Yanbin Yin

The Yin lab’s research falls into the Genomics and Bioinformatics Data Sciences. In relation to food for health 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-seq: http://bcb.unl.edu/dbCAN_seq

CGC-Finder: http://bcb.unl.edu/dbCAN2/download/Tools/

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

  1. 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
  2. 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
  3. Huang L, Zhang H, Wu P, Entwistle S, Li X, Yohe T, Yi H, Yang Z, Yin Y (2018) dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation, Nucleic Acids Res. 2018 Jan 4;46(D1):D516-D521. doi: 10.1093/nar/gkx894. PMID: 30053267
  4. Huo L, Zhang H, Huo X, Yang Y, Li X, Yin Y (2017) pHMM-tree: Phylogeny of Profile Hidden Markov Models, Bioinformatics. 2017 Apr 1;33(7):1093-1095. doi: 10.1093/bioinformatics/btw779. PMID: 28062446
  5. Ekstrom A, Yin Y (2016) ORFanFinder: automated identification of taxonomically restricted orphan genes, Bioinformatics. 2016 Jul 1;32(13):2053-5. doi: 10.1093/bioinformatics/btw122. PMID: 27153690
  6. 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