Brock University

Brock Biology



UCSC Genome




  • [11/07/2013] Dr. Monica Riley, a pioneer scientist in the fields of molecular biology and microbial genome analysis, a great mentor, and wonderful person, died from heart failure on October 11, 2013 in Richmond, CA at age of 87. A nice article about Monica Riley can be read at at here

  • [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 accommodating 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 available.

    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.