Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F: The mosaic genome of warm--blooded vertebrates. Science. 1985, 228: 953-958. 10.1126/science.4001930.
Article
CAS
PubMed
Google Scholar
Bernardi G: Structural and Evolutionary Genomics: Natural Selection in Genome Evolution. 2005, Elsevier Science Publishers Ltd
Google Scholar
Costantini M, Clay O, Auletta F, Bernardi G: Isochore Map of Human Chromosomes. Genome Research. 2006, 16: 536-541. 10.1101/gr.4910606.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bernardi G: The neoselectionist Theory of Genome Evolution. PNAS. 2007, 104 (20): 8385-8390. 10.1073/pnas.0701652104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Costantini M, Cammarano R, Bernardi G: The evolution of isochore patterns in vertebrate genomes. BMC Genomics. 2008, 10: 146-
Article
Google Scholar
Wu C, Li W: Evidence for higher rates of nucleotide substitution in rodents than in man. PNAS. 1985, 82: 1741-1745. 10.1073/pnas.82.6.1741.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gu X, Li W: Higher rates of amino acids substitution in rodents than in human. Mol Phylogenet Evol. 1992, 1: 211-214. 10.1016/1055-7903(92)90017-B.
Article
CAS
PubMed
Google Scholar
Holliday R: Understanding Ageing. 1995, Cambridge University Press, Cambridge, U.K
Book
Google Scholar
Eyre-Walker A, Hurst LD: The evolution of isochores. Nature Reviews Genetics. 2001, 2 (7): 549-555. 10.1038/35080577.
Article
CAS
PubMed
Google Scholar
Galtier N, Piganeau G, Mouchiroud D, Duret L: GC-Content Evolution in Mammalian Genomes: The Biased Gene Conversion Hypothesis. Genetics. 2001, 159 (2): 907-911.
CAS
PubMed
PubMed Central
Google Scholar
Duret L, Galtier N: Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes. Annual Review of Genomics and Human Genetics. 2009, 10: 285-311. 10.1146/annurev-genom-082908-150001.
Article
CAS
PubMed
Google Scholar
Chojnowski J, Franklin J, Katsu Y, et al: Patterns of Vertebrate Isochore Evolution Revealed by Comparison of Expressed Mammalian, Avian, and Crocodilian Genes. Journal of Molecular Evolution. 2007, 65 (3): 259-266. 10.1007/s00239-007-9003-2.
Article
CAS
PubMed
Google Scholar
Duret L: Evolution of synonymous codon usage in metazoans. Current Opinion in Genetics & Development. 2002, 12 (6): 640-649. 10.1016/S0959-437X(02)00353-2.
Article
CAS
Google Scholar
Konu O, Li M: Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. Journal of Molecular Evolution. 2002, 54: 35-41. 10.1007/s00239-001-0015-z.
Article
CAS
PubMed
Google Scholar
Versteeg R, van Schaik B, van Batenburg M, et al: The human transcriptome map reveals extremes in gene dentistry, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Research. 2003, 13 (9): 1998-2004. 10.1101/gr.1649303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vinogradov A: Isochores and tissue specificity. Nucleic Acids Research. 2003, 31 (17): 5212-5220. 10.1093/nar/gkg699.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arhondakis S, Auletta F, Torelli G, D'Onofrio G: Base composition and expression level of human genes. Gene. 2004, 325: 165-169.
Article
CAS
PubMed
Google Scholar
Comeron J: Selective and Mutational Patterns Associated With Gene Expression in Humans: Influences on Synonymous Composition and Intron Presence. Genetics. 2004, 167 (3): 1293-1304. 10.1534/genetics.104.026351.
Article
CAS
PubMed
PubMed Central
Google Scholar
Semon M, Mouchiroud D, Duret L: Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Human Molecular Genetics. 2005, 14 (3): 421-427.
Article
CAS
PubMed
Google Scholar
Vinogradov A: Dualism of gene GC content and CpG pattern in regard to expression in the human genome: Magnitude versus breadth. Trends in Genetics. 2005, 21 (12): 639-643. 10.1016/j.tig.2005.09.002.
Article
CAS
PubMed
Google Scholar
Arhondakis S, Clay O, Bernardi G: Compositional properties of human cDNA libraries: Practical implications. FEBS Letters. 2006, 580 (24): 5772-5778. 10.1016/j.febslet.2006.09.034.
Article
CAS
PubMed
Google Scholar
Arhondakis S, Clay O, Bernardi G: GC level and expression of human coding sequences. Biochemical and Biophysical Research Communications. 2008, 367 (3): 542-545. 10.1016/j.bbrc.2007.12.155.
Article
CAS
PubMed
Google Scholar
Mahmud A, Amore G, Bernardi G: Compositional Genome Contexts Affect Gene Expression Control in Sea Urchin Embryo. PLoS ONE. 2008, 3 (12): e4025-10.1371/journal.pone.0004025.
Article
PubMed
PubMed Central
Google Scholar
Caron H, van Schaik B, van der Mee M, et al: The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains. Science. 2001, 291 (5507): 1289-1292. 10.1126/science.1056794.
Article
CAS
PubMed
Google Scholar
Lercher M, Urrutia A, Pavlicek A, Hurst L: A unification of mosaic structures in the human genome. Human Molecular Genetics. 2003, 12 (19): 2411-2415. 10.1093/hmg/ddg251.
Article
CAS
PubMed
Google Scholar
Mouchiroud D, D'Onofrio G, Aissani B, et al: The distribution of genes in the human genome. Gene. 1991, 100: 181-187.
Article
CAS
PubMed
Google Scholar
Zoubak S, Clay O, Bernardi G: The gene distribution of the human genome. Gene. 1996, 174: 95-102. 10.1016/0378-1119(96)00393-9.
Article
CAS
PubMed
Google Scholar
Mijalski T, Harder A, Halder T, et al: Identification of coexpressed gene clusters in a comparative analysis. PNAS. 2005, 102 (24): 8621-8626. 10.1073/pnas.0407672102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Singer G, Lloyd A, Huminiecki L, Wolfe K: Clusters of Co-expressed Genes in Mammalian Genomes Are Conserved by Natural Selection. Molecular Biology and Evolution. 2005, 22 (3): 767-775.
Article
CAS
PubMed
Google Scholar
Wang Z, Gerstein M, Snyder M: RNA-seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics. 2009, 10: 57-63. 10.1038/nrg2484.
Article
CAS
PubMed
PubMed Central
Google Scholar
Metzker M: Sequencing technologies -- the next generation. Nature Reviews Genetics. 2010, 11: 31-46. 10.1038/nrg2626.
Article
CAS
PubMed
Google Scholar
Ozsolak F, Milos P: RNA sequencing: advances, challenges and opportunities. Nature Reviews Genetics. 2011, 12 (2): 87-98. 10.1038/nrg2934.
Article
CAS
PubMed
Google Scholar
Dalca A, Brudno M: Genome variation discovery with high-throughput sequencing data. Briefings in Bioinformatics. 2010, 11: bbp058-14.
Article
Google Scholar
Ng S, Buckingham K, Lee C, et al: Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics. 2010, 42: 30-35. 10.1038/ng.499.
Article
CAS
PubMed
Google Scholar
Wu T, Nacu S: Fast and SNP--tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010, 26 (7): 873-881. 10.1093/bioinformatics/btq057.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiang H, Zhu J, Chen Q, et al: Single--base resolution methylome of the silkworm reveals a sparse epigenomic map. Nature Biotechnology. 2010, 28 (5): 516-520. 10.1038/nbt.1626.
Article
CAS
PubMed
Google Scholar
Mortazavi A, Williams B, McCue K, et al: Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Kikuta H, Laplante M, Navratilova P, et al: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Research. 2007, 17 (5): 545-555. 10.1101/gr.6086307.
Article
CAS
PubMed
PubMed Central
Google Scholar
Navratilova P, Becker T: Genomic regulatory blocks in vertebrates and implications in human disease. Briefings in Functional Genomics & Proteomics. 2009, 8 (4): 333-342. 10.1093/bfgp/elp019.
Article
Google Scholar
Hiratani I, Leskovar A, Gilbert D: Differentiation--induced replication-timing changes are restricted to AT--rich/long interspersed nuclear element (LINE)--rich isochores. Proceedings of the National Academy of Sciences of the United States of America. 2004, 101 (48): 16861-16866. 10.1073/pnas.0406687101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ren L, Gao G, Zhao D: Developmental stage related patterns of codon usage and genomic GC content: Searching for evolutionary fingerprints with models of stem cell differentiation. Genome Biology. 2007, 8 (3):
Clay O, Bernardi G: GC3 of Genes Can Be Used as a Proxy for Isochore Base Composition: A Reply to Elhaik et al. Molecular Biology and Evolution. 2011, 28: 21-23. 10.1093/molbev/msq222.
Article
CAS
PubMed
Google Scholar
UCSC Genome Browser: 2011, [http://genome.ucsc.edu]
Frousios K, Iliopoulos CS, Mouchard L, et al: REAL: an efficient REad ALigner for next generation sequencing reads. Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology. 2010, New York, NY, USA: ACM, 154-159. BCB '10,
Chapter
Google Scholar
REad ALigner (REAL): 2011, [http://www.inf.kcl.ac.uk/pg/real/]
Navarro G, Raffinot M: Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences. 2002, Cambridge University Press
Book
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg S: Ultrafast and memory--efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009, 10 (3): R25+-
Article
PubMed
PubMed Central
Google Scholar
Li R, Li Y, Kristiansen K, Wang J: SOAP: short oligonucleotide alignment program. Bioinformatics. 2008, 24 (5): btn025-714.
Google Scholar
National Center for Biotechnology Information (NCBI): 2011, [ftp://ftp.ncbi.nlm.nih.gov]