Yanbin Yin

Professor Food Science & Technology University of Nebraska-Lincoln

Address: FIC 1901 N 21st St Rm 254
Lincoln NE 68588-6205
Phone: 402-472-4303 On-campus 2-4303
Email: yyin@unl.edu

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

Education

Ph D, Peking University, 2005

Areas of Expertise

Computational Biology

Featured Publications

Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Dhabalia Ashok A, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y (2024) Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nature Genetics. 2024 May;56(5):1018-1031. doi: 10.1038/s41588-024-01737-3. Epub 2024 May 1. PMID: 38693345

Zheng J, Ge Q, Yan Y, Zhang X, Huang L, Yin Y (2023) dbCAN3: automated carbohydrate-active enzyme and substrate annotation, Nucleic Acids Res. 2023 Jul 5;51(W1):W115-W121. doi: 10.1093/nar/gkad328. PMID: 37125649

Li T, Yin Y(2022) Critical assessment of pan-genomic analysis of metagenome-assembled genomes, Brieﬁngs in Bioinformatics, 2022 Nov 19;23(6):bbac413. doi: 10.1093/bib/bbac413. PMID: 36124775

Zheng B, He Y, Zhang P, Huo YX, Yin Y (2022) Polyphenol utilization proteins in human gut microbiome, Applied and Environmental Microbiology, 2022 Feb 8;88(3):e0185121. doi: 10.1128/AEM.01851-21. PMID: 34851722

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

Yanbin Yin

Contact

Education

Areas of Expertise

Featured Publications