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Oct 24, 2014
10/14
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Ye, Yuzhen; Choi, Jeong-Hyeon; Tang, Haixu
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This article is from BMC Bioinformatics , volume 12 . Abstract 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. Results: We developed a fast protein similarity search tool...
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113943
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Oct 16, 2014
10/14
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Kim, Sun, 1962-; Mardis, Elaine, 1962-; Tang, Haixu
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Includes bibliographical references and index
Topics: Genomes, Nucleotide sequence
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Oct 21, 2014
10/14
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Zhang, Quan; Rho, Mina; Tang, Haixu; Doak, Thomas G; Ye, Yuzhen
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This article is from Genome Biology , volume 14 . Abstract Background: Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders' sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. When spacers are expressed, they direct CRISPR-associated (Cas) proteins to silence complementary invading DNA. In order to characterize the invaders of human...
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053933
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Oct 26, 2014
10/14
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Foster, Patricia L.; Hanson, Andrew J.; Lee, Heewook; Popodi, Ellen M.; Tang, Haixu
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This article is from G3: Genes|Genomes|Genetics , volume 3 . Abstract By sequencing the genomes of 34 mutation accumulation lines of a mismatch-repair defective strain of Escherichia coli that had undergone a total of 12,750 generations, we identified 1625 spontaneous base-pair substitutions spread across the E. coli genome. These mutations are not distributed at random but, instead, fall into a wave-like spatial pattern that is repeated almost exactly in mirror image in the two separately...
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583449
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56
Oct 24, 2014
10/14
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Lee, Seungmook; Kwon, Min-Seok; Lee, Hyoung-Joo; Paik, Young-Ki; Tang, Haixu; Lee, Jae K; Park, Taesung
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This article is from BMC Bioinformatics , volume 12 . Abstract Background: Quantification of protein expression by means of mass spectrometry (MS) has been introduced in various proteomics studies. In particular, two label-free quantification methods, such as spectral counting and spectra feature analysis have been extensively investigated in a wide variety of proteomic studies. The cornerstone of both methods is peptide identification based on a proteomic database search and subsequent...
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234305
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Oct 25, 2014
10/14
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Peterson, Mark P; Whittaker, Danielle J; Ambreth, Shruthi; Sureshchandra, Suhas; Buechlein, Aaron; Podicheti, Ram; Choi, Jeong-Hyeon; Lai, Zhao; Mockatis, Keithanne; Colbourne, John; Tang, Haixu; Ketterson, Ellen D
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This article is from BMC Genomics , volume 13 . Abstract Background: Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the...
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476391
