Christian L. Barrett

TL;DR: A new hidden Markov model method (SAM-T98) for finding remote homologs of protein sequences is described and evaluated, which is optimized to recognize superfamilies, and would require parameter adjustment to be used to find family or fold relationships.

TL;DR: The extent to which the SAM-T98 implementation of a hidden Markov model procedure; PSI-BLAST; and the intermediate sequence search (ISS) procedure can detect evolutionary relationships between the members of the sequence database PDBD40-J is determined.

TL;DR: High-throughput, genome-wide measurements of RNA polymerase binding locations and mRNA transcript abundance, 5′ sequences and translation into proteins to determine the organizational structure of the Escherichia coli K-12 MG1655 genome provide an experimentally annotated transcription unit architecture.

TL;DR: The 82 base-pair deletion found in the rph-pyrE operon of many endpoints may function to relieve a pyrimidine biosynthesis defect present in MG1655, suggesting flexibility in overcoming regulatory challenges in the adaptation.

TL;DR: Analysis of the genome-wide distribution of the nucleoid-associated protein Fis in Escherichia coli using chromatin immunoprecipitation coupled with high-resolution whole genome-tiling microarrays indicates that A(6)-tracts in particular constitute a high-affinity signal that dictates Fis phasing in stretches of DNA containing multiple and variably spaced A-Tracts and AT-tractions.