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T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame C, Higgins DG, Heringa J. Notredame C, et al. Among authors: heringa j. J Mol Biol. 2000 Sep 8;302(1):205-17. doi: 10.1006/jmbi.2000.4042. J Mol Biol. 2000. PMID: 10964570
Multiple Sequence Alignment.
Bawono P, Dijkstra M, Pirovano W, Feenstra A, Abeln S, Heringa J. Bawono P, et al. Among authors: heringa j. Methods Mol Biol. 2017;1525:167-189. doi: 10.1007/978-1-4939-6622-6_8. Methods Mol Biol. 2017. PMID: 27896722
PRALINE: a versatile multiple sequence alignment toolkit.
Bawono P, Heringa J. Bawono P, et al. Among authors: heringa j. Methods Mol Biol. 2014;1079:245-62. doi: 10.1007/978-1-62703-646-7_16. Methods Mol Biol. 2014. PMID: 24170407
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: heringa j. 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.
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.
Ye K, Feenstra KA, Heringa J, Ijzerman AP, Marchiori E. Ye K, et al. Among authors: heringa j. Bioinformatics. 2008 Jan 1;24(1):18-25. doi: 10.1093/bioinformatics/btm537. Epub 2007 Nov 17. Bioinformatics. 2008. PMID: 18024975
AuberGene--a sensitive genome alignment tool.
Szklarczyk R, Heringa J. Szklarczyk R, et al. Among authors: heringa j. Bioinformatics. 2006 Jun 15;22(12):1431-6. doi: 10.1093/bioinformatics/btl112. Epub 2006 Apr 10. Bioinformatics. 2006. PMID: 16606686
Global multiple-sequence alignment with repeats.
Sammeth M, Heringa J. Sammeth M, et al. Among authors: heringa j. Proteins. 2006 Jul 1;64(1):263-74. doi: 10.1002/prot.20957. Proteins. 2006. PMID: 16609972
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.
Simossis VA, Heringa J. Simossis VA, et al. Among authors: heringa j. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W289-94. doi: 10.1093/nar/gki390. Nucleic Acids Res. 2005. PMID: 15980472 Free PMC article.
Homology-extended sequence alignment.
Simossis VA, Kleinjung J, Heringa J. Simossis VA, et al. Among authors: heringa j. Nucleic Acids Res. 2005 Feb 7;33(3):816-24. doi: 10.1093/nar/gki233. Print 2005. Nucleic Acids Res. 2005. PMID: 15699183 Free PMC article.
The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.
Simossis VA, Heringa J. Simossis VA, et al. Among authors: heringa j. Comput Biol Chem. 2004 Dec;28(5-6):351-66. doi: 10.1016/j.compbiolchem.2004.09.005. Comput Biol Chem. 2004. PMID: 15556476
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