Search PubMed⌕ Search

Biomedical subjects

Pouya Faridi

Publications and source records attributed to Pouya Faridi.

4 recordsLinked to original sources
PubMed2026

Expanding the human proteome with microproteins and peptideins.

A major scientific drive is to characterize the protein-coding genome, which is a primary basis for studying human health. But the fundamental question remains of what has been missed in previous analyses. Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states1-3, with major implications for biomedical science. However, a key gap in knowledge has been which ncORFs produce small microproteins or alternative protein molecules that contribute to the human proteome. Here we report the collaborative efforts of the TransCODE Consortium4 to produce a consensus landscape of protein-level evidence for ncORFs. We show that about 25% of a set of 7,264 ncORFs gives rise to detectable peptides in a large-scale analysis of 95,520 proteomics experiments. We develop an annotation framework for ncORF-encoded microproteins as human proteins and codify the new conceptual model of 'peptideins' as microproteins that have indeterminate potential as functional proteins. To probe the biological implications of peptideins, we create an evolutionary analysis approach, termed ORF relative branch length (ORBL), and determine that evolutionary constraint is common and associates with observation of ncORF-derived peptides. We then characterize a pan-essential cellular phenotype for one peptidein from the OLMALINC long non-coding RNA. Overall, we generate public research tools supported by GENCODE and PeptideAtlas and advance biomedical discovery for understudied components of the human proteome.

Humans↗
PubMed2025

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.

A major scientific drive is to characterize the protein-coding genome as it provides the primary basis for the study of human health. But the fundamental question remains: what has been missed in prior genomic analyses? Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states, with major implications for proteomics, genomics, and clinical science. However, the impact of ncORFs has been limited by the absence of a large-scale understanding of their contribution to the human proteome. Here, we report the collaborative efforts of stakeholders in proteomics, immunopeptidomics, Ribo-seq ORF discovery, and gene annotation, to produce a consensus landscape of protein-level evidence for ncORFs. We show that at least 25% of a set of 7,264 ncORFs give rise to translated gene products, yielding over 3,000 peptides in a pan-proteome analysis encompassing 3.8 billion mass spectra from 95,520 experiments. With these data, we developed an annotation framework for ncORFs and created public tools for researchers through GENCODE and PeptideAtlas. This work will provide a platform to advance ncORF-derived proteins in biomedical discovery and, beyond humans, diverse animals and plants where ncORFs are similarly observed.

GENCODE↗
PubMed2006

Medicinal smokes.

All through time, humans have used smoke of medicinal plants to cure illness. To the best of our knowledge, the ethnopharmacological aspects of natural products' smoke for therapy and health care have not been studied. Mono- and multi-ingredient herbal and non-herbal remedies administered as smoke from 50 countries across the 5 continents are reviewed. Most of the 265 plant species of mono-ingredient remedies studied belong to Asteraceae (10.6%), followed by Solanaceae (10.2%), Fabaceae (9.8%) and Apiaceae (5.3%). The most frequent medical indications for medicinal smoke are pulmonary (23.5%), neurological (21.8%) and dermatological (8.1%). Other uses of smoke are not exactly medical but beneficial to health, and include smoke as a preservative or a repellent and the social use of smoke. The three main methods for administering smoke are inhalation, which accounts for 71.5% of the indications; smoke directed at a specific organ or body part, which accounts for 24.5%; ambient smoke (passive smoking), which makes up the remaining 4.0%. Whereas inhalation is typically used in the treatment of pulmonary and neurological disorders and directed smoke in localized situations, such as dermatological and genito-urinary disorders, ambient smoke is not directed at the body at all but used as an air purifier. The advantages of smoke-based remedies are rapid delivery to the brain, more efficient absorption by the body and lower costs of production. This review highlights the fact that not enough is known about medicinal smoke and that a lot of natural products have potential for use as medicine in the smoke form. Furthermore, this review argues in favor of medicinal smoke extended use in modern medicine as a form of drug delivery and as a promising source of new active natural ingredients.

Administration, Inhalation↗