Jian Bing Fan

Summary

Affiliation: Illumina Inc
Country: USA

Publications

  1. ncbi request reprint BeadArray-based solutions for enabling the promise of pharmacogenomics
    Jian Bing Fan
    Illumina, San Diego, CA 92121, USA
    Biotechniques 39:583-8. 2005
  2. pmc High-throughput DNA methylation profiling using universal bead arrays
    Marina Bibikova
    Illumina, Inc, San Diego, California 92121, USA
    Genome Res 16:383-93. 2006
  3. pmc Highly sensitive and specific microRNA expression profiling using BeadArray technology
    Jing Chen
    Illumina, Inc 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Nucleic Acids Res 36:e87. 2008
  4. pmc Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples
    Craig April
    Illumina, Inc, San Diego, California, United States of America
    PLoS ONE 4:e8162. 2009
  5. pmc Highly parallel genome-wide expression analysis of single mammalian cells
    Jian Bing Fan
    Research and Development, Illumina, Inc, San Diego, California, United States of America
    PLoS ONE 7:e30794. 2012
  6. pmc Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform
    Monica M Reinholz
    Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, Minnesota 55905, USA
    BMC Med Genomics 3:60. 2010
  7. pmc Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples
    Maggie L Chow
    Department of Neuroscience, NIH UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, 8110 La Jolla Shores Dr Ste 201, La Jolla, CA 92093, USA
    BMC Genomics 12:449. 2011
  8. pmc Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay
    Mary E Winn
    Scripps Genomic Medicine and Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    BMC Genomics 12:412. 2011
  9. pmc Profiling alternatively spliced mRNA isoforms for prostate cancer classification
    Chaolin Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 7:202. 2006
  10. pmc A versatile assay for high-throughput gene expression profiling on universal array matrices
    Jian Bing Fan
    Illumina, Inc, San Diego, California 92121, USA
    Genome Res 14:878-85. 2004

Research Grants

  1. High-Throughput Methylation Profiling System
    Jian Bing Fan; Fiscal Year: 2005

Collaborators

Detail Information

Publications53

  1. ncbi request reprint BeadArray-based solutions for enabling the promise of pharmacogenomics
    Jian Bing Fan
    Illumina, San Diego, CA 92121, USA
    Biotechniques 39:583-8. 2005
    ..We will then demonstrate how microarray technologies-among them bead-based approaches-have emerged as a key enabler for bringing home the promise of PGx...
  2. pmc High-throughput DNA methylation profiling using universal bead arrays
    Marina Bibikova
    Illumina, Inc, San Diego, California 92121, USA
    Genome Res 16:383-93. 2006
    ..The technology should prove useful for DNA methylation analyses in large populations, with potential application to the classification and diagnosis of a broad range of cancers and other diseases...
  3. pmc Highly sensitive and specific microRNA expression profiling using BeadArray technology
    Jing Chen
    Illumina, Inc 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Nucleic Acids Res 36:e87. 2008
    ..85-0.90) and direct sequencing (R = 0.87-0.89). This method, in conjunction with the 96-sample array matrix should prove useful for high-throughput expression profiling of miRNAs in large numbers of tissue samples...
  4. pmc Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples
    Craig April
    Illumina, Inc, San Diego, California, United States of America
    PLoS ONE 4:e8162. 2009
    ..We have developed a gene expression assay (Whole-Genome DASL), capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE) specimens...
  5. pmc Highly parallel genome-wide expression analysis of single mammalian cells
    Jian Bing Fan
    Research and Development, Illumina, Inc, San Diego, California, United States of America
    PLoS ONE 7:e30794. 2012
    ..We have developed a high-throughput amplification method for generating robust gene expression profiles using single cell or low RNA inputs...
  6. pmc Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform
    Monica M Reinholz
    Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, Minnesota 55905, USA
    BMC Med Genomics 3:60. 2010
    ..5K) and 24,526-gene panel (24K) platforms at differentiating nine human epidermal growth factor receptor 2- positive (HER2+) and 11 HER2-negative (HER2-) paraffin-embedded breast tumors...
  7. pmc Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples
    Maggie L Chow
    Department of Neuroscience, NIH UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, 8110 La Jolla Shores Dr Ste 201, La Jolla, CA 92093, USA
    BMC Genomics 12:449. 2011
    ....
  8. pmc Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay
    Mary E Winn
    Scripps Genomic Medicine and Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    BMC Genomics 12:412. 2011
    ..We assessed the utility of the whole genome DASL assay in an analysis of peripheral whole blood gene expression profiles...
  9. pmc Profiling alternatively spliced mRNA isoforms for prostate cancer classification
    Chaolin Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 7:202. 2006
    ..Here, we investigate the advantage of using splice isoforms, which couple transcriptional and splicing regulation, for cancer classification...
  10. pmc A versatile assay for high-throughput gene expression profiling on universal array matrices
    Jian Bing Fan
    Illumina, Inc, San Diego, California 92121, USA
    Genome Res 14:878-85. 2004
    ..The combined high-throughput assay and readout system is accurate and efficient, and can cost-effectively profile the expression of hundreds of genes in thousands of samples...
  11. pmc Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays
    Marina Bibikova
    Genetic Analysis, Illumina, Inc, 9885 Towne Center Drive, San Diego, CA 92121, USA
    Am J Pathol 165:1799-807. 2004
    ..The DASL assay system should prove useful for high-throughput expression profiling of archived clinical samples...
  12. ncbi request reprint Gene expression profiles in formalin-fixed, paraffin-embedded tissues obtained with a novel assay for microarray analysis
    Marina Bibikova
    Illumina, Inc, San Diego, CA 92161, USA
    Clin Chem 50:2384-6. 2004
  13. ncbi request reprint Expression signatures that correlated with Gleason score and relapse in prostate cancer
    Marina Bibikova
    Illumina, Inc, 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Genomics 89:666-72. 2007
    ..007). These results suggest that the approach we used is effective for expression profiling in heterogeneous FFPE tissues for cancer diagnosis/prognosis biomarker discovery and validation...
  14. ncbi request reprint Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens
    Hai Ri Li
    Department of Cellular and Molecular Medicine, San Diego Supercomputer Center, University of California, San Diego, La Jolla 92093 0651, USA
    Cancer Res 66:4079-88. 2006
    ....
  15. pmc Human embryonic stem cells have a unique epigenetic signature
    Marina Bibikova
    Illumina, Inc, San Diego, California 92121, USA
    Genome Res 16:1075-83. 2006
    ..Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential...
  16. ncbi request reprint High-throughput SNP genotyping on universal bead arrays
    Richard Shen
    Illumina Inc, 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Mutat Res 573:70-82. 2005
    ..6 million genotypes per day in a robotics-assisted process. With a streamlined and comprehensive assay, this system brings a new level of flexibility, throughput, and affordability to genetic research...
  17. doi request reprint High density DNA methylation array with single CpG site resolution
    Marina Bibikova
    Illumina, Inc 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Genomics 98:288-95. 2011
    ..Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research...
  18. doi request reprint Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead arrays
    Marina Bibikova
    Illumina Inc, San Diego, CA, USA
    Methods Mol Biol 439:159-77. 2008
    ..Using the DASL Assay, gene expression analyses can be performed on routinely stored tumor specimens from patients with known outcomes...
  19. doi request reprint Genome-wide DNA methylation profiling
    Marina Bibikova
    Illumina, Inc, 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Wiley Interdiscip Rev Syst Biol Med 2:210-23. 2010
    ..Either whole- or reduced-genome approaches have been used to get the most comprehensive DNA methylation profiles in organisms of various genome sizes...
  20. doi request reprint GoldenGate assay for DNA methylation profiling
    Marina Bibikova
    Illumina Inc, San Diego, CA, USA
    Methods Mol Biol 507:149-63. 2009
    ..The Illumina GoldenGate Methylation technology should prove useful for DNA methylation analyses in large populations, with potential application to biomarker discovery and validation...
  21. ncbi request reprint A highly informative SNP linkage panel for human genetic studies
    Sarah Shaw Murray
    Illumina, Inc, 9885 Towne Centre Drive, San Diego, California 92121 1975, USA
    Nat Methods 1:113-7. 2004
    ..The potent combination of this SNP linkage panel with the multiplexed assay system provides a previously unattainable level of performance for linkage studies...
  22. doi request reprint Genomic profiling of 766 cancer-related genes in archived esophageal normal and carcinoma tissues
    Jing Chen
    Illumina Inc, San Diego, CA 92121, USA
    Int J Cancer 122:2249-54. 2008
    ..Taken together, our results demonstrated the utility of the BeadArray technology for high-throughput genetic analysis in FFPE tumor tissues and provided a detailed genetic profiling of cancer-related genes in human esophageal cancer...
  23. pmc Decoding randomly ordered DNA arrays
    Kevin L Gunderson
    Illumina, Inc, San Diego, California 92121, USA
    Genome Res 14:870-7. 2004
    ..The algorithm can be applied to any spatially fixed collection of objects or molecules that are associated with specific DNA sequences...
  24. doi request reprint Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assay
    Craig S April
    Illumina, Inc, San Diego, CA, USA
    Methods Mol Biol 784:77-98. 2011
    ..This technology is particularly useful for genome-wide expression profiling in degraded, archived material, including limited quantities of clinical samples, such as microdissected and biopsied materials...
  25. doi request reprint Genome-wide mapping of allele-specific protein-DNA interactions in human cells
    Nathaniel D Maynard
    Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Ave, La Jolla, California 92037, USA
    Nat Methods 5:307-9. 2008
    ..ChIP-SNP will facilitate the study of mechanisms of allele-specific gene expression...
  26. ncbi request reprint Highly parallel genomic assays
    Jian Bing Fan
    Illumina Inc, 9885 Towne Centre Drive, San Diego, California 92121, USA
    Nat Rev Genet 7:632-44. 2006
    ..In the future, most cancers might be staged by high-resolution molecular profiling rather than by gross cytological analysis. Here, we describe the key developments that enable highly parallel genomic assays...
  27. doi request reprint miRNA expression profiling using Illumina Universal BeadChips
    Jing Chen
    Illumina, Inc, San Diego, CA, USA
    Methods Mol Biol 822:103-16. 2012
    ..85-0.90) and direct sequencing (R = 0.87-0.89). This method should prove useful for high-throughput expression profiling of miRNAs in large numbers of tissue samples...
  28. ncbi request reprint Illumina universal bead arrays
    Jian Bing Fan
    Illumina, Inc, San Diego, California, USA
    Methods Enzymol 410:57-73. 2006
    ..This chapter describes the concept of the BeadArray technology, two different Array of Arrays formats, the assay scheme and protocol, the performance of the system, and its use in large-scale genetic, epigenetic, and expression studies...
  29. pmc Salinomycin induces cell death and differentiation in head and neck squamous cell carcinoma stem cells despite activation of epithelial-mesenchymal transition and Akt
    Selena Z Kuo
    Division of Otolaryngology Head and Neck Surgery, Department of Surgery, University of California, San Diego, San Diego, CA, USA
    BMC Cancer 12:556. 2012
    ..In our study we sought to determine the effects of salinomycin on head and neck squamous cell carcinoma (HNSCC) stem cells...
  30. pmc Whole-genome haplotyping by dilution, amplification, and sequencing
    Fiona Kaper
    Illumina, Inc, San Diego, CA 92122, USA
    Proc Natl Acad Sci U S A 110:5552-7. 2013
    ..The N50 for a Yoruba male DNA was 702 kb whereas the N50 for a European female DNA was 358 kb. Therefore, the strategy described here is suitable for haplotyping of a set of targeted regions as well as of the entire genome...
  31. doi request reprint Translational utility of next-generation sequencing
    Frank S Ong
    Illumina, Inc, San Diego, CA 92122, USA
    Genomics 102:137-9. 2013
    ....
  32. pmc Genome-wide methylation profiles reveal quantitative views of human aging rates
    Gregory Hannum
    Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
    Mol Cell 49:359-67. 2013
    ..Our model highlights specific components of the aging process and provides a quantitative readout for studying the role of methylation in age-related disease...
  33. pmc Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages
    Maggie L Chow
    Department of Neuroscience, NIH UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, La Jolla, California, United States of America
    PLoS Genet 8:e1002592. 2012
    ..Our results raise the hypothesis that genetic dysregulation in the developing brain leads to abnormal regional patterning, excess prefrontal neurons, cortical overgrowth, and neural dysfunction in autism...
  34. doi request reprint Unraveling epigenetic regulation in embryonic stem cells
    Marina Bibikova
    Illumina, Inc, San Diego, CA 92121, USA
    Cell Stem Cell 2:123-34. 2008
    ..Understanding the interactions among these factors will be critical to the development of improved strategies to reprogram differentiated cells or direct differentiation of pluripotent cells...
  35. pmc Nicotine promotes acquisition of stem cell and epithelial-to-mesenchymal properties in head and neck squamous cell carcinoma
    Michael Andrew Yu
    Division of Otolaryngology Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, CA, USA
    PLoS ONE 7:e51967. 2012
    ..Further characterization of such pathways remains a promising avenue for the understanding and treatment of tobacco-related cancers...
  36. doi request reprint Manifestation of diffuse yellowish keratoderma on the palms and soles in autosomal recessive congenital ichthyosis patients may be indicative of mutations in NIPAL4
    Afagh Alavi
    School of Biology, University of Tehran, Tehran, Iran
    J Dermatol 39:375-81. 2012
    ..We provide evidence suggesting presentation of this diffuse yellowish keratoderma may be indicative of mutations in NIPAL4, providing an easily assessable genotype-phenotype correlation...
  37. ncbi request reprint Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer
    Chen Wang
    Authors Affiliations Departments of Health Sciences Research, Medical Oncology, Obstetrics and Gynecology, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles Department of Research, Illumina, San Diego, California Departments of Cancer Biology and Biostatistics, University of Kansas Medical Center, Kansas City, Kansas and Vaccine and Gene Therapy Institute of Florida, Port St Lucie, Florida
    Cancer Res 74:3084-91. 2014
    ..Collectively, these results suggest that an epigenetically mediated immune response is a predictor of recurrence and, possibly, treatment response for HGS EOC. Cancer Res; 74(11); 3084-91. ©2014 AACR. ..
  38. ncbi request reprint Assessing DNA sequence variations in human ESTs in a phylogenetic context using high-density oligonucleotide arrays
    Jian Bing Fan
    Affymetrix, Inc 3380 Central Expressway, Santa Clara, California 95051, USA
    Genomics 80:351-60. 2002
    ....
  39. pmc Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters
    Young Soo Kwon
    Department of Cellular and Molecular Medicine, University of California at San Diego School of Medicine, La Jolla, CA 92093 0651, USA
    Proc Natl Acad Sci U S A 104:4852-7. 2007
    ..This study demonstrates the power of the ChIP-DSL technology in revealing regulatory gene expression programs that have been previously invisible in the human genome...
  40. ncbi request reprint Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence
    Louise C Laurent
    The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Stem Cells 26:1506-16. 2008
    ..We propose that miRNAs are coordinately controlled in hESCs, and are key regulators of pluripotence and differentiation. Disclosure of potential conflicts of interest is found at the end of this article...
  41. ncbi request reprint DNA methylation markers of surfactant proteins in lung cancer
    Zhenwu Lin
    Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
    Int J Oncol 31:181-91. 2007
    ..We speculate that SP-A1 and SP-D are subject to methylation/demethylation regulatory mechanisms and are involved in lung cancer pathogenesis by virtue of their function in innate host defense and/or regulation of inflammation...
  42. pmc Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression
    David Serre
    McGill University, Montreal, Quebec, Canada
    PLoS Genet 4:e1000006. 2008
    ....
  43. ncbi request reprint Epigenetic specificity of loss of imprinting of the IGF2 gene in Wilms tumors
    Hans T Bjornsson
    Center for Epigenetics, Institute of Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Natl Cancer Inst 99:1270-3. 2007
    ..Thus, epigenetic alterations in Wilms tumors are not widespread, supporting the gene and lineage specificity of LOI of IGF2...
  44. ncbi request reprint Profiling alternative splicing on fiber-optic arrays
    Joanne M Yeakley
    Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Nat Biotechnol 20:353-8. 2002
    ..Our approach may be useful in the large-scale analysis of the role of alternative splicing in development and disease...
  45. ncbi request reprint Allele-specific expression in the germline of patients with familial pancreatic cancer: an unbiased approach to cancer gene discovery
    Aik Choon Tan
    The Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
    Cancer Biol Ther 7:135-44. 2008
    ....
  46. pmc Salicylic acid-dependent expression of host genes in compatible Arabidopsis-virus interactions
    Zhonglian Huang
    Department of Plant Pathology, Iowa State University, Ames, Iowa 50011 1020, USA
    Plant Physiol 137:1147-59. 2005
    ....
  47. pmc Functional analysis of human microtubule-based motor proteins, the kinesins and dyneins, in mitosis/cytokinesis using RNA interference
    Changjun Zhu
    The Burnham Institute, La Jolla, CA 92037, USA
    Mol Biol Cell 16:3187-99. 2005
    ..Using immunofluorescence analysis, time-lapse microscopy, and rescue experiments, we investigate the roles of these 12 kinesins in detail...
  48. pmc DNA methylation signatures within the human brain
    Christine Ladd-Acosta
    Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Am J Hum Genet 81:1304-15. 2007
    ..These results were validated for all six genes tested in a replicate set of 57 samples. Our data suggest that DNA methylation signatures distinguish brain regions and may help account for region-specific functional specialization...
  49. ncbi request reprint Paternal origins of complete hydatidiform moles proven by whole genome single-nucleotide polymorphism haplotyping
    Jian Bing Fan
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Genomics 79:58-62. 2002
    ....
  50. ncbi request reprint Tobamovirus infection is independent of HSP101 mRNA induction and protein expression
    Tyrell Carr
    Department of Plant Pathology, Iowa State University, 351 Bessey Hall, Ames, 50011 1020, USA
    Virus Res 121:33-41. 2006
    ..Similar results were obtained for TMV infection in Nicotiana benthamiana plants silenced for HSP101, demonstrating that HSP101 is not necessary for efficient tobamovirus infection...
  51. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  52. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  53. ncbi request reprint Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infection
    Chunling Yang
    Department of Plant Pathology, Iowa State University, Ames, Iowa 50011, USA
    Mol Plant Microbe Interact 20:358-70. 2007
    ..The functions of these downregulated genes are consistent with viral symptoms, such as chlorosis and stunted growth, providing new insight into mechanisms of pathogenesis...

Research Grants1

  1. High-Throughput Methylation Profiling System
    Jian Bing Fan; Fiscal Year: 2005
    ....