In the same section
Peer-reviewed journal articles
Critical review of conformational B-cell epitope prediction methods.
Cia Beriain, G., Pucci, F., & Rooman, M. (2023). Critical review of conformational B-cell epitope prediction methods. Briefings in bioinformatics, 24(1). doi:10.1093/bib/bbac567
SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants.
Cia Beriain, G., Kwasigroch, J.-M., Rooman, M., & Pucci, F. (2022). SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants. Bioinformatics, 38(18), 4418-4419. doi:10.1093/bioinformatics/btac517
NPTX1 mutations trigger endoplasmic reticulum stress and cause autosomal dominant cerebellar ataxia
Coutelier, M., Jacoupy, M., Janer, A., Renaud, F., Auger, N., Saripella, G.-V., Ancien, F., Pucci, F., Rooman, M., Gilis, D., Larivière, R., Sgarioto, N., Valter, R., Guillot-Noel, L., Le Ber, I., Sayah, S., Charles, P., Nümann, A., Pauly, M. G., Helmchen, C., Deininger, N., Haack, T., Brais, B., Brice, A., Trégouët, D.-A., El Hachimi, K., Shoubridge, E., Durr, A., & Stevanin, G. (2022). NPTX1 mutations trigger endoplasmic reticulum stress and cause autosomal dominant cerebellar ataxia. Brain, 145(4), 1519-1534. doi:10.1093/brain/awab407
Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations.
Cia Beriain, G., Pucci, F., & Rooman, M. (2022). Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations. International journal of molecular sciences, 23(4). doi:10.3390/ijms23042078
MutaFrame—an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome
Ancien, F., Pucci, F., Vranken, W. F., & Rooman, M. (2022). MutaFrame—an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome. Bioinformatics, 38(1), 265-266. doi:10.1093/bioinformatics/btab453
Using metagenomic data to boost protein structure prediction and discovery
Hou, Q., Pucci, F., Pan, F., Xue, F., Rooman, M., & Feng, Q. (2022). Using metagenomic data to boost protein structure prediction and discovery. Computational and Structural Biotechnology Journal, 20, 434-442. doi:10.1016/j.csbj.2021.12.030
Artificial intelligence challenges for predicting the impact of mutations on protein stability.
Pucci, F., Schwersensky, M., & Rooman, M. (2022). Artificial intelligence challenges for predicting the impact of mutations on protein stability. Current opinion in structural biology, 72, 161-168. doi:10.1016/j.sbi.2021.11.001
BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
Basu, S. C., Assaf, S., Teheux, F., Rooman, M., & Pucci, F. (2021). BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins. Frontiers in bioinformatics, 1, 742843. doi:10.3389/fbinf.2021.742843
Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7
Pham, N. T. H., Létourneau, M., Fortier, M., Bégin, G., Al-Abdul-Wahid, S., Pucci, F., Folch, B., Rooman, M., Chatenet, D., St Pierre, Y., Lagüe, P., Calmettes, C., & Doucet, N. (2021). Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7. The Journal of biological chemistry, 297(5), 101308. doi:10.1016/j.jbc.2021.101308
Quantifying renin-angiotensin-system alterations in covid-19
Pucci, F., Annoni, F., Dos Santos, R. A. S., Taccone, F., & Rooman, M. (2021). Quantifying renin-angiotensin-system alterations in covid-19. Cells, 10(10), 2755. doi:10.3390/cells10102755
Discopolis 2.0: A new recursive version of the algorithm for uniform sampling of metabolic flux distributions with linear programming
Bogaerts, P., & Rooman, M. (2021). Discopolis 2.0: A new recursive version of the algorithm for uniform sampling of metabolic flux distributions with linear programming. IFAC-PapersOnLine, 54(3), 300-305. doi:10.1016/j.ifacol.2021.08.258
Prediction and evolution of the molecular fitness of sars-cov-2 variants: Introducing spikepro
Pucci, F., & Rooman, M. (2021). Prediction and evolution of the molecular fitness of sars-cov-2 variants: Introducing spikepro. Viruses, 13(5), 935. doi:10.3390/v13050935
In silico analysis of the molecular-level impact of smpd1 variants on niemann-pick disease severity
Ancien, F., Pucci, F., & Rooman, M. (2021). In silico analysis of the molecular-level impact of smpd1 variants on niemann-pick disease severity. International journal of molecular sciences, 22(9), 4516. doi:10.3390/ijms22094516
SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs.
Hou, Q., Pucci, F., Ancien, F., Kwasigroch, J.-M., Bourgeas, R., & Rooman, M. (2021). SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs. Bioinformatics. doi:10.1093/bioinformatics/btab034
Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness
Schwersensky, M., Rooman, M., & Pucci, F. (2020). Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness. BMC biology, 18(1), 146. doi:10.1186/s12915-020-00870-9
Modeling the Molecular Impact of SARS-CoV-2 Infection on the Renin-Angiotensin System
Pucci, F., Bogaerts, P., & Rooman, M. (2020). Modeling the Molecular Impact of SARS-CoV-2 Infection on the Renin-Angiotensin System. Viruses, 12(12), 1367. doi:10.3390/v12121367
Inhibition of aquaporin-1 prevents myocardial remodeling by blocking the transmembrane transport of hydrogen peroxide
Montiel, V., Bella, R., Michel, L. Y. M., Esfahani, H., De Mulder, D., Robinson, E. L., Deglasse, J.-P., Tiburcy, M., Chow, P. H., Jonas, J.-C. J., Gilon, P., Steinhorn, B., Michel, T., Beauloye, C., Bertrand, L., Farah, C., Dei Zotti, F., Debaix, H., Bouzin, C., Brusa, D., Horman, S., Vanoverschelde, J.-L., Bergmann, O., Gilis, D., Rooman, M., Ghigo, A., Geninatti-Crich, S., Yool, A., Zimmermann, W., Roderick, L., Devuyst, O., & Balligand, J. L. (2020). Inhibition of aquaporin-1 prevents myocardial remodeling by blocking the transmembrane transport of hydrogen peroxide. Science Translational Medicine, 12(564), eaay2176. doi:10.1126/scitranslmed.aay2176
Protein Thermal Stability Engineering Using HoTMuSiC.
Pucci, F., Kwasigroch, J.-M., & Rooman, M. (2020). Protein Thermal Stability Engineering Using HoTMuSiC. Methods in molecular biology, 2112, 59-73. doi:10.1007/978-1-0716-0270-6_5
SOLart: a structure-based method to predict protein solubility and aggregation
Hou, Q., Kwasigroch, J.-M., Rooman, M., & Pucci, F. (2020). SOLart: a structure-based method to predict protein solubility and aggregation. Bioinformatics, 36(5), 1445-1452. doi:10.1093/bioinformatics/btz773
Digenic inheritance of human primary microcephaly delineates centrosomal and non centrosomal pathways.
Duerinckx, S., Jacquemin, V., Drunat, S., Vial, Y., Passemard, S., Perazzolo, C., Massart, A., Soblet, J., Racapé, J., Desmyter, L., Badoer, C., Papadimitriou, S., Le Borgne, Y.-A., Lefort, A., Libert, F., De Maertelaer, V., Rooman, M., Costagliola, S., Verloes, A., Lenaerts, T., Pirson, I., & Abramowicz, M. (2020). Digenic inheritance of human primary microcephaly delineates centrosomal and non centrosomal pathways. Human mutation, 41(2), 512-524. doi:10.1002/humu.23948
DISCOPOLIS : an algorithm for uniform sampling of metabolic flux distributions via iterative sequences of linear programs
Bogaerts, P., & Rooman, M. (2019). DISCOPOLIS : an algorithm for uniform sampling of metabolic flux distributions via iterative sequences of linear programs. IFAC-PapersOnLine, 52-26, 269-274.
A comprehensive computational study of amino acid interactions in membrane proteins.
Mbaye, M. N., Hou, Q., Basu, S. C., Teheux, F., Pucci, F., & Rooman, M. (2019). A comprehensive computational study of amino acid interactions in membrane proteins. Scientific reports, 9(1), 12043. doi:10.1038/s41598-019-48541-2
Relation between DNA ionization potentials, single base substitutions and pathogenic variants
Pucci, F., & Rooman, M. (2019). Relation between DNA ionization potentials, single base substitutions and pathogenic variants. BMC genomics, 20, 551. doi:10.1186/s12864-019-5867-y
Rational antibiotic design: in silico structural comparison of the functional cavities of penicillin-binding proteins and ß-lactamases
Mbaye, M. N., Gilis, D., & Rooman, M. (2019). Rational antibiotic design: in silico structural comparison of the functional cavities of penicillin-binding proteins and ß-lactamases. Journal of biomolecular structure & dynamics, 37(1), 65-74. doi:10.1080/07391102.2017.1418678
Deciphering noise amplification and reduction in open chemical reaction networks
Pucci, F., & Rooman, M. (2018). Deciphering noise amplification and reduction in open chemical reaction networks. Journal of the Royal Society interface, 15(149), 20180805. doi:10.1098/rsif.2018.0805
Computational analysis of the amino acid interactions that promote or decrease protein solubility
Hou, Q., Bourgeas, R., Pucci, F., & Rooman, M. (2018). Computational analysis of the amino acid interactions that promote or decrease protein solubility. Scientific reports, 8(1), 14661. doi:10.1038/s41598-018-32988-w
Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome.
Raimondi, D., Orlando, G., Tabaro, F., Lenaerts, T., Rooman, M., Moreau, Y., & Vranken, W. F. (2018). Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome. Scientific reports, 8(1), 16980. doi:10.1038/s41598-018-34959-7
Quantification of biases in predictions of protein stability changes upon mutations.
Pucci, F., Bernaerts, K., Kwasigroch, J.-M., & Rooman, M. (2018). Quantification of biases in predictions of protein stability changes upon mutations. Bioinformatics, 34(21), 3659-3665. doi:10.1093/bioinformatics/bty348
Insights into noise modulation in oligomerization systems of increasing complexity
Pucci, F., & Rooman, M. (2018). Insights into noise modulation in oligomerization systems of increasing complexity. Physical Review E, 98(1), 012137. doi:10.1103/PhysRevE.98.012137
Lexicon Visualization Library and Javascript for Scientific data visualization
Tanyalçin, I., Ferte, J., Ancien, F., Smits, G., Rooman, M., & Vranken, W. F. (2018). Lexicon Visualization Library and Javascript for Scientific data visualization. Computing in science & engineering, 20, 50-65. doi:10.1109/MCSE.2018.011111125
Prediction and interpretation of deleterious coding variants in terms of protein structural stability
Ancien, F., Pucci, F., Godfroid, M., & Rooman, M. (2018). Prediction and interpretation of deleterious coding variants in terms of protein structural stability. Scientific reports, 8, 4480. doi:10.1038/s41598-018-22531-2
Intrinsic noise modulation in closed oligomerization-type system
Rooman, M., & Pucci, F. (2018). Intrinsic noise modulation in closed oligomerization-type system. IFAC-PapersOnLine, 51(2), 649-653. doi:10.1016/j.ifacol.2018.03.110
SCooP: an accurate and fast predictor of protein stability curves as a function of temperature.
Pucci, F., Kwasigroch, J.-M., & Rooman, M. (2017). SCooP: an accurate and fast predictor of protein stability curves as a function of temperature. Bioinformatics, 33(21), 3415-3422. doi:10.1093/bioinformatics/btx417
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins.
Raimondi, D., Tanyalçin, I., Ferte, J., Gazzo, A., Orlando, G., Lenaerts, T., Rooman, M., & Vranken, W. F. (2017). DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. Nucleic acids research, 45(W1), W201-W206. doi:10.1093/nar/gkx390
Physical and molecular bases of protein thermal stability and cold adaptation.
Pucci, F., & Rooman, M. (2017). Physical and molecular bases of protein thermal stability and cold adaptation. Current opinion in structural biology, 42, 117-128. doi:10.1016/j.sbi.2016.12.007
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence.
Dalkas, G. A., & Rooman, M. (2017). SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. BMC bioinformatics, 18(1), 95. doi:10.1186/s12859-017-1528-9
Improved insights into protein thermal stability: From the molecular to the structurome scale
Pucci, F., & Rooman, M. (2016). Improved insights into protein thermal stability: From the molecular to the structurome scale. Philosophical transactions - Royal Society. Mathematical, Physical and engineering sciences, 374(2080), 20160141. doi:10.1098/rsta.2016.0141
Single Mutations in the Transmembrane Domains of Maize Plasma Membrane Aquaporins Affect the Activity of Monomers within a Heterotetramer.
Berny, M. C., Gilis, D., Rooman, M., & Chaumont, F. (2016). Single Mutations in the Transmembrane Domains of Maize Plasma Membrane Aquaporins Affect the Activity of Monomers within a Heterotetramer. Molecular Plant, 9(7), 986-1003. doi:10.1016/j.molp.2016.04.006
High-quality thermodynamic data on the stability changes of proteins upon single-site mutations
Pucci, F., Bourgeas, R., & Rooman, M. (2016). High-quality thermodynamic data on the stability changes of proteins upon single-site mutations. Journal of physical and chemical reference data, 45(2), 023104. doi:10.1063/1.4947493
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects
Raimondi, D., Gazzo, A., Rooman, M., Lenaerts, T., & Vranken, W. (2016). Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects. Bioinformatics, 32(12), 1797-1804. doi:10.1093/bioinformatics/btw094
Probability distributions for multimeric systems are skew normal
Albert, J., & Rooman, M. (2016). Probability distributions for multimeric systems are skew normal. Journal of mathematical biology, 72(1-2), 157-169. doi:10.1007/s00285-015-0877-0
Stability strengths and weaknesses in protein structures detected by statistical potentials. Application to bovine seminal ribonuclease
De Laet, M., Gilis, D., & Rooman, M. (2016). Stability strengths and weaknesses in protein structures detected by statistical potentials. Application to bovine seminal ribonuclease. Proteins, 84(1), 143-158. doi:10.1002/prot.24962
Predicting protein thermal stability changes upon point mutations using statistical potentials: introducing HoTMuSiC
Pucci, F., Bourgeas, R., & Rooman, M. (2016). Predicting protein thermal stability changes upon point mutations using statistical potentials: introducing HoTMuSiC. Scientific reports, 6, 23257. doi:10.1038/srep23257
Towards an accurate prediction of the thermal stability of homologous proteins
Pucci, F., & Rooman, M. (2015). Towards an accurate prediction of the thermal stability of homologous proteins. Journal of biomolecular structure & dynamics, 34(5), 1132-1142. doi:10.1080/07391102.2015.1073631
Is the cell nucleus a necessary component in precise temporal patterning?
Albert, J., & Rooman, M. (2015). Is the cell nucleus a necessary component in precise temporal patterning? PloS one, 10(7), e0134239. doi:10.1371/journal.pone.0134239
Symmetry principles in optimization problems: an application to protein stability prediction
Pucci, F., Bernaerts, K., Teheux, F., Gilis, D., & Rooman, M. (2015). Symmetry principles in optimization problems: an application to protein stability prediction. IFAC-PapersOnLine, 48, 458-463. doi:10.1016/j.ifacol.2015.05.062
Cation-pi, amino-pi, pi-pi, and H-bond interactions stabilize antigen-antibody interfaces.
Dalkas, G. A., Teheux, F., Kwasigroch, J.-M., & Rooman, M. (2014). Cation-pi, amino-pi, pi-pi, and H-bond interactions stabilize antigen-antibody interfaces. Proteins, 82(9), 1734-1746. doi:10.1002/prot.24527
Stochastic noise reduction upon complexification: Positively correlated birth-death type systems.
Rooman, M., Albert, J., & Duerinckx, M. (2014). Stochastic noise reduction upon complexification: Positively correlated birth-death type systems. Journal of theoretical biology, 354, 113-123. doi:10.1016/j.jtbi.2014.03.007
Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations.
Rooman, M., & Wintjens, R. (2014). Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations. Journal of biomolecular structure & dynamics, 32(4), 532-545. doi:10.1080/07391102.2013.783508
Protein thermostability prediction within homologous families using temperature-dependent statistical potentials.
Pucci, F., Dhanani, M., Dehouck, Y., & Rooman, M. (2014). Protein thermostability prediction within homologous families using temperature-dependent statistical potentials. PloS one, 9(3), e91659. doi:10.1371/journal.pone.0091659
Modeling the Drosophila gene cluster regulation network for muscle development.
Haye, A., Albert, J., & Rooman, M. (2014). Modeling the Drosophila gene cluster regulation network for muscle development. PloS one, 9(3), e90285. doi:10.1371/journal.pone.0090285
Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials
Pucci, F., & Rooman, M. (2014). Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials. PLoS computational biology, 10(7), e1003689. doi:10.1371/journal.pcbi.1003689
BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations.
Dehouck, Y., Kwasigroch, J.-M., Rooman, M., & Gilis, D. (2013). BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations. Nucleic acids research, 41, 333-339. doi:10.1093/nar/gkt450
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
Moretti, R., Fleishman, S. S., Agius, R., Torchala, M., Bates, P. P., Kastritis, P. P., Rodrigues, J. J., Trellet, M., Bonvin, A. A., Gilis, D., Rooman, M., Dehouck, Y., et al. (2013). Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins, 81(11), 1980-1987. doi:10.1002/prot.24356
Structure-based mutant stability predictions on proteins of unknown structure.
Gonnelli, G., Rooman, M., & Dehouck, Y. (2012). Structure-based mutant stability predictions on proteins of unknown structure. Journal of biotechnology, 161(3), 287-293. doi:10.1016/j.jbiotec.2012.06.020
A conserved cysteine residue is involved in disulfide bond formation between plant plasma membrane aquaporin monomers.
Bienert, G. P., Cavez, D., Besserer, A., Berny, M. C., Gilis, D., Rooman, M., & Chaumont, F. (2012). A conserved cysteine residue is involved in disulfide bond formation between plant plasma membrane aquaporin monomers. Biochemical journal, 445(1), 101-111. doi:10.1042/BJ20111704
Design principles of a genetic alarm clock.
Albert, J., & Rooman, M. (2012). Design principles of a genetic alarm clock. PloS one, 7(11), e47256. doi:10.1371/journal.pone.0047256
Robust non-linear differential equation models of gene expression evolution across Drosophila development.
Haye, A., Albert, J., & Rooman, M. (2012). Robust non-linear differential equation models of gene expression evolution across Drosophila development. BMC research notes, 5, 46. doi:10.1186/1756-0500-5-46
Flanking domain stability modulates the aggregation kinetics of a polyglutamine disease protein.
Saunders, H. M., Gilis, D., Rooman, M., Dehouck, Y., Robertson, A. L., & Bottomley, S. P. (2011). Flanking domain stability modulates the aggregation kinetics of a polyglutamine disease protein. Protein science, 20(10), 1675-1681. doi:10.1002/pro.698
Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli.
Albert, J., & Rooman, M. (2011). Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli. Systems and Synthetic Biology, 5(1-2), 33-43. doi:10.1007/s11693-011-9079-2
Conformations consistent with charge migration observed in DNA and RNA X-ray structures
Rooman, M., Cauet, E., Liévin, J., & Wintjens, R. (2011). Conformations consistent with charge migration observed in DNA and RNA X-ray structures. Journal of biomolecular structure & dynamics, 28, 949-954.
PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.
Dehouck, Y., Kwasigroch, J.-M., Gilis, D., & Rooman, M. (2011). PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality. BMC bioinformatics, 12, 151. doi:10.1186/1471-2105-12-151
Robustness analysis of a linear dynamical model of the drosophila gene expression
Haye, A., Albert, J., & Rooman, M. (2011). Robustness analysis of a linear dynamical model of the drosophila gene expression. Lecture notes in computer science, 6685 LNBI, 242-252. doi:10.1007/978-3-642-21946-7_19
Detection of perturbation phases and developmental stages in organisms from DNA microarray time series data.
Rooman, M., Albert, J., Dehouck, Y., & Haye, A. (2011). Detection of perturbation phases and developmental stages in organisms from DNA microarray time series data. PloS one, 6(12), e27948. doi:10.1371/journal.pone.0027948
Evidence that interaction between conserved residues in transmembrane helices 2, 3 and 7 are crucial for human VPAC1 receptor activation.
Chugunov, A. O., Simms, J., Poyner, D. R., Dehouck, Y., Rooman, M., Gilis, D., & Langer, I. (2010). Evidence that interaction between conserved residues in transmembrane helices 2, 3 and 7 are crucial for human VPAC1 receptor activation. Molecular pharmacology. doi:10.1124/mol.110.063578
Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials.
Folch, B., Dehouck, Y., & Rooman, M. (2010). Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials. Biophysical journal, 98(4), 667-677. doi:10.1016/j.bpj.2009.10.050
Gene expression model (in)validation by Fourier analysis.
Konopka, T., & Rooman, M. (2010). Gene expression model (in)validation by Fourier analysis. B M C Systems Biology, 4, 123. doi:10.1186/1752-0509-4-123
Interaction among the gene products contributes to the regulation of gene expression
Albert, J., & Rooman, M. (2010). Interaction among the gene products contributes to the regulation of gene expression. IFAC proceedings volumes, 11(PART 1), 245-250. doi:10.3182/20100707-3-BE-2012.0025
The first peptides: the evolutionary transition between prebiotic amino acids and early proteins.
van der Gulik, P., Massar, S., Gilis, D., Buhrman, H., & Rooman, M. (2009). The first peptides: the evolutionary transition between prebiotic amino acids and early proteins. Journal of theoretical biology, 261(4), 531-539. doi:10.1016/j.jtbi.2009.09.004
Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.
Dehouck, Y., Grosfils, A., Folch, B., Gilis, D., Bogaerts, P., & Rooman, M. (2009). Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics, 25(19), 2537-2543. doi:10.1093/bioinformatics/btp445
Modeling the temporal evolution of the Drosophila gene expression from DNA microarray time series.
Haye, A., Dehouck, Y., Kwasigroch, J.-M., Bogaerts, P., & Rooman, M. (2009). Modeling the temporal evolution of the Drosophila gene expression from DNA microarray time series. Physical biology, 6(1), 016004. doi:10.1088/1478-3975/6/1/016004
A robust method for the joint estimation of yield coefficients and kinetic parameters in bioprocess models.
Vastemans, V., Rooman, M., & Bogaerts, P. (2009). A robust method for the joint estimation of yield coefficients and kinetic parameters in bioprocess models. Biotechnology progress, 25(3), 606-618. doi:10.1002/btpr.89
Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity
Dehouck, Y., Folch, B., & Rooman, M. (2008). Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity. Protein engineering, design & selection, 21(4), 275-278. doi:10.1093/protein/gzn001
Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence
Wintjens, R., Gilis, D., & Rooman, M. (2008). Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence. Proteins, 70(4), 1564-1577. doi:10.1002/prot.21650
Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials
Folch, B., Rooman, M., & Dehouck, Y. (2008). Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials. Journal of chemical information and modeling, 48(1), 119-127. doi:10.1021/ci700237g
SODa: an Mn/Fe superoxide dismutase prediction and design server
Kwasigroch, J.-M., Wintjens, R., Gilis, D., & Rooman, M. (2008). SODa: an Mn/Fe superoxide dismutase prediction and design server. BMC bioinformatics, 9, 257. doi:10.1186/1471-2105-9-257
Enhancing the stability and solubility of TEV protease using in silico design.
Cabrita, L. D., Gilis, D., Robertson, A. L., Dehouck, Y., Rooman, M., & Bottomley, S. P. (2007). Enhancing the stability and solubility of TEV protease using in silico design. Protein science, 16(11), 2360-2367. doi:10.1110/ps.072822507
Deformation of D-branes in three-dimensional anti-de Sitter black holes
Bieliavsky, P., Detournay, S., Rooman, M., & Spindel, P. (2006). Deformation of D-branes in three-dimensional anti-de Sitter black holes. Journal of physics. Conference series, 53(1), 059, 900-911. doi:10.1088/1742-6596/53/1/059
Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses.
Kwasigroch, J.-M., & Rooman, M. (2006). Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses. Bioinformatics, 22(14), 1800-1802. doi:10.1093/bioinformatics/btl176
A new generation of statistical potentials for proteins
Dehouck, Y., Gilis, D., & Rooman, M. (2006). A new generation of statistical potentials for proteins. Biophysical journal, 90(11), 4010-4017. doi:10.1529/biophysj.105.079434
Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches
Gilis, D., Biot, C., Buisine, E., Dehouck, Y., & Rooman, M. (2006). Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches. Journal of chemical information and modeling, 46(2), 884-893. doi:10.1021/ci050395b
Histidine-aromatic interactions in proteins and protein-ligand complexes
Cauet, E., Rooman, M., Wintjens, R., Liévin, J., & Biot, C. (2005). Histidine-aromatic interactions in proteins and protein-ligand complexes: quantum chemical study of X-ray and model structures. Journal of chemical theory and computation, 1(3), 472-483. doi:10.1021/ct049875k
Database-derived potentials dependent on protein size for in silico folding and design
Dehouck, Y., Gilis, D., & Rooman, M. (2004). Database-derived potentials dependent on protein size for in silico folding and design. Biophysical journal, 87(1), 171-181. doi:10.1529/biophysj.103.037861
Star products on extended massive non-rotating BTZ black holes
Bieliavsky, P., Detournay, S., Spindel, P., & Rooman, M. (2004). Star products on extended massive non-rotating BTZ black holes. The journal of high energy physics (Online), 8(6), 697-721.
Cation-pi/H-bond stair motifs at protein-DNA interfaces
Biot, C., Wintjens, R., & Rooman, M. (2004). Cation-pi/H-bond stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-π interactions. Journal of the American Chemical Society, 126(20), 6220-6221. doi:10.1021/ja049620g
Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons.
Wintjens, R., Noël, C., May, A. C. W., Gerbod, D., Dufernez, F., Capron, M., Viscogliosi, E., & Rooman, M. (2004). Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons. The Journal of biological chemistry, 279(10), 9248-9254. doi:10.1074/jbc.M312329200
Free-energy calculations of protein-ligand cation-pi and amino-pi interactions: from vacuum to proteinlike environments
Biot, C., Buisine, E., & Rooman, M. (2003). Free-energy calculations of protein-ligand cation-pi and amino-pi interactions: from vacuum to proteinlike environments. Journal of the American Chemical Society, 125(46), 13988-13994. doi:10.1021/ja035223e
Global geometry of the 2 + 1 rotating black hole
Bieliavsky, P., Detournay, S., Herquet, M., Rooman, M., & Spindel, P. (2003). Global geometry of the 2 + 1 rotating black hole. Physics letters. Section B, 570(3-4), 231-236. doi:10.1016/j.physletb.2003.07.055
Basis set and electron correlation effects on ab initio calculations of cation-pi/H-bond stair motifs
Wintjens, R., Biot, C., Rooman, M., & Liévin, J. (2003). Basis set and electron correlation effects on ab initio calculations of cation-pi/H-bond stair motifs. The Journal of Physical Chemistry. A, 107(32), 6249-6258. doi:10.1021/jp034103q
Sequence-structure signals of 3D domain swapping in proteins
Dehouck, Y., Biot, C., Gilis, D., Kwasigroch, J.-M., & Rooman, M. (2003). Sequence-structure signals of 3D domain swapping in proteins. Journal of Molecular Biology, 330(5), 1215-1225. doi:10.1016/S0022-2836(03)00614-4
In vitro and in silico design of alpha1-antitrypsin mutants with different conformational stabilities
Gilis, D., McLennan, H. R., Dehouck, Y., Cabrita, L. D., Rooman, M., & Bottomley, S. P. (2003). In vitro and in silico design of alpha1-antitrypsin mutants with different conformational stabilities. Journal of Molecular Biology, 325(3), 581-589. doi:10.1016/S0022-2836(02)01221-4
Regular poisson structures on massive non-rotating BTZ black holes
Bieliavsky, P., Rooman, M., & Spindel, P. (2002). Regular poisson structures on massive non-rotating BTZ black holes. Nuclear physics. B, 645(3), 349-364.
PoPMuSiC, rationally designing point mutations in protein structures
Kwasigroch, J.-M., Gilis, D., Dehouck, Y., & Rooman, M. (2002). PoPMuSiC, rationally designing point mutations in protein structures. Bioinformatics, 18(12), 1701-1702. doi:10.1093/bioinformatics/18.12.1701
What is paradoxical about Levinthal paradox?
Rooman, M., Dehouck, Y., Kwasigroch, J.-M., Biot, C., & Gilis, D. (2002). What is paradoxical about Levinthal paradox? Journal of biomolecular structure & dynamics, 20(3), 327-329. doi:10.1080/07391102.2002.10506850
Probing the energetic and structural role of amino acid/nucleobase cation-pi interactions in protein-ligand complexes.
Biot, C., Buisine, E., Kwasigroch, J.-M., Wintjens, R., & Rooman, M. (2002). Probing the energetic and structural role of amino acid/nucleobase cation-pi interactions in protein-ligand complexes. The Journal of biological chemistry, 277(43), 40816-40822. doi:10.1074/jbc.M205719200
Cation-pi/H-bond stair motifs at protein-DNA interfaces
Rooman, M., Liévin, J., Buisine, E., & Wintjens, R. (2002). Cation-pi/H-bond stair motifs at protein-DNA interfaces. Journal of Molecular Biology, 319(1), 67-76. doi:10.1016/S0022-2836(02)00263-2
Uniqueness of the asymptotic AdS3 geometry
Rooman, M., & Spindel, P. (2001). Uniqueness of the asymptotic AdS3 geometry. Classical and quantum gravity, 18(11), 2117-2123. doi:10.1088/0264-9381/18/11/309
Identification and ab initio simulations of early folding units in proteins
Gilis, D., & Rooman, M. (2001). Identification and ab initio simulations of early folding units in proteins. Proteins, 42(2), 164-176. doi:10.1002/1097-0134(20010201)42:2<164::AID-PROT30>3.0.CO;2-#
Holonomies, anomalies and the Fefferman-Graham ambiguity in AdS3 gravity
Rooman, M., & Spindel, P. (2001). Holonomies, anomalies and the Fefferman-Graham ambiguity in AdS3 gravity. Nuclear physics. B, 594(1-2), 329-353. doi:10.1016/S0550-3213(00)00636-2
Ab initio structure predictions using a hierarchic approach applied to 434 CRO and Drosophila homeodomain
Gilis, D., & Rooman, M. (2001). Ab initio structure predictions using a hierarchic approach applied to 434 CRO and Drosophila homeodomain. Theoretical Chemistry accounts, 106(1-2), 69-75. doi:10.1007/s002140000221
Updated on October 11, 2021