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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!
      • 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

          Show more
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          Get in touch!

           

           

           

           

          Email or on Twitter

           

           

           

          massa86@stanford.edu

          @CircDNA

        © 2019

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