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ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites.
Nucleic Acids Res. 2016 May 5;44(8):e72. doi: 10.1093/nar/gkv1518. Epub 2015 Dec 31.
Nucleic Acids Res. 2016.
PMID: 26721389
Free PMC article.
PRALINE: a versatile multiple sequence alignment toolkit.
Bawono P, Heringa J.
Bawono P, et al.
Methods Mol Biol. 2014;1079:245-62. doi: 10.1007/978-1-62703-646-7_16.
Methods Mol Biol. 2014.
PMID: 24170407
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Multiple Sequence Alignment.
Bawono P, Dijkstra M, Pirovano W, Feenstra A, Abeln S, Heringa J.
Bawono P, et al.
Methods Mol Biol. 2017;1525:167-189. doi: 10.1007/978-1-4939-6622-6_8.
Methods Mol Biol. 2017.
PMID: 27896722
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Motif-Aware PRALINE: Improving the alignment of motif regions.
Dijkstra M, Bawono P, Abeln S, Feenstra KA, Fokkink W, Heringa J.
Dijkstra M, et al. Among authors: bawono p.
PLoS Comput Biol. 2018 Nov 1;14(11):e1006547. doi: 10.1371/journal.pcbi.1006547. eCollection 2018 Nov.
PLoS Comput Biol. 2018.
PMID: 30383764
Free PMC article.
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Quantifying the displacement of mismatches in multiple sequence alignment benchmarks.
Bawono P, van der Velde A, Abeln S, Heringa J.
Bawono P, et al.
PLoS One. 2015 May 19;10(5):e0127431. doi: 10.1371/journal.pone.0127431. eCollection 2015.
PLoS One. 2015.
PMID: 25993129
Free PMC article.
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General secretion signal for the mycobacterial type VII secretion pathway.
Daleke MH, Ummels R, Bawono P, Heringa J, Vandenbroucke-Grauls CM, Luirink J, Bitter W.
Daleke MH, et al. Among authors: bawono p.
Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):11342-7. doi: 10.1073/pnas.1119453109. Epub 2012 Jun 25.
Proc Natl Acad Sci U S A. 2012.
PMID: 22733768
Free PMC article.
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