Education

• B.S. Biochemistry, Yantai University, China
• Ph.D. Bioinformatics, Peking University, China
• Postdoc Bioinformatics, University at Buffalo (SUNY) and University of Georgia at Athens

Research

Computational tools that are developed in our 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

Ongoing projects:

1. NSF CAREER (2017-2022): Evolutionary Genomics of Enzymes for Complex Carbohydrate Metabolism
2. NIH R15 (2015-2019): Orphan genes in pathogenic bacteria
3. DOE JGI (2016-): Genome sequencing of Zygnematales green algae
4. USDA ARS (2018-2020): Developing Genomics Resources for Tropical Perennial Crops Economically Important to the United States

Teaching and/or Extension Activities

• Bioinformatics, Computational Biology, Microbial Genomics

Publications 

• Entwistle S^, Li X^, Yin Y# (2019) Orphan genes shared by pathogenic genomes are more associated with bacterial pathogenicity, mSystems, in press
• 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-W10,1Web server issue 2018, doi:10.1093/nar/gky418
• Huang L*, Zhang H*, Wu P, Entwistle S+, Li X^, Yohe T+, Yi H, Yang Z, Yin Y#. dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation, Nucleic Acids Res. 46 (D1), D516-D5, database issue 2018, doi:10.1093/nar/gkx894
• Huo L, Zhang H, Huo X, Yang Y^, Li X^, Yin Y#. pHMM-tree: Phylogeny of Profile Hidden Markov Models, Bioinformatics, Apr 1;33(7):1093-1095, doi:10.1093/bioinformatics/
• Ekstrom A+, Yin Y# (2016) ORFanFinder: automated identification of taxonomically restricted orphan genes, Bioinformatics, Jul 1;32(13):2053-5. doi:10.1093/bioinformatics/btw122
• Hu L, Taujale R^, Song J, Guo J, Yin Y#. Draft genome sequence of Talaromyces verruculosus ("Penicillium verruculosum") strain TS63-9, a fungus with great potential for industrial production of polysaccharide-degrading enzymes, Journal of Biotechnology, 219:5-6. doi: 10.1016/j.jbiotec.2015.12.017. PMID: 26707807
• Nguyen M+, Ekstrom A+, Li X^ and Yin Y#. HGT-Finder: a new tool for horizontal gene transfer finding and application to Aspergillus genomes, Toxins, 7(10):4035-4053; doi:10.3390/toxins7104035. PubMed PMID: 26473921
• Yin Y*, Mao X*, Yang JC, Chen X and Xu Y. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. web server issue 2012, Jul;40(Web Server issue):W445-51. PubMed PMID: 22645317 [selected by DOE's Bioenergy Science Centers as one of the Key Advances for Biofuels Production, ESI Highly Cited (Top 1%) Paper in Biology & Biochemistry field [cited 640 times]

# corresponding authors, ^supervised grad students/postdocs, + supervised undergraduate students, * co-first authors