Identification of conserved regulatory elements by comparative genome analysis

B Lenhard, A Sandelin, L Mendoza, P Engström… - Journal of biology, 2003 - Springer
… to identifying regulatory elements presented here yields greater specificity than previous
approaches that were based purely on profile searches of single genomicgenome sequencing

Eukaryotic regulatory element conservation analysis and identification using comparative genomics

Y Liu, XS Liu, L Wei, RB Altman… - Genome Research, 2004 - genome.cshlp.org
… for identification of eukaryotic regulatory elements. In this paper, we presented a … analysis
of the conservation of known regulatory elements in human and S. cerevisiae by comparison

Comparative genomics using fugu: A tool for the identification of conserved vertebrate cisregulatory elements

B Venkatesh, WH Yap - Bioessays, 2005 - Wiley Online Library
… of conserved regulatory elements were identified between … genome is the smallest among
these model fish genomes,(57… genome for identifying conserved gene regulatory elements in …

Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery

M Kellis, N Patterson, B Birren, B Berger… - Journal of …, 2004 - liebertpub.com
… (2003) we used a comparative genomics approach to … to identify regulatory elements based
on their conservation patterns across all intergenic regions and the complete genome. The …

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

O Elemento, S Tavazoie - Genome biology, 2005 - Springer
… for discovering globally conserved regulatory elements between two genomes. The method
is … -scale comparative genomics approaches for finding transcriptional regulatory elements

The identification and functional characterisation of conserved regulatory elements in developmental genes

T Dickmeis, F Müller - Briefings in Functional Genomics, 2005 - academic.oup.com
identifying conserved regulatory elements of developmental genes by comparative genomics
This review focusses on the use of comparative genomics for the identification of cis-acting …

Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the α globin cluster

J Flint, C Tufarelli, J Peden, K Clark… - Human Molecular …, 2001 - academic.oup.com
… non-coding sequences identified many of the known regulatory elementsidentified most
of the known regulatory elements (Table 3), whereas previously defined criteria (10) identified

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements

D De Witte, J Van de Velde, D Decap, M Van Bel… - …, 2015 - academic.oup.com
… Robust algorithms for comparative genomics are expected to gain in power … conserved
within all organisms. The branch length score (BLS) was developed to quantify motif conservation

Discovery of regulatory elements in vertebrates through comparative genomics

A Prakash, M Tompa - Nature biotechnology, 2005 - nature.com
… In contrast, we compare various tools for their ability to identify regulatory elements and …
6 also identifies regulatory elements in human and mouse using a genome-wide analysis. …

Close sequence comparisons are sufficient to identify human cis-regulatory elements

S Prabhakar, F Poulin, M Shoukry, V Afzal… - Genome …, 2006 - genome.cshlp.org
identified cis-regulatory elements at diverse genomic loci and also tested numerous extremely
conserved … Human regulatory elements were identified with acceptable sensitivity (53%–…