Dissecting Biological "Dark Matter" with Single-Cell Genetic Analysis of Rare and Uncultivated TM7 Microbes from the Human Mouth

Autor: Marcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Lösekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, Szeto, Ernest, Platt, Darren, Hugenholtz, Philip, Relman, David A., Quake, Stephen R.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America, 2007 Jul . 104(29), 11889-11894.

Externí odkaz: https://www.jstor.org/stable/25436219

Challenging the workhorse: Comparative analysis of eukaryotic micro‐organisms for expressing monoclonal antibodies

Autor: Jiang, Hanxiao, Horwitz, Andrew A., Wright, Chapman, Tai, Anna, Znameroski, Elizabeth A., Tsegaye, Yoseph, Warbington, Hailley, Bower, Benjamin S., Alves, Christina, Co, Carl, Jonnalagadda, Kanvasri, Platt, Darren, Walter, Jessica M., Natarajan, Venkatesh, Ubersax, Jeffrey A., Cherry, Joel R., Love, J. Christopher

Publikováno v: Biotechnology and Bioengineering

For commercial protein therapeutics, Chinese hamster ovary (CHO) cells have an established history of safety, proven capability to express a wide range of therapeutic proteins and high volumetric productivities. Expanding global markets for therapeut

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::a3cd71ffa137ce571ec068e7e0dd8ec1
http://europepmc.org/articles/PMC6836876

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

Autor: Nijkamp Jurgen F, van den Broek Marcel, Datema Erwin, de Kok Stefan, Bosman Lizanne, Luttik Marijke A, Daran-Lapujade Pascale, Vongsangnak Wanwipa, Nielsen Jens, Heijne Wilbert HM, Klaassen Paul, Paddon Chris J, Platt Darren, Kötter Peter, van Ham Roeland C, Reinders Marcel JT, Pronk Jack T, de Ridder Dick, Daran Jean-Marc

Publikováno v: Microbial Cell Factories, Vol 11, Iss 1, p 36 (2012)

Abstract Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions

Externí odkaz: https://doaj.org/article/ecaf5fd426dc4ccd8a2f5c8bf6b3ac9f

An Annotation 'Minipipe' to Rapidly Assess Genomic Assemblies of 454 pyrosequencing Reads

Autor: Kuo, Alan, Grigoriev, Igor, Richardson, Paul, Platt, Darren

Publikováno v: Platt, Darren; Richardson, Paul; Grigoriev, Igor; & Kuo, Alan. (2008). An Annotation `Minipipe' to Rapidly Assess Genomic Assemblies of 454 pyrosequencing Reads. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/5th3n7sk
Kuo, Alan; Grigoriev, Igor; Richardson, Paul; & Platt, Darren. (2008). An annotation "minipipe" to rapidly assess genomic assemblies of 454 pyrosequencing reads. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/3qf5z8p7

The JGI Annotation Pipeline is routinely used to predict genes in assemblies of Sanger-sequenced eukaryotic genomes. In this study we instead use annotation to assess competing assemblies of a single genome sequenced using alternative technologies. T

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::a9c5fa470372dedd182065822a8b9e4b
http://www.escholarship.org/uc/item/5th3n7sk

VecFinder: Automated de novo identification and removal of vector and adapter sequence from genomic datasets

Autor: Zhang, Michael Y., Tu, Hank, Shapiro, Harris, Platt, Darren

Publikováno v: Zhang, Michael Y.; Tu, Hank; Shapiro, Harris; & Platt, Darren. (2007). VecFinder: Automated de novo identification and removal of vector and adapter sequence from genomic datasets. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/70g8b0m7

High-throughput Sanger sequencing requires DNA to be inserted into bacterial vectors for biological amplification. Adapter or linker oligonucleotides may also be attached to target DNA fragments to facilitate insertion into the vector. These vector a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::e1f66df1ac2dad367234613c52f6253b
http://www.escholarship.org/uc/item/70g8b0m7