Andrew I Su

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. doi request reprint BioGPS: building your own mash-up of gene annotations and expression profiles
    Chunlei Wu
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nucleic Acids Res 44:D313-6. 2016
  2. pmc A gene expression atlas of the domestic pig
    Tom C Freeman
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK
    BMC Biol 10:90. 2012
  3. pmc CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma
    Yue Hu
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS ONE 6:e25807. 2011
  4. pmc A task-based approach for Gene Ontology evaluation
    Erik L Clarke
    The Scripps Research Institute, La Jolla, CA, USA
    J Biomed Semantics 4:S4. 2013
  5. pmc Linking genes to diseases with a SNPedia-Gene Wiki mashup
    Benjamin M Good
    The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
    J Biomed Semantics 3:S6. 2012
  6. pmc The Gene Wiki: community intelligence applied to human gene annotation
    Jon W Huss
    Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
    Nucleic Acids Res 38:D633-9. 2010
  7. pmc BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources
    Chunlei Wu
    Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr, San Diego, CA 92121, USA
    Genome Biol 10:R130. 2009
  8. pmc Gene set enrichment in eQTL data identifies novel annotations and pathway regulators
    Chunlei Wu
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS Genet 4:e1000070. 2008
  9. pmc Building a biomedical semantic network in Wikipedia with Semantic Wiki Links
    Benjamin M Good
    The Scripps Research Institute, La Jolla, CA 92037, USA
    Database (Oxford) 2012:bar060. 2012
  10. pmc Identification of regulatory elements that control PPARγ expression in adipocyte progenitors
    Wen Ling Chou
    Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
    PLoS ONE 8:e72511. 2013

Collaborators

Detail Information

Publications30

  1. doi request reprint BioGPS: building your own mash-up of gene annotations and expression profiles
    Chunlei Wu
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nucleic Acids Res 44:D313-6. 2016
    ..We also added a new 'gene list' feature that allows users to save query results for future reference. ..
  2. pmc A gene expression atlas of the domestic pig
    Tom C Freeman
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK
    BMC Biol 10:90. 2012
    ..The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering...
  3. pmc CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma
    Yue Hu
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS ONE 6:e25807. 2011
    ..Our results suggest that SCC and AC utilize different branches of the Wnt pathway during oncogenesis...
  4. pmc A task-based approach for Gene Ontology evaluation
    Erik L Clarke
    The Scripps Research Institute, La Jolla, CA, USA
    J Biomed Semantics 4:S4. 2013
    ..This task-based approach yields quantitative assessments grounded in experimental data and anchored tightly to the primary use of the annotations...
  5. pmc Linking genes to diseases with a SNPedia-Gene Wiki mashup
    Benjamin M Good
    The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
    J Biomed Semantics 3:S6. 2012
    ..Here we show how advances in wiki technology and natural language processing can be used to automatically assemble 'meta-wikis' that present integrated views over the data collaboratively created in multiple source wikis...
  6. pmc The Gene Wiki: community intelligence applied to human gene annotation
    Jon W Huss
    Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
    Nucleic Acids Res 38:D633-9. 2010
    ..Gene Wiki articles are freely accessible within the Wikipedia web site, and additional links and information are available at http://en.wikipedia.org/wiki/Portal:Gene_Wiki...
  7. pmc BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources
    Chunlei Wu
    Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr, San Diego, CA 92121, USA
    Genome Biol 10:R130. 2009
    ..gnf.org, a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform...
  8. pmc Gene set enrichment in eQTL data identifies novel annotations and pathway regulators
    Chunlei Wu
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS Genet 4:e1000070. 2008
    ..We believe that the specific molecular hypotheses generated in this study will reveal many additional pathway members and regulators, and that the analysis approaches described herein will be broadly applicable to other eQTL data sets...
  9. pmc Building a biomedical semantic network in Wikipedia with Semantic Wiki Links
    Benjamin M Good
    The Scripps Research Institute, La Jolla, CA 92037, USA
    Database (Oxford) 2012:bar060. 2012
    ..DATABASE URL: http://en.wikipedia.org/wiki/Portal:Gene_Wiki...
  10. pmc Identification of regulatory elements that control PPARγ expression in adipocyte progenitors
    Wen Ling Chou
    Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
    PLoS ONE 8:e72511. 2013
    ....
  11. pmc Genomewide association analysis in diverse inbred mice: power and population structure
    Phillip McClurg
    Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
    Genetics 176:675-83. 2007
    ..These eQTL data confirmed that the MDP is a suitable mapping population for QTL discovery and that eQTL results can serve as a gold standard for relative measures of statistical power...
  12. pmc A gene wiki for community annotation of gene function
    Jon W Huss
    San Diego State University, Bioinformatics and Medical Informatics Graduate Program, San Diego, California, USA
    PLoS Biol 6:e175. 2008
  13. doi request reprint OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
    Tobias Meißner
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, CA, USA
    BMC Med Genomics 8:24. 2015
    ....
  14. pmc Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments
    Matthew D Shoulders
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell Rep 3:1279-92. 2013
    ....
  15. pmc BioGPS and MyGene.info: organizing online, gene-centric information
    Chunlei Wu
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nucleic Acids Res 41:D561-5. 2013
    ..Finally, we describe MyGene.info (http://mygene.info) and related web services that provide programmatic access to BioGPS...
  16. pmc Mining the Gene Wiki for functional genomic knowledge
    Benjamin M Good
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    BMC Genomics 12:603. 2011
    ..We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology...
  17. pmc Dizeez: an online game for human gene-disease annotation
    Salvatore Loguercio
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS ONE 8:e71171. 2013
    ..These early results provide a basic proof of principle that online games can be successfully applied to the challenge of gene annotation. Dizeez is available at http://genegames.org. ..
  18. pmc Microtask crowdsourcing for disease mention annotation in pubmed abstracts
    Benjamin M Good
    Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA, 92037, USA
    Pac Symp Biocomput 20:282-93. 2015
    ..Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402. ..
  19. pmc Omics Pipe: a community-based framework for reproducible multi-omics data analysis
    Kathleen M Fisch
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA and Department of Human Biology, J Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
    Bioinformatics 31:1724-8. 2015
    ....
  20. pmc Games with a scientific purpose
    Benjamin M Good
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Biol 12:135. 2011
    ..The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems...
  21. pmc The Gene Wiki in 2011: community intelligence applied to human gene annotation
    Benjamin M Good
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nucleic Acids Res 40:D1255-61. 2012
    ..All articles in the Gene Wiki can be freely accessed and edited at Wikipedia, and additional links and information can be found at the project's Wikipedia portal page: http://en.wikipedia.org/wiki/Portal:Gene_Wiki...
  22. pmc Crowdsourcing for bioinformatics
    Benjamin M Good
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Bioinformatics 29:1925-33. 2013
    ..Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains...
  23. pmc Zone-specific gene expression patterns in articular cartilage
    Shawn P Grogan
    The Scripps Research Institute and Shiley Center for Orthopaedic Research and Education, Scripps Clinic, La Jolla, California, USA
    Arthritis Rheum 65:418-28. 2013
    ..To identify novel genes and pathways specific to the superficial zone (SZ), middle zone (MZ), and deep zone (DZ) of normal articular cartilage...
  24. doi request reprint Identification of serum-derived sphingosine-1-phosphate as a small molecule regulator of YAP
    Eric Miller
    Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
    Chem Biol 19:955-62. 2012
    ..These results revealed potent small molecule regulators of YAP and suggest that S1P and LPA might modulate cell proliferation and tumorigenesis through YAP activation...
  25. pmc An efficient rapid system for profiling the cellular activities of molecular libraries
    Jonathan S Melnick
    Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 103:3153-8. 2006
    ..This methodology provides a powerful tool for unraveling the cellular biology and molecular pharmacology of both naturally occurring and synthetic chemical diversity...
  26. ncbi request reprint HierS: hierarchical scaffold clustering using topological chemical graphs
    Steven J Wilkens
    Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
    J Med Chem 48:3182-93. 2005
    ..In addition, biological data are coupled to scaffolds by the inclusion of activity histograms, which indicate how the compounds in each scaffold class performed in previous high-throughput screening campaigns...
  27. pmc Large-scale profiling of Rab GTPase trafficking networks: the membrome
    Cemal Gurkan
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Mol Biol Cell 16:3847-64. 2005
    ..An interactive website for exploring datasets comprising components of the Rab-regulated hubs that define the membrome of different cell and organ systems in both human and mouse is available at http://www.membrome.org/...
  28. pmc Comparative analysis of haplotype association mapping algorithms
    Phillip McClurg
    Genomics Institute of the Novartis Research Foundation, San Diego, USA
    BMC Bioinformatics 7:61. 2006
    ..As the availability of genotyping data grows in size and density, analysis of these haplotype association mapping methods should be of increasing value to the statistical genetics community...
  29. pmc A genome-wide RNAi screen for modifiers of the circadian clock in human cells
    Eric E Zhang
    Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
    Cell 139:199-210. 2009
    ..Coupled with data showing many of these pathways are clock regulated, we conclude the clock is interconnected with many aspects of cellular function...
  30. pmc Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies
    Nancy M Choi
    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Immunol 191:2393-402. 2013
    ..Thus, the Igh locus has evolved a complex system for the regulation of V(D)J rearrangement that is different for each of the four domains that comprise this locus. ..