-pattern matching. Proc. 13th Annual Symposium on Combinatorial Pattern Matching (CPM 2002), Lecture Notes in Computer Science 2373, pp. 115-132, Springer 2002.
T. Kivioja, M. Arvas, K. Kataja, M. Penttilä, H. Söderlund & E. Ukkonen: Assigning probes into a small number of pools separable by electrophoresis. Proc. Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB-2002), Bioinformatics 18, Suppl 1 (2002), S199-S206.
K. Palin, E. Ukkonen, A. Brazma & Jaak Vilo: Correlating gene promoters and expression in gene disruption experiments. Proc. European Conference on Computational Biology (ECCB-2002), Bioinformatics 18, Suppl 2 (2002), S172-S180.
E. Ukkonen: Finding founder sequences from a set of recombinants. Proc. Algorithms in Bioinformatics (WABI-2002), Lecture Notes in Computer Science 2452, pp. 277-286, Springer 2002. [PS]
G. Grahne, R. Hakli, M. Nykänen, H. Tamm & E. Ukkonen: Design and implementation of a string database query language. Information Systems 28 (2003), 347-369.
M. Koivisto, M. Perola, T. Varilo, W. Hennah, J. Ekelund, M. Lukk, L. Peltonen, E. Ukkonen & H. Mannila: An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries. Proc. Pacific Symposium on Biocomputing 2003, pp. 502-513, World Scientific 2003.
V. Mäkinen, G. Navarro & E. Ukkonen: Approximate matching of run-length compressed strings. Algorithmica 35 (2003), 347-369.
E. Ukkonen, L. Lemström & V. Mäkinen: Sweepline the music! Invited paper in: Computer Science in Perspective. Essays Dedicated to Thomas Ottmann. Lecture Notes in Computer Science 2598, pp. 330-342, Springer 2003. [PDF]
J. Rousu, A. Rantanen, H. Maaheimo, E. Pitkänen, K. Saarela & E. Ukkonen: A method for estimating metabolic fluxes from incomplete isotopomer information. Proc. Computational Methods in Systems Biology (CMBS 2003), Lecture Notes in Computer Science 2602, pp. 88-103, Springer 2003.
V. Mäkinen, G. Navarro & E. Ukkonen: Algorithms for transposition invariant string matching. Proc. 20th Ann. Symp. on Theoretical Aspects of Computer Science (STACS 2003), Lecture Notes in Computer Science 2607, pp. 191-202, Springer 2003. [PS]
H. Tamm & E. Ukkonen: Bideterministic automata and minimal representations of regular languages. Proc. Eighth Int. Conf. on Implementation and Application of Automata (CIAA 2003), Lecture Notes in Computer Science 2759, pp. 61-71, Springer 2003.
J. Kärkkäinen, G. Navarro & E. Ukkonen. Approximate String Matching on Ziv-Lempel Compressed Text. Journal of Discrete Algorithms 1(3/4), (2003), 313-338.
Th. Schlitt, K. Palin, J. Rung, S. Diekmann, M. Lappe, E. Ukkonen & A. Brazma: From gene networks to gene function. Genome Research 13 (2003), 2568-2576.
E. Ukkonen, K. Lemström & V. Mäkinen: Geometric algorithms for transposition invariant content--based music retrieval. Proc. Fourth Int. Conf. on Music Information Retrieval (ISMIR-2003), Johns Hopkins University, 2003, pp. 193-199.
T. Mielikäinen, J. Ravantti & E. Ukkonen: The computational complexity of orientation search in cryo--electron Microscopy. Fourth Int. Conf. on Computational Science, Lecture Notes in Computer Science 3036, pp. 231-238, Springer 2004.
H. Tamm, M. Nykänen & E. Ukkonen: Size reduction of multitape automata. Short paper in: Ninth Int. Conf. on Implementation and Application of Automata (CIAA 2004), Lecture Notes in Computer Science 3317, pp. 329-330, Springer 2004.
S. Burkhardt, K. Fredriksson, T. Ojamies, J. Ravantti & E. Ukkonen: Local approximate 3D matching of proteins in viral cryo--EM density maps. Proc. Second Int. Symp. on 3D Data Processing, Visualization, and Transmission (3DPVT 2004), pp. 979-886, IEEE Computer Society 2004.
H. Tamm & E. Ukkonen: Bideterministic automata and minimal representations of regular languages. Theoretical Computer Science 328 (2004), 135--149.
T. Kivioja, M. Arvas, M. Saloheimo, M. Penttilä & E. Ukkonen: Optimization of cDNA-AFLP experiments using genomic sequence data. Bioinformatics 21 (2005), 2573-2579.
G. Navarro, V. Mäkinen & E. Ukkonen: Transposition invariant string matching. J. Algorithms 56 (2005), 124--153.
K. Fredriksson, G. Navarro & E. Ukkonen: Sequential and indexed two-dimensional combinatorial template matching allowing rotations. Theoretical Computer Science 347 (2005), 239-275.
A. Rantanen, T. Mielikäinen, J. Rousu & E. Ukkonen: Planning isotopomer measurements for estimation of metabolic fluxes. Proc. German Conference on Bioinformatics (GCB 2005), Lecture Notes in Informatics 71, pp. 177-191, GI 2005.
E. Pitkänen, A. Rantanen, J. Rousu & E. Ukkonen: Finding Feasible Pathways in Metabolic Networks. Proc. Panhellenic Conference on Informatics 2005, Lecture Notes in Computer Science 3746, pp. 123-133, Springer 2005.
I. Autio, J.C. Borras, I. Immonen, P. Jalli & E. Ukkonen: A voting margin approach for the detection of retinal microaneurysms. Proc. IASTED Int. Conf. on Visualization, Imaging, and Image Processing (VIIP 2005), pp. 511-517, ACTA Press 2005.
P. Rastas, M. Koivisto, H. Mannila & Esko Ukkonen: A Hidden Markov Technique for Haplotype Reconstruction. Algorithms in Bioinformatics (WABI-2005), Lecture Notes in Computer Science 3692, pp. 140-151, Springer 2005. [PDF]
H. Tamm, M. Nykänen & E. Ukkonen: Size reduction of multitape automata. Tenth Int. Conf. on Implementation and Application of Automata (CIAA 2005), Lecture Notes in Computer Science 3845, pp. 307-318, Springer 2006.
T. Mielikäinen & E. Ukkonen: The complexity of matroid-greedoid intersection and weighted greedoid maximization. Discrete Applied Mathematics 154 (2006), 684-691.
O. Hallikas, K. Palin, N. Sinjushina, R. Rautiainen, J. Partanen, E. Ukkonen & J. Taipale: Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124 (January 13, 2006), 47-59.
A. Rantanen, T. Mielikäinen, J. Rousu, H. Maaheimo & E. Ukkonen: Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. Bioinformatics 22 (2006), 1198-1206.
H. Tamm, M. Nykänen & E. Ukkonen: On size reduction techniques for multitape automata. Theoretical Computer Science (in press).
A. Rantanen, H. Maaheimo, E. Pitkänen, J. Rousu & E. Ukkonen: Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation. Transactions on Computational Systems Biology (in press).
P. Parikka, E. Pitkänen, A. Rantanen, A. Akerlund & E. Ukkonen: Pathway Assistant: a web portal for metabolic modelling. Network Tools and Applications in Biology (NETTAB 2006) (in press).
K. Palin, J. Taipale & E. Ukkonen: Locating potential enhancer elements by comparative genomics using the EEL software. Nature Protocols 1 (2006), 368-374. [PDF]