Browsing HMS Scholarly Articles by Keyword "comparative sequence analysis"

Now showing items 1-5 of 5

    • Adaptive Mutations in the JC Virus Protein Capsid Are Associated with Progressive Multifocal Leukoencephalopathy (PML) 

      Sunyaev, Shamil R.; Lugovskoy, Alexey; Simon, Kenneth; Gorelik, Leonid (Public Library of Science, 2009)
      PML is a progressive and mostly fatal demyelinating disease caused by JC virus infection and destruction of infected oligodendrocytes in multiple brain foci of susceptible individuals. While JC virus is highly prevalent ...

    • Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies 

      Champion, Mia D.; Zeng, Qiandong; Nix, Eli B.; Nano, Francis E.; Keim, Paul; Kodira, Chinnappa D.; Koehrsen, Michael; Pearson, Matthew; Howarth, Clint; Larson, Lisa; White, Jared; Alvarado, Lucia; Forsman, Mats; Bearden, Scott W.; Sjöstedt, Anders; Titball, Richard; Michell, Stephen L.; Birren, Bruce; Borowsky, Mark L; Young, Sarah U.; Engels, Reinhard; Galagan, James E (Public Library of Science, 2009)
      Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its ...

    • Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication 

      Ma, Li-Jun; Ibrahim, Ashraf S.; Skory, Christopher; Grabherr, Manfred G.; Burger, Gertraud; Butler, Margi; Elias, Marek; Idnurm, Alexander; Lang, B. Franz; Sone, Teruo; Abe, Ayumi; Corrochano, Luis M.; Fu, Jianmin; Hansberg, Wilhelm; Kim, Jung-Mi; Kodira, Chinnappa D.; Koehrsen, Michael J.; Miranda-Saavedra, Diego; O'Leary, Sinead; Ortiz-Castellanos, Lucila; Poulter, Russell; Rodriguez-Romero, Julio; Ruiz-Herrera, José; Shen, Yao-Qing; Zeng, Qiandong; Birren, Bruce W.; Cuomo, Christina A.; Wickes, Brian L.; Calvo, Sarah E; Engels, Reinhard; Galagan, James E; Liu, Bo (Public Library of Science, 2009)
      Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic ...

    • High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs 

      Teonadi, Hidayat; Livny, Miron; Livny, Jonathan; Waldor, Matthew K (Public Library of Science, 2008)
      Background: Diverse bacterial genomes encode numerous small non-coding RNAs (sRNAs) that regulate myriad biological processes. While bioinformatic algorithms have proven effective in identifying sRNA-encoding loci, the ...

    • Hypermutable Non-Synonymous Sites are Under Stronger Negative Selection 

      Schmidt, Steffen; Gerasimova, Anna; Kondrashov, Fyodor A.; Adzuhbei, Ivan A.; Kondrashov, Alexey S.; Sunyaev, Shamil R. (Public Library of Science, 2008)
      Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by ...