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Published on Jan 1, 2014in BMC Genomics 3.73
Kerry K. Cooper11
Estimated H-index: 11
(United States Department of Agriculture),
Robert E. Mandrell51
Estimated H-index: 51
(United States Department of Agriculture)
+ 7 AuthorsMichelle Qiu Carter12
Estimated H-index: 12
(United States Department of Agriculture)
Background Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no c...
38 Citations Source Cite
Published on Jan 1, 2012in BMC Genomics 3.73
Chi-Ching Lee9
Estimated H-index: 9
(National Tsing Hua University),
Wei-Cheng Lo10
Estimated H-index: 10
(National Chiao Tung University)
+ 3 AuthorsPing-Chiang Lyu35
Estimated H-index: 35
(National Tsing Hua University)
Background Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable to perform thorough analyses of difficult-to-culture microorganisms due to limitations in sequencing technology. As modern techniques have dramatically increased sequencing rates and rapidly expanded the number of sequenced genomes, in addition to traditional taxonomic classifications which focus on t...
4 Citations Source Cite
Published on Dec 1, 2011in BMC Bioinformatics 2.21
Yuzhen Ye29
Estimated H-index: 29
(Indiana University Bloomington),
Jeong-Hyeon Choi25
Estimated H-index: 25
(Indiana University Bloomington),
Haixu Tang38
Estimated H-index: 38
(Indiana University)
Background Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets.
71 Citations Source Cite
Published on Dec 1, 2010in BMC Bioinformatics 2.21
Kirill Kryukov5
Estimated H-index: 5
(National Institute of Genetics),
Naruya Saitou46
Estimated H-index: 46
(National Institute of Genetics)
Background Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.
12 Citations Source Cite
Published on Jan 1, 2010in BMC Bioinformatics 2.21
Eduardo Corel3
Estimated H-index: 3
(University of Göttingen),
Florian Pitschi2
Estimated H-index: 2
+ 3 AuthorsClaudine Devauchelle6
Estimated H-index: 6
(Centre national de la recherche scientifique)
Background While multiple alignment is the first step of usual classification schemes for biological sequences, alignment-free methods are being increasingly used as alternatives when multiple alignments fail. Subword-based combinatorial methods are popular for their low algorithmic complexity (suffix trees ...) or exhaustivity (motif search), in general with fixed length word and/or number of mismatches. We developed previously a method to detect local similarities (the N-local decoding) based ...
7 Citations Source Cite
Published on Jan 1, 2010in BMC Genomics 3.73
Karlene H. Lynch12
Estimated H-index: 12
(University of Alberta),
Paul Stothard26
Estimated H-index: 26
(University of Alberta),
Jonathan J. Dennis27
Estimated H-index: 27
(University of Alberta)
Background The Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ...
35 Citations Source Cite
Published on Jan 1, 2009in BMC Genomics 3.73
Feng Ding13
Estimated H-index: 13
(Chinese Academy of Sciences),
Petrus Tang23
Estimated H-index: 23
(Chang Gung University)
+ 4 AuthorsCheng-Hsun Chiu48
Estimated H-index: 48
(Chang Gung University)
Background Streptococcus pneumoniae serotype 14 is one of the most common pneumococcal serotypes that cause invasive pneumococcal diseases worldwide. Serotype 14 often expresses resistance to a variety of antimicrobial agents, resulting in difficulties in treatment. To gain insight into the evolution of virulence and antimicrobial resistance traits in S. pneumoniae from the genome level, we sequenced the entire genome of a serotype 14 isolate (CGSP14), and carried out comprehensive comparison wi...
57 Citations Source Cite
Published on Dec 1, 2008in BMC Bioinformatics 2.21
Scott Christley19
Estimated H-index: 19
(University of Notre Dame),
Neil F. Lobo32
Estimated H-index: 32
(University of Notre Dame),
Gregory R. Madey28
Estimated H-index: 28
(University of Notre Dame)
Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more organisms. Studies indicate that these conserved regions are associated with micro RNAs, mRNA processing, development and transcription regulation. The identification and characterization of these elements among genomes is necessary for the further understanding of their functionality.
6 Citations Source Cite