Jessica C Mar

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc attract: A method for identifying core pathways that define cellular phenotypes
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS ONE 6:e25445. 2011
  2. pmc Variance of gene expression identifies altered network constraints in neurological disease
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Boston, United States of America
    PLoS Genet 7:e1002207. 2011
  3. pmc Defining an informativeness metric for clustering gene expression data
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 27:1094-100. 2011
  4. pmc Data-driven normalization strategies for high-throughput quantitative RT-PCR
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
    BMC Bioinformatics 10:110. 2009
  5. pmc Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
    Orit Rozenblatt-Rosen
    Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
    Nature 487:491-5. 2012
  6. doi request reprint nEASE: a method for gene ontology subclassification of high-throughput gene expression data
    Thomas W Chittenden
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA
    Bioinformatics 28:726-8. 2012
  7. pmc Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines
    Bo Zhao
    Department of Medicine and Microbiology and Molecular Genetics, Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:337-42. 2011
  8. pmc Genome-wide siRNA screen for mediators of NF-κB activation
    Benjamin E Gewurz
    Department of Medicine and Microbiology and Molecular Genetics, Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 109:2467-72. 2012
  9. pmc Viral perturbations of host networks reflect disease etiology
    Natali Gulbahce
    Center for Complex Networks Research CCNR and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002531. 2012
  10. pmc Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation
    Benjamin E Gewurz
    Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
    J Virol 85:6764-73. 2011

Collaborators

Detail Information

Publications14

  1. pmc attract: A method for identifying core pathways that define cellular phenotypes
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS ONE 6:e25445. 2011
    ..attract can be applied to a wide range of biological systems and is freely available as a Bioconductor package and has been incorporated into the MeV software system...
  2. pmc Variance of gene expression identifies altered network constraints in neurological disease
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Boston, United States of America
    PLoS Genet 7:e1002207. 2011
    ..Furthermore, modeling patterns of variability in gene expression could fundamentally alter the way in which we think about how cellular networks are affected by disease processes...
  3. pmc Defining an informativeness metric for clustering gene expression data
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 27:1094-100. 2011
    ....
  4. pmc Data-driven normalization strategies for high-throughput quantitative RT-PCR
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
    BMC Bioinformatics 10:110. 2009
    ..The use of appropriate normalization algorithms for qPCR-based data is therefore a highly important aspect of the data preprocessing pipeline...
  5. pmc Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
    Orit Rozenblatt-Rosen
    Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
    Nature 487:491-5. 2012
    ..Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate the prioritization of cancer-causing driver genes to advance the understanding of the genetic basis of human cancer...
  6. doi request reprint nEASE: a method for gene ontology subclassification of high-throughput gene expression data
    Thomas W Chittenden
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA
    Bioinformatics 28:726-8. 2012
    ..Here, we overview an open-source software version of the nEASE algorithm. nEASE can be used either stand-alone or as part of a pathway discovery pipeline...
  7. pmc Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines
    Bo Zhao
    Department of Medicine and Microbiology and Molecular Genetics, Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:337-42. 2011
    ..EBNA3C also up-regulated MYC 1.3-fold and down-regulated CDKN2A exons 2 and 3, shared by p16 and p14, 1.4-fold, with false discovery rates < 5 × 10(-4)...
  8. pmc Genome-wide siRNA screen for mediators of NF-κB activation
    Benjamin E Gewurz
    Department of Medicine and Microbiology and Molecular Genetics, Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 109:2467-72. 2012
    ..Down-modulators of LMP1 mediated NFκB activation were also identified. These experiments identify multiple targets to inhibit or stimulate LMP1-, IL-1β-, or TNFα-mediated canonical NFκB activation...
  9. pmc Viral perturbations of host networks reflect disease etiology
    Natali Gulbahce
    Center for Complex Networks Research CCNR and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002531. 2012
    ..The topological proximity found between cellular targets of viral proteins and disease genes was exploited to uncover a novel pathway linking HPV to Fanconi anemia...
  10. pmc Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation
    Benjamin E Gewurz
    Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
    J Virol 85:6764-73. 2011
    ..001-fold and >2-fold changes. Thus, canonical NF-κB activation is critical for almost all LMP1 TES2 RNA effects in HEK-293 cells and a more significant therapeutic target than previously appreciated...
  11. pmc Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth
    Bo Zhao
    Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:14902-7. 2011
    ..The primed RBL program likely supports antigen-induced proliferation...
  12. pmc Therapeutic implications of GIPC1 silencing in cancer
    Thomas W Chittenden
    Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, United States America
    PLoS ONE 5:e15581. 2010
    ..Taken together, these data indicate that GIPC1 inhibition may represent a new target for therapeutic development for the treatment of human cancers...
  13. pmc Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Huntington Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 7:R119. 2006
    ..However, the starting point for all cellular gene expression, the transcription of RNA, has not been described and measured in a population of living cells...
  14. pmc Decomposition of gene expression state space trajectories
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
    PLoS Comput Biol 5:e1000626. 2009
    ..Using functional enrichment analyses, specific biological examples and an analysis of the trajectories and their core and transient components we provide a validation of our hypothesis using the Huang et al. (2005) dataset...