He Group  
Home|People|Projects|Publications|FAQs|Links|News|Contact Us

Asiyah Yu Lin

Postdoctoral Research Fellow

Asiyah has interdisciplinary backgrounds in the areas of pediatrics, immunology, and medical informatics. She is a MD specialized in pediatrics in China, a PhD in medical informatics in Japan, and a postdoctorial fellow in immunology-oriented informatics research in the USA. Asiyah also has multi-industry working experience: she worked as a web content manager in China, a web developer for a company in Japan, and a bioinformatics technical staff in Riken CDB in Japan. Currently, Asiyah is a postdoctoral research fellow in Oliver He's laboratory in the University of Michigan Medical School, Ann Arbor, Michigan, USA.

Asiyah's current research is focused on medical ontology development and ontology applications in the areas of translational and biomedical research.

EDUCATION

WORKING EXPERIENCE

  • He Laboratory, Unit of Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA 
    Postdoctoral Fellow, Dec 2010-present
    Research Focuses: Ontology development and applications, Semantic Web, Ontology-based analysis on different biomedical data (e.g., vaccines, host-pathogen interactions, adverse events, and cell lines)

  • Genomics Laboratory, RIKEN Center for Developmental Biology (CDB), Kobe, Japan
    Bioinformatician, May 2009-Nov. 2010
    Research Focuses: data assembly of next generation sequencer Roche 454
    Development of an EST database for non-model organisms


  • Translational Research Informatics Center, Kobe, Japan
    Part-time researcher, 2003-2004
    Working on the development of integrated databases for genetic and metabolic pathways of Diabetes

  • http://www.motor-japan.com
    Administrator and developer of this website since 2004,Programming in PHP and MySQL

  • Shenzhen E-sun Internet Co.,Ltd., Shenzhen, China
    Content Manager & Project Manager, 2000 to 2002

  • Caimao Hospital, Wuhan, China
    Pediatrician, 1996 to 1997

SPECIAL TRAINING

  • Computational & Comparative Genomics, November 2009. Cold Spring Harbor Laboratory, N.Y., USA.
    One week course on computational genomics: sequence similarity searching and comparison, multi alignment, phylogenetic tree, etc.
  • The sixth Summer School on Ontological Engineering and the Semantic Web, July 2008. Madrid, Spain.
    One week course on ontology and semantic web technology held by Open University (UK).
  • NIIT, August 2002- October, 2002, Shenzhen, China
    Relational database design and SQL

SKILLS

  • Bioinformatics: development of biomedical ontologies and databases; Semantic Web; High throughput sequence analysis; Network analysis.
  • Programming skills: SPARQL, OWL, PHP, MySQL, Perl, XML, HTML
  • Wet-lab biotechnology: PCR, genotyping, immunological tests, monoclonal antibody technology
  • Languages: Chinese (native), English (near native), Japanese (good)

Membership

  • Consortium of Ontology for Biomedical Investigations (OBI) ontology development
  • Consortium of Cell Line Ontology ( CLO) ontology development
  • International Conferences on Biomedical Ontologies (ICBO; since 2011)
  • International Society for Biocurator (2009-2011)

ONTOLOGIES

Asiyah has developed many ontologies as primary developer. The following ontologies have been actively developed and maintained by her:

  1. Ontology of Genetic Susceptibility Factros (OGSF)
    http://code.google.com/p/ogsf/
  2. Brucellosis Ontology (IDOBRU)
    http://sourceforge.net/projects/idobru/
  3. Ontology for Genetic Interval (OGI)
    http://bioportal.bioontology.org/ontologies/1100
  4. Ontology of Glucose Metabolism Disorder (OGMD)
    http://bioportal.bioontology.org/ontologies/1085

Asiyah has also actively participated in development of many community-based ontologies, including:

  1. VO (Vaccine Ontology)
    http://www.violinet.org/vaccineontology
  2. Ontology of Adverse Events (OAE)
    http://www.oae-ontology.org/
  3. Ontology for Biomedical Investigations (OBI)
    http://obi-ontology.org
  4. Ontology for General Medical Science (OGMS)
    http://code.google.com/p/ogms/
  5. Informed Consent Ontology (ICO)
    https://code.google.com/p/ico-ontology/
  6. Cell Line Ontology (CLO)
    http://www.clo-ontology.org/
  7. TDF Ontology for health behavior changes

The following ontologies were primarily developed by Asiyah but have not been actively maintained:

  1. COG (Cluster of orthologous Groups) Analysis Ontology (CAO)
    http://cao.svn.sourceforge.net/
  2. Ontology for disease genetic investigation (ODGI)
    http://bioportal.bioontology.org/ontologies/1086
  3. Ontology of Geographical Region (OGR)
    http://bioportal.bioontology.org/ontologies/1087

SELECTED PUBLICATION LIST

Papers published in He lab (Since 2011):

Papers published before joining He lab:


He Lab |Ontobee|OntoFox|OAE|VO|Genomesh|Ignet|miniTUBA|PHIDIAS|VIOLIN
He Group
University of Michigan Medical School
Ann Arbor, MI 48109
U of M NIAIDNIAID