[7/27/2012] A database of Comparative Cellular and Molecular
Biology of Longevity (CCMBL) was developed in collaboration with
Jeff Stuart's lab, and it is available at here. PubMed
entry for the paper describing the database.
[6/24/2012] Our recent study identifies transposable elements
as an important contributor to tandom repeats in the human
genome. Details is available in Ahmed and Liang, Comparative Functional
Genomics, 2012, 947089.
PubMed Link; Free access to the full article.
[8/3/2011] We have recently developed pBWA, a parallel version of the
Burrows-Wheeler Aligner (BWA), which is an efficient program that
aligns relatively short nucleotide sequences against a long
reference sequence such as the human genome. pBWA is freely available at Source Forge.
[4/2/2011] A dataset representing 483 Alu insertions with incomplete
insertion sequences identified using ME-SCAN as described in
Witherspoon et al, BMC Genomics 11:410, 2010 has been
deposited. These entries are denoted by a letter "i" at the end
of the dbRIP accession#, e.g.: "1000002i" for differentiating
from the regular RIP entries. They may be upgraded to the
regular entries later once complete sequence information becomes
available. The data is available by setting the "sequence
integrity level" to "incomplete" in SearchdbRIP. Please note
that the data is only available in hg19.
[3/30/2011] dbRIP v2h released: added new L1 RIP data based on Kidd et
al. Cell 143:837-1847, 2010 from Fosmid-end sequencing. Total
entries retrieved and curated: 191 (135 novel, 56 overlapping
with existing RIPs in dbRIP). The data can be checked using
author name, e.g. "Kidd" or "Eichler" in SearchdbRIP.
[10/5/2010] A new and stable dbRIP ID system is
implemented in this test version. This system uses 7-digit
numerical IDs, with the first digit used to indicate the major
type of retrotransposons (1xxxxxx, 2xxxxxx, 3xxxxxx, 4xxxxxxx
for Alu, L1, SVA and HERV, respectively). For example, dbRIP
1000001 is an Alu RIP, while 2000100 is a L1 SVA. The remaining
5 digits (5-9) are saved for new types of RIPs and for
existing types that exceed 1 million in number.
[10/5/2010] dbRIP obtained its new and permernent URL:
[9/1/2010] HERV RIP data is added. For HERV RIPs with the
presence of both full length LTR and solo-LTR, we provide both
versions of the sequences and genotype data whenever
Research in this laboratory is supported in part by
grants form the Canada Research Chair program, Canadian Foundation of Innovation
(CFI), Natural Sciences & Engineering Research Council of Canada
(NSERC), Ministry of Research and Innovation and Brock University.