Literature DB >> 17060616

Discovery of principles of nature from mathematical modeling of DNA microarray data.

Orly Alter1.   

Abstract

Mesh：

Year:  2006        PMID： 17060616      PMCID： PMC1637536          DOI： 10.1073/pnas.0607650103

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


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  21 in total

1.  Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.

Authors:  Orly Alter; Patrick O Brown; David Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-11       Impact factor: 11.205

2.  A genomewide oscillation in transcription gates DNA replication and cell cycle.

Authors:  Robert R Klevecz; James Bolen; Gerald Forrest; Douglas B Murray
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-20       Impact factor: 11.205

3.  Response experiments for nonlinear systems with application to reaction kinetics and genetics.

Authors:  Marcel O Vlad; Adam Arkin; John Ross
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-29       Impact factor: 11.205

4.  Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription.

Authors:  Orly Alter; Gene H Golub
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-15       Impact factor: 11.205

5.  Quantized generation time in mammalian cells as an expression of the cellular clock.

Authors:  R R Klevecz
Journal:  Proc Natl Acad Sci U S A       Date:  1976-11       Impact factor: 11.205

Review 6.  Exploring the new world of the genome with DNA microarrays.

Authors:  P O Brown; D Botstein
Journal:  Nat Genet       Date:  1999-01       Impact factor: 38.330

7.  Cell cycle synchronization of Gonyaulax polyedra by filtration: quantized generation times.

Authors:  K Homma; J W Hastings
Journal:  J Biol Rhythms       Date:  1988       Impact factor: 3.182

8.  Yeast origin recognition complex is involved in DNA replication and transcriptional silencing.

Authors:  G Micklem; A Rowley; J Harwood; K Nasmyth; J F Diffley
Journal:  Nature       Date:  1993-11-04       Impact factor: 49.962

9.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

Authors:  P T Spellman; G Sherlock; M Q Zhang; V R Iyer; K Anders; M B Eisen; P O Brown; D Botstein; B Futcher
Journal:  Mol Biol Cell       Date:  1998-12       Impact factor: 4.138

10.  Cohesin relocation from sites of chromosomal loading to places of convergent transcription.

Authors:  Armelle Lengronne; Yuki Katou; Saori Mori; Shihori Yokobayashi; Gavin P Kelly; Takehiko Itoh; Yoshinori Watanabe; Katsuhiko Shirahige; Frank Uhlmann
Journal:  Nature       Date:  2004-06-30       Impact factor: 49.962
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  13 in total

1.  A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies.

Authors:  Larsson Omberg; Gene H Golub; Orly Alter
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-14       Impact factor: 11.205

2.  Biological uncertainty.

Authors:  Joseph P Zbilut; Alessandro Giuliani
Journal:  Theory Biosci       Date:  2008-03-27       Impact factor: 1.919

Review 3.  Understanding genetic variation - the value of systems biology.

Authors:  Marc-Thorsten Hütt
Journal:  Br J Clin Pharmacol       Date:  2014-04       Impact factor: 4.335

4.  Deciphering life history transcriptomes in different environments.

Authors:  William J Etges; Meredith V Trotter; Cássia C de Oliveira; Subhash Rajpurohit; Allen G Gibbs; Shripad Tuljapurkar
Journal:  Mol Ecol       Date:  2014-12-31       Impact factor: 6.185

5.  SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism.

Authors:  Nicolas M Bertagnolli; Justin A Drake; Jason M Tennessen; Orly Alter
Journal:  PLoS One       Date:  2013-11-25       Impact factor: 3.240

6.  Free energy rhythms in Saccharomyces cerevisiae: a dynamic perspective with implications for ribosomal biogenesis.

Authors:  A Gross; Caroline M Li; F Remacle; R D Levine
Journal:  Biochemistry       Date:  2013-02-20       Impact factor: 3.162

7.  Tensor decomposition reveals concurrent evolutionary convergences and divergences and correlations with structural motifs in ribosomal RNA.

Authors:  Chaitanya Muralidhara; Andrew M Gross; Robin R Gutell; Orly Alter
Journal:  PLoS One       Date:  2011-04-29       Impact factor: 3.240

8.  GSVD comparison of patient-matched normal and tumor aCGH profiles reveals global copy-number alterations predicting glioblastoma multiforme survival.

Authors:  Cheng H Lee; Benjamin O Alpert; Preethi Sankaranarayanan; Orly Alter
Journal:  PLoS One       Date:  2012-01-23       Impact factor: 3.240

9.  Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression.

Authors:  Larsson Omberg; Joel R Meyerson; Kayta Kobayashi; Lucy S Drury; John F X Diffley; Orly Alter
Journal:  Mol Syst Biol       Date:  2009-10-13       Impact factor: 11.429

10.  A novel multi-scale modeling approach to infer whole genome divergence.

Authors:  Eli Reuveni; Alessandro Giuliani
Journal:  Evol Bioinform Online       Date:  2012-11-14       Impact factor: 1.625
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