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  • Make Your Own
  • Bio
  • Education
  • Publications
  • Outreach and Science Communication
  • What's on my Mind?
  • Travel and Nature
  • Get in touch!
  • …  
    • Make Your Own
    • Bio
    • Education
    • Publications
    • Outreach and Science Communication
    • What's on my Mind?
    • Travel and Nature
    • Get in touch!
    • Make Your Own
    • Bio
    • Education
    • Publications
    • Outreach and Science Communication
    • What's on my Mind?
    • Travel and Nature
    • Get in touch!
    • …  
      • Make Your Own
      • Bio
      • Education
      • Publications
      • Outreach and Science Communication
      • What's on my Mind?
      • Travel and Nature
      • Get in touch!
      •  

         

         

         

         

      • Welcome to the World of Circular DNA!

        Thank you to the Beckman Foundation for highlighting our work on Circular DNA! Click here to read the story.

        Note: This website will migrate to www.circulome.net in 2022

         

        I'm Massa and I work at the interface of Biophysics, Bioengineering, and Genomics. Currently, I am an Arnold O. Beckman and AHA Postdoctoral Fellow at Stanford University.

        My projects are focused on understanding the fundamentals of how multicellular organisms process information and respond to genetic and environmental change. This, in turn, requires identification and analysis of intercellular variation. Cellular heterogeneity is evident from the various cell types that make up our bodies, yet elements that manifest genomic diversity are seldom annotated and questions of their biogenesis and function remain largely unanswered. Thus, we often assume that all cells within an organism operate according to the same static genome. My work, a fusion of biophysics and genomics, challenges this assumption by providing evidence for cell-type-specific, programmed genomic heterogeneity at a number of previously assumed-to-be static genomic elements.

        Future work is focused on the following questions:

        1. How much variation is there between differentiated cells in a single organism and among individuals?
        2. Which variations drive functional diversity and competition between stem cells within a single lineage?
        3. How do differentiated cells program differential chromosome dynamics?
        4. Which variants facilitate repeated adaptations to new environments?

        The outcome will be novel tools in synthetic biology, single-cell biophysics, and mathematical modelling. By combining these tools with expertise in physics, bioengineering, and human and model-system genomics, my future group will aim to lay the necessary groundwork for elucidating how cells collectively perform systems-level functions in healthy and diseased states.

        Science Benefits from Diversity!!

        The quality of the scientific-research enterprise, and its ability to meet the needs of, and positively impact the lives of individuals, communities, nations, and the world is inextricably linked to the individuals/scientists involved. Each person’s unique life experiences yields a unique approach to novel problems. As a result, diversity is essential to success in the sciences, yet there have been systemic barriers to minorities (underrepresented with respect to race, ethnicity, or gender) who wish to enter STEM careers.

      • Education

        “Different roads sometimes lead to the same castle.” –George R.R. Martin

        Stanford University Medical School

        2015- Present

        Stanford Medicine Dean's and Arnold O. Beckman Fellow

        University of Texas at Dallas

        2015

        PhD in Biomedical Engineering

        University of Texas at Dallas

        2013

        PhD in Molecular Cell Biology and Biophysics

        University of Leeds

        2012

        Visiting Researcher

        University of Texas at Dallas

        2010

        MS in Molecular and Cell Biology

        University of Texas at Dallas

        2008

        BS in Cell Biology and Biophysics (Fast Track)

        Richland College, DCCCD

        2005-2006

        Various classes in various disciplines

      • Publications

        2012-Current

         

        Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273

         

        Dae-Eun Jeong, Matthew McCoy, Karen Artiles, Orkan Ilbay, Andrew Fire*, Kari Nadeau, Helen Park, Brooke Betts, Scott Boyd, Ramona Hoh, and Massa Shoura*

        *Co-Corresponding

        Context-dependent DNA Polymerization Effects Can Masquerade as DNA Modification Signals

        Yusuke Takahash*, Massa J. Shoura*, Andrew Fire, Shinichi Morishita

        *Co-first

        In Review

        mRNA vaccination compared to infection elicits an IgG-predominant response with greater SARS-CoV-2 specificity and similar decrease in variant spike recognition

        Katharina Röltgen, Sandra CA Nielsen, Prabhu S Arunachalam, Fan Yang, Ramona A Hoh, Oliver F Wirz, Alexandra S Lee, Fei Gao, Vamsee Mallajosyula, Chunfeng Li, Emily Haraguchi, Massa J. Shoura, James L Wilbur, Jacob N Wohlstadter, Mark M Davis, Benjamin A Pinsky, George B Sigal, Bali Pulendran, Kari C Nadeau, Scott D Boyd

        MedRxiv, 2021

        An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes

        Lamia Wahba*, Nimit Jain*, Andrew Z. Fire*, Massa J. Shoura*, Karen Artiles*, Matthew J. McCoy*, Dea-Eun Jeaong*

        mSphere, 2020 *All authors contributed equally to this work. Author order was chosen randomly

        Extrachromosomal DNA – relieving heredity constraints, accelerating tumour evolution​

        Chris Bailey, Massa J. Shoura, Paul S.Mischel, Charles Swanton

        Annals of Oncology, 2020

         

         

        Loop-closure Kinetics Reveal a Stable, Right-handed DNA Intermediate in Cre Recombination

        Massa J. Shoura, Stefan M Giovan, Alexandre V Vetcher, Riccardo Ziraldo, Andreas Hanke, Stephen D. Levene

        Nucleic Acids Research, 2020

        Recompleting the Caenorhabditis elegans Genome

        Jun Yoshimura*, Kazuki Ichikawa*, Massa J. Shoura*, Karen L Artiles*, Idan Gabdank, Lamia Wahba, Cheryl L Smith, Mark L Edgley, Ann E Rougvie, Andrew Z Fire, Shinichi Morishita, Erich M Schwarz

        Genome research, 2019 *co-first

        Featured on cover

        Securing the Future of Research Computing in the Biosciences

        Joanna Leng, Massa Shoura, Tom CB McLeish, Alan N Real, Mariann Hardey, James McCafferty, Neil A Ranson, Sarah A Harris

        PloS Comp. Bio., 2019

        Deconvolution of Nucleic-Acid Length Distributions: a gel electrophoresis analysis tool and applications

        Riccardo Ziraldo, Massa J. Shoura*, Andrew Z Fire, Stephen D Levene*

        Nucleic Acids Research, 2019 *co-corrosponding

        Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens

        Massa J. Shoura*, Idan Gabdank, Loren Hansen, Jason Merker, Jason Gotlib, Stephen D Levene, Andrew Z Fire*

        G3: Genes, Genomes, Genetics, 2017 *co-corrosponding

        Featured by various media outlets and Science Magazine

        http://genestogenomes.org/circulomes-vary-based-on-cell-type/

        https://www.sciencedaily.com/releases/2017/09/170911163239.htm

        https://www.sciencemagazinedigital.org/sciencemagazine/09_june_2017?pg=16#pg16

         

        Contribution of Fluorophore Dynamics and Solvation to Resonant Energy Transfer in Protein-DNA Complexes: a molecular-dynamics study

        Massa J. Shoura, RJK Udayana Ranatunga, Sarah A Harris, Steven O Nielsen, Stephen D Levene

        Biophysical Journal, 2014

        Understanding DNA Looping Through Cre-Recombination Kinetics

        Massa J. Shoura, Stephen D Levene

        Discrete and Topological Models in Molecular Biology pp 405-418, 2014

        Featured on cover

        The Thermodynamics of DNA Loop Formation, from J to Z

        Stephen D Levene, Stefan M Giovan, Andreas Hanke, Massa J. Shoura

        Biochemical Society Transactions, 2013

        Measurements of DNA-loop Formation via Cre-mediated Recombination

        Massa J. Shoura, Alexandre A Vetcher, Stefan M Giovan, Farah Bardai, Anusha Bharadwaj, Matthew R Kesinger, Stephen D Levene

        Nucleic Acids Research, 2012

        Featured by various media outlets

        https://www.sciencedaily.com/releases/2012/08/120813115530.htm

        https://www.bioopticsworld.com/bioimaging/fluorescence/article/16432525/fluorescent-light-tags-and-tracks-dna-looping

      • Outreach and Science Communication

        Last update: Dec 2020

         

        Ensuring that COVID-19-related journalism is as evidence-based as possible

        https://www.sciline.org/covid/expert-quotes-origins

        Did SARS-CoV-2 escape from a lab?

        https://www.genengnews.com/insights/controversy-aside-why-the-source-of-covid-19-matters/

        An Open Letter: Response to NSF 20-587 GRFP

        https://jasonjwilliamsny.github.io/grfp2020/#signatories

        BaMBA!

        https://bioscope.ucdavis.edu/author/srwyatt/

        Genomics and Biophysics in Santa Cruz

        https://www.biophysics.org/past-thematic-meetings/genome-biophysics-integrating-genomics-and-biophysics-to-understand-structural-and-functional-aspects-of-genomes

        Letters to a Pre-Scientist (Sci Pen-Pal)

        https://www.prescientist.org/for-scientists/sign-up/

        Face Recognition or Phrenology is a pseudoscience. Technologies based on this pseudoscience will never be accurate. Current applications of this "technology" exacerbate social injustice and has no place in a democratic society.

        https://www.vox.com/recode/2020/6/10/21287194/amazon-microsoft-ibm-facial-recognition-moratorium-police

      • What's on my mind?

        Updated Nov 2021

         

      • Sights from the Road*

        *All pictures below are copyrighted and not to be used without permission

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        Get in touch!

         

         

         

         

        Email or on Twitter

         

         

         

        massa86@stanford.edu

        @CircDNA

      © 2019

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