Research Output 2002 2019

2012

Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module

Pool, R., Heringa, J., Hoefling, M., Schulz, R., Smith, J. C. & Feenstra, K. A., 5 May 2012, In : Journal of Computational Chemistry. 33, 12, p. 1207-14 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Python
Canonical Ensemble
Molecular dynamics
Flexibility
Module

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

Beisser, D., Grohme, M., Kopka, J., Frohme, M., Schill, R. O., Hengherr, S., Dandekar, T., Klau, G. W., Dittrich, M. & Müller, T., 2012, In : BMC Systems Biology. 6, 72

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Tardigrada
Metabolome
Expressed Sequence Tags
Metabolites
Metabolic Networks and Pathways

Robustness and accuracy of functional modules in integrated network analysis

Beisser, D., Brunkorst, S., Dandekar, T., Klau, G. W., Dittrich, M. & Müller, T., 2012, In : Bioinformatics. 28, 14, p. 1887-1894

Research output: Contribution to JournalArticleAcademicpeer-review

Lymphoma, Large B-Cell, Diffuse
Network Analysis
Electric network analysis
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Gene expression

Thought problems from adolescence to adulthood: measurement invariance and longitudinal heritability

Abdellaoui, A., de Moor, M. H. M., Geels, L. M., van Beek, J. H. D. A., Willemsen, G. & Boomsma, D. I., 2012, In : Behavior Genetics. 42, 1, p. 19-29

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
adolescence
heritability
adulthood
Age Groups
Statistical Factor Analysis
2011

Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins.

Abeln, S. & Frenkel, D., 2011, In : Biophysical Journal. 100, 3, p. 693

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Proteins
Water
Amino Acids
Structural Models
Protein Folding

Analyzing the Functional Properties of the Creatine Kinase System with Multiscale 'Sloppy' Modeling

Hettling, J. & van Beek, J. H. G. M., 2011, In : PLoS Computational Biology. 7, 8, e1002130.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
phosphocreatine
Multiscale Modeling
Adenosinetriphosphate
Mitochondria
creatine kinase

Correction: Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins. Biophys. J. 100:693–700

Abeln, S. & Frenkel, D., 17 Aug 2011, In : Biophysical Journal. 101, 4, p. 1014-1014 1 p.

Research output: Contribution to JournalErratumAcademic

Open Access

Fluxes of Life: Bioinformatics for Metabolic Flux Quantification in Isotopic Non-Steady-State

Binsl, T. W., 2011

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Lagrangian Relaxation Applied to Sparse Global Network Alignment

El-Kebir, M., Heringa, J. & Klau, G. W., 2011, Pattern Recognition in Bioinformatics: 6th IAPR International Conference on PRIB 2011, Delft, The Netherlands, November 2-4, 2011, Proceedings. Loog, M., Wessels, L., Reinders, M. J. T. & de Ridder, D. (eds.). Berlin: Springer, p. 225-236 12 p. (Lecture Notes in Computer Science; vol. 7036).

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Open Access
File
Topology
Molecular interactions
Electric network analysis
Linear programming
Proteins

Protein analysis tools and services at IBIVU.

Brandt, B. W. & Heringa, J., 2011, In : Journal of Integrative Bioinformatics. 8, p. 168

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Simulating the physiology of athletes during endurance sports events: modelling human energy conversion and metabolism

van Beek, J. H. G. M., Supandi, F. B., Gavai, A., de Graaf, A. A., Binsl, T. W. & Hettling, H., 2011, In : Philosophical Transactions of the Royal Society A. Mathematical, Physical and Engineering Sciences. 369, 1954, p. 4295-4315 20 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
athletes
physiology
endurance
Physiology
energy conversion

The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in Saccharomyces cerevisiae

Bonzanni, N., Zhang, N., Oliver, S. G. & Fisher, J., 2011, In : Bioinformatics. 27, 13, p. 283-287

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Proteolysis
Transcription factors
Saccharomyces Cerevisiae
Proteasome Endopeptidase Complex
Transcription Factor

Towards Use-Case Driven Self-Management of Distributed Systems

Haydarlou, R., 2011, Delft University of Technology. 203 p.

Research output: Book / ReportBookAcademicpeer-review

Managers
Formal languages
Knowledge representation
Software design
Semantic Web
2010

Accurate confidence aware clustering of array CGH tumor profiles.

van Houte, B. P. P. & Heringa, J., 2010, In : Bioinformatics. 26, p. 6-14

Research output: Contribution to JournalArticleAcademicpeer-review

Comparative Genomics
Confidence
Cluster Analysis
Tumors
Tumor

Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach

Hettling, H., Heringa, J. & van Beek, J. H. G. M., 2010, In : BMC Bioinformatics. 11, Suppl. 10, p. O9

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

A vision and strategy for the virtual physiological human in 2010 and beyond

Hunter, P., Coveney, P. V., de Bono, B., Diaz, V., Fenner, J., Frangi, A. F., Harris, P., Hose, R., Kohl, P., Lawford, P., McCormack, K., Mendes, M., Omholt, S., Quarteroni, A., Skar, J., Tegner, J., Thomas, S. R., Tollis, I., Tsamardinos, I., van Beek, J. H. G. M. & 1 othersViceconti, M., 2010, In : Philosophical Transactions of the Royal Society A. Mathematical, Physical and Engineering Sciences. 368, 1920, p. 2595-2614

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Communication
sustaining
Information and Communication Technology
Open Source Software
education

CGHnormaliter: a bioconductor package for normalization of array CGH data with many CNAs.

van Houte, B. P. P., Binsl, T. W., Hettling, H. & Heringa, J., 2010, In : Bioinformatics. 26, p. 1366-1367

Research output: Contribution to JournalArticleAcademicpeer-review

Comparative Genomic Hybridization
Licensure
Normalization
Visualization
Availability

Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy.

Binsl, T. W., Alders, D. J. C., Heringa, J., Groeneveld, A. B. J. & van Beek, J. H. G. M., 2010, In : Bioinformatics. 26, 5, p. 653-660

Research output: Contribution to JournalArticleAcademicpeer-review

Isotope Labeling
Biopsy
Snapshot
Isotopes
Quantification

In vitro evolution of styrene monooxygenase from Pseudomonas putida CA-3 for improved epoxide synthesis

Gursky, L. J., Nikodinovic-Runic, J., Feenstra, K. A. & O'Connor, K. E., 2010, In : Applied Microbiology and Biotechnology. 85, 4, p. 995-1004 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

styrene oxide
Pseudomonas putida
Epoxy Compounds
Styrene
Indigo Carmine

J. Electron Density Fingerprints (EDprints):Virtual Screening Using Assembled Information of Electron Density.

Kooistra, A. J., Binsl, T. W., van Beek, J. H. G. M., de Graaf, C. & Heringa, J., 2010, In : Journal of Chemical Information and Modeling. 50, 10, p. 1772-1780

Research output: Contribution to JournalArticleAcademicpeer-review

Carrier concentration
Screening
Molecules

Multi-Harmony: detecting functional specificity from sequence alignment

Brandt, B. W., Feenstra, K. A. & Heringa, J., Jul 2010, In : Nucleic Acids Research. 38, Web Server issue, p. W35-40

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Sequence Alignment
Proteins
Ligands
Amino Acids

Multiple alignment of transmembrane protein sequences

Pirovano, W. A., Abeln, S., Feenstra, K. A. & Heringa, J., 2010, Structural Bioinformatics of Membrane Proteins. Frishman, D. (ed.). Vienna: Springer-Verlag, p. 103-122 400 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Protein secondary strructure prediction.

Pirovano, W. A. & Heringa, J., 2010, In : Methods in Molecular Biology. 609, p. 327-348

Research output: Contribution to JournalArticleAcademicpeer-review

Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories

Vinga, S., Neves, A. S., Santos, H., Brandt, B. W. & Kooijman, S. A. L. M., 2010, In : Philosophical Transactions of the Royal Society B. Biological Sciences. 365, 1557, p. 3429-3442

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Theory
System theory
Budgets
Organizations
Systems Biology
2009

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations.

van Houte, B. P. P., Binsl, T. W., Hettling, H., Pirovano, W. A. & Heringa, J., 2009, In : BMC Genomics. 10, p. 401

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Comparative Genomic Hybridization
Neoplasms
Gene Expression

Comprehensive genomic analysis of cell wall genes in Aspergillus nidulans

de Groot, P. W. J., Brandt, B. W., Horiuchi, H., Ram, A. F. J., de Koster, C. G. & Klis, F. M., 2009, In : Fungal Genetics and Biology. 46, 1, p. S72-S81

Research output: Contribution to JournalArticleAcademicpeer-review

Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development

Bonzanni, N., Krepska, E., Feenstra, K. A., Fokkink, W. J., Kielmann, T., Bal, H. E. & Heringa, J., 15 Aug 2009, In : Bioinformatics. 25, 16, p. 2049-56 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Predictive Modeling
Biological Phenomena
Developmental Biology
Caenorhabditis elegans
MicroRNAs

Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain

Liefhebber, J. M. P., Brandt, B. W., Broer, J., Spaan, W. J. M. & van Leeuwen, H. C., 2009, In : Virology Journal. 6, p. 62

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Viral Structural Proteins
Hepacivirus
Membranes
Proteins
Static Electricity

PhyloPars: estimation of missing parameter values using phylogeny.

Bruggeman, J., Heringa, J. & Brandt, B. W., 2009, In : Nucleic Acids Research. 37, p. W179-W184

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Phylogeny
Systems Biology
Ecology

RNA structure prediction from evolutionary patterns of nucleotide composition.

Smit, S., Knight, R. & Heringa, J., 2009, In : Nucleic Acids Research. 37, p. 1378-1386

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Nucleotides
RNA
Riboswitch
Catalytic RNA
Base Pairing

Robust modelling, measurement and analysis of human and animal metabolic systems

van Beek, J. H. G. M., Hauschild, A. C., Hettling, H. & Binsl, T. W., 2009, In : Philosophical Transactions of the Royal Society A. Mathematical, Physical and Engineering Sciences. 367, 1895, p. 1971-1992

Research output: Contribution to JournalArticleAcademicpeer-review

animals
Animals
Phosphates
Fluxes
Petri nets

Structure and function analysis of flexible alignment regions in proteins.

Pirovano, W. A., van der Reijden, A., Feenstra, K. A. & Heringa, J., 2009, In : BMC Bioinformatics. 10, 13, p. P6

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

The 2008 update of the Aspergillus nidulans genome annotation: A community effort

Wortman, J. R., Gilsenan, J. M., Joardar, V., Deegan, J., Clutterbuck, J., Andersen, M. R., Archer, D., Bencina, M., Braus, G., Coutinho, P., von Döhren, H., Doonan, J., Driessen, A. J. M., Durek, P., Espeso, E., Fekete, E., Flipphi, M., Estrada, C. G., Geysens, S., Goldman, G. & 66 othersde Groot, P. W. J., Hansen, K., Harris, S. D., Heinekamp, T., Helmstaedt, K., Henrissat, B., Hofmann, G., Homan, T., Horio, T., Horiuchi, H., James, S., Jones, M., Karaffa, L., Karányi, Z., Kato, M., Keller, N., Kelly, D. E., Kiel, J. A. K. W., Kim, J-M., van der Klei, I. J., Klis, F. M., Kovalchuk, A., Krasevec, N., Kubicek, C. P., Liu, B., MacCabe, A., Meyer, V., Mirabito, P., Miskei, M., Mos, M., Mullins, J., Nelson, D. R., Nielsen, J., Oakley, B. R., Osmani, S. A., Pakula, T., Paszewski, A., Paulsen, I., Pilsyk, S., Pócsi, I., Punt, P. J., Ram, A. F. J., Ren, Q., Robellet, X., Robson, G., Seiboth, B., van Solingen, P., Specht, T., Sun, J., Taheri-Talesh, N., Takeshita, N., Ussery, D., vanKuyk, P. A., Visser, H., van de Vondervoort, P. J. I., de Vries, R. P., Walton, J., Xiang, X., Xiong, Y., Zeng, A. P., Brandt, B. W., Cornell, M. J., van den Hondel, C. A. M. J. J., Visser, J., Oliver, S. G. & Turner, G., 2009, In : Fungal Genetics and Biology. 46, 1, p. S2-S13

Research output: Contribution to JournalArticleAcademicpeer-review

webPRC: the profile comparer for alignment-based searching of public domain databases.

Brandt, B. W. & Heringa, J., 2009, In : Nucleic Acids Research. 37, p. W48-W52

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Sequence Alignment
Public Sector
Databases
Proteins

What can formal methods bring to systems biology?

Bonzanni, N., Feenstra, K. A., Fokkink, W. J. & Krepska, E., 2009, In : Lecture Notes in Computer Science. 5850, p. 16-22

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
2008

Disordered flanks prevent peptide aggregation

Abeln, S. & Frenkel, D., Dec 2008, In : PLoS Computational Biology. 4, 12, e1000241.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Peptides
peptide
Aggregation
Agglomeration
peptides

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting

Ye, K., Feenstra, K. A., Heringa, J., Ijzerman, A. P. & Marchiori, E., 1 Jan 2008, In : Bioinformatics. 24, 1, p. 18-25 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Feature Weighting
Multiple Sequence Alignment
Sequence Alignment
Specificity
Learning systems

On defining the dynamics of hydrophobic patches on protein surfaces

Lijnzaad, P., Feenstra, K. A., Heringa, J. & Holstege, F. C. P., Jul 2008, In : Proteins. 72, 1, p. 105-14 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Membrane Proteins
Phospholipases A
Molecular dynamics
Proteins
Molecular Dynamics Simulation

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

Pirovano, W., Feenstra, K. A. & Heringa, J., 15 Feb 2008, In : Bioinformatics. 24, 4, p. 492-7 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Alignment
Proteins
Protein
Membrane
Membrane Proteins
2007

Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants

Feenstra, K. A., Starikov, E. B., Urlacher, V. B., Commandeur, J. N. M. & Vermeulen, N. P. E., Mar 2007, In : Protein Science. 16, 3, p. 420-31 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

lauric acid
Hydroxylation
Energy barriers
Statistics
Hydrogen

LIGAND-PROTEIN DOCKING AND MOLECULAR DYNAMICS SIMULATIONS AND APPLICATIONS IN CYTOCHROMES P450

Vermeulen, N. P. E., de Graaf, C., Stjernschantz, E., Feenstra, A. & Oostenbrink, B. C., 2007, In : Drug Metabolism Reviews. 39, p. 13-13

Research output: Contribution to JournalArticleProfessional

Sequence harmony: detecting functional specificity from alignments

Feenstra, K. A., Pirovano, W., Krab, K. & Heringa, J., Jul 2007, In : Nucleic Acids Research. 35, Web Server issue, p. W495-8

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Sequence Alignment
Proteins
alternative oxidase

Using phylogeny to improve genome-wide distant homology recognition

Abeln, S., Teubner, C. & Deane, C. M., 19 Jan 2007, In : PLoS Computational Biology. 3, 1, p. 0073-0083 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Phylogeny
homology
Homology
Genome
phylogeny
2005

Automated docking and virtual screening of substrates of cytochromes P450

Vermeulen, NPE., De Graaf, C., Feenstra, AF. & Oostenbrink, BC., 2005, In : Drug Metabolism Reviews. 37, p. 13-13

Research output: Contribution to JournalArticleProfessional

How old is your fold?

Winstanley, H. F., Abeln, S. & Deane, C. M., Jun 2005, In : Bioinformatics. 21, SUPPL. 1

Research output: Contribution to JournalArticleAcademicpeer-review

Fold
Proteins
Protein Structure
Phylogeny
Protein
2004

Automated docking and molecular dynamics simulations of substrate binding in cytochromes P450

Vermeulen, NPE., de Graaf, C., van Lipzig, MMH. & Feenstra, AF., Aug 2004, In : Drug Metabolism Reviews. 36, p. 15-15

Research output: Contribution to JournalArticleProfessional

In silico prediction and experimental validation of drug binding and metabolism: The case of Cytochromes P450

Vermeulen, NPE., Keizers, P., van Lipzig, MMH., de Graaf, C., Venhorst, J., Feenstra, AE. & Commandeur, JNM., Oct 2004, In : European Journal of Pharmaceutical Sciences. 23, p. S9-S9

Research output: Contribution to JournalArticleProfessional

2002

A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides

Feenstra, K. A., Peter, C., Scheek, R. M., van Gunsteren, W. F. & Mark, A. E., Jul 2002, In : Journal of Biomolecular NMR. 23, 3, p. 181-94 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Nuclear magnetic resonance
Sampling
Peptides
Molecular Dynamics Simulation
Conformations