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3BIO-BioInfo Team Publications

Peer-reviewed journal articles

 


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  

 

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  

 

Artificial intelligence challenges for predicting the impact of mutations on protein stability.

Pucci, F., Schwersensky, M., & Rooman, M. (2021). 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  

 

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  

 

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. (2021). NPTX1 mutations trigger endoplasmic reticulum stress and cause autosomal dominant cerebellar ataxia. Brain. doi:10.1093/brain/awab407  

 

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  

 

Optimality of the genetic code with respect to protein stability and amino-acid frequencies

Gilis, D., Massar, S., Cerf, N., & Rooman, M. (2001). Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biology, 2, 0049.  

 

Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations

Iurcu-Mustata, G., Van Belle, D., Wintjens, R., Prévost, M., & Rooman, M. (2001). Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations. Biopolymers, 59(3), 145-159. doi:10.1002/1097-0282(200109)59:3<145::AID-BIP1014>3.0.CO;2-Z  

 

PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins.

Gilis, D., & Rooman, M. (2000). PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. Protein engineering, 13(12), 849-856.  

 

Updated on October 11, 2021