Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation

ES Nakayasu, M Gritsenko, PD Piehowski, Y Gao… - Nature …, 2021 - nature.com
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new
disease biomarkers. However, certain critical steps of study design such as cohort selection …

Biomarkers for wound healing and their evaluation

S Patel, A Maheshwari, A Chandra - Journal of wound care, 2016 - magonlinelibrary.com
A biological marker (biomarker) is a substance used as an indicator of biological state.
Advances in genomics, proteomics and molecular pathology have generated many …

Integrating transcriptome and proteome profiling: Strategies and applications

D Kumar, G Bansal, A Narang, T Basak, T Abbas… - …, 2016 - Wiley Online Library
Discovering the gene expression signature associated with a cellular state is one of the
basic quests in majority of biological studies. For most of the clinical and cellular …

Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin

A Ghosh, SP Pandey, DC Joshi, P Rana… - Nucleic Acids …, 2023 - academic.oup.com
Nuclear-retained long non-coding RNAs (lncRNAs) including MALAT1 have emerged as
critical regulators of many molecular processes including transcription, alternative splicing …

Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery

PY Lee, J Osman, TY Low, R Jamal - Bioanalysis, 2019 - Taylor & Francis
Plasma and serum are widely used for proteomics-based biomarker discovery. However,
analysis of these biofluids is highly challenging due to the complexity and wide dynamic …

Exploring affinity chromatography in proteomics: a comprehensive review

I Chamrád, R Simerský, R Lenobel, O Novák - Analytica Chimica Acta, 2024 - Elsevier
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass
spectrometry and bioinformatics, together with separation methods, has brought many …

Big data, integrative omics and network biology

P Tolani, S Gupta, K Yadav, S Aggarwal… - Advances in protein …, 2021 - Elsevier
A cell integrates various signals through a network of biomolecules that crosstalk to
synergistically regulate the replication, transcription, translation and other metabolic …

False discovery rate: the Achilles' heel of proteogenomics

S Aggarwal, A Raj, D Kumar, D Dash… - Briefings in …, 2022 - academic.oup.com
Proteogenomics refers to the integrated analysis of the genome and proteome that
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …

[HTML][HTML] Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples

PJ Boersema, T Geiger, JR Wiśniewski… - Molecular & cellular …, 2013 - Elsevier
Cells secrete a large number of proteins to communicate with their surroundings.
Furthermore, plasma membrane proteins and intracellular proteins can be released into the …

Integrated plasma proteomics identifies tuberculosis-specific diagnostic biomarkers

HF Schiff, NF Walker, C Ugarte-Gil, M Tebruegge… - JCI …, 2024 - pmc.ncbi.nlm.nih.gov
BACKGROUND Novel biomarkers to identify infectious patients transmitting Mycobacterium
tuberculosis are urgently needed to control the global tuberculosis (TB) pandemic. We …