Katarzyna Wilczek-Boney

Publications (2)62.4 Total impact

• Article: A catalog of reference genomes from the human microbiome.

  Karen E Nelson, George M Weinstock, Sarah K Highlander, Kim C Worley, Heather Huot Creasy, Jennifer Russo Wortman, Douglas B Rusch, Makedonka Mitreva, Erica Sodergren, Asif T Chinwalla, [......], Sandra W Clifton, Emma Allen-Vercoe, Ashlee M Earl, Candace N Farmer, Konstantinos Liolios, Michael G Surette, Qiang Xu, Craig Pohl, Katarzyna Wilczek-Boney, Dianhui Zhu
  [show abstract] [hide abstract]
  ABSTRACT: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
  Science 05/2010; 328(5981):994-9. · 31.20 Impact Factor
• Source

  Available from: Marcelo F Gouveia Nogueira

  Article: The genome sequence of taurine cattle: a window to ruminant biology and evolution.

  Christine G Elsik, Ross L Tellam, Kim C Worley, Richard A Gibbs, Donna M Muzny, George M Weinstock, David L Adelson, Evan E Eichler, Laura Elnitski, Roderic Guigó, [......], Ashley J Waardenberg, Zhiquan Wang, Robert Ward, Rosemarie Weikard, Thomas H Welsh, Stephen N White, Laurens G Wilming, Kris R Wunderlich, Jianqi Yang, Feng-Qi Zhao
  [show abstract] [hide abstract]
  ABSTRACT: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
  Science 05/2009; 324(5926):522-8. · 31.20 Impact Factor