Public Resources

Stanford Human OligoExome Resource: 

• “Stanford Human OligoExome is a scalable oligonucleotide management system for genomic analysis and high-throughput resequencing. This set of capture oligonucleotides will cover the CCDS exon space and a high proportion of related regulatory regions from the human genome.” - Stanford Medicine: Ji Research Group, Division of Oncology
• Related Publication: Natsoulis, Georges et al. “A flexible approach for highly multiplexed candidate gene targeted resequencing.” PloS one vol. 6,6 (2011): e21088. doi:10.1371/journal.pone.0021088

MitoPhenome - Mitochondria Phenome Knowledgebase

• The site offers data tools, databases, and research findings that explore mitochondrial DNA variations, their role in disease mechanisms, and broader genomic studies.

Yeast deletion project and proteomics of mitochondria database

• “The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function.” (The Health Sciences Library System)
  
• Related Publication: Gu, Zhenglong et al. “Role of duplicate genes in genetic robustness against null mutations.” Nature vol. 421,6918 (2003): 63-6. doi:10.1038/nature01198 

Chemical DNA Synthesis Cycle

• This chart describes the steps and detailed mechanisms involved in oligonucleotide synthesis. Initially a reference tool for the Stanford Genome Technology Center Oligo Facility, the chart is now available for public use. The idea behind this updated version of the chart was to consolidate all pertinent aspects of the cycle, including side reactions, in to one convenient location, with the sole purpose of educating anyone interested in chemical DNA synthesis.

Yeast Fitness Database (supplementing "The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes". Science 18 April 2008: Vol. 320. no. 5874, pp. 362 - 365)

• “Genetics aims to understand the relation between genotype and phenotype. However, because complete deletion of most yeast genes ( approximately 80%) has no obvious phenotypic consequence in rich medium, it is difficult to study their functions.” (Hillenmeyer et. al. 1)

Yeast genome deletion project

Blast site for checking putative sequences against the sequenced primers

• The Basic Local Alignment Search Tool (BLAST), a bioinformatics program used to find regions of similarity between biological sequences. The site offers various specialized searches, such as SmartBLAST, Primer-BLAST, and CD-search, and provides options for downloading the BLAST tool or accessing it through cloud services and APIs.

Yeast deletion project and proteomics of mitochondria database

Saccharomyces cerevisiae YJM789 Genome Project

• Related Publication: W. Wei, J.H. McCusker, R.W. Hyman, T. Jones, Y. Ning, Z. Cao, Z. Gu, D. Bruno, M. Miranda, M. Nguyen, J. Wilhelmy, C. Komp, R. Tamse, X. Wang, P. Jia, P. Luedi, P.J. Oefner, L. David, F.S. Dietrich, Y. Li, R.W. Davis, & L.M. Steinmetz, Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789, Proc. Natl. Acad. Sci. U.S.A. 104.31 (2007): 12825-12830, https://doi.org/10.1073/pnas.0701291104.

Candida albicans sequencing

• Related Publication: Odds, Frank C et al. “Candida albicans genome sequence: a platform for genomics in the absence of genetics.” Genome biology vol. 5,7 (2004): 230. doi:10.1186/gb-2004-5-7-230

C. neoformans sequencing project