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by Bultet, Lisandra Aguilar and Aguilar-Rodríguez, José and Ahrens, Christian H and Ahrné, Erik Lennart and Ai, Ni and Aimo, Lucila and Akalin, Altuna and Aleksiev, Tyanko and Alocci, Davide and Altenhoff, Adrian and Alves, Isabel and Ambrosini, Giovanna and Pedone, Pascale Anderle and Angelino, Paolo and Anisimova, Maria and Appel, Ron and Argoud-Puy, Ghislaine and Arnold, Konstantin and Arpat, Bulak and Artimo, Panu and Ascencao, Kelly and Auchincloss, Andrea and Axelsen, Kristian and Gerritsen, Vivienne Baillie and Bairoch, Amos and Bansal, Parit and Baratin, Delphine and Barbato, Alessandro and Barbié, Valérie and Barras, David and Barreiro, Maria and Barret, Sophie and Bastian, Frederic and Neto, Teresamanuela Batista and Baudis, Michael and Beaudoing, Emmanuel and Beckmann, Jacques S and Bekkar, Amel Kawter and Ben Hamida Cammoun, Leila and Benmohammed, Sara and Bernard, Madeleine and Bertelli, Claire and Bertoni, Martino and Bienert, Stefan and Bignucolo, Olivier and Bilbao, Aivett and Bilican, Adem and Blank, Diana and Blatter, Marie-Claude and Blum, Lorenz and Bocquet, Jocelyne and Boeckmann, Brigitte and Bolleman, Jerven Tjalling and Bordoli, Lorenza and Bosshard, Lars and Bouchet, Gerard and Bougueleret, Lydie and Boutet, Emmanuel and Bovigny, Christophe and Bratulic, Sinisa and Breuza, Lionel and Bridge, Alan James and Britan, Aurore and Brito, Francisco and Frazão, Josias Brito and Bruggmann, Rémy and Bucher, Philipp and Burdet, Frédéric and Burger, Lukas and Cabello, Elena Maria and Gomez, Ruben Martin Cabezon and Calderon, Sandra and Cannarozzi, Gina and Carl, Sarah and Casas, Cristina Casals and Catherinet, Sebastien and Périer, Rouayda Cavin and Charpilloz, Christophe and Chaskar, Prasad Datatray and Chen, Weihua and Pepe, Anush Chiappino and Chopard, Bastien and Chu, Hoi Yee and Civic, Natacha and Claassen, Manfred and Clottu, Sylvie and Colombo, Martino and Cosandier, Isabelle and Coudert, Elisabeth and Crespo, Isaac and Creus, Marc and Cuche, Béatrice and Cuendet, Michel A and Cusin, Isabelle and Daga, Neha and Daina, Antoine and Dauvillier, Jér Ôme and David, Fabrice and Davydov, Iakov and De Sa Ricca Manadelo Ferreira, Mariana and ... and SIB Swiss Inst Bioinformatics
Nucleic Acids Research, ISSN 0305-1048, 2016, Volume 44, Issue 1, pp. D27 - D37
The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the... 
PROTEIN MODELS | QUALITY | REGULATORY SITES | LANDSCAPE | KNOWLEDGEBASE | ARCHIVE | BIOCHEMISTRY & MOLECULAR BIOLOGY | REPOSITORY | EXPRESSION DATA | TOOLS | PREDICTION | Database Issue
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 2014, Volume 42, Issue 5, pp. 2848 - 2855
Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput... 
ORGANIZATION | PROTEIN | DROSOPHILA GENOME | CHROMATIN | GENE | TRANSCRIPTION FACTORIES | DNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | IN-VIVO | DYNAMICS | PRINCIPLES | Models, Molecular | Chromosomes - chemistry | Interphase - genetics | Computer Simulation | DNA, Superhelical - chemistry | Chromatin - chemistry | Computational Biology
Journal Article
L’Espace géographique, ISSN 0046-2497, 2018, Volume 47, Issue 4, pp. 323 - 345
Au cours des dernières décennies, les résidences fermées se sont multipliées dans la troisième métropole française, Marseille. La dynamique d'enclosure prend... 
Journal Article
Espace Geographique, ISSN 0046-2497, 2018, Volume 47, Issue 4, pp. 323 - 345
Journal Article
Scientific Reports, ISSN 2045-2322, 12/2017, Volume 7, Issue 1, pp. 6309 - 9
We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir... 
SITE-SPECIFIC RECOMBINATION | MECHANISM | CAPSIDS | DNA | MULTIDISCIPLINARY SCIENCES | KNOTS | Proteins
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 08/2013, Volume 41, Issue 14, pp. 6808 - 6815
Using numerical simulations of pairs of long polymeric chains confined in microscopic cylinders, we investigate consequences of double-strand DNA breaks... 
ORGANIZATION | UNLINKING | FILAMENTS | REPLICATION | DNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | RESOLUTION | SEGREGATION | RECA PROTEIN | ESCHERICHIA-COLI CHROMOSOME | E. COLI | Models, Molecular | DNA Breaks, Double-Stranded | Monte Carlo Method | Chromosomes, Bacterial - chemistry | Computational Biology
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 02/2018, Volume 46, Issue 4, pp. 1648 - 1660
Abstract Using molecular dynamics simulations, we show here that growing plectonemes resulting from transcription-induced supercoiling have the ability to... 
ORGANIZATION | COLI TOPOISOMERASE-IV | 3D GENOME | SINGLE-MOLECULE | GENOME ARCHITECTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | COHESIN | TOPOLOGICAL DOMAINS | ENHANCERS | DNA-MOLECULES | PRINCIPLES | Computational Biology
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 01/2019, Volume 47, Issue 2, pp. 521 - 532
Abstract Topologically associating domains (TADs) are megabase-sized building blocks of interphase chromosomes in higher eukaryotes. TADs are chromosomal... 
ORGANIZATION | CHROMATIN LOOPS | DNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | RNA-TRANSCRIPTION | COHESIN | TOPOLOGICAL DOMAINS | ATTACHMENT SITES | PRINCIPLES | MAMMALIAN GENOMES | TORSIONAL TENSION | Promoter Regions, Genetic | Chromatin | DNA, Superhelical | Enhancer Elements, Genetic | Transcription, Genetic | Chromosomes - chemistry | Models, Genetic | Survey and Summary
Journal Article
Bioinformatics, ISSN 1367-4803, 10/2018, Volume 34, Issue 19, pp. 3402 - 3404
Abstract Summary The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of... 
SLIPKNOTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 10/2009, Volume 37, Issue 19, pp. 6316 - 6322
Using freely jointed polymer model we compare equilibrium properties of crowded polymer chains whose segments are either permeable or not permeable for other... 
CHROMATIN FIBER | CELLS | REPLICATION | TOPOISOMERASES | NUCLEAR ARCHITECTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | IN-VIVO | COMPUTER-SIMULATION | RING POLYMERS | INTERPHASE NUCLEI | SUPERCOILED DNA | Models, Molecular | Biopolymers - chemistry | Chromosomes - chemistry | Computational Biology
Journal Article
Nucleic Acids Research, ISSN 1362-4962, 01/2010, Volume 38, Issue 21, pp. 7410 - 7421
Using numerical simulations, we investigate the underlying physical effects responsible for the overall organization of chromosomal territories in interphase... 
Journal Article
Methods in Molecular Biology, ISSN 1064-3745, 2017, Volume 1624, pp. 339 - 372
A detailed protocol of molecular dynamics simulations of supercoiled DNA molecules that can be in addition knotted or catenated is described. We also describe... 
Molecular dynamics | Supercoiled DNA | DNA gyrase | DNA topoisomerases | DNA knots and catenanes | DNA Gyrase - metabolism | Computational Biology - methods | DNA - chemistry | Algorithms | DNA, Superhelical - chemistry | Nucleic Acid Conformation | DNA, Catenated - chemistry | Molecular Dynamics Simulation
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 9/2008, Volume 36, Issue 15, pp. 4956 - 4963
Despite the fact that in living cells DNA molecules are long and highly crowded, they are rarely knotted. DNA knotting interferes with the normal functioning... 
TOPOLOGY | LOCAL JUXTAPOSITION GEOMETRY | MECHANISM | HOMEOSTATIC CONTROL | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | GYRASE | PLASMID PBR322 | TOPOISOMERASE-IV | KNOTS | II TOPOISOMERASES | Models, Molecular | Nucleic Acid Conformation | Monte Carlo Method | Computer Simulation | DNA, Circular - chemistry | DNA, Superhelical - chemistry | Computational Biology
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 09/2014, Volume 42, Issue 16, pp. 10425 - 10432
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 11/2010, Volume 38, Issue 21, pp. 7410 - 7421
Using numerical simulations, we investigate the underlying physical effects responsible for the overall organization of chromosomal territories in interphase... 
ORDER | SHAPE | PROTEIN | CHROMATIN | LAMIN-B RECEPTOR | BIOCHEMISTRY & MOLECULAR BIOLOGY | CHROMOSOME TERRITORIES | GENES | DYNAMICS | CELL-CYCLE | Chromosomes - ultrastructure | Transcription, Genetic | Models, Genetic | Chromosomes - genetics | Computational Biology
Journal Article