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Yanbin Yin

yyin@unl.edu

402-472-4303

The Yin lab’s research falls into the Genomics and Bioinformatics Data Sciences. In relation to food for health and personalized nutrition research, our lab has been studying carbohydrate active enzymes (CAZymes) and CAZyme gene clusters (CGCs, also known as polysaccharide utilization loci or PULs) in both plants and microbes. We develop new computational models and informatics tools (e.g., dbCAN) that help automatically identify CAZymes and CGCs in the gut microbiome that can build, modify, and break down various complex carbohydrates. We are also interested in data mining gut microbial and viral microbiome for other important genetic elements (e.g., orphan genes, horizontally transferred genes, anti-CRISPR genes) to enhance their biotechnological and biomedical applications and understand genome biology/evolution.

 

Computational tools that are developed in the Yin lab include:

dbCAN: http://bcb.unl.edu/dbCAN2

Run_dbCAN: https://github.com/linnabrown/run_dbcan

dbCAN-PUL: http://bcb.unl.edu/dbCAN_PUL/home

eCAMI: https://github.com/yinlabniu/eCAMI

dbCAN-seq: http://bcb.unl.edu/dbCAN_seq

AcrFinder: http://bcb.unl.edu/AcrFinder

AcrDB: http://bcb.unl.edu/AcrDB

ORFanFinder: https://github.com/yinlabniu/ORFanFinder

ORFanDB: http://bcb.unl.edu/ORFanDB

HGT-Finder: https://github.com/yinlabniu/HGT-Finder

pHMM-tree: http://bcb.unl.edu/pHMM-Tree/source/index.php

PlantCAZyme: http://bcb.unl.edu/plantcazyme

 

Featured Publications

Ausland C, Zheng J, Yi H, Yang B, Li T, Feng X, Zheng B, Yin Y (2021) dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates, Nucleic Acids Res., 2021 Jan 8;49(D1):D523-D528. 10.1093/nar/gkaa742. PMID: 32941621


Xu J, Zhang H, Zheng J, Dovoedo P, Yin Y (2020) eCAMI: simultaneous classification and motif identification for enzyme annotation, Bioinformatics, 2020 Apr 1;36(7):2068-2075. doi:10.1093/bioinformatics/btz908. PMID: 31794006


Entwistle S, Li X, Yin Y (2019) Orphan genes shared by pathogenic genomes are more associated with bacterial pathogenicity, mSystems, 2019 Feb 12;4(1). pii: e00290-18. doi: 10.1128/mSystems.00290-18. PMID: 30801025


Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk P, Xu Y, Yin Y (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation, Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101. doi: 10.1093/nar/gky418. PMID: 29771380


Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y (2012) dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012 Jul;40(W1):W445-51. doi: 10.1093/nar/gks479. PMID: 22645317