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Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
...of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; 5Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, USA Cryptococcus neoformans is an opportunistic fungal pathogen...
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LETTER: Temperature-Regulated Transcription in the Pathogenic Fungus Cryptococcus neoformans
- Barbara R. Steen,
- Tian Lian,
- Scott Zuyderduyn,
- William Kim MacDonald,
- Marco Marra,
- Steven J.M. Jones,
- and James W. Kronstad
Genome Res. September 1, 2002 12: 1386-1400; doi:10.1101/gr.80202
...-dependent protein kinase controls virulence of the fungal pathogen Cryptococcus neoformans. Mol. Cell. Biol. 21 : 3179 – 3191 . ↵ Ewing B. , Green P. ( 1998 ) Base-calling of automated sequencer traces using phred , II: Error probabilities. Genome Res. 8 : 186 – 194 . ↵ Ewing B. , Hillier L. , Wendl M.C. , Green P...
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PERSPECTIVE: Genomics of the fungal kingdom: Insights into eukaryotic biology
- James E. Galagan,
- Matthew R. Henn,
- Li-Jun Ma,
- Christina A. Cuomo,
- and Bruce Birren
Genome Res. December 2005 15: 1620-1631; doi:10.1101/gr.3767105
....e., pathogenicity), thus allowing these traits to be explored through comparison. View this table: In this window In a new window Table 2. Fungal and Oomycete projects in progress a Access to these fungal genomic data is available through a growing number of online resources. These resources include the Broad...
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RESOURCE: Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
- Christopher D. Fjell,
- Ian Bosdet,
- Jacqueline E. Schein,
- Steven J.M. Jones,
- and Marco A. Marra
Genome Res. June 2003 13: 1244-1249; doi:10.1101/gr.819303
...., Heitman, J., Jones, S.J., Marra, M.A., et al. 2002 . Physical maps for analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans . Genome Res. 9 : 1445 –1453. ↵ Soderlund, C., Longden, I. and Mott, R. 1997 . FPC: a system for building contigs from restriction fingerprinted clones...
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Methods: Gene prediction and verification in a compact genome with numerous small introns
- Aaron E. Tenney,
- Randall H. Brown,
- Charles Vaske,
- Jennifer K. Lodge,
- Tamara L. Doering,
- and Michael R. Brent
Genome Res. November 2004 14: 2330-2335; Published in Advance October 12, 2004, doi:10.1101/gr.2816704
.... In this paper, we demonstrate that reverse transcription-polymerase chain reaction (RT–PCR) and direct sequencing based on predicted gene structures satisfy this need, at least for single-celled eukaryotes. The TWINSCAN gene prediction algorithm was adapted for the fungal pathogen Cryptococcus neoformans...
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METHODS: Software for Automated Analysis of DNA Fingerprinting Gels
- Daniel R. Fuhrmann,
- Martin I. Krzywinski,
- Readman Chiu,
- Parvaneh Saeedi,
- Jacqueline E. Schein,
- Ian E. Bosdet,
- Asif Chinwalla,
- LaDeana W. Hillier,
- Robert H. Waterston,
- John D. McPherson,
- Steven J.M. Jones,
- and Marco A. Marra
Genome Res. May 1, 2003 13: 940-953; doi:10.1101/gr.904303
...efforts aimed at bacterial, fungal, plant, and animal s. Although BandLeader's performance is excellent, there is room for incremental improvement. With continued careful modeling and algorithm improvement, we see the potential for increased bandcalling performance, with gains in sensitivity, specificity...

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