Literature DB >> 16924100

Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments.

William Salerno1, Paul Havlak, Jonathan Miller.   

Abstract

A power-law distribution of the length of perfectly conserved sequence from mouse/human whole-genome intersection and alignment is exhibited. Spatial correlations of these elements within the mouse genome are studied. It is argued that these power-law distributions and correlations are comprised in part by functional noncoding sequence and ought to be accounted for in estimating the statistical significance of apparent sequence conservation. These inter-genomic correlations of conservation are placed in the context of previously observed intra-genomic correlations, and their possible origins and consequences are discussed.

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Year:  2006        PMID： 16924100      PMCID： PMC1559763          DOI： 10.1073/pnas.0605735103

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  24 in total

1.  Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes.

Authors:  Benjamin Audit; Cedric Vaillant; Alain Arneodo; Yves d'Aubenton-Carafa; Claude Thermes
Journal:  J Mol Biol       Date:  2002-03-01       Impact factor: 5.469

2.  LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

Authors:  Michael Brudno; Chuong B Do; Gregory M Cooper; Michael F Kim; Eugene Davydov; Eric D Green; Arend Sidow; Serafim Batzoglou
Journal:  Genome Res       Date:  2003-03-12       Impact factor: 9.043

3.  The UCSC Genome Browser Database.

Authors:  D Karolchik; R Baertsch; M Diekhans; T S Furey; A Hinrichs; Y T Lu; K M Roskin; M Schwartz; C W Sugnet; D J Thomas; R J Weber; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

Review 4.  RNA regulation: a new genetics?

Authors:  John S Mattick
Journal:  Nat Rev Genet       Date:  2004-04       Impact factor: 53.242

5.  Evolution of long-range fractal correlations and 1/f noise in DNA base sequences.

Authors: 
Journal:  Phys Rev Lett       Date:  1992-06-22       Impact factor: 9.161

6.  Distribution and intensity of constraint in mammalian genomic sequence.

Authors:  Gregory M Cooper; Eric A Stone; George Asimenos; Eric D Green; Serafim Batzoglou; Arend Sidow
Journal:  Genome Res       Date:  2005-06-17       Impact factor: 9.043

7.  Expansion-modification systems: A model for spatial 1/f spectra.

Authors: 
Journal:  Phys Rev A       Date:  1991-05-15       Impact factor: 3.140

8.  Human-mouse alignments with BLASTZ.

Authors:  Scott Schwartz; W James Kent; Arian Smit; Zheng Zhang; Robert Baertsch; Ross C Hardison; David Haussler; Webb Miller
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043

9.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

10.  MicroRNA enrichment among short 'ultraconserved' sequences in insects.

Authors:  T Tran; P Havlak; J Miller
Journal:  Nucleic Acids Res       Date:  2006-05-12       Impact factor: 16.971
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  9 in total

1.  Comparing the Statistical Fate of Paralogous and Orthologous Sequences.

Authors:  Florian Massip; Michael Sheinman; Sophie Schbath; Peter F Arndt
Journal:  Genetics       Date:  2016-07-29       Impact factor: 4.562

2.  Algebraic distribution of segmental duplication lengths in whole-genome sequence self-alignments.

Authors:  Kun Gao; Jonathan Miller
Journal:  PLoS One       Date:  2011-07-14       Impact factor: 3.240

3.  Information measure for long-range correlated sequences: the case of the 24 human chromosomes.

Authors:  A Carbone
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

4.  Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome.

Authors:  Wentian Li; Jan Freudenberg; Pedro Miramontes
Journal:  BMC Bioinformatics       Date:  2014-01-03       Impact factor: 3.169

5.  Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics.

Authors:  Dimitris Polychronopoulos; Diamantis Sellis; Yannis Almirantis
Journal:  PLoS One       Date:  2014-05-02       Impact factor: 3.240

6.  How evolution of genomes is reflected in exact DNA sequence match statistics.

Authors:  Florian Massip; Michael Sheinman; Sophie Schbath; Peter F Arndt
Journal:  Mol Biol Evol       Date:  2014-11-13       Impact factor: 16.240

Review 7.  Conserved non-coding elements: developmental gene regulation meets genome organization.

Authors:  Dimitris Polychronopoulos; James W D King; Alexander J Nash; Ge Tan; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2017-12-15       Impact factor: 16.971

8.  Primary orthologs from local sequence context.

Authors:  Kun Gao; Jonathan Miller
Journal:  BMC Bioinformatics       Date:  2020-02-06       Impact factor: 3.169

9.  Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells.

Authors:  Peili Gu; Jeffrey G Reid; Xiaolian Gao; Chad A Shaw; Chad Creighton; Peter L Tran; Xiaochuan Zhou; Rafal B Drabek; David L Steffen; David M Hoang; Michelle K Weiss; Arash O Naghavi; Jad El-daye; Mahjabeen F Khan; Glen B Legge; David A Wheeler; Richard A Gibbs; Jonathan N Miller; Austin J Cooney; Preethi H Gunaratne
Journal:  PLoS One       Date:  2008-07-02       Impact factor: 3.240
  9 in total

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