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

• Ph.D., Medical Informatics, March 2009
  Graduate School of Medicine, Kobe University, Kobe, Japan
• M.Sc., Immunology, July 2000
  Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
• M.D., Pediatrics, July 1996
  Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China

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):

• Lin Y, He Y. The Ontology of Genetic Susceptibility Factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. Journal of Biomedical Semantics. 2014, 5:19. doi:10.1186/2041-1480-5-19.
• Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer TC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The Cell Line Ontology. Journal of Biomedical Semantics. Accepted for publication on 3 March 2014.
• He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, Li X, Patel M, Zhao B, Chung M, Ostrow J, Sylora A, Dungarani P, Ulysse G, Kochhar K, Vidri B, Strait K, Jourdian GW, Xiang Z. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Research. 2014. 42 (D1): D1124-D1132. doi: 10.1093/nar/gkt1133. First published online: November 19, 2013. [PDF]. PMID: 24259431.
• Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
• Lin Y, He Y. Ontology modeling of genetic susceptibility to adverse events following vaccination. Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)". International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . Full-length proceeding paper. [http://ceur-ws.org/Vol-1061/Paper3_vdos2013.pdf]
• Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Journal of Biomedical Semantics. 2012, 3:17. PMID: 23256535. PMCID: PMC3639077.
• Lin Y, He Y. New era of developing and using ontologies for microbiology research and diagnosis. Journal of Microbiology and Diagnosis. 2012. 1:e107. doi:10.4172/2161- 0703.1000e107.
• Lin Y, Xiang Z, He Y. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. [Epub ahead of print] PMID: 22041276. PMCID: PMC3217896.
• Lin Y, Xiang Z, He Y. Towards a Semantic Web application: Ontology-driven ortholog clustering analysis. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO-2011), Buffalo, NY, USA, July 28-30, 2011. Page 33 - 40. [http://ceur-ws.org/Vol-833/paper5.pdf]

Papers published before joining He lab:

• Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach ” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010.
• Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009.
• Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34.
• Yu Lin, Norihiro Sakamoto (2008) “Ontology Driven Modeling for the Knowledge of Genetic Susceptibility to Disease” Kobe Journal of Medical Sciences (Vol.54 No.6, pp.290-303) Ph.D. defense thesis paper.
• Lin Yu, Guo Masuda, Hiroyuki Hoshimoto, Norihiro Sakamoto (2004) “GeneticDiabetes as a metabolic pathway databases in Diabetes Mellitus” The 24th Joint Conference on Medical Informatics, Nagoya, 26th-28th Nov.,2004.
• Yu Lin, Guanxin Shen, Xiaolin Wang (2000) “The construction, expression of anti-TFR scFv and 3D molecular modeling in the Internet”. M.Sc. defense thesis paper (in Chinese).