corr in DNA (2010)

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2010

Alain Arneodo, Cedric Vaillant, Benjamin Audit, Françoise Argoul, Yves d'Aubenton-Carafa, Claude Thermes (2010), "Multi-scale coding of genomic information: From DNA sequence to genome structure and function", Physics Reports, 498(2-3):45-188.
[ abstract]
Labrini Athanasopoulou, Stavros Athanasopoulos, Kostas Karamanos, and Yannis Almirantis (2010), "Scaling properties and fractality in the distribution of coding segments in eukaryotic genomes revealed through a block entropy approach", Physical Review E , 82:051917.
[ abstract]
protein

Nirmalya Bandyopadhyay, Tamer Kahveci (2010), "GBA Manager: an online tool for querying low-complexity regions in proteins", Journal of Computational Biology, 17(1):73-77.
[ abstract]
repeats

CR Beck, P Collier, C Macfarlane, M Malig, JM Kidd, EE Eichler, RM Badge, JV Moran (2010), "LINE-1 retrotransposition activity in human genomes", Cell, 141(7):1159-1170.
D Bielinska (2010), "Four-component spectral representation of DNA sequences", Journal of Mathematical Chemistry, 47:41-51.
A Caballero, H Quesada (2010), "Homoplasy and distribution of AFLP fragments: an analysis in silico of the genome of different species", Molecular Biology and Evolution, 27(5):1139-1151.
Carlo Cattani (2010), "Fractals and hidden symmetries in DNA", Mathematical Problems in Engineering: Theory, Methods and Applications, 2010:507056.
[ abstract]
CL Chen, A Rappailles, L Duquenne, M Huvet, G Guilbaud, L Farinelli, B Audit, Y d'Aubenton-Carafa, A Arneodo, O Hyrien, C Thermes (2010), "Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes", Genome Research, 20(4):447-457.
Hong-Da Chen, Wen-Lang Fan, Sing-Guan Kong, Hoong-Chien Lee (2010), "Universal global imprints of genome growth and evolution -- equivalent length and cumulative mutation density", PLoS ONE, 5(4):e9844.
[ abstract]
Robertas Damasevicius (2010), "Complexity estimation of genetic sequences using information-theoretic and Frequency analysis methods", Informatica, 21(1):13-30.
[abstract]
E Elhaik, D Graur, K Josic (2010), "Comparative testing of DNA segmentation algorithms using benchmark simulations", Molecular Biology and Evolution, 27(5):1015-1024.
[ abstract]
isochore

Eran Elhaik, Dan Graur, Kresimir Josic, Giddy Landan (2010), "Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm", Nucleic Acids Research, 38(15):e158.
[ abstract]
R Gemayel, MD Vinces, M Legendre, KJ Verstrepen (2010), "Variable tandem repeats accelerate evolution of coding and regulatory sequences", Annual Review of Genetics, 44:445-477.
[abstract]
sequence

Richard E. Green, Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas, Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer, Hernán A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof, Barbara Höber, Barbara Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic, Zeljko Kucan, Ivan Gusic, Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich, Svante Pääbo (2010), "A draft sequence of the Neandertal genome", Science, 328(5979):710-722.
[ abstract]
M Hackenberg, Barturen G, Carpena P, Luque-Escamilla PL, Previti C, Oliver JL. (2010), "Prediction of CpG-island function: CpG clustering vs. sliding-window methods", BMC Genomics, 11:327.
Jorn Hameister, Werner E Helm, Marc-Thorsten Hutt, Manuel Dehnert (2010), "Systematics of short-range correlations in eukaryotic genomes", in Advances in Data Analysis, Data Handling and Business Intelligence. Studies in Classification, Data Analysis, and Knowledge Organization, pp.627-637 (Springer).
[ abstract]
Franziska Hoffgaard, Philipp Weil, Kay Hamacher (2010), "BioPhysConnectoR: connecting sequence information and biophysical models", BMC Bioinformatics, 11:199.
[ abstract]
repeats

F Hormozdiari, I Hajirasouliha, P Dao, F Hach, D Yorukoglu, C Alkan, EE Eichler, SC Sahinalp (2010), "Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery", Bioinformatics, 26(12):i350-i357.
MV Jose, T Govezensky, JR Bobadilla (2010), "Fractional Brownian motion in DNA sequences of bacterial chromosomes: a renormalization group approach", Revista Mexicana de Fisica E, 56(1):69-74.
Kevin N. Laland, John Odling-Smee, Sean Myles (2010), "How culture shaped the human genome: bringing genetics and the human sciences together", Nature Review Genetics, 11:137-148.
[ abstract]
repeats

Albert R. La Spada, J. Paul Taylor (2010), "Repeat expansion disease: progress and puzzles in disease pathogenesis", Nature Reviews Genetics, 11(4):247-258.
[ abstract]
isochore

Denise B Lynch, Mary E Logue, Geraldine Butler, Kenneth H Wolfe (2010), "Chromosomal G+C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres", Genome Biology and Evolution, 2:572-583.
[ abstract]
repeats

Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki (2010), "Storage and retrieval of highly repetitive sequence collections", Journal of Computational Biology, 17(3): 281-308.
[ abstract]
isochore

Scott Mann, Yi-Ping Phoebe Chen (2010), "Bacterial genomnic G+C composition-eliciting environmental adaptation", Genomics, 95:7-15.
[ abstract]
isochore

Scott Mann, Jinyan Li, Yi-Ping Phoebe Chen (2010), "Insights into bacterial genome composition through variable target GC content profiling", Journal of Computational Biology, 17(1): 79-96.
[ abstract]
J Moukhtar, C Faivre-Moskalenko, P Milani, B Audit, C Vaillant, E Fontaine, F Mongelard, G Lavorel, P St-Jean, P Bouvet, F Argoul, A Arneodo (2010), "Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments" Journal of Physical Chemistry B, 114(15):5125-5143.
[ abstract]
isochore

Satoshi OOta, Kazuhiro Kawamura, Yosuke Kawai, Naruya Saitou (2010), "A new framework for studying the isochore evolution: estimation of the equilibrium GC content based on the temporal mutation rate model", Genome Biology and Evolution, 2:558-571.
[ abstract]
protein

Susanne Pape, Franziska Hoffgaard, Kay Hamacher (2010), "Distance-dependent classification of amino acids by information theory", Proteins, 78(10):2322-2328.
[ abstract]
A Provata, P Katsaloulis (2010), "Hierarchical multifractal representation of symbolic sequences and application to human chromosomes", Physical Review E , 81:026102.
[ abstract]
Sheila M Reynolds, Jeff A Bilmes, William Stafford Noble (2010), "Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens", PLoS Computational Biology, 6(7): e1000834.
[ abstract]
isochore

Jonathan Romiguier, Vincent Ranwez, Emmanuel JP Douzery, and Nicolas Galtier (2010), "Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes", Genome Research, 20(8):1001-1009.
[abstract]
T Ryba, I Hiratani, J Lu, M Itoh, M Kulik, J Zhang, S Dalton, DM Gilbert (2010), "Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types", Genome Research, 20:761-770.
[ abstract]
RV Sole (2010), "Genome size, self-organization and DNA's dark matter", Complexity, 16(1):20-23.
[ abstract]
repeats

JC Tan, Tan A, Checkley L, Honsa CM, Ferdig MT (2010), "Variable numbers of tandem repeats in Plasmodium falciparum genes", Journal of Molecular Evolution, 71(4):268-278.
[ abstract]
A Varriale, G Bernardi (2010), "Distribution of DNA methylation, CpGs, and CpG islands in human isochores", Genomics, 95(1):25-28.
a/symmetry

Shu-Jun Wei, Min Shi, Xue-Xin Chen, Michael J. Sharkey, Cornelis van Achterberg, Gong-Yin Ye, Jun-Hua He (2010), "New views on strand asymmetry in insect mitochondrial genomes" PLoS ONE, 5:e12708.
[ abstract]
Hao Wu, Brian Caffo, Harris A Jaffee, Rafael A Irizarry, Andrew P Feinberg (2010), "Redefining CpG islands using hidden Markov models", Biostatistics, 11(3):499-514.
[ abstract]
Wenqian Zhang, Wenwu Wu, Wenchao Lin, Pengfang Zhou, Li Dai, Yang Zhang, Jingfei Huang, Deli Zhang (2010), "Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses", PLoS ONE, 5(10): e13303.
[ abstract]
W Q Zhou, H Yan (2010), "Relationship between periodic dinucleotides and the nucleosome structure revealed by alpha shape modeling," Chemical Physics Letters, 489(4-6):225-228.