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IBIVU Group Publications

[ 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 |   2000 | 1999 ]

Publications 2018
Meike H. van der Ree, Louis Jansen, Matthijs R.A. Welkers, Hendrik W. Reesin, K. Anton Feenstra, and Neeltje A. Kootstra. (2018) Deep sequencing identifies hepatitis B virus core protein signatures in chronic hepatitis B patients, Antiviral Research in press
Annika Jacobsen, Linda J. W. Bosch, Sanne R. Martens-De Kemp, Beatriz Carvalho, Anke H. Sillars-Hardebol, Richard J. Dobson, Emanuele De Rinaldis, Gerrit A. Meijer, Sanne Abeln, Jaap Heringa, Remond J.A. Fijneman, and K. Anton Feenstra. (2018) Aurora kinase A (AURKA) interaction with Wnt and Ras-MAPK signalling pathways in colorectal cancer, Scientific Reports 8 p. 7522
K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filippe B. dos Santos, Douwe Molenaar, Bas Teusink, Huub J. C. Hoefsloot, and Jaap Heringa. Training for translation between disciplines: a philosophy for life and data sciences curricula, Bioinformatics 34 p. 4-12
Publications 2017
Punto Bawono, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, Jaap Heringa. (2017) Multiple sequence alignment, Methods in Molecular BIology 1525 p. 167-189
Qingzhen Hou, Paul de Geest, Wim F. Vranken, Jaap Heringa and K. Anton Feenstra. (2017) Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest, Bioinformatics 33 p. 1479-1487
Publications 2016
Hou, Q., Lensink, M.F., Heringa, J. and Feenstra, K.A. (2016). CLUB-MARTINI: Selecting favourable interactions amongst available candidates, a coarse-grained simulation approach to scoring docking decoys. PLoS ONE 11: e0155251.
Jacobsen, A., Heijmans, N., Verkaar, F., Smit, M.J., Heringa, J.*, van Amerongen, R.* and Feenstra, K.A.* (2016). Construction and experimental validation of a Petri Net model of Wnt/β-catenin signaling. PLoS ONE 11: e0155743. * joint senior author
Haydarlou, R., Jacobsen, A., Bonzanni, N., Feenstra, K.A., Abeln, S. and Heringa, J. (2016). BioASF: A Framework for automatically generating executable pathway models specified in BioPAX. Bioinformatics 32:i60-i69.
van Dijk, E., Varilly, P., Knowles, T.P.J., Frenkel, D. and Abeln, S. (2016). Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation. Physical Review Letters 116(7): 078101.
Publications 2015
Lelieveld, S.*, Schutte, J.*, Dijkstra, M.J.J., Bawono, P., Kinston, S.J., Gottgens B., Heringa, J., Bozanni, N. (2015). ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites Nucl. Acids Res. (2015). * joint first author
van den Broek, E., Dijkstra, M.J.J., Krijgsman, O., Sie, D., Haan, J.C., Traets, J.J.H., van de Wiel, M.A., Nagtegaal, I., D., Punt, C.J.A., Carvalho, B., Ylstra, B., Abeln, S., Meijer, Gerrit A., Fijneman, Remond J. A. (2015). High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer PLoS ONE (2015)
Stringer, B., Merono-Penuela, A., Loizou, A., Abeln, S., Heringa, J. (2015). To SCRY Linked Data: Extending SPARQL the Easy Way Proceedings of the 1st International Diversity++ Workshop co-located with the 14th International Semantic Web Conference (ISWC 2015)
Predrag, K., Kannin, A., Dijkstra, M.J.J., Abeln, S., Camilloni, C., Vendruscolo, M. (2015). Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations PLoS. Comp. Biol. (2015)
Hou, Q., Dulith, B.E., Huynen, M.H., Heringa, J., Feenstra, A. (2015). Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case BMC Bioinformatics (2015)
May, A., Brandt, B. W., El-Kebir, M., Klau, G. W., Zaura, E., Crielaard, W., Heringa, J.*, Abeln, S.* (2015). metaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics, Advance Acesss. * joint last authors
Bawono, P., Van der Velde, A., Abeln, S., Heringa, J. (2015). Quantifying the displacement of mismatches in multiple sequence alignment benchmarks. PLoS ONE, e0127431.
May, A., Abeln, S., Buijs, M. J., Heringa, J., Crielaard, W., Brandt, B. W. (2015). NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. Nucleic Acids Res., 43: W301-W305.
van Dijk, E., Hoogeveen, A., Abeln, S. (2015). The hydrophobic temperature dependence of amino acids directly calculated from protein structures. PLoS Comp. Biol.,11: e1004277.
Publications 2014
Dinkla, K.*, El-Kebir, M.*, Bucur, C.-I., Siderius, M., Smit, M.J., Westenberg M.A. and Klau, G.W. (2014). eXamine: Exploring annotated modules in networks. BMC Bioinformatics, 15: 201. * joint first authors highlyaccessed
El-Kebir, M.*, Brandt, B.W.*, Heringa, J. and Klau, G.W. (2014). NatalieQ: A web server for protein-protein interaction network querying. BMC Systems Biology, 7: 80. * joint first authors highlyaccessed
May, A., Abeln, S., Crielaard, W., Heringa, J. and Brandt, B.W. (2014). Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinformatics, 30(11): 1530-1538.
Bawono, P. and Heringa, J. (2014). Phylogenetic Analyses. Comprehensive Biomedical Physics, 1st edition.
Bawono, P. and Heringa, J. (2014). PRALINE: a versatile multiple sequence alignment toolkit. Methods Mol. Biol., 1079: 245-262.
May, A.*, Pool, R.*, van Dijk, E., Bijlard, J., Abeln, S., Heringa, J., Feenstra, K.A. (2014). Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. Bioinformatics, 30(3): 326-334. * joint first authors
Abeln, S., Vendruscolo, M., Dobson, C.M. and Frenkel, D. (2014). A simple lattice model that captures protein folding, aggregation and amyloid formation. PLoS ONE, 9(1): e85185.
Publications 2013
Gijsbers, E.F., Feenstra, K.A., van Nuenen, A.C., Navis, M., Heringa, J., Schuitemaker, H. and Kootstra, N.A. (2013). HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in Gag. PLoS ONE, 8(12): e81235.
Ni, R., Abeln, S., Schor, M., Stuart, M.A.C. and Bolhuis, P.G. (2013). Interplay between folding anda ssembly of fibril-forming polypeptides. PRL, 111: 058101.
Edwards, H., Abeln, S. and Deane, C.M. (2013). Exploring fold space preferences of new-born and ancient protein superfamilies. PLoS Comp. Biol., 9(11): e1003325.
Van den Kerkhof, T.L.G.M., Feenstra, K.A., Euler, Z., van Gils, M.J., Rijsdijk, L.W.E., Boeser-Nunnink, B.D., Heringa, J., Schuitemaker, H. and Sanders R.W. (2013). HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity. Retrovirology, 10: 102. highlyaccessed
El-Kebir, M., Marschall, T., Wohlers, I., Patterson, M., Heringa, J., Schönhuth, A. and Klau, G.W. (2013). Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics, 14(Suppl 15): S18.
Hettling, H., Alders, D.J.C., Heringa, J., Binsl, T.W., Groeneveld, A.B. and van Beek, J.H.G.M. (2013). Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies. BMC Systems Biology, 7: 82.
Willemsen,T., Feenstra, K.A. and Groth, P. (2013). Building executable biological pathway models automatically from BioPAX. 3rd International Workshop on Linked Science 2013 — Supporting Reproducibility, Scientific Investigations and Experiments (LISC2013). Sydney. pp. 2-14.
Bonzanni, N.*, Garg, A.*, Feenstra, K.A.*, Kinston, S., Miranda-Saavedra, D., Schutte, J., Heringa, J., Xenarios, I. and Göttgens, B. (2013). Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinformatics, 29(13): i80-i88. * joint first authors
Abeln, S., Molenaar, D., Feenstra, K.A., Hoefsloot, H.C.J., Teusink, B. and Heringa, J. (2013). Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. Briefings in Bioinformatics, 14(5): 589-598.
El-Kebir, M., van der Kuip, M., van Furth, A.M. and Kirschner, D.E. (2013). Computational modeling of tuberculous meningitis reveals an important role for tumor necrosis factor-α. J. Theor. Biol., 328: 43-53.
De Vries-van Leeuwen, I.J., Da Costa Pereira, D., Flach, K.D., Piersma, S.R., Haase, C., Bier, D., Yalcin, Z., Michalides, R., Feenstra, K.A., Jiménez, C.R, De Greef, T.F.A., Brunsveld, L., Ottmann, C., Zwart, W. and De Boer, A.H. (2013). 14-3-3 protein interaction with the estrogen receptor alpha F-domain provides a drug target interface. Proc. Natl. Acad. Sci. U. S. A., 110(22): 8894-8899.
Haitjema, A.*, Brandt, B.W.*, Ameziane, N., May, P., Heringa, J., de Winter, J.P., Joenje, H. and Dorsman, J.C. (2013). A protein prioritization approach tailored for the FA/BRCA pathway. PLoS ONE, 8(4): e62017. * joint first authors
Pajić, V., Pavlović-Lažetić, G., Beljanski, M., Brandt, B.W. and Pajić, M. (2013). Towards a database for genotype-phenotype association research: Mining data from encyclopedia. Int. J. Data Min. Bioinform., 7(2): 196-213.
Canzar, S.*, El-Kebir, M.*, Pool, R., Elbassioni, K., Mark, A.E., Geerke, D.P., Stougie, L. and Klau, G.W. (2013). Charge group partitioning in biomolecular simulation. J. Comput. Biol., 20(3): 188-198. * joint first authors
Staiger, C., Cadot, S., Györffy, B., Wessels, L.F.A. and Klau, G.W. (2013). Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis. Frontiers in Genetics, 4: 289.
Fröhlich, H. and Klau, G.W. (2013). Reconstructing consensus Bayesian network structures with application to learning molecular interaction networks. In: T. Beissbarth et al. (Eds.), Proc. of German Conference on Bioinformatics, Open Access Series in Informatics.
Buhrman, H., van der Gulik, P.T.S., Klau, G.W., Schaffner, C., Speijer, D. and Stougie L. (2013). A realistic model under which the genetic code is optimal. J. Mol. Evol, 77(4): 170-184.
Böcker, S., Canzar, S. and Klau, G.W. (2013). The generalized Robinson-Foulds metric. In: A. Darling and J. Stoye (Eds.): WABI 2013, Proc. of the 13th Annual International Workshop on Algorithms in Bioinformatics, LNCS, 8126: 156-169.
Canzar, S., Elbassioni, K., Klau, G.W. and Mestre, J. (2013). On tree-constrained matchings and generalizations. Algorithmica, 1-22.
Wohlers, I., Andonov, R. and Klau, G.W. (2013). DALIX: Optimal DALI protein structure alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(1): 26-36.
Chimani, M., Gutwenger, C., Jünger, M., Klau, G.W., Klein, K. and Mutzel, P. (2013). Open Graph Drawing Framework (OGDF). In: Handbook of Graph Drawing and Visualization. Roberto Tamassia (ed.), CRC Press.
Publications 2012
Wohlers, I., Malod-Dognin, N., Andonov, R. and Klau, G.W. (2012). CSA: Comprehensive comparison of pairwise protein structure alignments. Nucleic Acids Res., 40(W1): 303-309.
Bonder, M.J., Abeln, S., Zaura E. and Brandt, B.W. (2012). Comparing clustering and pre-processing in taxonomy analysis. Bioinformatics, 28(22): 2891-2897.
Daleke, M.H., Ummels, R., Bawono, P., Heringa, J., Vandenbroucke-Grauls, C.M., Luirink, J. and Bitter, W. (2012). General secretion signal for the mycobacterial type VII secretion pathway. Proc. Natl. Acad. Sci. U. S. A., 109(28): 11342-11347.
Brandt, B.W., Bonder, M.J., Huse, S.M. and Zaura, E. (2012). TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage. Nucleic Acids Res., 40: W82-W87.
Canzar, S., El-Kebir, M., Pool, R., Elbassioni, K., Malde, A.K., Mark, A.E., Geerke, D.P., Stougie, L. and Klau, G. (2012). Charge group partitioning in biomolecular simulation. in: Research in Computational Molecular Biology, Procedeeding of 16th Annual International Conference, RECOMB 2012, Barcelona, Spain, April 21-24, 2012. Lecture Notes in Computer Science, 7262: 29-43.
Pool, R., Heringa, J., Hoefling, M., Schulz, R., Smith, J.C. and Feenstra, K.A. (2012). Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. J. Comput. Chem., 33(12): 1207-1214.
Publications 2011
El-Kebir, M., Heringa, J. and Klau, G.W. (2011). Lagrangian relaxation applied to sparse global network alignment. In: Proc. 6th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2011), Delft, The Netherlands, November 2-4 2011, Lecture Notes in Computer Science 7036: 225-236.
Canzar, S. and El-Kebir, M., Heringa, J. and Klau, G.W. (2011). A mathematical programming approach to marker-assisted gene pyramiding. In: Proc. 11th International Workshop, WABI 2011, Saarbrücken, Germany,September 5-7, 2011, Lecture Notes in Computer Science 6833: 26-38.
van Beek, J.H.G.M., Supandi, F., Gavai, A.K., de Graaf, A.A., Binsl, T.W. and Hettling, H. (2011). Simulating the physiology of athletes during endurance sports events: modelling human energy conversion and metabolism. Philos. Transact. A Math. Phys. Eng. Sci., 369(1954): 4295-4315.
Brandt, B.W. and Heringa, J. (2011). Protein analysis tools and services at IBIVU. J. Integr. Bioinform., 8(2): 168.
Hettling, H. and van Beek, J.H.G.M. (2011). Analyzing the functional properties of the creatine kinase system with multiscale 'sloppy' modeling, PLoS Comput. Biol., 7(8): e1002130.
Marino S., El-Kebir, M. and Kirschner D. (2011). A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis. J. Theor. Biol., 280(1): 50-62.
Bonzanni, N., Zhang, N., Oliver, S.G. and Fisher, J. (2011). The role of proteasome-mediated proteolysis in modulating activity of potentially harmful transcription factor activity in Saccharomyces cerevisiae. Bioinformatics, 27(13): i282-i287.
Fallahi-Sichani M., El-Kebir M., Marino S., Kirschner, D.E. and Linderman, J.J. (2011). Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation. J. Immunol., 186(6): 3472-3483.
Abeln, S. and Frenkel, D. (2011). Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins. Biophys J., 100(3): 693-700.
Publications 2010
Binsl T.W., de Graaf A.A., Venema K., Heringa J., Maathuis A., de Waard P. and van Beek, J.H.G.M. (2010). Measuring non-steady-state metabolic fluxes in starch-converting faecal microbiota in vitro, Benef. Microbes, 1(4): 391-405.
Hettling, H., Heringa, J. and van Beek, J.H.G.M. (2010). Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach, BMC Bioinformatics, 11(Suppl 10): O9.
Pool, R. and Bolhuis, P.G. (2010). The influence of micelle formation on the stability of colloid surfactant mixtures, Phys Chem Chem Phys, 12(44): 14789-14797.
Pirovano, W., Abeln, S., Feenstra, K.A. and Heringa, J. (2010). Multiple alignment of membrane protein sequences, In: Structural Bioinformatics of Membrane Proteins (D. Frishman, Ed.), Springer: Wien, New York. ISBN: 9783709100448.
Vinga, S., Neves, A.R., Santos, H., Brandt, B.W. and Kooijman, S.A.L.M. (2010). Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories, Philos. Trans. R. Soc. Lond. B Biol. Sci., 365(1557): 3429-3442.
Kooistra, A.J., Binsl, T.W., van Beek, J.H.G.M., de Graaf, C. and Heringa, J. (2010). Electron density fingerprints (EDprints): virtual screening using assembled information of electron density, J. Chem. Inf. Model. 50: 1772-1780.
Moreau, Y. and Heringa, J. (2010). Yves Moreau and Jaap Heringa, on behalf of the ECCB10 organizing and steering committees, Bioinformatics, 26(18): i412-413.
Brandt, B.W.*, Feenstra, K.A.* and Heringa, J. (2010). Multi-Harmony: detecting functional specificity from sequence alignment, Nucleic Acids Res., 38: W35-W40. * joint first authors
Van Houte, B.P.P., Binsl, T.W., Hettling, H. and Heringa, J. (2010). CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs, Bioinformatics, 26(10): 1366-1367.
Binsl, T.W., Alders, D.J.C., Heringa, J., Groeneveld, A.B.J. and van Beek, J.H.G.M. (2010). Computational quantification of metabolic fluxes from a single isotope snapshot: Application to an animal biopsy, Bioinformatics, 26(5): 653-660.
Gursky, L.J., Nikodinovic-Runic, J., Feenstra, K.A. and O'Connor, K.E. (2010). In vitro evolution of styrene monooxygenase from Pseudomonas putida CA-3 for improved epoxide synthesis, Appl. Microbiol. Biotechnol., 85(4): 995-1004.
Van Houte, B.P.P. and Heringa, J. (2010). Accurate confidence aware clustering of array CGH tumor profiles, Bioinformatics, 26(1): 6-14.
Pirovano, W. and Heringa, J. (2010). Protein secondary structure prediction, Methods Mol. Biol., 609: 327-348.
Publications 2009
Papp, B., Teusink, B. and Notebaart, R.A. (2009). A critical view of metabolic network adaptations, HFSP JOURNAL, 3(1): 24-35.
Pastink, M.I., Teusink, B., Hols, P., Visser, S., de Vos, W.M. and Hugenholtz, J. (2009). Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria, Applied and Environmental Microbiology, 75(11): 3627-3633.
Santos, F., Teusink, B., Molenaar, D., van Heck, M., Wels, M., Sieuwerts, S., de Vos, W.M. and Hugenholtz, J. (2009). Effect of amino acid availability on Vitamin B-12 production in Lactobacillus reuteri, Applied and Environmental Microbiology, 75(12): 3930-3936.
Teusink, B., Wiersma, A., Jacobs, L, Notebaart, R.A. and Smid, E.J. (2009). Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation, PLOS Comp. Biol., 5(6): e1000410.
Verouden, M.P.H., Notebaart, R.A., Westerhuis, J.A., van der Werf, M.J. Teusink, B. and Smilde, A.K. (2009). Multi-way analysis of flux distributions across multiple conditions, J. of Chemometrics, 23(7-8): 406-420.
Santos, F., Teusink, B., de Vos, W.M. and Hugenholtz, J. (2009). The evidence that pseudovitamin B-12 is biologically active in mammals is still lacking - a comment on Molina et al.'s (2009) experimental design, J. of Appl. Microbiol., 107(5): 1763-1763.
Molenaar, D., van Berlo, R., de Ridder, D. and Teusink, B. (2009). Shifts in growth strategies reflect tradeoffs in cellular economics, Mol. Systems Biol., 5: 323.
Bonzanni, N., Feenstra, K.A., Fokkink, W.J. and Krepska, E. (2009). What can formal methods bring to systems biology?, in Proc. 16th Symposium on Formal Methods - FM'09, Eindhoven, Lecture Notes in Computer Science 5850: 16-22, Springer.
Van Houte, B.P.P., Binsl, T.W., Hettling, H., Pirovano, W. and Heringa, J. (2009). CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations, BMC Genomics, 10: 401.
Bonzanni, N., Krepska, E., Feenstra, K.A., Fokkink, W., Kielmann, T., Bal, H. and Heringa, J. (2009). Executing multicellular differentiation: quantitative predictive modelling of C. elegans vulval development, Bioinformatics, 25(16): 2049-2056.
Pirovano, W., van der Reijden, A., Feenstra, K.A. and Heringa, J. (2009). Structure and function analysis of flexible alignment regions in proteins, BMC Bioinformatics, 10(Suppl 13): P6.
Van Beek, J.H.G.M., Hauschild, A.-C., Hettling, H. and Binsl, T.W. (2009). Robust modeling measurement and analysis of human and animal metabolic systems, Phil. Trans. A, 367(1895): 1971-1992.
Liefhebber, J.M.P., Brandt, B.W., Broer, R., Spaan, W.J.M and van Leeuwen, H.C. (2009). Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain, Virology J., 6: 62. highlyaccessed
Bruggeman, J., Heringa, J. and Brandt, B.W. (2009). PhyloPars: estimation of missing parameter values using phylogeny, Nucleic Acids Res., 37: W179-W184.
Brandt, B.W. and Heringa, J. (2009). webPRC: the Profile Comparer for alignment-based searching of public domain databases, Nucleic Acids Res., 37: W48-W52.
Smit, S., Knight, R. and Heringa, J. (2009). RNA structure prediction from evolutionary patterns of nucleotide composition, Nucleic Acids Res., 37: 1378-1386.
De Groot, P.W.J., Brandt, B.W., Horiuchi, H., Ram, A.F.J., De Koster, C.G. and Klis, F.M. (2009). Comprehensive genomic analysis of cell wall genes in Aspergillus nidulans, Fungal Genetics and Biology, 46(1): S72-S81.
Wortman, J.R., Gilsenan, J.M., ..... Brandt, B.W., Cornell, M.J., van den Hondel, C.A.M.J.J., Visser, J., Oliver, S.G. and Turner G. (2009). The 2008 update of the Aspergillus nidulans genome annotation: a community effort, Fungal Genetics and Biology, 46(1): S2-S13.
Butz, M., Van Ooyen, A. and Wörgötter, F (2009). A model for cortical rewiring following deafferentation and focal stroke, Frontiers in Computational Neuroscience, 3.
Jansen, R., Linkenkaer-Hansen, K., Heistek, T., Timmerman, J., Mansvelder, H.D., Brussaard, A.B., De Gunst, M., and Van Ooyen, A. (2009). Inbred mouse strains differ in multiple hippocampal activity traits, Eur. J. Neuroscience, 30: 1092-1100.
Koene, R.A., Tijms, B., Van Hees, P., Postma, F., De Ridder, A., Ramakers, G.J.A, Van Pelt, J., and Van Ooyen, A. (2009). NETMORPH: A framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies, Neuroinformatics, 7: 195-210.
Kaiser, M., Hilgetag, C.C. and Van Ooyen, A. (2009). A simple rule for axon outgrowth and synaptic competition generates realistic connection lengths and filling fractions, Cerebral cortex, 19: 3001-3010.
Van Elburg, R.A.J. and Van Ooyen, A. (2009). Generalization of the event-based Carnevale-Hines integration scheme for integrate-and-fire models, Neural Computation, 21: 1913-1930.
Butz, M., Wörgötter, F. and Van Ooyen, A. (2009). Activity-dependent structural plasticity, Brain Research Reviews, 60: 287-305.
Montez, T., Poil, S.-S., Jones, B., Manshanden, I., Verbunt, J.P.A., Van Dijk, B. W., Brussaard, A. B., Van Ooyen, A., Stam, C. J., Scheltens, P. and Linkenkaer-Hansen, K. (2009). Altered temporal correlations in parietal alpha and prefrontal theta oscillations in early-stage Alzheimer disease, PNAS, 106: 1614-1619.
Feng, Z-P, Zhang, Z., van Kesteren, R.E., Straub, V.A., van Nierop, P., Jin, K., Nejatbakhsh, N., Goldberg, J.I., Spencer, G.E., Yeoman, M.S., Wildering, W., Coorssen, J.R., Croll, R.P., Buck, L.T., Syed, N.I. and Smit, A.B. (2009). Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis, BMC Genomics, 10: 451.
Publications 2008
Pirovano, W., Feenstra, K.A. and Heringa, J. (2008). The meaning of alignment: lessons from structural diversity, BMC Bioinformatics, 9(1): 556. highlyaccessed
Feenstra, K.A., Bastianelli, G. and Heringa, J. (2008). Predicting protein interactions from functional specificity, in: From Computational Biophysics to Systems Biology. pp. 89-92. Eds. U.H.E. Hansmann, J.H. Meinke, S. Mohanty, W. Nadler and O. Zimmermann, John von Neumann Institute for Computing, Jülich, NIC Series, Vol. 40.
Pirovano, W. and Heringa, J. (2008). Multiple sequence alignment, Methods Mol. Biol., 452: 143-161.
Krepska, E. Bonzanni, N., Feenstra, K.A., Fokkink, W., Kielmann, T., Bal, H.E. and Heringa, J. (2008). Design issues for qualitative modelling of biological cells with petri nets, Formal Meth. in Syst. Biol., 5054: 48-62
Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context, Nucleic Acids Res., 36: W255-W259.
Ivliev, A.E., 't Hoen, P.A.C., Villerius, M.P., den Dunnen, J.T. and Brandt, B.W. (2008). Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data, Nucleic Acids Res., 36: W327-W331.
Jancura, P., Heringa, J. and Marchiori, E. (2008). Dividing Protein Interaction Networks by Growing Orthologous Articulations, Third IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008. Springer, 2008.
Jancura, P., Heringa, J. and Marchiori, E. (2008). Divide, Align and Full-Search for Discovering Conserved Protein Complexes, Proceedings of the Sixth European Conference on Evolutionary Computation, Machine Learning and Datamining in Bioinformatics. LNCS 4973, pp. 73-84.
Heringa, J. (2008). Sequence Similarity, Encyclopedia of Life Sciences - Handbook of Human Molecular Evolution, John Wiley & Sons Ltd, Chichester, UK.
Vajda, I., Van Pelt, J., Wolters, P., Chiappalone, M., Martinoia, S., Van Someren, E. and Van Ooyen, A. (2008). Low-frequency stimulation induces stable transitions in stereotypical activity in cortical networks, Biophysical J., 94: 5028-5039.
Pirovano, W., Feenstra, K.A. and Heringa, J. (2008). PRALINETM: a strategy for improved multiple alignment of transmembrane proteins, Bioinformatics, 24(4): 492-497.
Smit, S., Rother, K., Heringa, J. and Knight, R. (2008). From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal, RNA, 14(3): 410-416.
Lijnzaad, P., Feenstra, K. A., Heringa, J. and Holstege, F.C.P. (2008). On defining the dynamics of hydrophobic patches on protein surfaces, Proteins: Struct. Func. Bioinf., 72: 105-114 (2008)
Ye, K., Feenstra, K.A, Heringa, J., IJzerman, A.P. and Marchiori, E. (2008). Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine Learning approach for feature weighting, Bioinformatics, 24(1): 18-25.
Horner, D.S., Pirovano, W. and Pesole, G. (2008). Correlated substitution analysis and the prediction of amino acid structural contacts, Brief. Bioinform., 9(1): 46-56.
Publications 2007
S. Smit, J. Widmann and R. Knight (2007). Evolutionary rates vary among rRNA structural elements, Nucleic Acids Res., 35(10): 3339-3354.
Szklarczyk, R., Heringa, J., Kosakovsky Pond, S. and Nekrutenko, A. (2007). Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function but follows a genomic trend, Proc. Natl. Acad. Sci. USA, 104(31): 12807-12812.
Chung, W.-Y., Wadhawan, S., Szklarczyk, R. and Nekrutenko, A. (2007). A First look at ARFome: dual-coding genes in mammalian genomes, PLoS Comp. Biol., 3(5): e91.
Pang, C.N.I., Lin, K., Wouters, M.A., Heringa, J. and George, R.A. (2007). Identifying foldable regions in protein sequence from the hydrophobic signal, Nucleic Acids Res., 36: 578-588.
Marchiori, E., Moore, J.H. and Rajapakse, J.C. (Eds.) (2007). Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 5th European Conference, LNCS 4447, Springer.
Feenstra, K.A., Pirovano, W., Krab, K. and Heringa, J. (2007). Sequence Harmony: detecting functional specificity from alignments, Nucleic Acids Res., 35: W495-W498.
Heringa, J. and Pirovano, W. (2007). Sequence similarity searches, In: Bioinformatics, Method Express Series (Dear, P. ed.), Scion Publishing Ltd, Oxfordshire, UK, pp. 39-67
T.W. Binsl, K.M. Mullen, I.H.M. van Stokkum, J. Heringa and J.H.G.M. van Beek (2007). FluxSimulator: An R package to simulate isotopomer distributions in metabolic networks, Journal of Statistical Software, 18(7).
Feenstra, K.A., Starikov, E.B., Urlacher, V.B., Commandeur, J.N.M. and Vermeulen, N.P.E. (2007). Combining Substrate Dynamics, Binding Statistics and Reactivity to Rationalize Regioselective Metabolism of Octane and Lauric Acid by CYP102A1 and Mutants, Prot. Sci., 16: 420-431.
M.C. Codrea, C.R. Jimenez, S. Piersma, J. Heringa and E. Marchiori (2007). Robust peak detection and alignment of nanoLC-FT mass spectrometry data, The Fifth European Conference on Evolutionary Computation, Machine Learning and Datamining. Springer, LNCS 4447, Pages 35-46.
M.C. Codrea, C.R. Jimenez, J. Heringa and E. Marchiori (2007). Tools for computational processing of LC-MS datasets: a user's perspective, Computer Methods and Programs in Biomedicine, Elsevier, Volume 86, Issue 3, Pages 281-290.
K.J.A. Vanhoutte, C. Laarakkers, E. Marchiori, P. Pickkers, J.F.M. Wetzels, J.L. Willems, L.P. van den Heuvel, F.G.M. Russel and R. Masereeuw (2007). Biomarker discovery with SELDI-TOF MS in human urine associated with early renal injury: evaluation with computational analytical tools, Nephrology Dialysis Transplantation, 22(10): 2932-2943.
Linkenkaer-Hansen, K., Smit, D. J. A., Barkil, A., Van Beijsterveldt, T. E. M., Brussaard, A. B., Boomsma, D. I., Van Ooyen, A. and De Geus, E. J. C. (2007). Genetic contributions to long-range temporal correlations in ongoing oscillations, J. Neuroscience 27: 13882-13889.
Krottje, J. K. and Van Ooyen, A. (2007). A mathematical framework for modelling axon guidance, Bulletin of Mathematical Biology, 69:3-31.
Jong, K., Marchiori, E., van der Vaart, A., Chin S., Carvalho, B., Tijssen, M., Eijk, P.P., van den IJssel, P, Grabsch, H., Quirke, P.m, Oudejans, J.J., Meijer, G.A., Caldas, C. and Ylstra, B. (2007). Cross-Platform Array Comparative Genomic Hybridization (array CGH) Meta-analysis separates hematopoietic and mesenchymal from epithelial tumors, Oncogene 26: 1499-1506.
Publications 2006
Pirovano, W.*, Feenstra, K.A.* and Heringa, J. (2006). Sequence Comparison by Sequence Harmony Identifies Subtype Specific Functional Sites, Nucleic Acids Res., 34(22): 6540-6548.   * joint first authors
Feenstra, K.A., Pirovano, W. and Heringa, J. (2006). Sub-type Specific Sites for SMAD Receptor Binding Identified by Sequence Comparison using "Sequence Harmony". In: From Computational Biophysics to Systems Biology. Forchungszentrum Jülich, Germany; World Scientific, London, Vol. 34, pp 73-78.
Graham, B. P. and Van Ooyen, A. (2006). Mathematical modelling and numerical simulation of the morphological development of neurons, BMC Neuroscience 7 (Suppl 1): S9.
Marchiori, E.*, Pirovano, W., Heringa, J. and Feenstra, K.A.* (2006). A feature selection algorithm for detecting subtype specific sites for Smad receptor binding, Bio-ICMLA06 (IEEE), 168-173. Full-Text preprint.   * equal contribution
Patist, J.P., Kowalczyk, W. and Marchiori, E. (2006). Maintaining Gaussian mixture models of data streams under block evolution. International Conference on Computational Science, Springer,pp. 1071-1074.
Feenstra, K.A., Hofstetter, K., Bosch, R., Schmid, A., Commandeur, J.N.M. and Vermeulen, N.P.E. (2006). Enantioselective substrate binding in a monooxygenase protein model by molecular dynamics and Docking. Biophys. J., 91: 3206-3216
E. Marchiori, C. Jimenez, M. West-Nielsen and N. Heegaard. Robust SVM-based biomarker selection with noisy mass spectrometric proteomic data. In Applications of Evolutionary Computing. EvoBIO: Evolutionary Computation and Machine Learning in Bioinformatics. Springer, pp. 79-90, LNCS 3907, 2006.
Lentz, O., Feenstra, A., Habicher, T., Hauer, B., Schmid, R.D. and Urlacher, V.B. (2006). Altering the Regioselectivity of Cytochrome P450 CYP102A3 of Bacillus subtilis by Using a New Versatile Assay System, ChemBioChem 7: 345-350.
Simossis, V.A. and Heringa, J. (2005). Local structure prediction of proteins. In: Computational Methods for Protein Structure Prediction and Modeling (Xu, Y., Xu, D., Liang J, Eds.), Springer-Verlag, GmbH, in press.
van Nierop, P., Bertrand, S., Munno, D. W., Gouwenberg, Y., van Minnen, J., Spafford, J. D., Syed, N. I., Bertrand, D. and Smit, A. B. (2006). Identification and functional expression of a family of nicotinic acetylcholine receptor subunits in the central nervous system of the mollusc Lymnaea stagnalis. J Biol Chem 281, 1680-1691.
Van Ooyen, A. and Roelfsema, P. R. (2006). Envisioning the reward. (Preview of Shuler and Bear, 2006, Science 311: 1606-1609). Neuron 50:188-190.
Steuber, V., Willshaw, D., Van Ooyen, A. (2006). Generation of time delays: simplified models of intracellular signalling in cerebellar Purkinje cells. Network: Computation in Neural Systems, 17:173-191.
Janulevicius, A., Van Pelt, J. and Van Ooyen, A. (2006). Compartment volume influences microtubule dynamic instability: a model study. Biophysical J. 90:788-798.
Szklarczyk, R. and Heringa, J. (2006). AuberGene - a sensitive genome alignment tool, Bioinformatics, 22 (12), 1431-1436.
Sammeth, M. and Heringa, J. (2006). Global multiple sequence alignment with repeats. Prot. Struct. Funct. Bioinf. 64, 263-274.
Publications 2005
De Graaf, C., Vermeulen, N.P.E. and Feenstra, K.A. (2005). Cytochrome P450 in Silico: An Integrative Modeling Approach J. Med. Chem., 48:2725-55.
Keizers, P.H.J., de Graaf, C., Kanter, Oostenbrink, C., Feenstra, K.A., Vermeulen, N.P.E. and Commandeur, J.N.M. (2005). Metabolic Regio- And Stereoselectivity Of Cytochrome P450 2D6 Towards 3, 4-methylenedioxy-N-alkyl-amphetamines: In Silico Predictions And Experimental Validation. J. Med. Chem., 48:6117-27.
M. West-Nielsen, E.V. Hogdall, E. Marchiori, C.K. Hogdall, C. Schou and N.H.H. Heegaard. Sample handling for mass spectrometric proteomic investigations of human sera. Analytical Chemistry, vol. 77, no. 16, 5114-5123, 2005.
E. Marchiori, N. Heegaard, C. Jimenez and M. West-Nielsen. Feature Selection for Classification with Proteomic Data of Mixed Quality. Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. CIBCB , pp. 385-391, 2005.
E. Marchiori and M. Sebag. Bayesian Learning with Local Support Vector Machines for Cancer Classification with Gene Expression Data. In Applications of Evolutionary Computing. EvoBIO: Evolutionary Computation and Bioinformatics. Springer,pp.74-83, 2005.
Celie, P. H., Kasheverov, I. E., Mordvintsev, D. Y., Hogg, R. C., van Nierop, P., van Elk, R., van Rossum-Fikkert, S. E., Zhmak, M. N., Bertrand, D., Tsetlin, V., et al. (2005a). Crystal structure of nicotinic acetylcholine receptor homolog AChBP in complex with an alpha-conotoxin PnIA variant. Nat Struct Mol Biol 12, 582-588.
van Nierop, P., Bertrand, S., Munno, D. W., Gouwenberg, Y., van Minnen, J., Spafford, J. D., Syed, N. I., Bertrand, D. and Smit, A. B. (2005a). Identification and functional expression of a family nicotinic acetylcholine receptor subunits in the central nervous system of the mollusc lymnaea stagnalis. J Biol Chem.
Bosman, L., Lodder, J. C., Van Ooyen, A. and Brussaard, A. B. (2005). Role of synaptic inhibition in spatiotemporal patterning of cortical activity. In: Van Pelt, J. Kamermans, M., Levelt, C. N., Van Ooyen, A., Ramakers, G. J. A., Roelfsema, P. R. (eds.) Development, Dynamics and Pathology of Neuronal Networks: From Molecules to Functional Circuits, Progress in Brain Research 147, Elsevier, Amsterdam, pp. 201-204.
Van Ooyen (2005). Competition in neurite outgrowth and the development of nerve connections. In: Van Pelt, J. Kamermans, M., Levelt, C. N., Van Ooyen, A., Ramakers, G. J. A., Roelfsema, P. R. (eds.) Development, Dynamics and Pathology of Neuronal Networks: From Molecules to Functional Circuits, Progress in Brain Research 147, Elsevier, Amsterdam, pp. 81-99.
Kiddie, G., McLean, D., Van Ooyen, A., Graham, B. (2005). Biologically plausible models of neurite outgrowth. In: Van Pelt, J. Kamermans, M., Levelt, C. N., Van Ooyen, A., Ramakers, G. J. A., Roelfsema, P. R. (eds.) Development, Dynamics and Pathology of Neuronal Networks: From Molecules to Functional Circuits, Progress in Brain Research 147, Elsevier, Amsterdam, pp. 67-80.
Roelfsema, P. R. and Van Ooyen, A. (2005). Attention-gated reinforcement learning of internal representations for classification. Neural Computation 17, 2176-2214.
Kleinjung, J. and Fraternali, F. (2005). POPSCOMP: An automated interaction analysis of biomolecular complexes, Nucleic Acids Research 33 (Web Server issue), W342-W346. Full Text (Open Access)
George, R.A., Lin, K. and Heringa J. (2005). Scooby-Domain: prediction of globular domains in protein sequence, Nucleic Acids Res., 33 (Web Server issue), W160-W163. Full Text (Open Access)
Simossis V.A. and Heringa J. (2005). PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res., 33 (Web Server Issue), W289-294. Full Text (Open Access)
Simossis V.A., Kleinjung, J. and Heringa J. (2005). Homology-extended sequence alignment. Nucleic Acids Res., 33(3):816-824. Full Text (Open Access)
Lin K., Simossis V.A., Taylor W.R. and Heringa J. (2005). A simple and fast secondary structure prediction algorithm using hidden neural networks. Bioinformatics. 21(2):152-9. (Epub 2004 Sep 17). Abstract
Heringa J. (2005). Protein domains. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Vol. 7 (Subramaniam, Ed.), Section 6: Comparative Methods for Structure Analysis and Prediction (Taylor, W.R., Section Ed.); Chapter 68, pp. 3283-3297, Wiley Interscience, ISBN: 0-470-84974-6.
Fraternali F. and Kleinjung J. (2005). Molecular simulations in structure prediction. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Vol. 7 (Subramaniam, Ed.), Section 6: Comparative Methods for Structure Analysis and Prediction (Taylor, W.R., Section Ed.), Chapter 74, pp. 3346-3352, Wiley Interscience, ISBN: 0-470-84974-6.
Publications 2004
Heringa J. (2004). Protein sequence analysis and prediction of secondary structural features. In: Compact Handbook of Computational Biology (Konopka A.K., and Crabbe M.J.C., Eds,), New York, Marcel Dekker, pp. 99 - 185.
Konopka A.K., Bucher P., Crabbe M.J.C., Crochemore M., Heringa J., Lisacek F., Makalowska I., Makalowski W., Pesole G., Saccone C., Sagot M.-F., Sarai A., Stadler P. and Taylor W.R. (2004). Computational Biology: Annotated Glossary of Terms, In: Compact Handbook of Computational Biology (Konopka A.K., Crabbe M.J.C., eds.), New York: Marcel Dekker, pp. 451 - 501.
Konopka A.K., and Heringa J. (2004). A dictionary of programs for sequence analysis, In: Compact Handbook of Computational Biology (Konopka A.K., Crabbe M.J.C., eds.) New York: Marcel Dekker, pp. 503 - 536.
Simossis V.A. and Heringa J. (2004). The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. Comp. Biol. Chem. 28(5-6), 351-366. Abstract
Vaccaro L., Cross K.J., Kleinjung J., Straus S.K. , Thomas D.J., Wharton S.A., Skehel J.J. and Fraternali F. (2004). Plasticity of Influenza Haemagglutinin Fusion Peptides and their Interaction with Lipid Bilayers, Biophys. J. 88, 25-36. Abstract
Szklarczyk, R. and Heringa, J. (2004). Tracking repeats using significance and transitivity. Bioinformatics 20 Suppl. 1, i311-i317.
Simossis V.A. and Heringa J. (2004). Integrating protein secondary structure prediction and multiple Sequence Alignment, Current Protein and Peptide Science, 5(4):249-266. Abstract
Kleinjung J., Romein J., Lin K. and Heringa J. (2004). Contact-based sequence alignment, Nucleic Acids Research 32(8), 2464-2473. Full Text (Open Access)
Shojaee-Moradie F., Chan M.P.Y., Telfer M.A., Brandenburg D., Sundermann E., Eckey H., Kleinjung J., Schaefer A. and Jones R.H. (2004). Effect of thyroid hormone binding proteins on insulin receptor binding of B1-thyronine-insulin analogues, Biochemical J. 381(1), 51-57. Abstract
K. Jong, E. Marchiori, A. van der Vaart, G. Meijer and B. Ylstra. (tool website) Automatic Breakpoint Identification and Smoothing of Array Comparative Genomic Hybridization Data. Bioinformatics, 20:3636-3637, 2004.
K. Jong, E. Marchiori and A. van der Vaart. Analysis of Proteomic Pattern Data for Cancer Detection. In Applications of Evolutionary Computing. EvoBIO: Evolutionary Computation and Bioinformatics. Springer, pp. 41-51, 2004.
K. Jong, E. Marchiori, M. Sebag and A. van der Vaart. Feature Selection in Proteomic Pattern Data with Support Vector Machines. In CIBCB , pp. 41-48, IEEE, 2004.
Publications 2003
Simossis V.A. and Heringa J. (2003). The PRALINE Online Server: Optimising progressive multiple alignment on the web. Comp. Biol. Chem. 27(4-5), 511-519. Abstract
Romein J.W., Heringa J. and Bal H.E. (2003). A Million-Fold Speed Improvement in Genomic Repeats Detection, SuperComputing'03, Phoenix, AZ, November, 2003. Full Text
George R.A. and Heringa J. (2003). An analysis of protein domain linkers: their classification and role in protein folding, Prot. Engineer. 15, 871-879. Abstract
Simossis V.A., Kleinjung J. and Heringa J. (2003). An overview of multiple sequence alignment. In: Current Protocols in Bioinformatics (eds. A.D.Baxevanis, D.B.Davison), Chapter 3.7, John Wiley & Sons. Availability
Cavallo L., Kleinjung J. and Fraternali F. (2003). POPS: a fast algorithm for Solvent Accessible Surface Areas at atomic and residue level, Nucleic Acids Research 31, 3364-3366. Full Text (Open Access)
Lin K., Kleinjung J., Taylor W. and Heringa J. (2003). Testing homolgy with CAO: A contact-based Markov model of protein evolution, Comp. Biol. Chem. 27, 93-102. Abstract
Kleinjung J., Fraternali F., Martin S.R. and Bayley P.M. (2003). Thermal Unfolding Simulations of Apo-calmodulin using Leap-dynamics, Proteins 50, 648-656. Abstract
George R.A., Kleinjung J. and Heringa J. (2003). Predicting protein structural domains from sequence data. In: Bioinformatics and Genomes - Current Perspectives. Pp. 1-26. Horizon Scientific Press, Norfolk, England. ISBN 1-898486-47-6. Availability
Publications 2002
Heringa J. (2002). Protein sequence analysis and prediction of secondary structural features, Bentham Press, New York (in press).
Taylor W.R., Heringa J., Baud F. and Flores T.P. (2002). A Fourier analysis of symmetry in proteins, Protein Eng. 15(2), 79-89. Abstract
Heringa J. (2002). Sequence Similarity, In: Encyclopedia of the Human Genome. Nature Publishing Group, London. ISBN: 0333803868 Availability
Kleinjung J., Douglas N. and Heringa J. (2002). Parallelized multiple alignment. Bioinformatics 18(9), 1270-1271. Abstract
Heringa J. (2002). Local weighting schemes for protein multiple sequence alignment, Comp. Chem. 26, 459-477. Abstract
George R.A. and Heringa J. (2002). Protein domain identification and improved sequence similarity searching using PSI-BLAST, Proteins: Struct. Func. Gen. 48, 672-681. Abstract
George R.A. and Heringa J.(2002). SnapDRAGON - a method to delineate protein structural domains from sequence data, J. Mol. Biol. 316, 839-851. Abstract
Publications 2001
Heringa J. (2001). Post-genome informatics. Comp. Chem. 25, 425-426. Abstract
Weljie A. and Heringa J. (2001). Sequence alignment of Ca-binding proteins. In: Methods in Molecular Biology, Vol 173: Calcium-binding Protocols, Vol 2 (Vogel, H.J., ed.), Humana Press, Totowa, N.J., pp 231-253. ISBN: 0896036898
Publications 2000
Heringa J. (2000). Predicting secondary structure from protein sequences, In: Bioinformatics: Sequence, structure and databanks, pp 113-141, Practical Approach Series (Higgins D., Taylor W.R., eds), Oxford University Press. ISBN: 0199637911
Pollock D.D. and Heringa J. (2000). RECOMB98: Computational molecular biology: Pre-and post-genomics. Comp. Chem. 24, pp 133-134. Abstract
Kleinjung J., Bayley P. and Fraternali F. (2000). Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution, FEBS Lett. 470(3), 257-262. Abstract
Notredame C., Higgins D.G. and Heringa J. (2000). T-Coffee: a novel method for fast and accurate multiple sequence alignment, J. Mol. Biol. 302, 205-217. Abstract
George R.A. and Heringa J. (2000). The REPRO server: finding protein internal sequence repeats through the Web. Trends in Biochemical Sciences 25, 515-517. Abstract
Publications 1999
Martin S.R., Lu A.Q., Xiao J., Kleinjung J., Beckingham K. and Bayley P.M. (1999). Conformational and metal-binding properties of androcam, a testis-specific, calmodulin-related protein from Drosophila, Protein Sci. 8(11), 2444-2454. Abstract
Heringa J. and Argos P. (1999). Strain in protein structures as viewed through nonrotameric side chains: II. Effects upon ligand binding. Proteins: Struct. Func. and Gen. 37, 44-55. Abstract
Heringa J. and Argos P. (1999). Strain in protein structures as viewed through nonrotameric side chains: I. Their position and interaction, Proteins: Struct. Func. and Gen. 37, 30-43. Abstract
Heringa J. (1999). Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment, Comp. Chem. 23, 341-364. Abstract
Publications 1998
Langosch D. and Heringa J. (1998). Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils, Proteins: Struct. Func. and Gen. 31, 150-159. Abstract
Heringa J. (1998). Detection of internal repeats: how common are they? Cur. Op. Struct. Biol. 8, 338-345. Abstract
Publications 1997
Heringa J., Frishman D. and Argos P. (1997). Computational methods relating protein sequence and structure, In: Proteins: A Comprehensive Treatise, Vol. 1, Principles of protein structure (Allen G., ed.) pp 171-277, JAI Press. ISBN: 1559386711
Heringa J. and Taylor W.R. (1997). Three-dimensional domain duplication, swapping and stealing. Cur. Op. Struct. Biol. 7, 416-421. Abstract

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