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Human-mouse genome comparisons to locate regulatory sites
Elucidating the human transcriptional regulatory network is a challenge of the post-genomic era. Technical progress so far is impressive, including detailed understanding of regulatory mechanisms forExpand
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The Ess1 prolyl isomerase is required for transcription termination of small noncoding RNAs via the Nrd1 pathway.
Genome-wide studies have identified abundant small, noncoding RNAs, including small nuclear RNAs, small nucleolar RNAs (snoRNAs), cryptic unstable transcripts (CUTs), and upstream regulatory RNAsExpand
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Widespread Antisense Transcription in Escherichia coli
ABSTRACT The vast majority of annotated transcripts in bacteria are mRNAs. Here we identify ~1,000 antisense transcripts in the model bacterium Escherichia coli. We propose that these transcripts areExpand
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Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus
We find that genome-wide DNA transfer by conjugation in mycobacteria affords bacteria that reproduce by binary fission the same advantages of sexual reproduction, and may explain the genomicExpand
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Decoding human regulatory circuits.
Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, deExpand
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Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast
The packaging of eukaryotic DNA into chromatin has profound consequences for gene regulation, as well as for other DNA transactions such as recombination, replication and repair. Understanding howExpand
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Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection
ABSTRACT Salmonella enterica serovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highlyExpand
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Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme
To study local structures in proteins, we previously developed an autoassociative artificial neural network (autoANN) and clustering tool to discover intrinsic features of macromolecular structures.Expand
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Bayesian Clustering with Variable and Transformation Selections
SUMMARY The clustering problem has attracted much attention from both statisticians and computer scientists in the past fifty years. Methods such as hierarchical clustering and the K-means method areExpand
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Draft Genome Sequence of MKD8, a Conjugal Recipient Mycobacterium smegmatis Strain
ABSTRACT We report an annotated draft genome sequence of the Mycobacterium smegmatis strain MKD8. This strain acts as a recipient during conjugation with the reference M. smegmatis strain mc2155.Expand
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