Centre intégratif de génomique

Equipe principale | CIG Services communs | Groupe Benton | Groupe Fajas | Groupe Fankhauser | Groupe Franken | Groupe Gambetta | Groupe Gatfield | Groupe Larsch | Groupe Michalik | Groupe Reymond | Groupe Roignant | Groupe van Leeuwen | Groupe Vastenhouw | Groupe Vjestica | Plateforme de biostatistique | Plateforme Genomics Technologies Facility (GTF) | Plateforme Protein Analysis Facility (PAF)
Publications | Mémoires et thèses

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69 publications

2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2006 | 2005 | 2004 | 2003 | 2002 |
2019
Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.
Schvartzman J.B., Hernández P., Krimer D.B., Dorier J., Stasiak A., 2019/08/22. Nucleic acids research, 47 (14) pp. 7182-7198. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_55CCC896580F]
Are TADs supercoiled?
Racko D., Benedetti F., Dorier J., Stasiak A., 2019/01/25. Nucleic acids research, 47 (2) pp. 521-532. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_12BCCBEC8B1A]
KnotProt 2.0: a database of proteins with knots and other entangled structures.
Dabrowski-Tumanski P., Rubach P., Goundaroulis D., Dorier J., Sulkowski P., Millett K.C., Rawdon E.J., Stasiak A., Sulkowska J.I., 2019/01/08. Nucleic acids research, 47 (D1) pp. D367-D375. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_CACEFF8F3AA5]
2018
Two convergent pathways of DNA knotting in replicating DNA molecules as revealed by θ-curve analysis.
O'Donnol D., Stasiak A., Buck D., 2018/09/28. Nucleic acids research, 46 (17) pp. 9181-9188. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A21115AE0E58]
Identification and nanomechanical characterization of the fundamental single-strand protofilaments of amyloid α-synuclein fibrils.
Ruggeri F.S., Benedetti F., Knowles TPJ, Lashuel H.A., Sekatskii S., Dietler G., 2018. Proceedings of the National Academy of Sciences of the United States of America, 115 (28) pp. 7230-7235. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A49EC9CE5710]
 
Periodic Motion of Sedimenting Flexible Knots
Gruziel M., Thyagarajan K., Dietler G., Stasiak A., Ekiel-Jeżewska M.L., Szymczak P., 2018. Physical Review Letters, 121 (12) p. 127801. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_86C1997A4259]
2017
Studies of global and local entanglements of individual protein chains using the concept of knotoids.
Goundaroulis D., Dorier J., Benedetti F., Stasiak A., 2017/07/24. Scientific reports, 7 (1) p. 6309. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D27975D9E8ED]
 
Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization.
Japaridze A., Muskhelishvili G., Benedetti F., Gavriilidou A.F., Zenobi R., De Los Rios P., Longo G., Dietler G., 2017. Nano Letters, 17 (3) pp. 1938-1948. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6CDAD1F0847A]
 
Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.
Racko D., Benedetti F., Dorier J., Burnier Y., Stasiak A., 2017. Methods in Molecular Biology, 1624 pp. 339-372. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E48F1B04C7E2]
Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
Goundaroulis D., Gügümcü N., Lambropoulou S., Dorier J., Stasiak A., Kauffman L., 2017. Polymers, 9 (9) p. 444. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_72C4DA5C17D4]
2016
 
Model of DNA topology simplification has come full (supercoiled) circle after two decades of research: Comment on "Disentangling DNA molecules" by Alexander Vologodskii.
Stasiak A., 2016/06/17. Physics of life reviews, 18 pp. 154-157.
[DOI][Pmid][serval:BIB_ABC1B1429C43]
How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation.
Rawdon E.J., Dorier J., Racko D., Millett K.C., Stasiak A., 2016/06/02. Nucleic acids research, 44 (10) pp. 4528-4538. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_0E0CBB4E996B]
In Search of Functional Advantages of Knots in Proteins.
Dabrowski-Tumanski P., Stasiak A., Sulkowska J.I., 2016. PLoS One, 11 (11) pp. e0165986. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B15CF13C8D83]
2015
Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.
Benedetti F., Japaridze A., Dorier J., Racko D., Kwapich R., Burnier Y., Dietler G., Stasiak A., 2015. Nucleic Acids Research, 43 (4) pp. 2390-2399.
[URN][DOI][WoS][Pmid][serval:BIB_202F278D6524]
Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules.
Cebrián J., Kadomatsu-Hermosa M.J., Castán A., Martínez V., Parra C., Fernández-Nestosa M.J., Schaerer C., Martínez-Robles M.L., Hernández P., Krimer D.B. et al., 2015. Nucleic Acids Research, 43 (4) pp. e24.
[URN][DOI][WoS][Pmid][serval:BIB_D98515AFF191]
Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation.
Racko D., Benedetti F., Dorier J., Burnier Y., Stasiak A., 2015. Nucleic Acids Research, 43 (15) pp. 7229-7236.
[URN][DOI][WoS][Pmid][serval:BIB_A7486614D0B2]
KnotProt: a database of proteins with knots and slipknots.
Jamroz M., Niemyska W., Rawdon E.J., Stasiak A., Millett K.C., Sulkowski P., Sulkowska J.I., 2015. Nucleic Acids Research, 43 (Database issue) pp. D306-D314.
[URN][DOI][WoS][Pmid][serval:BIB_5E3AE35DDBFA]
 
Presence control of DNA repair controllers.
Stasiak A., 2015. Cell Cycle, 14 (14) p. 2199. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_583B1E0E73F5]
Subknots in ideal knots, random knots, and knotted proteins.
Rawdon E.J., Millett K.C., Stasiak A., 2015. Scientific Reports, 5 p. 8928.
[URN][DOI][WoS][Pmid][serval:BIB_4E22520D9806]
2014
Effects of supercoiling on enhancer-promoter contacts.
Benedetti F., Dorier J., Stasiak A., 2014. Nucleic Acids Research, 42 (16) pp. 10425-10432.
[URN][DOI][WoS][Pmid][serval:BIB_60CC627662F8]
 
Force-induced globule-coil transition in laminin binding protein and its role for viral-cell membrane fusion.
Zaitsev B.N., Benedetti F., Mikhaylov A.G., Korneev D.V., Sekatskii S.K., Karakouz T., Belavin P.A., Netesova N.A., Protopopova E.V., Konovalova S.N. et al., 2014. Journal of Molecular Recognition, 27 (12) pp. 727-738. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0D5BB837E25A]
Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.
Benedetti F., Dorier J., Burnier Y., Stasiak A., 2014. Nucleic Acids Research, 42 (5) pp. 2848-2855.
[URN][DOI][WoS][Pmid][serval:BIB_A6B3945F65A0]
2013
 
Identifying knots in proteins.
Millett K.C., Rawdon E.J., Stasiak A., Sułkowska J.I., 2013. Biochemical Society Transactions, 41 (2) pp. 533-537.
[DOI][WoS][Pmid][serval:BIB_9E0FB0902957]
 
Knot localization in proteins.
Rawdon E.J., Millett K.C., Sulkowska J.I., Stasiak A., 2013. Biochemical Society Transactions, 41 (2) pp. 538-541.
[DOI][WoS][Pmid][serval:BIB_E6F5CE3DF11E]
Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes.
Dorier J., Stasiak A., 2013. Nucleic Acids Research, 41 (14) pp. 6808-6815.
[URN][DOI][WoS][Pmid][serval:BIB_F265DFDD4281]
Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots.
Weber C., Carlen M., Dietler G., Rawdon E.J., Stasiak A., 2013. Scientific Reports, 3 p. 1091.
[URN][DOI][WoS][Pmid][serval:BIB_EF01E9CB67B3]
 
Topological aspects of DNA function and protein folding.
Stasiak A., Bates A.D., Buck D.E., Harris S.A., Sumners de W, 2013. Biochemical Society Transactions, 41 (2) pp. 491-493.
[DOI][WoS][Pmid][serval:BIB_F6365372C12F]
2012
 
Conservation of complex knotting and slipknotting patterns in proteins.
Sulkowska J.I., Rawdon E.J., Millett K.C., Onuchic J.N., Stasiak A., 2012. Proceedings of the National Academy of Sciences of the United States of America, 109 (26) pp. E1715-E1723.
[DOI][WoS][Pmid][serval:BIB_20EC3B5942F1]
Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots.
Reith D., Cifra P., Stasiak A., Virnau P., 2012. Nucleic Acids Research, 40 (11) pp. 5129-5137.
[URN][DOI][WoS][Pmid][serval:BIB_4D5FAD702911]
Probing Rad51-DNA interactions by changing DNA twist.
Atwell S., Disseau L., Stasiak A.Z., Stasiak A., Renodon-Cornière A., Takahashi M., Viovy J.L., Cappello G., 2012. Nucleic Acids Research, 40 (22) pp. 11769-11776.
[URN][DOI][WoS][Pmid][serval:BIB_F52D1167F718]
 
Saccharomyces cerevisiae Dmc1 and Rad51 Proteins Preferentially Function with Tid1 and Rad54 Proteins, Respectively, to Promote DNA Strand Invasion during Genetic Recombination.
Nimonkar A.V., Dombrowski C.C., Siino J.S., Stasiak A.Z., Stasiak A., Kowalczykowski S.C., 2012. Journal of Biological Chemistry, 287 (34) pp. 28727-28737.
[DOI][WoS][Pmid][serval:BIB_D442EA44C09F]
2011
Cooperative kinking at distant sites in mechanically stressed DNA.
Lionberger T.A., Demurtas D., Witz G., Dorier J., Lillian T., Meyhöfer E., Stasiak A., 2011. Nucleic Acids Research, 39 (22) pp. 9820-9832.
[URN][DOI][WoS][Pmid][serval:BIB_AAD051219F59]
 
Cumulative Shapes of Knotted Polymers
Rawdon Eric J., Millett Kenneth C., Tran Vy T., Stasiak Andrzej, 2011. Progress of Theoretical Physics Supplement, 191 pp. 165-171. Peer-reviewed.
[WoS][serval:BIB_E3E207286AFD]
 
DNA knots and DNA supercoiling.
Witz G., Dietler G., Stasiak A., 2011. Cell Cycle, 10 (9) pp. 1339 - 1340.
[DOI][WoS][Pmid][serval:BIB_D0B3B4E4B323]
 
Nullification of small knots
Ernst Claus, Montemayor Anthony, Stasiak Andrzej, 2011. Progress of Theoretical Physics Supplement, 191 pp. 66-77. Peer-reviewed.
[WoS][serval:BIB_DB7A53E81CD2]
 
Role of topological exclusion in formation and organization of chromosomal territories
Dorier Julien, Stasiak Andrzej, 2011. Progress of Theoretical Physics Supplement, 191 pp. 46-54. Peer-reviewed.
[WoS][serval:BIB_2E510889DD8C]
 
Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases.
Witz G., Dietler G., Stasiak A., 2011. Proceedings of the National Academy of Sciences of the United States of America, 108 (9) pp. 3608-3611. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0770B1E1A91E]
2010
A histone-fold complex and FANCM form a conserved DNA-remodeling complex to maintain genome stability.
Yan Z., Delannoy M., Ling C., Daee D., Osman F., Muniandy P.A., Shen X., Oostra A.B., Du H., Steltenpool J. et al., 2010. Molecular Cell, 37 (6) pp. 865-878. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_48630B959492]
Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination.
Buisson R., Dion-Côté A.M., Coulombe Y., Launay H., Cai H., Stasiak A.Z., Stasiak A., Xia B., Masson J.Y., 2010. Nature Structural and Molecular Biology, 17 (10) pp. 1247-1254. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F9FEB5C7E1CF]
Design of potent inhibitors of human RAD51 recombinase based on BRC motifs of BRCA2 protein: modeling and experimental validation of a chimera peptide.
Nomme J., Renodon-Cornière A., Asanomi Y., Sakaguchi K., Stasiak A.Z., Stasiak A., Norden B., Tran V., Takahashi M., 2010. Journal of Medicinal Chemistry, 53 (15) pp. 5782-5791.
[URN][DOI][WoS][Pmid][serval:BIB_501909E7F3E7]
DNA supercoiling and its role in DNA decatenation and unknotting.
Witz G., Stasiak A., 2010. Nucleic Acids Research, 38 (7) pp. 2119-2133. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0F19F8CEC35D]
 
ParA2, a Vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on DNA.
Hui M.P., Galkin V.E., Yu X., Stasiak A.Z., Stasiak A., Waldor M.K., Egelman E.H., 2010. Proceedings of the National Academy of Sciences of the United States of America, 107 (10) pp. 4590-4595.
[DOI][WoS][Pmid][serval:BIB_6FAEA31F23C9]
 
Symmetry-breaking in cumulative measures of shapes of polymer models.
Millett K.C., Rawdon E.J., Tran T.V., Stasiak A., 2010. Journal of Chemical Physics, 133 (15) p. 154113.
[DOI][WoS][Pmid][serval:BIB_357CEB0096EE]
The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture.
Dorier J., Stasiak A., 2010. Nucleic Acids Research, 38 (21) pp. 7410-7421. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5D2209110663]
2009
A partial ordering of knots and links through diagrammatic unknotting
Diao Y., Ernst C., Stasiak A., 2009. Journal of Knot Theory and its Ramifications, 18 (4) pp. 505-522. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_E9F6D0EED72F]
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles.
Demurtas D., Amzallag A., Rawdon E.J., Maddocks J.H., Dubochet J., Stasiak A., 2009. Nucleic Acids Research, 37 (9) pp. 2882-2893. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BC7848C64B2B]
 
DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting.
Marenduzzo D., Orlandini E., Stasiak A., Sumners de W, Tubiana L., Micheletti C., 2009. Proceedings of the National Academy of Sciences of the United States of America, 106 (52) pp. 22269-22274. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_89D4E77514A2]
 
Effect of knotting on polymer shapes and their enveloping ellipsoids.
Millett K.C., Plunkett P., Piatek M., Rawdon E.J., Stasiak A., 2009. Journal of Chemical Physics, 130 (16) p. 165104. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EF24549906CD]
 
Inhibitory effect of DNA supercoiling on DNA knotting
Dorier J., Burnier Y., Stasiak A., 2009. Bussei Kenkyu, 92 (1) pp. 84-88. Peer-reviewed.
[serval:BIB_B3C1D95595C0]
Interplay of DNA supercoiling and catenation during the segregation of sister duplexes.
Martínez-Robles M.L., Witz G., Hernández P., Schvartzman J.B., Stasiak A., Krimer D.B., 2009. Nucleic Acids Research, 37 (15) pp. 5126-5137. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C26EB08DD54C]
 
MRE11-RAD50-NBS1 is a critical regulator of FANCD2 stability and function during DNA double-strand break repair.
Roques C., Coulombe Y., Delannoy M., Vignard J., Grossi S., Brodeur I., Rodrigue A., Gautier J., Stasiak A.Z., Stasiak A. et al., 2009. The EMBO journal, 28 (16) pp. 2400-2413. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FC743A0ACC8B]
Shapes of knotted cyclic polymers
Millett K.C., Plunkett P., Piatek M., Rawdon E.J., Stasiak A., 2009. Bussei Kenkyu, 92 (1) pp. 32-37. Peer-reviewed.
[URN][serval:BIB_2F88CF511535]
Topological origins of chromosomal territories.
Dorier J., Stasiak A., 2009. Nucleic Acids Research, 37 (19) pp. 6316-6322. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E01F9D39E9FE]
2008
DNA supercoiling inhibits DNA knotting.
Burnier Y., Dorier J., Stasiak A., 2008/09. Nucleic Acids Research, 36 (15) pp. 4956-4963. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_681FC248BD52]
Functional and structural basis for a bacteriophage homolog of human RAD52.
Ploquin M., Bransi A., Paquet E.R., Stasiak A.Z., Stasiak A., Yu X., Cieslinska A.M., Egelman E.H., Moineau S., Masson J.Y., 2008/08. Current Biology, 18 (15) pp. 1142-1146. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2CCD57AED525]
3D visualization software to analyze topological outcomes of topoisomerase reactions.
Darcy I.K., Scharein R.G., Stasiak A., 2008/06. Nucleic Acids Research, 36 (11) pp. 3515-3521. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_179198ADDF98]
 
Scaling behavior and equilibrium lengths of knotted polymers
Rawdon E., Dobay A., Kern J.C., Millett K.C., Piatek M., Plunkett P., Stasiak A., 2008/06. Macromolecules, 41 (12) pp. 4444-4451. Peer-reviewed.
[DOI][WoS][serval:BIB_25B197F30C73]
 
A glycine-arginine domain in control of the human MRE11 DNA repair protein.
Déry U., Coulombe Y., Rodrigue A., Stasiak A., Richard S., Masson J.Y., 2008/05. Molecular and Cellular Biology, 28 (9) pp. 3058-3069. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_02AB3CC30E0D]
 
Effect of Knotting on the Shape of Polymers
Rawdon E. J., Kern J. C., Piatek M., Plunkett P., Stasiak A., Millett K. C., 2008. Macromolecules, 41 (21) pp. 8281-8287. Peer-reviewed.
[DOI][WoS][serval:BIB_1A3C409C3553]
 
RecA-DNA complexes
Stasiak A.Z., Stasiak A., 2008. CHEMTRACTS-Biochemistry and Molecular Biology, 21 pp. 399-405.
[serval:BIB_A6C711050795]
 
The Fanconi anemia protein FANCM can promote branch migration of Holliday junctions and replication forks.
Gari K., Décaillet C., Stasiak A.Z., Stasiak A., Constantinou A., 2008/01. Molecular Cell, 29 (1) pp. 141-148. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5826A5E32C17]
2006
3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy.
Amzallag A., Vaillant C., Jacob M., Unser M., Bednar J., Kahn J.D., Dubochet J., Stasiak A., Maddocks J.H., 2006. Nucleic Acids Research, 34 (18) pp. e125. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A662BC1558A2]
 
Thermodynamics, kinetics and mechanics of biopolymers
Bhattachrjeee S.M., Micheletti C., Stasiak A., 2006. Journal of Physics: Condensed Matter, 18 pp. N/A. Peer-reviewed.
[DOI][WoS][serval:BIB_86D48CF78497]
2005
 
The average inter-crossing number of equilateral random walks and polygons
Diao Y., Dobay A., Stasiak A., 2005. Journal of Physics A: Mathematical and General, 38 (35) pp. 7601-7616.
[DOI][WoS][serval:BIB_31F454720298]
2004
 
DNA circles
Stasiak A., 2004., 1er Séminaire Transalpin de Physique Les Diablerets - Suisse - 2003 pp. 13-51 dans De Los Rios P., Dietler G., Fourcade B., Peroni C. (eds.) Living matter: a new challenge to physicists ?, Frontier Group.
[serval:BIB_DB99D3F18B84]
2003
 
Life cycle of a biologist.
Stasiak A., 2003. EMBO reports, 4 (5) p. 457.
[DOI][serval:BIB_18CDA5132921]
 
The first lady of DNA.
Stasiak A., 2003. EMBO reports, 4 (1) p. 14.
[DOI][serval:BIB_1F0E271E656C]
 
Topoisomerases
Stasiak A., 2003. dans Cooper D.N. (eds.) Encyclopedia of the human genome., Nature Publishing Group.
[serval:BIB_E688E9F19B12]
2002
 
Quantization of energy and writhe in self-repelling knots
Hoidn P., Kusner R.B., Stasiak A., 2002. New Journal of Physics, 4 pp. 20.1-20.11. Peer-reviewed.
[DOI][WoS][serval:BIB_447497EF5428]
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