Peng, Y. Z. | bioRxiv Science

bioRxiv2023

OmicsPharLeuDB: an integrative database for mining pharmacogenomic data in acute lymphoblastic leukemia

Leukemia is one of the most common hematological malignancies in children. Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds of approved drugs and experimental chemical compounds. However, until now, no comprehensive databases have been specifically designed for leukemia. Therefore, we have developed OmicsPharLeuDB (mugpeng.shinyapps.io/leu_web_english_peng_v2/), a database that includes the largest published studies investigating the viability response of human leukemia cell lines to chemical compound treatment, and the association between drug sensitivity and multi-omics, and also provides a user-friendly interactive website allowing the user to assess drug sensitivity data from a different platform and find the potential relationship between drugs and omics.

bioinformatics↗

bioRxiv2020

A thousand metagenome-assembled genomes of Akkermansia reveal new phylogroups and geographical and functional variations in human gut

The present study revealed the genomic architecture of Akkermansia in human gut by analyzing 1,119 near-complete metagenome-assembled genomes, 84 public available genomes, and 1 newly sequenced A. glycaniphila strain. We found that 1) the genomes of Akkermansia formed 4 species (including 2 candidate species) with distinct interspecies similarity and differed genomic characteristics, and 2) the population of A. muciniphila was structured by 3 previously identified phylogroups (Amuc I, II, and III) referring to 1,132 genomes and 1 new phylogroup (defined as Amuc IV) that contained 62 genomes. Amuc III was presented in Chinese population and Amuc IV was mainly distributed in western populations. A large number of gene of functions, pathways, and carbohydrate active enzymes that specifically associated to phylogroups. Our findings based on over a thousand genomes strengthened the previous knowledge and provided new insights into the population structure and ecology of Akkermansia in human gut.

genomics↗