Journal of Computer Science & Systems Biology

Stephen F. Kingsmore

Publications

• Research Article
  Management of High-Throughput DNA Sequencing Projects: Alpheus
  Author(s): Neil A. Miller, Stephen F. Kingsmore, Andrew D. Farmer, Raymond J. Langley, Joann Mudge, John A. Crow, Alvaro J. Gonzalez, Faye D. Schilkey, Ryan J. Kim, Jennifer van Velkinburgh, Gregory D. May, C. Forrest Black, M. Kathy Myers, John P. Utsey, Nicholas S. Frost, Selene M. Virk, David J. Sugarbaker, Raphael Bueno, Stephen R. Gullans, Susan M. Baxter, Steve W. Day and Ernest F. RetzelNeil A. Miller, Stephen F. Kingsmore, Andrew D. Farmer, Raymond J. Langley, Joann Mudge, John A. Crow, Alvaro J. Gonzalez, Faye D. Schilkey, Ryan J. Kim, Jennifer van Velkinburgh, Gregory D. May, C. Forrest Black, M. Kathy Myers, John P. Utsey, Nicholas S. Frost, Selene M. Virk, David J. Sugarbaker, Raphael Bueno, Stephen R. Gullans, Susan M. Baxter, Steve W. Day and Ernest F. Retzel
  
  High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multigigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem’s SOLiD (sequencing-by-ligation). enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymor.. Read More»
  DOI: 10.4172/jcsb.1000013

  Abstract PDF