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Items: 1 to 50 of 93

1.

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, Borgne YL, Lefort A, Libert F, Maertelaer V, Rooman M, Costagliola S, Verloes A, Lenaerts T, Pirson I, Abramowicz M.

Hum Mutat. 2019 Nov 7. doi: 10.1002/humu.23948. [Epub ahead of print]

PMID:
31696992
2.

SOLart: a structure-based method to predict protein solubility and aggregation.

Hou Q, Kwasigroch JM, Rooman M, Pucci F.

Bioinformatics. 2019 Oct 11. pii: btz773. doi: 10.1093/bioinformatics/btz773. [Epub ahead of print]

PMID:
31603466
3.

A comprehensive computational study of amino acid interactions in membrane proteins.

Mbaye MN, Hou Q, Basu S, Teheux F, Pucci F, Rooman M.

Sci Rep. 2019 Aug 19;9(1):12043. doi: 10.1038/s41598-019-48541-2.

4.

Relation between DNA ionization potentials, single base substitutions and pathogenic variants.

Pucci F, Rooman M.

BMC Genomics. 2019 Jul 16;20(Suppl 8):551. doi: 10.1186/s12864-019-5867-y.

5.

Deciphering noise amplification and reduction in open chemical reaction networks.

Pucci F, Rooman M.

J R Soc Interface. 2018 Dec 21;15(149):20180805. doi: 10.1098/rsif.2018.0805.

PMID:
30958227
6.

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 WF.

Sci Rep. 2018 Nov 19;8(1):16980. doi: 10.1038/s41598-018-34959-7.

7.

Computational analysis of the amino acid interactions that promote or decrease protein solubility.

Hou Q, Bourgeas R, Pucci F, Rooman M.

Sci Rep. 2018 Oct 2;8(1):14661. doi: 10.1038/s41598-018-32988-w.

8.

Insights into noise modulation in oligomerization systems of increasing complexity.

Pucci F, Rooman M.

Phys Rev E. 2018 Jul;98(1-1):012137. doi: 10.1103/PhysRevE.98.012137.

PMID:
30110836
9.

Quantification of biases in predictions of protein stability changes upon mutations.

Pucci F, Bernaerts KV, Kwasigroch JM, Rooman M.

Bioinformatics. 2018 Nov 1;34(21):3659-3665. doi: 10.1093/bioinformatics/bty348.

PMID:
29718106
10.

Prediction and interpretation of deleterious coding variants in terms of protein structural stability.

Ancien F, Pucci F, Godfroid M, Rooman M.

Sci Rep. 2018 Mar 14;8(1):4480. doi: 10.1038/s41598-018-22531-2.

11.

Rational antibiotic design: in silico structural comparison of the functional cavities of penicillin-binding proteins and ß-lactamases.

Mbaye MN, Gilis D, Rooman M.

J Biomol Struct Dyn. 2019 Jan;37(1):65-74. doi: 10.1080/07391102.2017.1418678. Epub 2018 Jan 17.

PMID:
29251560
12.

SCooP: an accurate and fast predictor of protein stability curves as a function of temperature.

Pucci F, Kwasigroch JM, Rooman M.

Bioinformatics. 2017 Nov 1;33(21):3415-3422. doi: 10.1093/bioinformatics/btx417.

PMID:
29036273
13.

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins.

Raimondi D, Tanyalcin I, Ferté J, Gazzo A, Orlando G, Lenaerts T, Rooman M, Vranken W.

Nucleic Acids Res. 2017 Jul 3;45(W1):W201-W206. doi: 10.1093/nar/gkx390.

14.

SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence.

Dalkas GA, Rooman M.

BMC Bioinformatics. 2017 Feb 10;18(1):95. doi: 10.1186/s12859-017-1528-9.

15.

Physical and molecular bases of protein thermal stability and cold adaptation.

Pucci F, Rooman M.

Curr Opin Struct Biol. 2017 Feb;42:117-128. doi: 10.1016/j.sbi.2016.12.007. Epub 2016 Dec 29. Review.

PMID:
28040640
16.

Improved insights into protein thermal stability: from the molecular to the structurome scale.

Pucci F, Rooman M.

Philos Trans A Math Phys Eng Sci. 2016 Nov 13;374(2080). pii: 20160141.

17.

Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects.

Raimondi D, Gazzo AM, Rooman M, Lenaerts T, Vranken WF.

Bioinformatics. 2016 Jun 15;32(12):1797-804. doi: 10.1093/bioinformatics/btw094. Epub 2016 Feb 18.

PMID:
27153718
18.

Single Mutations in the Transmembrane Domains of Maize Plasma Membrane Aquaporins Affect the Activity of Monomers within a Heterotetramer.

Berny MC, Gilis D, Rooman M, Chaumont F.

Mol Plant. 2016 Jul 6;9(7):986-1003. doi: 10.1016/j.molp.2016.04.006. Epub 2016 Apr 19.

19.
20.

Stability strengths and weaknesses in protein structures detected by statistical potentials: Application to bovine seminal ribonuclease.

De Laet M, Gilis D, Rooman M.

Proteins. 2016 Jan;84(1):143-58. doi: 10.1002/prot.24962. Epub 2015 Dec 9.

PMID:
26573727
21.

Is the Cell Nucleus a Necessary Component in Precise Temporal Patterning?

Albert J, Rooman M.

PLoS One. 2015 Jul 30;10(7):e0134239. doi: 10.1371/journal.pone.0134239. eCollection 2015.

22.

Towards an accurate prediction of the thermal stability of homologous proteins.

Pucci F, Rooman M.

J Biomol Struct Dyn. 2016 May;34(5):1132-42. doi: 10.1080/07391102.2015.1073631. Epub 2015 Sep 1.

PMID:
26198299
23.

Probability distributions for multimeric systems.

Albert J, Rooman M.

J Math Biol. 2016 Jan;72(1-2):157-69. doi: 10.1007/s00285-015-0877-0. Epub 2015 Apr 4.

PMID:
25840518
24.

Stability curve prediction of homologous proteins using temperature-dependent statistical potentials.

Pucci F, Rooman M.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003689. doi: 10.1371/journal.pcbi.1003689. eCollection 2014 Jul.

25.

Protein thermostability prediction within homologous families using temperature-dependent statistical potentials.

Pucci F, Dhanani M, Dehouck Y, Rooman M.

PLoS One. 2014 Mar 19;9(3):e91659. doi: 10.1371/journal.pone.0091659. eCollection 2014.

26.

Stochastic noise reduction upon complexification: positively correlated birth-death type systems.

Rooman M, Albert J, Duerinckx M.

J Theor Biol. 2014 Aug 7;354:113-23. doi: 10.1016/j.jtbi.2014.03.007. Epub 2014 Mar 14.

PMID:
24632443
27.

Modeling the Drosophila gene cluster regulation network for muscle development.

Haye A, Albert J, Rooman M.

PLoS One. 2014 Mar 3;9(3):e90285. doi: 10.1371/journal.pone.0090285. eCollection 2014.

28.

Cation-π, amino-π, π-π, and H-bond interactions stabilize antigen-antibody interfaces.

Dalkas GA, Teheux F, Kwasigroch JM, Rooman M.

Proteins. 2014 Sep;82(9):1734-46. doi: 10.1002/prot.24527. Epub 2014 Feb 18.

29.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.

Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.

30.

BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations.

Dehouck Y, Kwasigroch JM, Rooman M, Gilis D.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W333-9. doi: 10.1093/nar/gkt450. Epub 2013 May 30.

31.

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.

J Biomol Struct Dyn. 2014 Apr;32(4):532-45. doi: 10.1080/07391102.2013.783508. Epub 2013 Apr 13.

32.

Design principles of a genetic alarm clock.

Albert J, Rooman M.

PLoS One. 2012;7(11):e47256. doi: 10.1371/journal.pone.0047256. Epub 2012 Nov 7.

33.

Structure-based mutant stability predictions on proteins of unknown structure.

Gonnelli G, Rooman M, Dehouck Y.

J Biotechnol. 2012 Oct 31;161(3):287-93. doi: 10.1016/j.jbiotec.2012.06.020. Epub 2012 Jul 8.

PMID:
22782143
34.

A conserved cysteine residue is involved in disulfide bond formation between plant plasma membrane aquaporin monomers.

Bienert GP, Cavez D, Besserer A, Berny MC, Gilis D, Rooman M, Chaumont F.

Biochem J. 2012 Jul 1;445(1):101-11. doi: 10.1042/BJ20111704.

PMID:
22506965
35.

Robust non-linear differential equation models of gene expression evolution across Drosophila development.

Haye A, Albert J, Rooman M.

BMC Res Notes. 2012 Jan 19;5:46. doi: 10.1186/1756-0500-5-46.

36.

Detection of perturbation phases and developmental stages in organisms from DNA microarray time series data.

Rooman M, Albert J, Dehouck Y, Haye A.

PLoS One. 2011;6(12):e27948. doi: 10.1371/journal.pone.0027948. Epub 2011 Dec 15.

37.

Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli.

Albert J, Rooman M.

Syst Synth Biol. 2011 Jun;5(1-2):33-43. doi: 10.1007/s11693-011-9079-2. Epub 2011 Feb 26.

38.

Flanking domain stability modulates the aggregation kinetics of a polyglutamine disease protein.

Saunders HM, Gilis D, Rooman M, Dehouck Y, Robertson AL, Bottomley SP.

Protein Sci. 2011 Oct;20(10):1675-81. doi: 10.1002/pro.698. Epub 2011 Aug 18.

39.

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.

Dehouck Y, Kwasigroch JM, Gilis D, Rooman M.

BMC Bioinformatics. 2011 May 13;12:151. doi: 10.1186/1471-2105-12-151.

40.

Conformations consistent with charge migration observed in DNA and RNA X-ray structures.

Rooman M, Cauët E, Liévin J, Wintjens R.

J Biomol Struct Dyn. 2011 Jun;28(6):949-53.

PMID:
21469755
41.

Gene expression model (in)validation by Fourier analysis.

Konopka T, Rooman M.

BMC Syst Biol. 2010 Sep 3;4:123. doi: 10.1186/1752-0509-4-123.

42.

Evidence that interaction between conserved residues in transmembrane helices 2, 3, and 7 are crucial for human VPAC1 receptor activation.

Chugunov AO, Simms J, Poyner DR, Dehouck Y, Rooman M, Gilis D, Langer I.

Mol Pharmacol. 2010 Sep;78(3):394-401. doi: 10.1124/mol.110.063578. Epub 2010 Jun 23.

PMID:
20573782
43.

Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials.

Folch B, Dehouck Y, Rooman M.

Biophys J. 2010 Feb 17;98(4):667-77. doi: 10.1016/j.bpj.2009.10.050.

44.

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.

J Theor Biol. 2009 Dec 21;261(4):531-9. doi: 10.1016/j.jtbi.2009.09.004. Epub 2009 Sep 15.

PMID:
19761777
45.

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.

Bioinformatics. 2009 Oct 1;25(19):2537-43. doi: 10.1093/bioinformatics/btp445. Epub 2009 Aug 3.

PMID:
19654118
46.

A robust method for the joint estimation of yield coefficients and kinetic parameters in bioprocess models.

Vastemans V, Rooman M, Bogaerts P.

Biotechnol Prog. 2009 May-Jun;25(3):606-18. doi: 10.1002/btpr.89.

PMID:
19455623
47.

Modeling the temporal evolution of the Drosophila gene expression from DNA microarray time series.

Haye A, Dehouck Y, Kwasigroch JM, Bogaerts P, Rooman M.

Phys Biol. 2009 Jan 27;6(1):016004. doi: 10.1088/1478-3975/6/1/016004.

PMID:
19171963
48.

SODa: an Mn/Fe superoxide dismutase prediction and design server.

Kwasigroch JM, Wintjens R, Gilis D, Rooman M.

BMC Bioinformatics. 2008 Jun 2;9:257. doi: 10.1186/1471-2105-9-257.

49.

Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity.

Dehouck Y, Folch B, Rooman M.

Protein Eng Des Sel. 2008 Apr;21(4):275-8. doi: 10.1093/protein/gzn001. Epub 2008 Feb 2.

PMID:
18245807
50.

Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials.

Folch B, Rooman M, Dehouck Y.

J Chem Inf Model. 2008 Jan;48(1):119-27. Epub 2007 Dec 28.

PMID:
18161956

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