VCFcontam: A Machine Learning Approach to Estimate Cross-Sample Contamination from Variant Call Data

Autor: Catherine K. Foo, James Han, Evan McCartney-Melstad, Ke Bi

The quality of genotyping calls resulting from DNA sequencing is reliant on high quality starting genetic material. One factor that can reduce sample quality and lead to misleading genotyping results is genetic contamination of a sample by another so

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::3fa2fd5f43c05d7b0d2e43b5207a58ca
https://doi.org/10.1101/2021.03.12.435007

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

Autor: Jonathan S. Weissman, Elizabeth R. Gavis, Catherine K. Foo, Nicolette G. Belletier, Joshua G. Dunn

Publikováno v: eLife
eLife, Vol 2 (2013)

Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8bf33b3fb42d9fca5dc00cd4b8264c09
https://pubmed.ncbi.nlm.nih.gov/24302569

Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers

Autor: Thomas D. Wu, Maria N. Lorenzo, Nicholas J. Skelton, Yvonne Franke, Chaitali Parikh, Wenlin Yuan, Marlena Jackson, Vasantharajan Janakiraman, Meredith Sagolla, Kui Lin, Barbara J. Brandhuber, Jeremy Stinson, Catherine K. Foo, Eric Stawiski, Hong Li, Wen-I Wu, Joseph Guillory, Somasekar Seshagiri, Jiansheng Wu, David Stokoe, Howard M. Stern, Noelyn M. Kljavin, Subhra Chaudhuri, Jesus Rondon, Brian Lee, Jie Lin, Krista K. Bowman

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America. 109(47)

The protein kinase v-akt murine thymoma viral oncogene homolog (AKT), a key regulator of cell survival and proliferation, is frequently hyperactivated in human cancers. Intramolecular pleckstrin homology (PH) domain–kinase domain (KD) interactions

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::96cc0089503155df42b9c7a1b89a93e2
https://pubmed.ncbi.nlm.nih.gov/23134728

Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays

Autor: Anita Sil, Catherine K. Foo, Mark Voorhies

Publikováno v: Voorhies, Mark; Foo, Catherine K; & Sil, Anita. (2011). Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays. BMC Microbiology, 11(1), 216. doi: http://dx.doi.org/10.1186/1471-2180-11-216. Retrieved from: http://www.escholarship.org/uc/item/7nv4f93d
BMC Microbiology
BMC Microbiology, Vol 11, Iss 1, p 216 (2011)

Background The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genome-wide studies to experimen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::daceea0a49c28938be4478e99b21fb10
https://doi.org/10.1186/1471-2180-11-216

Validation Study for Automated Nucleic Acid Extraction From Frozen Tissue, Peripheral Blood, and Formalin-Fixed Paraffin-Embedded Tissue

Autor: Mita Patel, Kimberly Lung, Catherine K. Foo, Anibal Cordero, Jeff Catalano, Petros Giannikopoulos

Publikováno v: American Journal of Clinical Pathology. 144:A240-A240

Nucleic acid extraction is a key step in many molecular laboratories. Obtaining DNA and RNA of sufficient quality and quantity is critical for the next-generation sequencing assays performed at our facility. To improve efficiency of our lab process,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::47aee248054f938df69fcffca54fa07d
https://doi.org/10.1093/ajcp/144.suppl2.240