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Publications of Author

1. Radek Szklarczyk, Jaap Heringa
   Tracking repeats using significance and transitivity. [Citation Graph (0, 0)][DBLP]
   ISMB/ECCB (Supplement of Bioinformatics), 2004, pp:311-317 [Conf]
   
2. John W. Romein, Jaap Heringa, Henri E. Bal
   A Million-Fold Speed Improvement in Genomic Repeats Detection. [Citation Graph (0, 0)][DBLP]
   SC, 2003, pp:20- [Conf]
   
3. Jens Kleinjung, Nigel Douglas, Jaap Heringa
   Parallelized multiple alignment. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2002, v:18, n:9, pp:1270-1271 [Journal]
   
4. Kuang Lin, Victor A. Simossis, William R. Taylor, Jaap Heringa
   A simple and fast secondary structure prediction method using hidden neural networks. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2005, v:21, n:2, pp:152-159 [Journal]
   
5. Radek Szklarczyk, Jaap Heringa
   AuberGene - a sensitive genome alignment tool. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2006, v:22, n:12, pp:1431-1436 [Journal]
   
6. Jaap Heringa
   Post-genome Informatics: Minoru Kanehisa, Oxford University Press, Oxford, 2000, 148 pages. [Citation Graph (0, 0)][DBLP]
   Computers & Chemistry, 2001, v:25, n:4, pp:425-426 [Journal]
   
7. Jaap Heringa
   Local Weighting Schemes for Protein Multiple Sequence Alignment. [Citation Graph (0, 0)][DBLP]
   Computers & Chemistry, 2002, v:26, n:5, pp:459-477 [Journal]
   
8. Jaap Heringa
   The Evolution and Recognition of Protein Sequence Repeats. [Citation Graph (0, 0)][DBLP]
   Computers & Chemistry, 1994, v:18, n:3, pp:233-243 [Journal]
   
9. Jaap Heringa
   Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment. [Citation Graph (0, 0)][DBLP]
   Computers & Chemistry, 1999, v:23, n:3-4, pp:341-364 [Journal]
   
10. Kuang Lin, Jens Kleinjung, William R. Taylor, Jaap Heringa
    Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. [Citation Graph (0, 0)][DBLP]
    Computational Biology and Chemistry, 2003, v:27, n:2, pp:93-102 [Journal]
    
11. David D. Pollock, Jaap Heringa
    RECOMB98. Computational Molecular Biology: Pre- and Post-genomics, March 22-25, 1998, New York. [Citation Graph (0, 0)][DBLP]
    Computers & Chemistry, 2000, v:24, n:1, pp:133-134 [Journal]
    
12. Victor A. Simossis, Jaap Heringa
    The PRALINE online server: optimising progressive multiple alignment on the web. [Citation Graph (0, 0)][DBLP]
    Computational Biology and Chemistry, 2003, v:27, n:4-5, pp:511-519 [Journal]
    
13. Victor A. Simossis, Jaap Heringa
    The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. [Citation Graph (0, 0)][DBLP]
    Computational Biology and Chemistry, 2004, v:28, n:5-6, pp:351-366 [Journal]
    
14. Richard A. George, Kuang Lin, Jaap Heringa
    Scooby-domain: prediction of globular domains in protein sequence. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:160-163 [Journal]
    
15. Victor A. Simossis, Jaap Heringa
    PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:289-294 [Journal]
    
16. Marius C. Codrea, Connie R. Jimenez, Jaap Heringa, Elena Marchiori
    Tools for computational processing of LC-MS datasets: A user's perspective. [Citation Graph (0, 0)][DBLP]
    Computer Methods and Programs in Biomedicine, 2007, v:86, n:3, pp:281-290 [Journal]
    
17. Marius C. Codrea, Connie R. Jimenez, Sander Piersma, Jaap Heringa, Elena Marchiori
    Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data. [Citation Graph (0, 0)][DBLP]
    EvoBIO, 2007, pp:35-46 [Conf]
    
18. 
    Divide, Align and Full-Search for Discovering Conserved Protein Complexes. [Citation Graph (, )][DBLP]
    
    
19. 
    A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding. [Citation Graph (, )][DBLP]
    
    
20. 
    Dividing Protein Interaction Networks by Growing Orthologous Articulations. [Citation Graph (, )][DBLP]
    
    
21. 
    Design Issues for Qualitative Modelling of Biological Cells with Petri Nets. [Citation Graph (, )][DBLP]
    
    
22. 
    Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. [Citation Graph (, )][DBLP]
    
    
23. 
    PRALINE^TM: a strategy for improved multiple alignment of transmembrane proteins. [Citation Graph (, )][DBLP]
    
    
24. 
    Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. [Citation Graph (, )][DBLP]
    
    
25. 
    Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. [Citation Graph (, )][DBLP]
    
    
26. 
    Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy. [Citation Graph (, )][DBLP]
    
    
27. 
    Accurate confidence aware clustering of array CGH tumor profiles. [Citation Graph (, )][DBLP]
    
    
28. 
    CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs. [Citation Graph (, )][DBLP]
    
    
29. 
    The meaning of alignment: lessons from structural diversity. [Citation Graph (, )][DBLP]
    
    
30. 
    Structure and function analysis of flexible alignment regions in proteins. [Citation Graph (, )][DBLP]