The Mason Lab

Integrative Functional Genomics


our interests

Research

We aim to use and improve technological methods in molecular genetics, so we can more accurately map the molecular networks of the genome and their changes over time. We leverage clinical cases which can reveal the most about the human genome: the most peculiar cases in human genetics, the most aggressive cancers, and the most striking brain malformations. We continually curate a functional annotation map of the human genome from experimental and computational work, and have the fortunate opportunity to work with patients and families who refine and inform our genomic hypotheses, thus improving our models of the genomic elements responsible for development and disease, and detailing the genetic structures that engineer human biology.

  • Cancer & Rare
    diseases
  • Epigenome and
    Epitranscriptome
  • Genome assembly
    & evolution
  • Neurogenetics
  • Space Genomics and
    Genome Technology
  • Metagenomics

who we are

lab members

“Researchers often want Bioinformaticians to be Biomagicians, people who can make significant results out of non-significant data, or Biomorticians, people who can bury data that disagree with the researcher's prior hypothesis.”
-Dan Masys

Former members: Sheng Li (Ph.D. 2015 - Instructor of Bioinformatics, Weill Cornell Medical College), Yogesh Saletore (Ph.D. 2015), Russell Durrett, Paul Zumbo, Altuna Akalin

publications

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  • Peter H Sudmant et al., “An integrated map of structural variation in 2,504 human genomes”, Nature, 526, pp 75-81, Feb 2015.

  • Peter H Sudmant et al., “An integrated map of structural variation in 2,504 human genomes”, Nature, 526, pp 75-81, Feb 2015.

  • Anton G Henssen et al., “Genomic DNA transposition induced by human PGBD5”, eLIFE, 4, Sep 2015.

  • Anton G Henssen et al., “Genomic DNA transposition induced by human PGBD5”, eLIFE, 4, Sep 2015.

  • Ash A Alizadeh et al., “Toward understanding and exploiting tumor heterogeneity”, Nature Medicine, 21, pp 846–853, Aug 2015.

  • Ash A Alizadeh et al., “Toward understanding and exploiting tumor heterogeneity”, Nature Medicine, 21, pp 846–853, Aug 2015.

  • Ebrahim Afshinnekoo et al., “Modern Methods for Delineating Metagenomic Complexity”, Cell Systems, 1, pp 6-7, Jul 2015.

  • Ebrahim Afshinnekoo et al., “Modern Methods for Delineating Metagenomic Complexity”, Cell Systems, 1, pp 6-7, Jul 2015.

  • Ebrahim Afshinnekoo et al., “Geospatial Resolution of Human and Bacterial Diversity from City-scale Metagenomics”, Cell Systems, 1, pp 72–87, Feb 2015.

  • Ebrahim Afshinnekoo et al., “Geospatial Resolution of Human and Bacterial Diversity from City-scale Metagenomics”, Cell Systems, 1, pp 72–87, Feb 2015.

  • Leonard Lipovich et al., “High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans”, J Comp Neurol, Aug 2015.

  • Leonard Lipovich et al., “High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans”, J Comp Neurol, Aug 2015.

  • Matthew Pendleton et al., “Assembly and diploid architecture of an individual human genome via single-molecule technologies”, Nature Methods, 12, pp 780–786, Jun 2015.

  • Matthew Pendleton et al., “Assembly and diploid architecture of an individual human genome via single-molecule technologies”, Nature Methods, 12, pp 780–786, Jun 2015.

  • Bastian Linder, Anya V Grozhik, Anthony O Olarerin-George, Cem Meydan, Christopher E Mason & Samie R Jaffrey, “Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome”, Nature Methods, 12, pp 767–772, Jun 2015.

  • Bastian Linder, Anya V Grozhik, Anthony O Olarerin-George, Cem Meydan, Christopher E Mason & Samie R Jaffrey, “Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome”, Nature Methods, 12, pp 767–772, Jun 2015.

  • Amy S Gargis, et al., “Good laboratory practice for clinical next-generation sequencing informatics pipelines”, Nature Biotechnology, 33, pp 689–693, Jul 2015.

  • Amy S Gargis, et al., “Good laboratory practice for clinical next-generation sequencing informatics pipelines”, Nature Biotechnology, 33, pp 689–693, Jul 2015.

  • Sagar Chhangawala, Gabe Rudy, Christopher E. Mason, & Jeffrey A. Rosenfeld “The impact of read length on quantification of differentially expressed genes and splice junction detection”, Genome Biology, 16:131, Dec 2015.

  • Sagar Chhangawala, Gabe Rudy, Christopher E. Mason, & Jeffrey A. Rosenfeld “The impact of read length on quantification of differentially expressed genes and splice junction detection”, Genome Biology, 16:131, Dec 2015.

  • Alan H. Shih, et al., “Mutational Cooperativity Linked to Combinatorial Epigenetic Gain of Function in Acute Myeloid Leukemia”, Cancer Cell, 27, pp 502-515

  • Alan H. Shih, et al., “Mutational Cooperativity Linked to Combinatorial Epigenetic Gain of Function in Acute Myeloid Leukemia”, Cancer Cell, 27, pp 502-515

  • Francine E. Garrett-Bakelman, Caroline K. Sheridan, Thadeous J. Kacmarczyk, Jennifer Ishii, Doron Betel, Alicia Alonso, Christopher E. Mason, Maria E. Figueroa, & Ari M. Melnick, “Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution”, J Visualized Experiments, (96): 52246, Feb 2015.

  • Francine E. Garrett-Bakelman, Caroline K. Sheridan, Thadeous J. Kacmarczyk, Jennifer Ishii, Doron Betel, Alicia Alonso, Christopher E. Mason, Maria E. Figueroa, & Ari M. Melnick, “Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution”, J Visualized Experiments, (96): 52246, Feb 2015.

  • Wenhuo Hu, et al., “miR-29a maintains mouse hematopoietic stem cell self-renewal by regulating Dnmt3a”, Blood, 125, pp 2206-2216, Apr 2015.

  • Wenhuo Hu, et al., “miR-29a maintains mouse hematopoietic stem cell self-renewal by regulating Dnmt3a”, Blood, 125, pp 2206-2216, Apr 2015.

  • Xinxia Peng et al., “Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)”, Nucleic Acids Research, 43, D737-42, Jan 2015.

  • Xinxia Peng et al., “Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)”, Nucleic Acids Research, 43, D737-42, Jan 2015.

  • Matthew I. Bellgard, et al., “Rare Disease Research Roadmap: Navigating the bioinformatics and translational challenges for improved patient health outcomes”, Health Policy and Technology, 3, 4, pp 325–335, Dec 2014.

  • Matthew I. Bellgard, et al., “Rare Disease Research Roadmap: Navigating the bioinformatics and translational challenges for improved patient health outcomes”, Health Policy and Technology, 3, 4, pp 325–335, Dec 2014.

  • Inna Dubchak et al., “An Integrative Computational Approach for Prioritization of Genomic Variants”, PLoS ONE 9(12): e114903, Dec 2014.

  • Inna Dubchak et al., “An Integrative Computational Approach for Prioritization of Genomic Variants”, PLoS ONE 9(12): e114903, Dec 2014.

  • Raajit Rampal et al., “DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia”, 9, pp 1841–1855, Dec 2014.

  • Raajit Rampal et al., “DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia”, 9, pp 1841–1855, Dec 2014.

  • Altuna Akalin, Vedran Franke, Kristian Vlahoviček, Christopher E. Mason, & Dirk Schübeler, “genomation: a toolkit to summarize, annotate and visualize genomic intervals”, Bioinformatics, 31, pp 1127-1129, Nov 2014.

  • Altuna Akalin, Vedran Franke, Kristian Vlahoviček, Christopher E. Mason, & Dirk Schübeler, “genomation: a toolkit to summarize, annotate and visualize genomic intervals”, Bioinformatics, 31, pp 1127-1129, Nov 2014.

  • Niina Haiminen, et al., “Comparative exomics of Phalaris cultivars under salt stress”, BMC Genomics, 15(Suppl 6):S18, Oct 2014.

  • Niina Haiminen, et al., “Comparative exomics of Phalaris cultivars under salt stress”, BMC Genomics, 15(Suppl 6):S18, Oct 2014.

  • Sheng Li et al., “Dynamic evolution of clonal epialleles revealed by methclone”, Genome Biology, 15(9):472, Sep 2014.

  • Sheng Li et al., “Dynamic evolution of clonal epialleles revealed by methclone”, Genome Biology, 15(9):472, Sep 2014.

  • M Brian Couger, et al., “Enabling large-scale next-generation sequence assembly with Blacklight”, Concurrency and Computation Practice and Experience, 26(13), pp 2157-2166, Sep 2014.

  • M Brian Couger, et al., “Enabling large-scale next-generation sequence assembly with Blacklight”, Concurrency and Computation Practice and Experience, 26(13), pp 2157-2166, Sep 2014.

  • Sarah A. Munro et al. “Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures”, Nature Communications, 25;5:5125, Sep 2014.

  • Sarah A. Munro et al. “Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures”, Nature Communications, 25;5:5125, Sep 2014.

  • Joshua Xu, Zhenqiang Su, Huixiao Hong, Jean Thierry-Mieg, Danielle Thierry-Mieg, David P. Kreil, Christopher E. Mason, Weida Tong & Leming Shi. “Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq”, Scientific Data, 1:140020, Feb 2014

  • Joshua Xu, Zhenqiang Su, Huixiao Hong, Jean Thierry-Mieg, Danielle Thierry-Mieg, David P. Kreil, Christopher E. Mason, Weida Tong & Leming Shi. “Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq”, Scientific Data, 1:140020, Feb 2014

  • Seqc/Maqc-Iii Consortium, “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium,” Nature biotechnology, vol. 32, iss. 9, pp. 903-914, Sep 2014.

    Seqc/Maqc-Iii Consortium, “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium,” Nature biotechnology, vol. 32, iss. 9, pp. 903-914, Sep 2014.

  • Seqc/Maqc-Iii Consortium, “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium,” Nature biotechnology, vol. 32, iss. 9, pp. 903-914, Sep 2014.

  • Sheng Li et al., “Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study,” Nature biotechnology, vol. 32, iss. 9, pp. 915-925, Sep 2014.

    Sheng Li et al., “Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study,” Nature biotechnology, vol. 32, iss. 9, pp. 915-925, Sep 2014.

  • Sheng Li et al., “Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study,” Nature biotechnology, vol. 32, iss. 9, pp. 915-925, Sep 2014.

  • Detecting and correcting systematic variation in large-scale RNA sequencing data

    Sheng Li, Paweł P. Łabaj, Paul Zumbo, Peter Sykacek, Wei Shi, Leming Shi, John Phan, Po-Yen Wu, May Wang, Charles Wang, Danielle Thierry-Mieg, Jean Thierry-Mieg, David P. Kreil, and Christopher E. Mason, “Detecting and correcting systematic variation in large-scale RNA sequencing data,” Nature biotechnology, vol. 32, iss. 9, pp. 888-895, Sep 2014.

  • Sheng Li, Paweł P. Łabaj, Paul Zumbo, Peter Sykacek, Wei Shi, Leming Shi, John Phan, Po-Yen Wu, May Wang, Charles Wang, Danielle Thierry-Mieg, Jean Thierry-Mieg, David P. Kreil, and Christopher E. Mason, “Detecting and correcting systematic variation in large-scale RNA sequencing data,” Nature biotechnology, vol. 32, iss. 9, pp. 888-895, Sep 2014.

  • Cell-cycle reprogramming for PI3k inhibition overrides a relapse-specific c481s BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma

    David Chiron et al., “Cell-cycle reprogramming for PI3k inhibition overrides a relapse-specific c481s BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma,” Cancer discovery, vol. 4, iss. 9, pp. 1022-1035, Sep 2014.

  • David Chiron et al., “Cell-cycle reprogramming for PI3k inhibition overrides a relapse-specific c481s BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma,” Cancer discovery, vol. 4, iss. 9, pp. 1022-1035, Sep 2014.

  • Assessment and improvement of indian-origin rhesus macaque and mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data

    Xinxia Peng, Lenore Pipes, Hao Xiong, Richard R. Green, Daniel C. Jones, Walter L. Ruzzo, Gary P. Schroth, Christopher E. Mason, Robert E. Palermo, and Michael G. Katze, “Assessment and improvement of indian-origin rhesus macaque and mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data,” Journal of medical primatology, p. n/a–n/a, May 2014.

  • Xinxia Peng, Lenore Pipes, Hao Xiong, Richard R. Green, Daniel C. Jones, Walter L. Ruzzo, Gary P. Schroth, Christopher E. Mason, Robert E. Palermo, and Michael G. Katze, “Assessment and improvement of indian-origin rhesus macaque and mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data,” Journal of medical primatology, p. n/a–n/a, May 2014.

  • A rat RNA-seq transcriptomic BodyMap across 11 organs and 4 developmental stages

    Ying Yu et al., “A rat RNA-seq transcriptomic BodyMap across 11 organs and 4 developmental stages,” Nature communications, vol. 5, Feb 2014.

  • Ying Yu et al., “A rat RNA-seq transcriptomic BodyMap across 11 organs and 4 developmental stages,” Nature communications, vol. 5, Feb 2014.

  • Systems analysis of human multigene disorders

    Christopher E. Mason, Sandra G. Porter and Todd M. Smith, Systems analysis of human multigene disorders, Chapter. Systems biology and integrated computational frameworks for rapid characterization of multi-omic data, 2014.

  • Christopher E. Mason, Sandra G. Porter and Todd M. Smith, Systems analysis of human multigene disorders, Chapter. Systems biology and integrated computational frameworks for rapid characterization of multi-omic data, 2014.

  • The pivotal regulatory landscape of RNA modifications

    Sheng Li and Christopher E. Mason, “The pivotal regulatory landscape of RNA modifications,” Annual review of genomics and human genetics, vol. 15, iss. 1, pp. 127-150, 2014.

  • Sheng Li and Christopher E. Mason, “The pivotal regulatory landscape of RNA modifications,” Annual review of genomics and human genetics, vol. 15, iss. 1, pp. 127-150, 2014.

  • Small heat shock proteins hspb7 and hspb12 regulate early steps of cardiac morphogenesis

    Gabriel E. Rosenfeld, Emily J. Mercer, Christopher E. Mason, and Todd Evans, “Small heat shock proteins hspb7 and hspb12 regulate early steps of cardiac morphogenesis,” Developmental biology, vol. 381, iss. 2, pp. 389-400, Sep 2013.

  • Gabriel E. Rosenfeld, Emily J. Mercer, Christopher E. Mason, and Todd Evans, “Small heat shock proteins hspb7 and hspb12 regulate early steps of cardiac morphogenesis,” Developmental biology, vol. 381, iss. 2, pp. 389-400, Sep 2013.

  • Induction of sarcomas by mutant IDH2

    Chao Lu et al., “Induction of sarcomas by mutant IDH2,” Genes & development, vol. 27, iss. 18, pp. 1986-1998, Sep 2013.

  • Chao Lu et al., “Induction of sarcomas by mutant IDH2,” Genes & development, vol. 27, iss. 18, pp. 1986-1998, Sep 2013.

  • Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

    Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, and Doron Betel, “Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data,” Genome biology, vol. 14, iss. 9, p. R95, Sep 2013.

  • Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, and Doron Betel, “Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data,” Genome biology, vol. 14, iss. 9, p. R95, Sep 2013.

  • Crowdfunding genomics and bioinformatics

    Pamela Cameron, David W. Corne, Christopher E. Mason, and Jeffrey Rosenfeld, “Crowdfunding genomics and bioinformatics,” Genome biology, vol. 14, iss. 9, p. 134, Sep 2013.

  • Pamela Cameron, David W. Corne, Christopher E. Mason, and Jeffrey Rosenfeld, “Crowdfunding genomics and bioinformatics,” Genome biology, vol. 14, iss. 9, p. 134, Sep 2013.

  • Identification of kinase fusion oncogenes in post-chernobyl radiation-induced thyroid cancers

    Julio C. Ricarte-Filho et al., “Identification of kinase fusion oncogenes in post-chernobyl radiation-induced thyroid cancers,” The journal of clinical investigation, vol. 123, iss. 11, pp. 4935-4944, Nov 2013.

  • Julio C. Ricarte-Filho et al., “Identification of kinase fusion oncogenes in post-chernobyl radiation-induced thyroid cancers,” The journal of clinical investigation, vol. 123, iss. 11, pp. 4935-4944, Nov 2013.

  • Deletion of asxl1 results in myelodysplasia and severe developmental defects in vivo

    Omar Abdel-Wahab et al., “Deletion of asxl1 results in myelodysplasia and severe developmental defects in vivo,” The journal of experimental medicine, vol. 210, iss. 12, pp. 2641-2659, Nov 2013.

  • Omar Abdel-Wahab et al., “Deletion of asxl1 results in myelodysplasia and severe developmental defects in vivo,” The journal of experimental medicine, vol. 210, iss. 12, pp. 2641-2659, Nov 2013.

  • Systematic evaluation of spliced alignment programs for RNA-seq data

    Pär. G. Engströmne et al., “Systematic evaluation of spliced alignment programs for RNA-seq data,” Nature methods, Nov 2013.

  • Pär. G. Engströmne et al., “Systematic evaluation of spliced alignment programs for RNA-seq data,” Nature methods, Nov 2013.

  • Pervasive sequence patents cover the entire human genome

    Jeffrey Rosenfeld and Christopher E. Mason, “Pervasive sequence patents cover the entire human genome,” Genome medicine, vol. 5, iss. 3, p. 27, Mar 2013.

  • Jeffrey Rosenfeld and Christopher E. Mason, “Pervasive sequence patents cover the entire human genome,” Genome medicine, vol. 5, iss. 3, p. 27, Mar 2013.

  • David Chiron, Peter Martin, Maurizio Di Liberto, Xiangao Huang, Scott Ely, Brian J. Lannutti, John P. Leonard, Christopher E. Mason, and Selina Chen-Kiang, “Induction of prolonged early g1 arrest by CDK4/CDK6 inhibition reprograms lymphoma cells for durable PI3Kδ inhibition through PIK3IP1,” Cell cycle (georgetown, tex.), vol. 12, iss. 12, pp. 1892-1900, Jun 2013.

    David Chiron, Peter Martin, Maurizio Di Liberto, Xiangao Huang, Scott Ely, Brian J. Lannutti, John P. Leonard, Christopher E. Mason, and Selina Chen-Kiang, “Induction of prolonged early g1 arrest by CDK4/CDK6 inhibition reprograms lymphoma cells for durable PI3Kδ inhibition through PIK3IP1,” Cell cycle (georgetown, tex.), vol. 12, iss. 12, pp. 1892-1900, Jun 2013.

  • David Chiron, Peter Martin, Maurizio Di Liberto, Xiangao Huang, Scott Ely, Brian J. Lannutti, John P. Leonard, Christopher E. Mason, and Selina Chen-Kiang, “Induction of prolonged early g1 arrest by CDK4/CDK6 inhibition reprograms lymphoma cells for durable PI3Kδ inhibition through PIK3IP1,” Cell cycle (georgetown, tex.), vol. 12, iss. 12, pp. 1892-1900, Jun 2013.

  • Xinghua Pan et al., “Two methods for full-length RNA sequencing for low quantities of cells and single cells,” Proceedings of the national academy of sciences of the united states of america, vol. 110, iss. 2, pp. 594-599, Jan 2013.

    Xinghua Pan et al., “Two methods for full-length RNA sequencing for low quantities of cells and single cells,” Proceedings of the national academy of sciences of the united states of america, vol. 110, iss. 2, pp. 594-599, Jan 2013.

  • Xinghua Pan et al., “Two methods for full-length RNA sequencing for low quantities of cells and single cells,” Proceedings of the national academy of sciences of the united states of america, vol. 110, iss. 2, pp. 594-599, Jan 2013.

  • The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics

    Lenore Pipes et al., “The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics,” Nucleic acids research, vol. 41, iss. Database issue, p. D906–914, Jan 2013.

  • Lenore Pipes et al., “The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics,” Nucleic acids research, vol. 41, iss. Database issue, p. D906–914, Jan 2013.

  • Novel RNA regulatory mechanisms revealed in the epitranscriptome

    Yogesh Saletore, Selina Chen-Kiang, and Christopher E. Mason, “Novel RNA regulatory mechanisms revealed in the epitranscriptome,” RNA biology, vol. 10, iss. 3, 2013.

  • Yogesh Saletore, Selina Chen-Kiang, and Christopher E. Mason, “Novel RNA regulatory mechanisms revealed in the epitranscriptome,” RNA biology, vol. 10, iss. 3, 2013.

  • An optimized algorithm for detecting and annotating regional differential methylation

    Sheng Li et al., “An optimized algorithm for detecting and annotating regional differential methylation,” BMC bioinformatics, vol. 14 Suppl 5, p. S10, 2013.

  • Sheng Li et al., “An optimized algorithm for detecting and annotating regional differential methylation,” BMC bioinformatics, vol. 14 Suppl 5, p. S10, 2013.

  • Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia

    Julia A. Meyer et al., “Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia,” Nature genetics, vol. 45, iss. 3, pp. 290-294, 2013.

  • Julia A. Meyer et al., “Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia,” Nature genetics, vol. 45, iss. 3, pp. 290-294, 2013.

  • Paul Zumbo and Christopher E. Mason, Genome analysis: current procedures and applications, Chapter Molecular methods for profiling the RNA world, 2013.

    Paul Zumbo and Christopher E. Mason, Genome analysis: current procedures and applications, Chapter Molecular methods for profiling the RNA world, 2013.

  • Paul Zumbo and Christopher E. Mason, Genome analysis: current procedures and applications, Chapter Molecular methods for profiling the RNA world, 2013.

  • A hybrid mechanism of action for BCL6 in b cells defined by formation of functionally distinct complexes at enhancers and promoters

    Katerina Hatzi et al., “A hybrid mechanism of action for BCL6 in b cells defined by formation of functionally distinct complexes at enhancers and promoters,” Cell reports, vol. 4, iss. 3, pp. 578-588, 2013.

  • Katerina Hatzi et al., “A hybrid mechanism of action for BCL6 in b cells defined by formation of functionally distinct complexes at enhancers and promoters,” Cell reports, vol. 4, iss. 3, pp. 578-588, 2013.

  • The birth of the epitranscriptome: deciphering the function of RNA modifications

    Yogesh Saletore, Kate Meyer, Jonas Korlach, Igor D. Vilfan, Samie Jaffrey, and Christopher E. Mason, “The birth of the epitranscriptome: deciphering the function of RNA modifications,” Genome biology, vol. 13, iss. 10, p. 175, Oct 2012.

  • Yogesh Saletore, Kate Meyer, Jonas Korlach, Igor D. Vilfan, Samie Jaffrey, and Christopher E. Mason, “The birth of the epitranscriptome: deciphering the function of RNA modifications,” Genome biology, vol. 13, iss. 10, p. 175, Oct 2012.

  • methylKit: a comprehensive r package for the analysis of genome-wide DNA methylation profiles

    Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E. Garrett-Bakelman, Maria E. Figueroa, Ari Melnick, and Christopher E. Mason, “methylKit: a comprehensive r package for the analysis of genome-wide DNA methylation profiles,” Genome biology, vol. 13, iss. 10, p. R87, Oct 2012.

  • Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E. Garrett-Bakelman, Maria E. Figueroa, Ari Melnick, and Christopher E. Mason, “methylKit: a comprehensive r package for the analysis of genome-wide DNA methylation profiles,” Genome biology, vol. 13, iss. 10, p. R87, Oct 2012.

  • ENU mutagenesis in mice identifies candidate genes for hypogonadism

    Jeffrey Weiss et al., “ENU mutagenesis in mice identifies candidate genes for hypogonadism,” Mammalian genome: official journal of the international mammalian genome society, vol. 23, iss. 5-6, pp. 346-355, Jun 2012.

  • Jeffrey Weiss et al., “ENU mutagenesis in mice identifies candidate genes for hypogonadism,” Mammalian genome: official journal of the international mammalian genome society, vol. 23, iss. 5-6, pp. 346-355, Jun 2012.

  • Detecting false-positive signals in exome sequencing

    Karin V. Fuentes Fajardo, David Adams, Christopher E. Mason, Murat Sincan, Cynthia Tifft, Camilo Toro, Cornelius F. Boerkoel, William Gahl, and Thomas Markello, “Detecting false-positive signals in exome sequencing,” Human mutation, vol. 33, iss. 4, pp. 609-613, Apr 2012.

  • Karin V. Fuentes Fajardo, David Adams, Christopher E. Mason, Murat Sincan, Cynthia Tifft, Camilo Toro, Cornelius F. Boerkoel, William Gahl, and Thomas Markello, “Detecting false-positive signals in exome sequencing,” Human mutation, vol. 33, iss. 4, pp. 609-613, Apr 2012.

  • Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis

    Lambert Busque et al., “Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis,” Nature genetics, vol. 44, iss. 11, pp. 1179-1181, 2012.

  • Lambert Busque et al., “Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis,” Nature genetics, vol. 44, iss. 11, pp. 1179-1181, 2012.

  • A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar

    George H. Perry, Darryl Reeves, Páll Melsted, Aakrosh Ratan, Webb Miller, Katelyn Michelini, Jr Louis Edward E, Jonathan K. Pritchard, Christopher E. Mason, and Yoav Gilad, “A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar,” Genome biology and evolution, vol. 4, iss. 2, pp. 126-135, 2012.

  • George H. Perry, Darryl Reeves, Páll Melsted, Aakrosh Ratan, Webb Miller, Katelyn Michelini, Jr Louis Edward E, Jonathan K. Pritchard, Christopher E. Mason, and Yoav Gilad, “A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar,” Genome biology and evolution, vol. 4, iss. 2, pp. 126-135, 2012.

  • Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia

    Altuna Akalin et al., “Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia,” PLoS genetics, vol. 8, iss. 6, p. e1002781, 2012.

  • Altuna Akalin et al., “Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia,” PLoS genetics, vol. 8, iss. 6, p. e1002781, 2012.

  • Jeffrey A. Rosenfeld, Christopher E. Mason, and Todd M. Smith, “Limitations of the human reference genome for personalized genomics,” PloS one, vol. 7, iss. 7, p. e40294,  2012.

    Jeffrey A. Rosenfeld, Christopher E. Mason, and Todd M. Smith, “Limitations of the human reference genome for personalized genomics,” PloS one, vol. 7, iss. 7, p. e40294, 2012.

  • Jeffrey A. Rosenfeld, Christopher E. Mason, and Todd M. Smith, “Limitations of the human reference genome for personalized genomics,” PloS one, vol. 7, iss. 7, p. e40294, 2012.

  • A complex chromosomal rearrangement involving chromosomes 2, 5, and x in autism spectrum disorder

    Karina Griesi-Oliveira et al., “A complex chromosomal rearrangement involving chromosomes 2, 5, and x in autism spectrum disorder,” American journal of medical genetics. part b, neuropsychiatric genetics: the official publication of the international society of psychiatric genetics, vol. {159B}, iss. 5, pp. 529-536, 2012.

  • Karina Griesi-Oliveira et al., “A complex chromosomal rearrangement involving chromosomes 2, 5, and x in autism spectrum disorder,” American journal of medical genetics. part b, neuropsychiatric genetics: the official publication of the international society of psychiatric genetics, vol. {159B}, iss. 5, pp. 529-536, 2012.

  • Faster sequencers, larger datasets, new challenges

    Christopher E. Mason and Olivier Elemento, “Faster sequencers, larger datasets, new challenges,” Genome biology, vol. 13, iss. 3, p. 314, 2012.

  • Christopher E. Mason and Olivier Elemento, “Faster sequencers, larger datasets, new challenges,” Genome biology, vol. 13, iss. 3, p. 314, 2012.

  • Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons

    Kate D. Meyer, Yogesh Saletore, Paul Zumbo, Olivier Elemento, Christopher E. Mason, and Samie R. Jaffrey, “Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons,” Cell, vol. 149, iss. 7, pp. 1635-1646, 2012.

  • Kate D. Meyer, Yogesh Saletore, Paul Zumbo, Olivier Elemento, Christopher E. Mason, and Samie R. Jaffrey, “Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons,” Cell, vol. 149, iss. 7, pp. 1635-1646, 2012.

  • Multiple recurrent de novo CNVs, including duplications of the 7q11.23 williams syndrome region, are strongly associated with autism

    Stephan J. Sanders et al., “Multiple recurrent de novo CNVs, including duplications of the 7q11.23 williams syndrome region, are strongly associated with autism,” Neuron, vol. 70, iss. 5, pp. 863-885, Jun 2011.

  • Stephan J. Sanders et al., “Multiple recurrent de novo CNVs, including duplications of the 7q11.23 williams syndrome region, are strongly associated with autism,” Neuron, vol. 70, iss. 5, pp. 863-885, Jun 2011.

  • L-histidine decarboxylase and tourette’s syndrome

    Gulhan A. Ercan-Sencicek et al., “L-histidine decarboxylase and tourette’s syndrome,” The new england journal of medicine, vol. 362, iss. 20, pp. 1901-1908, May 2010.

  • Gulhan A. Ercan-Sencicek et al., “L-histidine decarboxylase and tourette’s syndrome,” The new england journal of medicine, vol. 362, iss. 20, pp. 1901-1908, May 2010.

  • Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

    Christopher E. Mason, Feng-Jue Shu, Cheng Wang, Ryan M. Session, Roland G. Kallen, Neil Sidell, Tianwei Yu, Mei Hui Liu, Edwin Cheung, and Caleb B. Kallen, “Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements,” Nucleic acids research, vol. 38, iss. 7, pp. 2355-2368, Apr 2010.

  • Christopher E. Mason, Feng-Jue Shu, Cheng Wang, Ryan M. Session, Roland G. Kallen, Neil Sidell, Tianwei Yu, Mei Hui Liu, Edwin Cheung, and Caleb B. Kallen, “Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements,” Nucleic acids research, vol. 38, iss. 7, pp. 2355-2368, Apr 2010.

  • Standardizing the next generation of bioinformatics software development with BioHDF (HDF5)

    Christopher E. Mason, Paul Zumbo, Stephan Sanders, Mike Folk, Dana Robinson, Ruth Aydt, Martin Gollery, Mark Welsh, Eric N. Olson, and Todd M. Smith, “Standardizing the next generation of bioinformatics software development with BioHDF (HDF5),” Advances in experimental medicine and biology, vol. 680, pp. 693-700, 2010.

  • Christopher E. Mason, Paul Zumbo, Stephan Sanders, Mike Folk, Dana Robinson, Ruth Aydt, Martin Gollery, Mark Welsh, Eric N. Olson, and Todd M. Smith, “Standardizing the next generation of bioinformatics software development with BioHDF (HDF5),” Advances in experimental medicine and biology, vol. 680, pp. 693-700, 2010.

  • The syndrome of pachygyria, mental retardation, and arachnoid cysts maps to 11p15

    Kaya Bilguvar et al., “The syndrome of pachygyria, mental retardation, and arachnoid cysts maps to 11p15,” American journal of medical genetics. part a, vol. {149A}, iss. 11, pp. 2569-2572, Nov 2009.

  • Kaya Bilguvar et al., “The syndrome of pachygyria, mental retardation, and arachnoid cysts maps to 11p15,” American journal of medical genetics. part a, vol. {149A}, iss. 11, pp. 2569-2572, Nov 2009.

  • Genomic mapping of binding regions for the ecdysone receptor protein complex

    Zareen Gauhar, Ling V. Sun, Sujun Hua, Christopher E. Mason, Florian Fuchs, Tong-Ruei Li, Michael Boutros, and Kevin P. White, “Genomic mapping of binding regions for the ecdysone receptor protein complex,” Genome research, vol. 19, iss. 6, pp. 1006-1013, Jun 2009.

  • Zareen Gauhar, Ling V. Sun, Sujun Hua, Christopher E. Mason, Florian Fuchs, Tong-Ruei Li, Michael Boutros, and Kevin P. White, “Genomic mapping of binding regions for the ecdysone receptor protein complex,” Genome research, vol. 19, iss. 6, pp. 1006-1013, Jun 2009.

  • Christopher E. Mason, Matthew W. State, and Steven O. Moldin, Kaplan & Sadock’s Comprehensive Textbook of Psychiatry, Ninth ed., Book 1, Chapter 11: "Genome, Transcriptome, and Proteome: The molecular genetics and biochemistry underlying the neurobiology of mental disorders", Benjamin J. Sadock, Virginia A. Sadock, Pedro Ruiz, and Harold I. Kaplan, Eds., Philadelphia: Wolters Kluwer Health/Lippincott Williams & Wilkins, 2009.

    Christopher E. Mason, Matthew W. State, and Steven O. Moldin, Kaplan & sadock’s comprehensive textbook of psychiatry, Ninth ed., Book 1, Chapter 11: "Genome, Transcriptome, and Proteome: The molecular genetics and biochemistry underlying the neurobiology of mental disorders", Benjamin J. Sadock, Virginia A. Sadock, Pedro Ruiz, and Harold I. Kaplan, Eds., Philadelphia: Wolters Kluwer Health/Lippincott Williams & Wilkins, 2009.

  • Christopher E. Mason, Matthew W. State, and Steven O. Moldin, Kaplan & sadock’s comprehensive textbook of psychiatry, Ninth ed., Book 1, Chapter 11: "Genome, Transcriptome, and Proteome: The molecular genetics and biochemistry underlying the neurobiology of mental disorders", Benjamin J. Sadock, Virginia A. Sadock, Pedro Ruiz, and Harold I. Kaplan, Eds., Philadelphia: Wolters Kluwer Health/Lippincott Williams & Wilkins, 2009.

  • Functional and evolutionary insights into human brain development through global transcriptome analysis

    Matthew B. Johnson, Yuka Imamura Kawasawa, Christopher E. Mason, Zeljka Krsnik, Giovanni Coppola, Darko Bogdanovi., Daniel H. Geschwind, Shrikant M. Mane, Matthew W. State, and Nenad Sestan, “Functional and evolutionary insights into human brain development through global transcriptome analysis,” Neuron, vol. 62, iss. 4, pp. 494-509, 2009.

  • Matthew B. Johnson, Yuka Imamura Kawasawa, Christopher E. Mason, Zeljka Krsnik, Giovanni Coppola, Darko Bogdanovi., Daniel H. Geschwind, Shrikant M. Mane, Matthew W. State, and Nenad Sestan, “Functional and evolutionary insights into human brain development through global transcriptome analysis,” Neuron, vol. 62, iss. 4, pp. 494-509, 2009.

  • A novel heterozygous deletion within the 3′ region of the PAX6 gene causing isolated aniridia in a large family group

    Fatih Bayrakli et al., “A novel heterozygous deletion within the 3′ region of the PAX6 gene causing isolated aniridia in a large family group,” Journal of clinical neuroscience: official journal of the neurosurgical society of australasia, vol. 16, iss. 12, pp. 1610-1614, 2009.

  • Fatih Bayrakli et al., “A novel heterozygous deletion within the 3′ region of the PAX6 gene causing isolated aniridia in a large family group,” Journal of clinical neuroscience: official journal of the neurosurgical society of australasia, vol. 16, iss. 12, pp. 1610-1614, 2009.

  • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

    John C. Marioni, Christopher E. Mason, Shrikant M. Mane, Matthew Stephens, and Yoav Gilad, “RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays,” Genome research, vol. 18, iss. 9, pp. 1509-1517, Sep 2008.

  • John C. Marioni, Christopher E. Mason, Shrikant M. Mane, Matthew Stephens, and Yoav Gilad, “RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays,” Genome research, vol. 18, iss. 9, pp. 1509-1517, Sep 2008.

  • Molecular characterization of a patient with 3p deletion syndrome and a review of the literature

    Thomas V. Fernandez et al., “Molecular characterization of a patient with 3p deletion syndrome and a review of the literature,” American journal of medical genetics. part a, vol. {146A}, iss. 21, pp. 2746-2752, Nov 2008.

  • Thomas V. Fernandez et al., “Molecular characterization of a patient with 3p deletion syndrome and a review of the literature,” American journal of medical genetics. part a, vol. {146A}, iss. 21, pp. 2746-2752, Nov 2008.

  • Novel NTRK1 mutations cause hereditary sensory and autonomic neuropathy type IV: demonstration of a founder mutation in the turkish population

    Beyhan Tüysüz et al., “Novel NTRK1 mutations cause hereditary sensory and autonomic neuropathy type IV: demonstration of a founder mutation in the turkish population,” Neurogenetics, vol. 9, iss. 2, pp. 119-125, May 2008.

  • Beyhan Tüysüz et al., “Novel NTRK1 mutations cause hereditary sensory and autonomic neuropathy type IV: demonstration of a founder mutation in the turkish population,” Neurogenetics, vol. 9, iss. 2, pp. 119-125, May 2008.

  • Susceptibility loci for intracranial aneurysm in european and japanese populations

    Kaya Bilguvar et al., “Susceptibility loci for intracranial aneurysm in european and japanese populations,” Nature genetics, vol. 40, iss. 12, pp. 1472-1477, Dec 2008.

  • Kaya Bilguvar et al., “Susceptibility loci for intracranial aneurysm in european and japanese populations,” Nature genetics, vol. 40, iss. 12, pp. 1472-1477, Dec 2008.

  • ChIpping at the human genome to characterize functional estrogen response elements

    Christopher E. Mason, RG Kallen, S. Hua, KP White, T. Yu, C. Wang, and Kallen CB, “ChIpping at the human genome to characterize functional estrogen response elements,” Reproductive sciences, vol. 15, iss. 1, p. 48, 2008.

  • Christopher E. Mason, RG Kallen, S. Hua, KP White, T. Yu, C. Wang, and Kallen CB, “ChIpping at the human genome to characterize functional estrogen response elements,” Reproductive sciences, vol. 15, iss. 1, p. 48, 2008.

  • Enhanced function annotations for drosophila serine proteases: a case study for systematic annotation of multi-member gene families

    Parantu K. Shah, Lokesh P. Tripathi, Lars Juhl Jensen, Murad Gahnim, Christopher E. Mason, Eileen E. Furlong, Veronica Rodrigues, Kevin P. White, Peer Bork, and R. Sowdhamini, “Enhanced function annotations for drosophila serine proteases: a case study for systematic annotation of multi-member gene families,” Gene, vol. 407, iss. 1-2, pp. 199-215, 2008.

  • Parantu K. Shah, Lokesh P. Tripathi, Lars Juhl Jensen, Murad Gahnim, Christopher E. Mason, Eileen E. Furlong, Veronica Rodrigues, Kevin P. White, Peer Bork, and R. Sowdhamini, “Enhanced function annotations for drosophila serine proteases: a case study for systematic annotation of multi-member gene families,” Gene, vol. 407, iss. 1-2, pp. 199-215, 2008.

  • Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression

    Sujun Hua, Caleb B. Kallen, Ruby Dhar, Maria T. Baquero, Christopher E. Mason, Beth A. Russell, Parantu K. Shah, Jiang Liu, Andrey Khramtsov, Maria S. Tretiakova, Thomas N. Krausz, Olufunmilayo I. Olopade, David L. Rimm, and Kevin P. White, “Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression,” Molecular systems biology, vol. 4, p. 188, 2008.

  • Sujun Hua, Caleb B. Kallen, Ruby Dhar, Maria T. Baquero, Christopher E. Mason, Beth A. Russell, Parantu K. Shah, Jiang Liu, Andrey Khramtsov, Maria S. Tretiakova, Thomas N. Krausz, Olufunmilayo I. Olopade, David L. Rimm, and Kevin P. White, “Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression,” Molecular systems biology, vol. 4, p. 188, 2008.

  • Developmental stage and level of codon usage bias in drosophila

    Saverio Vicario, Christopher E. Mason, Kevin P. White, and Jeffrey R. Powell, “Developmental stage and level of codon usage bias in drosophila,” Molecular biology and evolution, vol. 25, iss. 11, pp. 2269-2277, 2008.

  • Saverio Vicario, Christopher E. Mason, Kevin P. White, and Jeffrey R. Powell, “Developmental stage and level of codon usage bias in drosophila,” Molecular biology and evolution, vol. 25, iss. 11, pp. 2269-2277, 2008.

  • Personalized genomic medicine with a patchwork, partially owned genome

    Christopher E. Mason, Michael R. Seringhaus, and Clara Sattler de Sousa e Brito, “Personalized genomic medicine with a patchwork, partially owned genome,” The yale journal of biology and medicine, vol. 80, iss. 4, pp. 145-151, Dec 2007.

  • Christopher E. Mason, Michael R. Seringhaus, and Clara Sattler de Sousa e Brito, “Personalized genomic medicine with a patchwork, partially owned genome,” The yale journal of biology and medicine, vol. 80, iss. 4, pp. 145-151, Dec 2007.

  • A novel syndrome of cerebral cavernous malformation and greig cephalopolysyndactyly. laboratory investigation

    Kaya Bilguvar et al., “A novel syndrome of cerebral cavernous malformation and greig cephalopolysyndactyly. laboratory investigation,” Journal of neurosurgery, vol. 107, iss. 6 Suppl, pp. 495-499, Dec 2007.

  • Kaya Bilguvar et al., “A novel syndrome of cerebral cavernous malformation and greig cephalopolysyndactyly. laboratory investigation,” Journal of neurosurgery, vol. 107, iss. 6 Suppl, pp. 495-499, Dec 2007.

  • Rapid identification of disease-causing mutations using copy number analysis within linkage intervals

    Fatih Bayrakli, Kaya Bilguvar, Christopher E. Mason, Michael L. DiLuna, Yasar Bayri, Levent Gungor, Murat Terzi, Shrikant M. Mane, Richard P. Lifton, Matthew W. State, and Murat Gunel, “Rapid identification of disease-causing mutations using copy number analysis within linkage intervals,” Human mutation, vol. 28, iss. 12, pp. 1236-1240, Dec 2007.

  • Fatih Bayrakli, Kaya Bilguvar, Christopher E. Mason, Michael L. DiLuna, Yasar Bayri, Levent Gungor, Murat Terzi, Shrikant M. Mane, Richard P. Lifton, Matthew W. State, and Murat Gunel, “Rapid identification of disease-causing mutations using copy number analysis within linkage intervals,” Human mutation, vol. 28, iss. 12, pp. 1236-1240, Dec 2007.

  • Identification of tightly regulated groups of genes during drosophila melanogaster embryogenesis

    Sean D. Hooper, Stephanie Boué, Roland Krause, Lars J. Jensen, Christopher E. Mason, Murad Ghanim, Kevin P. White, Eileen E. M. Furlong, and Peer Bork, “Identification of tightly regulated groups of genes during drosophila melanogaster embryogenesis,” Molecular systems biology, vol. 3, p. 72, 2007.

  • Sean D. Hooper, Stephanie Boué, Roland Krause, Lars J. Jensen, Christopher E. Mason, Murad Ghanim, Kevin P. White, Eileen E. M. Furlong, and Peer Bork, “Identification of tightly regulated groups of genes during drosophila melanogaster embryogenesis,” Molecular systems biology, vol. 3, p. 72, 2007.

  • Genome evolution between drosophila melanogaster and drosophila pseudoobscura

    Christopher E. Mason, “Genome evolution between drosophila melanogaster and drosophila pseudoobscura,” PhD Thesis, 2006.

  • Christopher E. Mason, “Genome evolution between drosophila melanogaster and drosophila pseudoobscura,” PhD Thesis, 2006.

  • A gene expression map for the euchromatic genome of drosophila melanogaster

    Viktor Stolc, Zareen Gauhar, Christopher E. Mason, Gabor Halasz, Marinus F. van Batenburg, Scott A. Rifkin, Sujun Hua, Tine Herreman, Waraporn Tongprasit, Paolo Emilio Barbano, Harmen J. Bussemaker, and Kevin P. White, “A gene expression map for the euchromatic genome of drosophila melanogaster,” Science (new york, N.Y.), vol. 306, iss. 5696, pp. 655-660, 2004.

  • Viktor Stolc, Zareen Gauhar, Christopher E. Mason, Gabor Halasz, Marinus F. van Batenburg, Scott A. Rifkin, Sujun Hua, Tine Herreman, Waraporn Tongprasit, Paolo Emilio Barbano, Harmen J. Bussemaker, and Kevin P. White, “A gene expression map for the euchromatic genome of drosophila melanogaster,” Science (new york, N.Y.), vol. 306, iss. 5696, pp. 655-660, 2004.

  • Low-contact-angle polydimethyl siloxane (PDMS) membranes for fabricating micro-bioarrays

    S. D. Gillmor, B. J. Larson, J. M. Braun, C. E. Mason, L. E. Cruz-Barba, F. Denes, and M. G. Lagally, “Low-contact-angle polydimethyl siloxane (PDMS) membranes for fabricating micro-bioarrays,” in Microtechnologies in medicine amp; biology 2nd annual international IEEE-EMB special topic conference on, 2002, pp. 51-56.

  • S. D. Gillmor, B. J. Larson, J. M. Braun, C. E. Mason, L. E. Cruz-Barba, F. Denes, and M. G. Lagally, “Low-contact-angle polydimethyl siloxane (PDMS) membranes for fabricating micro-bioarrays,” in Microtechnologies in medicine amp; biology 2nd annual international IEEE-EMB special topic conference on, 2002, pp. 51-56.


Courses & Programs

Professor: Christopher E. Mason
Description: The rapid advancement of Next-Generation Sequencing (NGS) has opened a wealth of opportunities for research in many fields: cancer biology, epigenetics, tumor evolution, microbiome and infectious disease dynamics, neuro-degeneration, personalized medicine, and improved diagnosis and risk assessment for patients. Moreover, there are emerging, faster NGS technologies that promise comprehensive molecular portraits of disease and actionable clinical results for doctors within a single day. Scientists and physicians will be better equipped to design studies and help patients if they possess an intricate knowledge of these molecular-profiling methods, their biological context, and their applicability to specific cases and diseases. Finally, a rich understanding of the complexity of the human genome is essential for the proper annotation of characterization of any new mutations/modifications found, since large-scale efforts at tumor and normal genome sequencing have dramatically altered our view of the normal genome and epigenome.
Thus, in this 10-week course, students will build a strong foundation of knowledge of NGS technologies (both existing and emerging), learn the applications of these technologies for basic and clinical research, and finally learn the essential tools for the analysis, integration, and application of these data relative to other public databases and phenotype repositories. We have a broad range of expertise being contributed from many leaders in the field.

Professor: Christopher E. Mason
Description: This course will introduce participants to the biochemical background, data collection, and data analysis frameworks for next-gen sequencing (NGS). Over the course of this workshop, they will learn how to handle the enormous amounts of data that are generated by these methods, and how to approach their analysis, from re-sequencing, RNA-Seq, ChIP-Seq, or other NGS datasets.
Prerequisites: Participants should be comfortable with using the UNIX command line, and should have a good knowledge of the UCSC genome browser.

Professors: Carl Blobel and Christopher E. Mason
Description: This course is required for all 1st and 2nd year PBSB graduate students, but is open to all WGSMS students. It is designed to train students in scientific presentation and critique. The structure is a formalized, in depth "journal club". Each 1st year student will choose a paper from a list provided by the Course Directors. Each 2nd year student will select a paper in their thesis field, subject to approval of the Course Directors. Each session will consist of a student formally presenting their selected paper to the class, which is expected to serve as a critical audience. The presentation should consist of an introduction of the relevant background literature, an objective presentation of the study, a subjective analysis/critique of the work, and suggestions for future work. Presentations by 2nd year students will be scheduled first, giving the 1st year students the opportunity to learn from their more senior colleagues. Grading will be based on presentation quality and contribution to constructive feedback.

Undergraduate Research Scholars Program in Bioengineering
Description: This is a pilot independent study research program that enables students to work on a bioengineering related project with a participating faculty member for up to two semesters. Students selected to participate in the program will be eligible to receive funding to support project costs as well as conference travel. The program is generously funded by the Rose Sandholm grant.

Office & Lab


Christopher Mason
Institute for Computational Biomedicine
Weill Cornell Medical College
Dept of Physiology and Biophysics
1305 York Ave, 13th floor, Rm Y13-04
New York, NY 10021


Wet lab
Weill Cornell Medical College
Belfer Research Building BRB 1062-A01
413 East 69th St
New York, NY 10021

Mailing Addresses


Dry Lab
Mason Lab c/o ⟨contact⟩
Weill Cornell Medical College
Dept of Physiology & Biophysics
510 East 70th Street E-509
New York, NY 10065


Wet lab
Mason Lab c/o ⟨contact⟩
Weill Cornell Medical College
Belfer Research Building BRB 1062-A01
413 East 69th St
New York, NY 10021

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