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  • Bio
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  • What's on my Mind?
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  • …  
    • Bio
    • Education
    • Publications
    • Outreach and Science Communication
    • What's on my Mind?
    • Travel and Nature
    • Get in touch!
Fair Fight
  • Bio
  • Education
  • Publications
  • Outreach and Science Communication
  • What's on my Mind?
  • Travel and Nature
  • Get in touch!
  • …  
    • Bio
    • Education
    • Publications
    • Outreach and Science Communication
    • What's on my Mind?
    • Travel and Nature
    • Get in touch!
Fair Fight
  • Bio
  • Education
  • Publications
  • Outreach and Science Communication
  • What's on my Mind?
  • Travel and Nature
  • Get in touch!
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    • This website will migrate to www.circulome.net in 2021

      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

      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​

      ChrisBailey, 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 Monthly. Jan/Feb. 2021

      "When you took your oath of office, you put your hand on the Bible and swore to uphold the Constitution. You did not put your hand on the Constitution and swear to uphold the Bible."

    • 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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