IBIVU - Vrije Universiteit


		IBIVU Group Publications

[ 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 ]

♠ Publications 2010

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; doi: 10.1093/bioinformatics/btq018

Van Houte, B.P.P. and Heringa, J. (2010). Accurate confidence aware clustering of array CGH tumor profiles, Bioinformatics, 26(1): 6-14.

♠ 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?, Proc. 16th Symposium on Formal Methods - FM'09, Eindhoven, Lecture Notes in Computer Science, Springer, in press.

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, J., 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.

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., 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.

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). PRALINE^TM: a strategy for improved multiple alignment of transmembrane proteins, Bioinformatics, 24(2): 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., 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., 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., 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., 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, 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, 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, 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, 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., 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., 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., 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., 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., 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., 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., F.J.J.de 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, 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, 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., 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., 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, B. Ylstra. (tool website) Automatic Breakpoint Identification and Smoothing of Array Comparative Genomic Hybridization Data. Bioinformatics, 20:3636-3637, 2004.

K. Jong, E. Marchiori, 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, 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., 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

IBIVU Group Publications