Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach

Autor: Tommi Välikangas, Tomi Suomi, Courtney E. Chandler, Alison J. Scott, Bao Q. Tran, Robert K. Ernst, David R. Goodlett, Laura L. Elo

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-18 (2022)

Longitudinal proteomics holds great promise for biomarker discovery, but the data interpretation has remained a challenge. Here, the authors evaluate several tools to detect longitudinal differential expression in proteomics data and introduce RolDE,

Externí odkaz: https://doaj.org/article/b79a18593db04cd9a2786773cf4f290f

Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms

Autor: Jeffrey A. Freiberg, Yoann Le Breton, Bao Q. Tran, Alison J. Scott, Janette M. Harro, Robert K. Ernst, Young Ah Goo, Emmanuel F. Mongodin, David R. Goodlett, Kevin S. McIver, Mark E. Shirtliff

Publikováno v: mSystems, Vol 1, Iss 6 (2016)

ABSTRACT To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stag

Externí odkaz: https://doaj.org/article/50dac4ebd33841f7a2835b84722aa5a8

Phosphoproteomic and transcriptomic analyses reveal multiple functions for Aspergillus nidulans MpkA independent of cell wall stress

Autor: Jyothi Kumar, Walker Huso, Liliane Fraga Costa Ribeiro, Cynthia Chelius, Bao Q. Tran, Stephen Lincoln, Young Ah Goo, Ranjan Srivastava, Steven D. Harris, Mark R. Marten

Publikováno v: Fungal Genetics and Biology. 125:1-12

The protein kinase MpkA plays a prominent role in the cell wall integrity signaling (CWIS) pathway, acting as the terminal MAPK activating expression of genes which encode cell wall biosynthetic enzymes and other repair functions. Numerous studies fo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::022de312d8ed534131fda9c78fcd9891
https://doi.org/10.1016/j.fgb.2019.01.003

Rapid denaturing organic digestion method for targeted protein identification and characterization

Autor: Bao Q Tran, David P. A. Kilgour, Jonathan M. Oyler

Bottom-up mass spectrometry-based protein analysis methods employing protease digestion are routinely used to identify and characterize proteins with high specificity and sensitivity. Method performance is generally measured by sequence coverage capa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0bfe16d3c6c3057d705602713fed27d2
https://irep.ntu.ac.uk/id/eprint/42560/1/1426606_a1594_Kilgour.pdf

Comprehensive Analysis of Aspergillus nidulans PKA Phosphorylome Identifies a Novel Mode of CreA Regulation

Autor: Leandro José de Assis, Gustavo H. Goldman, Jessica J. J. Ramsey, Steven D. Harris, Nisha S. Naik, Lucas Ferreira Ribeiro, Bao Q. Tran, Stephen Lincoln, Jyothi Kumar, Simin Hossain, Mevlut Ulas, Young Ah Goo, Marc Ostermeier, Özgür Bayram, Karthik Boppidi, Liliane Fraga Costa Ribeiro, Mark R. Marten, Ranjan Srivastava, Cynthia Chelius

Publikováno v: Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
mBio, Vol 10, Iss 2 (2019)
mBio, Vol 10, Iss 2, p e02825-18 (2019)

In filamentous fungi, an important kinase responsible for adaptation to changes in available nutrients is cyclic AMP (cAMP)-dependent protein kinase (protein kinase A [PKA]). This kinase has been well characterized at a molecular level, but its syste

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d0f2a5e624f172b638aabbe8e8cb8c2e
https://doi.org/10.1128/mbio.02825-18