Yongchao Ge

Summary

Affiliation: Mount Sinai School of Medicine
Country: USA

Publications

  1. pmc flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding
    Yongchao Ge
    Department of Neurology and Center of Translational System Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Bioinformatics 28:2052-8. 2012
  2. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
  3. doi request reprint Multiple testing and its applications to microarrays
    Yongchao Ge
    Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Stat Methods Med Res 18:543-63. 2009
  4. pmc Role of CpG context and content in evolutionary signatures of brain DNA methylation
    Yurong Xin
    Department of Psychiatry, Columbia University and the New York State Psychiatric Institute, New York, NY, USA
    Epigenetics 6:1308-18. 2011
  5. pmc MethylomeDB: a database of DNA methylation profiles of the brain
    Yurong Xin
    Department of Psychiatry, Columbia University and the New York State Psychiatric Institute, New York, NY 10032, USA
    Nucleic Acids Res 40:D1245-9. 2012
  6. pmc Localized mucosal response to intranasal live attenuated influenza vaccine in adults
    María Inés Barría
    Department of Microbiology, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Infect Dis 207:115-24. 2013
  7. pmc Development of a novel peptide microarray for large-scale epitope mapping of food allergens
    Jing Lin
    Pediatric Allergy and Immunology, Mount Sinai School of Medicine, New York, NY 10029 6574, USA
    J Allergy Clin Immunol 124:315-22, 322.e1-3. 2009
  8. pmc Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network
    Yen Sin Ang
    Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
    Cell 145:183-97. 2011
  9. doi request reprint A comprehensive evaluation of human plasmacytoid dendritic cells using small volumes of human blood
    Hannah Phipps-Yonas
    Department of Microbiology, Mount Sinai School of Medicine, New York, New York, USA
    J Interferon Cytokine Res 28:501-7. 2008
  10. pmc Coregulation mapping based on individual phenotypic variation in response to virus infection
    German Nudelman
    Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Immunome Res 6:2. 2010

Collaborators

  • Fernand Hayot
  • Yen Sin Ang
  • Olga Troyanskaya
  • Thomas W Mittag
  • John Danias
  • Xiujun Zhao
  • Lampros Panagis
  • Jing Lin
  • Wayne G Shreffler
  • Julie Wang
  • Hugh Sampson
  • Yurong Xin
  • Stuart C Sealfon
  • FATEMEH G HAGHIGHI
  • Thomas A Kraus
  • Thomas M Moran
  • María Inés Barría
  • Steven Mortillo
  • Venugopalan D Nair
  • Benjamin Chanrion
  • Stephanie M Engel
  • Anne H O'Donnell
  • Maria Milekic
  • German Nudelman
  • Xonia Carvajal-Vergara
  • Hannah Phipps-Yonas
  • Frederique Ruf
  • Robert C Gentleman
  • Erica Scher
  • Jose Luis Garrido
  • David Banach
  • Cheryl Stein
  • Ronald L Davis
  • Ramiro Costa
  • Maria Chikina
  • Jaeyun Kim
  • Natarajan Balasubramaniyan
  • Deanna L Benson
  • Kuangfu Hsiao
  • Shekhar B Patil
  • Yuya Okawa
  • Alice Elste
  • George W Huntley
  • Victoria Arango
  • Andrew J Dwork
  • Aleksandar Stankov
  • Jay A Gingrich
  • Gorazd Rosoklija
  • Jose L Garrido
  • Lisa J Edelmann
  • Ana Sevilla
  • Klaske D Lichtenbelt
  • Jamie L Duke
  • Lisa Kellerman
  • Dung Fang Lee
  • Madhu Kumar
  • Rhoda S Sperling
  • Bruce D Gelb
  • Betty Chang
  • Marta Rodríguez-García
  • Avinash Waghray
  • Marco Tartaglia
  • Ninette Cohen
  • Aaron D Kaplan
  • Yungtai Lo
  • Sunita L d'Souza
  • Steven H Kleinstein
  • Ihor R Lemischka
  • Roye Rozov
  • Jianzhong Hu
  • Jeremy Seto
  • Lei Yang
  • Jie Su
  • Sherly Pardo
  • Tricia Singh
  • James G Wetmur
  • Martine Loubeau
  • Christoph Schaniel
  • Eric D Adler
  • Boris Michael Hartmann
  • Ke Jiang
  • Myung June Park
  • Badrinath Roysam
  • Gang Lin
  • Gordon Smyth
  • Friedrich Leisch
  • Luke Tierney
  • Cheng Li
  • Marcel Dettling
  • Rafael Irizarry

Detail Information

Publications17

  1. pmc flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding
    Yongchao Ge
    Department of Neurology and Center of Translational System Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Bioinformatics 28:2052-8. 2012
    ..The latter approach cannot be applied directly to high-dimensional data as the computational time and memory become unmanageable and the estimated histogram is unreliable. An algorithm without these two problems would be very useful...
  2. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
    ..We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples...
  3. doi request reprint Multiple testing and its applications to microarrays
    Yongchao Ge
    Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Stat Methods Med Res 18:543-63. 2009
    ..The advantages and disadvantages of these methods are discussed. These methods are applied to gene expression data from two microarray studies and the properties of these multiple testing procedures are compared...
  4. pmc Role of CpG context and content in evolutionary signatures of brain DNA methylation
    Yurong Xin
    Department of Psychiatry, Columbia University and the New York State Psychiatric Institute, New York, NY, USA
    Epigenetics 6:1308-18. 2011
    ..We identify key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease...
  5. pmc MethylomeDB: a database of DNA methylation profiles of the brain
    Yurong Xin
    Department of Psychiatry, Columbia University and the New York State Psychiatric Institute, New York, NY 10032, USA
    Nucleic Acids Res 40:D1245-9. 2012
    ....
  6. pmc Localized mucosal response to intranasal live attenuated influenza vaccine in adults
    María Inés Barría
    Department of Microbiology, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Infect Dis 207:115-24. 2013
    ..The measure of successful vaccination with the inactivated vaccine is a systemic rise in immunoglobulin G (IgG) level, but for the LAIV no such correlate has been established...
  7. pmc Development of a novel peptide microarray for large-scale epitope mapping of food allergens
    Jing Lin
    Pediatric Allergy and Immunology, Mount Sinai School of Medicine, New York, NY 10029 6574, USA
    J Allergy Clin Immunol 124:315-22, 322.e1-3. 2009
    ..The peptide microarray is a novel assay that facilitates high-throughput screening of peptides with a small quantity of sample...
  8. pmc Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network
    Yen Sin Ang
    Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
    Cell 145:183-97. 2011
    ..We propose an integrated model of transcriptional and epigenetic control, mediated by select trxG members, for the maintenance of ES cell self-renewal and somatic cell reprogramming...
  9. doi request reprint A comprehensive evaluation of human plasmacytoid dendritic cells using small volumes of human blood
    Hannah Phipps-Yonas
    Department of Microbiology, Mount Sinai School of Medicine, New York, New York, USA
    J Interferon Cytokine Res 28:501-7. 2008
    ..In addition, we have used multiplex enzyme-linked immunosorbent assays to measure secreted proteins. We demonstrate the validity of this technique and document its potential for use with blood from human study populations...
  10. pmc Coregulation mapping based on individual phenotypic variation in response to virus infection
    German Nudelman
    Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Immunome Res 6:2. 2010
    ..CONCLUSIONS: MDS mapping based on correlation in conjunction with TF enrichment analysis represents a useful computational method to generate predictions underlying gene coregulation across a population...
  11. pmc Gene expression changes in areas of focal loss of retinal ganglion cells in the retina of DBA/2J mice
    Lampros Panagis
    Departments of Ophthalmology, Mount Sinai School of Medicine, New York, New York, USA
    Invest Ophthalmol Vis Sci 51:2024-34. 2010
    ....
  12. doi request reprint Peripheral blood cytokine profiling during pregnancy and post-partum periods
    Thomas A Kraus
    Department of Obstetrics, Gynecology and Reproductive Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
    Am J Reprod Immunol 64:411-26. 2010
    ..This immunologic adaptation may contribute to pregnancy-related alterations in disease susceptibility and severity of infections from viral pathogens such as influenza virus...
  13. pmc Methyl-Analyzer--whole genome DNA methylation profiling
    Yurong Xin
    Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, NY 10032, USA
    Bioinformatics 27:2296-7. 2011
    ..Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution...
  14. pmc Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells
    Venugopalan D Nair
    Department of Neurology, Mount Sinai School of Medicine, New York, New York, USA
    Mol Cell Biol 32:4861-76. 2012
    ..Taken together, these results suggest that cell cycle-dependent association and dissociation of LSD1 with chromatin mediates short-time-scale gene expression changes during embryonic stem cell cycle progression...
  15. pmc Compensatory redistribution of neuroligins and N-cadherin following deletion of synaptic β1-integrin
    Steven Mortillo
    Department of Neuroscience, Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York, USA
    J Comp Neurol 520:2041-52. 2012
    ..Together, our findings demonstrate unequivocally that β1-integrin is an integral synaptic adhesion protein, and suggest that adhesive function at the synapse reflects a cooperative and dynamic network of multiple CAM families...
  16. pmc Noise propagation and scaling in regulation of gonadotrope biosynthesis
    Frederique Ruf
    Department of Neurology, Mount Sinai School of Medicine, New York, New York, USA
    Biophys J 93:4474-80. 2007
    ..These results explain the basis for variation in cellular responses in an important mammalian signaling pathway leading to gene induction...
  17. pmc Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome
    Xonia Carvajal-Vergara
    Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
    Nature 465:808-12. 2010
    ..These features correlate with a potential hypertrophic state. We also provide molecular insights into signalling pathways that may promote the disease phenotype...