Simon M Lin

Summary

Affiliation: Northwestern University
Country: USA

Publications

  1. ncbi request reprint Interpreting microarray results with gene ontology and MeSH
    John D Osborne
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
    Methods Mol Biol 377:223-42. 2007
  2. pmc Model-based variance-stabilizing transformation for Illumina microarray data
    Simon M Lin
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
    Nucleic Acids Res 36:e11. 2008
  3. doi request reprint lumi: a pipeline for processing Illumina microarray
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 24:1547-8. 2008
  4. ncbi request reprint A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays
    Chia Ju Lee
    Computational Biology and Bioinformatics Program, Northwestemrn University, Evanston, IL 60208, USA
    Int J Comput Biol Drug Des 1:396-405. 2008
  5. pmc From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
    Pan Du
    The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 25:i63-8. 2009
  6. 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
  7. pmc A collection of bioconductor methods to visualize gene-list annotations
    Gang Feng
    Northwestern University Biomedical Informatics Center NUBIC, part of the Northwestern CTSA and The Robert H, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    BMC Res Notes 3:10. 2010
  8. pmc Annotating the human genome with Disease Ontology
    John D Osborne
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    BMC Genomics 10:S6. 2009
  9. pmc ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    Lihua J Zhu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    BMC Bioinformatics 11:237. 2010
  10. ncbi request reprint Improved prediction of treatment response using microarrays and existing biological knowledge
    Simon M Lin
    Northwestern University, Robert H Lurie Cancer Center, Chicago, IL 60611, USA
    Pharmacogenomics 7:495-501. 2006

Collaborators

Detail Information

Publications30

  1. ncbi request reprint Interpreting microarray results with gene ontology and MeSH
    John D Osborne
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
    Methods Mol Biol 377:223-42. 2007
    ..Examples of searching GO with DAVID, EASE, and GOMiner are provided along with an interpretation of results. The mining of MeSH using high-density array pattern interpreter with a set of gene identifiers is also described...
  2. pmc Model-based variance-stabilizing transformation for Illumina microarray data
    Simon M Lin
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
    Nucleic Acids Res 36:e11. 2008
    ..The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org...
  3. doi request reprint lumi: a pipeline for processing Illumina microarray
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 24:1547-8. 2008
    ..Availability: The lumi Bioconductor package, www.bioconductor.org..
  4. ncbi request reprint A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays
    Chia Ju Lee
    Computational Biology and Bioinformatics Program, Northwestemrn University, Evanston, IL 60208, USA
    Int J Comput Biol Drug Des 1:396-405. 2008
    ..In addition to the performance improvement, the general divide-and-conquer strategy can be applied to any other normalisation algorithms without modifying the underlying implementation...
  5. pmc From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
    Pan Du
    The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 25:i63-8. 2009
    ..The resultant DOLite has been used in the Functional Disease Ontology (FunDO) Web application at http://www.projects.bioinformatics.northwestern.edu/fundo...
  6. 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...
  7. pmc A collection of bioconductor methods to visualize gene-list annotations
    Gang Feng
    Northwestern University Biomedical Informatics Center NUBIC, part of the Northwestern CTSA and The Robert H, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    BMC Res Notes 3:10. 2010
    ..abstract:..
  8. pmc Annotating the human genome with Disease Ontology
    John D Osborne
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    BMC Genomics 10:S6. 2009
    ..The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases...
  9. pmc ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    Lihua J Zhu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    BMC Bioinformatics 11:237. 2010
    ..However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome...
  10. ncbi request reprint Improved prediction of treatment response using microarrays and existing biological knowledge
    Simon M Lin
    Northwestern University, Robert H Lurie Cancer Center, Chicago, IL 60611, USA
    Pharmacogenomics 7:495-501. 2006
    ..For clinical studies, particularly Phase I or I/II studies, this technique is exceptionally advantageous...
  11. ncbi request reprint What is mzXML good for?
    Simon M Lin
    Northwestern University, Robert H Lurie Cancer Center, Chicago, IL 60611, USA
    Expert Rev Proteomics 2:839-45. 2005
    ..With these limitations in mind, the authors conclude that mzXML is, nonetheless, an indispensable data exchange format for proteomics...
  12. pmc Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donors
    Haixi Miao
    Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
    PLoS ONE 3:e2847. 2008
    ....
  13. doi request reprint Using the bioconductor GeneAnswers package to interpret gene lists
    Gang Feng
    Biomedical Informatics Center, Clinical and Translational Sciences Institute, Northwestern University, Chicago, IL, USA
    Methods Mol Biol 802:101-12. 2012
    ..Several network analysis methods are included in GeneAnswers, and the tutorial highlights the conditions under which each type of analysis is most beneficial and provides sample code...
  14. pmc Visual presentation as a welcome alternative to textual presentation of gene annotation information
    Jairav Desai
    The Biomedical Informatics Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
    Adv Exp Med Biol 680:709-15. 2010
    ..Moreover, the survey participants provided many constructive comments that will specify the development of a phase-two project (http://128.248.174.241/) to visually annotate each gene in the human genome...
  15. pmc Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma
    Antonia Navarro
    Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS ONE 7:e33284. 2012
    ..Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities remains unknown...
  16. pmc Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
    Pan Du
    Northwestern University Biomedical Informatics Center NUBIC, NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    BMC Bioinformatics 11:587. 2010
    ..Both Beta-value and M-value statistics have been used as metrics to measure methylation levels. However, there are no detailed studies of their relations and their strengths and limitations...
  17. pmc BALB/c mice genetically susceptible to proteoglycan-induced arthritis and spondylitis show colony-dependent differences in disease penetrance
    Balint Farkas
    Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, 1735 W, Harrison Street, Cohn Research Building, Chicago, IL 60612, USA
    Arthritis Res Ther 11:R21. 2009
    ....
  18. pmc Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors
    Thomas J Lukas
    Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, E Chicago Ave, Chicago, IL 60611, USA
    Genome Biol 9:R111. 2008
    ....
  19. ncbi request reprint Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University Chicago, IL 60611, USA
    Bioinformatics 22:2059-65. 2006
    ..This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods...
  20. pmc Epithelial regulation of mesenchymal tissue behavior
    Corrie L Gallant-Behm
    Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
    J Invest Dermatol 131:892-9. 2011
    ..These results support the idea that soluble factors produced by the epithelium in response to injury may influence fibroblast behavior and regulate scar formation in vivo...
  21. ncbi request reprint 2009 and beyond: the decade of personalised medicine
    Pan Du
    The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    Int J Comput Biol Drug Des 1:329-33. 2008
    ....
  22. ncbi request reprint MedlineR: an open source library in R for Medline literature data mining
    Simon M Lin
    Duke Comprehensive Cancer Center, Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
    Bioinformatics 20:3659-61. 2004
    ..We provide MedlineR as a library foundation for bioinformaticians and statisticians to build more sophisticated literature data mining applications...
  23. ncbi request reprint Microarray analysis: a comparative approach
    Kimberly F Johnson
    Duke Bioinformatics Shared Resource, Box 3958, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cancer Ther 1:237-8. 2002
  24. pmc RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells
    Luiz O F Penalva
    Department of Molecular Genetics and Microbiology, Center for RNA Biology, 414 Jones Building, Research Drive, Duke University Medical Center, Durham, North Carolina 27710, USA
    Mol Cancer 3:24. 2004
    ....
  25. ncbi request reprint Irrational exuberance in clinical proteomics
    Simon M Lin
    Clin Cancer Res 11:7963-4. 2005
  26. ncbi request reprint Gene expression profiles of the rat brain both immediately and 3 months following acute sarin exposure
    Tirupapuliyur V Damodaran
    Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
    Biochem Pharmacol 71:497-520. 2006
    ..Our model also predicts that besides dose and duration of post-treatment period, age and possibly other factors may be playing important roles in the regulation of pathways, leading to the neurotoxicity...
  27. pmc Transcriptional profiling of the Sonic hedgehog response: a critical role for N-myc in proliferation of neuronal precursors
    Trudy G Oliver
    Department of Pharmacology and Cancer Biology and Bioinformatics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 100:7331-6. 2003
    ..Finally, cyclin D1 and N-myc are overexpressed in murine medulloblastoma. These findings suggest that cyclin D1 and N-myc are important mediators of Shh-induced proliferation and tumorigenesis...
  28. ncbi request reprint Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma
    Trudy G Oliver
    Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
    Development 132:2425-39. 2005
    ..The identification and molecular characterization of pre-neoplastic cells provides insight into the early steps in medulloblastoma formation, and may yield important markers for early detection and therapy of this disease...