Zobrazeno 1 - 10
of 177
pro vyhledávání: '"Esko Ukkonen"'
Publikováno v:
Bioinformatics
Motivation Position-specific probability matrices (PPMs, also called position-specific weight matrices) have been the dominating model for transcription factor (TF)-binding motifs in DNA. There is, however, increasing recent evidence of better perfor
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4fa5c60b115791df20ecab64d67f3986
https://pubmed.ncbi.nlm.nih.gov/31999322
https://pubmed.ncbi.nlm.nih.gov/31999322
Publikováno v:
Bioinformatics
Bioinformatics, 2017, 33 (6), pp.799-806. ⟨10.1093/bioinformatics/btw321⟩
Bioinformatics, Oxford University Press (OUP), 2017, 33 (6), pp.799-806. ⟨10.1093/bioinformatics/btw321⟩
Bioinformatics, 2017, 33 (6), pp.799-806. ⟨10.1093/bioinformatics/btw321⟩
Bioinformatics, Oxford University Press (OUP), 2017, 33 (6), pp.799-806. ⟨10.1093/bioinformatics/btw321⟩
New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50,000 bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilisation of the reads in, e.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6235fdfd98d53a603d4095fc76f2dadf
http://hdl.handle.net/10138/182781
http://hdl.handle.net/10138/182781
Publikováno v:
Bioinformatics. 33:514-521
Motivation While the position weight matrix (PWM) is the most popular model for sequence motifs, there is growing evidence of the usefulness of more advanced models such as first-order Markov representations, and such models are also becoming availab
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7e75c3183a728d0db777344589c55c10
https://doi.org/10.1093/bioinformatics/btw683
https://doi.org/10.1093/bioinformatics/btw683
Autor:
Travis Gagie, Sophie Sverdlov, Dominik Kempa, Esko Ukkonen, Jarkko Toivonen, Leena Salmela, Alexandre P. Francisco
Publikováno v:
bioRxiv
Position weight matrices (PWMs) are the standard way to model binding site affinities in bioinformatics. However, they assume that symbol occurrences are position independent and, hence, they do not take into account symbols co-occurrence at differen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f707fa1f9e60f40c52109b81b1e4a629
https://doi.org/10.1101/143024
https://doi.org/10.1101/143024
Publikováno v:
Theoretical Computer Science. 548:1-13
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has applications in t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f9a8df886f19b3c46a63320b01b069f
https://doi.org/10.1016/j.tcs.2014.06.032
https://doi.org/10.1016/j.tcs.2014.06.032
The longest common substring with $k$-mismatches problem is to find, given two strings $S_1$ and $S_2$, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance between $A_1$ and $A_2$ is $\le k$. We introduce a practical
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::436e3282efbb048f96ad20622be756c4
https://aaltodoc.aalto.fi/handle/123456789/25527
https://aaltodoc.aalto.fi/handle/123456789/25527
Autor:
Jarkko Toivonen, Jussi Taipale, Arttu Jolma, Jian Yan, Nicholas M. Luscombe, Mikko Taipale, Ekaterina Morgunova, Kimmo Palin, Kazuhiro R. Nitta, Tom Whitington, Patrick Lemaire, Martin Enge, Timothy P. Hughes, Esko Ukkonen, Teemu Kivioja, Gong-Hong Wei, Pasi Rastas, Renaud Vincentelli, Juan M. Vaquerizas
Publikováno v:
Cell. 152(1-2):327-339
SummaryAlthough 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 the sequence-specific binding of human TFs using high
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9820ef8889f379d9f623e43f3f37fcd6
Publikováno v:
University of Helsinki
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::58bf0cc762ae412f7697902abb528a63
https://doi.org/10.1007/978-1-4939-2864-4_296
https://doi.org/10.1007/978-1-4939-2864-4_296
Autor:
Jussi Taipale, Arttu Jolma, Lu Cheng, Jian Yan, Esko Ukkonen, Mikko Taipale, Shaheynoor Talukder, Juan M. Vaquerizas, Gong-Hong Wei, Kimmo Palin, Martin Bonke, Martin Enge, Nicholas M. Luscombe, Jarkko Toivonen, Teemu Kivioja, Timothy P. Hughes, Mikko J. Sillanpää
Publikováno v:
Genome Research
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 this information is encoded in a pattern of specific s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1e3e1ddb0fa052bab5503b4483832ac5
https://doi.org/10.1101/gr.100552.109
https://doi.org/10.1101/gr.100552.109
Publikováno v:
Nucleic Acids Research
In some dimeric cases of transcription factor (TF) binding, the specificity of dimeric motifs has been observed to differ notably from what would be expected were the two factors to bind to DNA independently of each other. Current motif discovery met
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9737d0d00f0d2f4641835ad841eb625a
https://doi.org/10.1093/nar/gky027
https://doi.org/10.1093/nar/gky027