Bingqiang Liu

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We present a new algorithm, BOBRO, for prediction of cis-regulatory motifs in a given set of promoter sequences. The algorithm substantially improves the prediction accuracy and extends the scope of applicability of the existing programs based on two key new ideas: (i) we developed a highly effective method for reliably assessing the possibility for each(More)
MOTIVATION We present an integrated toolkit, BoBro2.0, for prediction and analysis of cis-regulatory motifs. This toolkit can (i) reliably identify statistically significant cis-regulatory motifs at a genome scale; (ii) accurately scan for all motif instances of a query motif in specified genomic regions using a novel method for P-value estimation; (iii)(More)
DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are(More)
We present a new computational method for solving a classical problem, the identification problem of cis-regulatory motifs in a given set of promoter sequences, based on one key new idea. Instead of scoring candidate motifs individually like in all the existing motif-finding programs, our method scores groups of candidate motifs with similar sequences,(More)
The Clostridium genus of bacteria contains the most widely studied biofuel-producing organisms such as Clostridium thermocellum and also some human pathogens, plus a few less characterized strains. Here, we present a comparative genomic analysis of 40 fully sequenced clostridial genomes, paying a particular attention to the biomass degradation ones. Our(More)
Regulons are the basic units of the response system in a bacterial cell, and each consists of a set of transcriptionally co-regulated operons. Regulon elucidation is the basis for studying the bacterial global transcriptional regulation network. In this study, we designed a novel co-regulation score between a pair of operons based on accurate operon(More)
High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal the very complex structures of transcriptomes. However, it is an important and highly challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms. In this study, we present a novel de novo assembler, BinPacker,(More)
Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed by the available genomic and transcriptomic data, providing new(More)
Increased flux through the hexosamine biosynthetic pathway and the corresponding increase in intracellular glycosylation of proteins via O-linked β-N-acetylglucosamine (O-GlcNAc) is sufficient to induce insulin resistance (IR) in multiple systems. Previously, our group used shotgun proteomics to identify multiple rodent adipocytokines and secreted proteins(More)