Research Topics
| Jian Bing FanSummaryAffiliation: Illumina Inc Country: USA Publications
Research Grants
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Detail Information
Publications
BeadArray-based solutions for enabling the promise of pharmacogenomicsJian-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...
High-throughput DNA methylation profiling using universal bead arraysMarina 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...- Highly parallel genome-wide expression analysis of single mammalian cellsJian 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... - Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platformMonica 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... - Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samplesMaggie 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.... - Gene expression profiling of human whole blood samples with the Illumina WG-DASL assayMary 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... - Profiling alternatively spliced mRNA isoforms for prostate cancer classificationChaolin 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... - A versatile assay for high-throughput gene expression profiling on universal array matricesJian 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... - Expression signatures that correlated with Gleason score and relapse in prostate cancerMarina 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... - Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samplesCraig 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... - High-throughput SNP genotyping on universal bead arraysRichard 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... 
High density DNA methylation array with single CpG site resolutionMarina 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...- A highly informative SNP linkage panel for human genetic studiesSarah 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... - Genome-wide DNA methylation profilingMarina 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... - Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assayCraig 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... - Highly sensitive and specific microRNA expression profiling using BeadArray technologyJing 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... - Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead arraysMarina 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... - miRNA expression profiling using Illumina Universal BeadChipsJing 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... - Genomic profiling of 766 cancer-related genes in archived esophageal normal and carcinoma tissuesJing 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... - GoldenGate assay for DNA methylation profilingMarina 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... - Genome-wide mapping of allele-specific protein-DNA interactions in human cellsNathaniel 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... - Whole-genome haplotyping by dilution, amplification, and sequencingFiona Kaper
Illumina, Inc, San Diego, CA 92122
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... - Genome-wide methylation profiles reveal quantitative views of human aging ratesGregory 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... - Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature agesMaggie 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... - Nicotine promotes acquisition of stem cell and epithelial-to-mesenchymal properties in head and neck squamous cell carcinomaMichael 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... - Manifestation of diffuse yellowish keratoderma on the palms and soles in autosomal recessive congenital ichthyosis patients may be indicative of mutations in NIPAL4Afagh 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... - Salinomycin induces cell death and differentiation in head and neck squamous cell carcinoma stem cells despite activation of epithelial-mesenchymal transition and AktSelena 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... - Unraveling epigenetic regulation in embryonic stem cellsMarina 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... - Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expressionDavid Serre
McGill University, Montreal, Quebec, Canada
PLoS Genet 4:e1000006. 2008.... - Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequenceLouise 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... - Gene expression profiles in formalin-fixed, paraffin-embedded tissues obtained with a novel assay for microarray analysisMarina Bibikova
Illumina, Inc, San Diego, CA 92161, USA
Clin Chem 50:2384-6. 2004 - DNA methylation markers of surfactant proteins in lung cancerZhenwu 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... - Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arraysMarina 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... - Decoding randomly ordered DNA arraysKevin 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... - Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promotersYoung 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... - Assessing DNA sequence variations in human ESTs in a phylogenetic context using high-density oligonucleotide arraysJian-Bing Fan
Affymetrix, Inc. 3380 Central Expressway, Santa Clara, California 95051, USA
Genomics 80:351-60. 2002.... - Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimensHai-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.... - Salicylic acid-dependent expression of host genes in compatible Arabidopsis-virus interactionsZhonglian Huang
Department of Plant Pathology, Iowa State University, Ames, Iowa 50011-1020, USA
Plant Physiol 137:1147-59. 2005.... - Functional analysis of human microtubule-based motor proteins, the kinesins and dyneins, in mitosis/cytokinesis using RNA interferenceChangjun 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... - Profiling alternative splicing on fiber-optic arraysJoanne 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... - Paternal origins of complete hydatidiform moles proven by whole genome single-nucleotide polymorphism haplotypingJian-Bing Fan
Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
Genomics 79:58-62. 2002.... - Tobamovirus infection is independent of HSP101 mRNA induction and protein expressionTyrell 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... - DNA methylation signatures within the human brainChristine 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... - Genome-wide detection and characterization of positive selection in human populationsPardis C Sabeti
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Nature 449:913-8. 2007.... - A second generation human haplotype map of over 3.1 million SNPsKelly 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... - Epigenetic specificity of loss of imprinting of the IGF2 gene in Wilms tumorsHans 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... - Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infectionChunling 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... - Illumina universal bead arraysJian-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... - Human embryonic stem cells have a unique epigenetic signatureMarina 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... - Highly parallel genomic assaysJian-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... - Allele-specific expression in the germline of patients with familial pancreatic cancer: an unbiased approach to cancer gene discoveryAik Choon Tan
The Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
Cancer Biol Ther 7:135-44. 2008....
Research Grants
- High-Throughput Methylation Profiling SystemJian Bing Fan; Fiscal Year: 2005....