Yanbin Yin

Teaching and/or Extension Activities:
Bioinformatics, Computational Biology, Microbial Genomics

Research Area:

Our lab’s research falls into the Genomics and Bioinformatics Data Sciences. Our long-term research interests include: (i) developing new computational tools (softwares, databases and web servers) to facilitate genomics research, and (ii) characterizing important genetic elements in genomes and metagenomes to enhance their biotechnological and biomedical applications and understand genome biology/evolution. Specifically, we have been studying orphan genes, horizontally transferred genes, anti-CRISPR genes, and CAZymes (carbohydrate active enzymes) in bacteria, archaea, fungi, algae, plants, and viruses.

 

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

 Lab website: http://bcb.unl.edu/

Five Selected 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


  
Yanbin Yin
Associate Professor

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

Contact Information:
253 Food Innovation Center
Lincoln, NE 68588-6205
402 472 4303
yyin@unl.edu