• Publications
  • Influence
DNA-Binding Specificities of Human Transcription Factors
Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed theExpand
  • 827
  • 69
On-line construction of suffix trees
  • E. Ukkonen
  • Mathematics, Computer Science
  • Algorithmica
  • 1 September 1995
An on-line algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the stringExpand
  • 912
  • 53
Approximate String Matching with q-grams and Maximal Matches
  • E. Ukkonen
  • Mathematics, Computer Science
  • Theor. Comput. Sci.
  • 6 January 1992
We study approximate string matching in connection with two string distance functions that are computable in linear time. The first function is based on the so-called $q$-grams. An algorithm is givenExpand
  • 627
  • 48
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
The genetic code-the binding specificity of all transfer-RNAs--defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and thisExpand
  • 352
  • 35
Algorithms for Approximate String Matching
  • E. Ukkonen
  • Computer Science, Mathematics
  • Inf. Control.
  • 1 March 1985
The edit distance between strings a 1 … a m and b 1 … b n is the minimum cost s of a sequence of editing steps (insertions, deletions, changes) that convert one string into the other. A well-knownExpand
  • 584
  • 34
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
Members of the large ETS family of transcription factors (TFs) have highly similar DNA‐binding domains (DBDs)—yet they have diverse functions and activities in physiology and oncogenesis. SomeExpand
  • 420
  • 32
Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity
Understanding the regulation of human gene expression requires knowledge of the "second genetic code," which consists of the binding specificities of transcription factors (TFs) and the combinatorialExpand
  • 480
  • 30
Finding Approximate Patterns in Strings
  • E. Ukkonen
  • Mathematics, Computer Science
  • J. Algorithms
  • 1 March 1985
Let p (the pattern) be a string and t ≥ 0 an integer. The problem of locating in any string a substring whose edit distance from p is at most a given constant t is considered. An algorithm isExpand
  • 404
  • 28
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling
Homozygosity for the G allele of rs6983267 at 8q24 increases colorectal cancer (CRC) risk ∼1.5 fold. We report here that the risk allele G shows copy number increase during CRC development. OurExpand
  • 463
  • 19
A global map of human gene expression
To the Editor Although there is only one human genome sequence, different genes are expressed in many different cell types and tissues, as well as in different developmental stages or diseases. TheExpand
  • 349
  • 17