Joshua A. Shapiro, Ph.D.

Research Interests

• Causes and consequences of genotypic and phenotypic diversity

• Genomic signatures of selection and demography

• Evolution of expression patterns and expression regulation

Experience

• Senior Data Scientist 2022-present
  Data Scientist 2019-2022
  Childhood Cancer Data Lab of Alex’s Lemonade Stand Foundation

• Assistant Professor 2013-2019
  Visiting Assistant Professor 2011-2013
  Department of Biology, Bryn Mawr College

• Associate Professional Specialist 2011-2013
  Lecturer 2008-2009
  Post-Doctoral Research Associate 2006-2011
  Lewis-Sigler Institute for Integrative Genomics, Princeton University
  Advisor: Dr. Leonid Kruglyak

• Graduate Research 2000-2006
  Department of Ecology and Evolution, University of Chicago
  Advisor: Dr. Chung-I Wu

• Laboratory Technician 2000
  Department of Cell Biology, University of Virginia
  Supervisor: Dr. P. Prabhakara Reddi

• Fulbright Scholar 1999
  Centre for Research on Introduced Marine Pests, CSIRO, Australia

Education

• Ph.D. University of Chicago Department of Ecology and Evolution    2007
  Dissertation: Selection and Structure in Drosophila Populations During the Process of Speciation
  Advisor: Dr. Chung-I Wu

• B.A. Williams College Biology    1998
  Summa Cum Laude with Highest Honors
  Thesis: Population Structure and Gene Flow in Chorus Frog Tadpoles (Pseudacris triseriata) on North Government Island
  Advisor: Dr. David Smith

Publications

• Hawkins AG, Shapiro JA, Spielman SJ, Mejia DS, Prasad DV, Ichihara N, et al. 2026. The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.
  Cell Genomics 6:101283.

• Lee MK, Azizgolshani N, Shapiro JA, Nguyen LN, Kolling FW, Zanazzi GJ, et al. 2024 Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors.
  Nature Communications 15:3634.

• Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, et al. 2023. OpenPBTA: The Open Pediatric Brain Tumor Atlas.
  Cell Genomics 3:100340.

• Dang MT, Gonzalez MV, Gaonkar KS, Rathi KS, Young P, Arif S, et al. 2021. Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality.
  <a href=“https://doi.org/10.1016/j.celrep.2021.108917> [Cell Reports]{.joirnal 34(13):108917.

• Guo X, Zhang R, Li Y, Wang Z, Ishchuk OP, Ahmad KM, Wee J, Piskur J, Shapiro JA, Gu Z. 2020. evolution of fungal pathogen Candida glabrata by genome-wide analysis of genetic variations.
  Methods 176:82-90.

• Hyson P, Shapiro JA, Wien MW. 2015. Draft genome sequence of Exiguobacterium sp. strain BMC-KP, an environmental isolate from Bryn Mawr, Pennsylvania.
  Genome Announcements 3:10.1128/genomea.01164-15.

• Naseer N, Shapiro JA, Chander M. 2014. RNA-seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor.
  PLOS One 9(8):e106181.

• Andersen EC*, Gerke JP*, Shapiro JA*, Crissman JR, Ghosh R, Bloom JS, Félix M-A, Kruglyak L. 2012. Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity.
  Nature Genetics 44:285-290.

• Ghosh R, Andersen EX, Shapiro JA, Gerke JP, Kruglyak L. 2012. Natural variation in a chloride channel subunit confers avermectin resistance in C. elegans.
  Science 355:574-578.

• Lu X-M*, Shapiro JA*, Ting C-T, Li Y, Li C, Xu J, Chen Y-J, Greenberg AJ, Li S-H, Wu C-I. 2010. Genome-wide mis-expression of X-linked vs. autosomal genes associated with hybrid male sterility.
  Genome Research 20:1097-1102.

• Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy A, Kruglyak L. 2010. Dissection of genetically complex traits with extremely large pools of yeast segregants.
  Nature 464:1039-1042.

• Schacherer J*, Shapiro JA*, Ruderfer DM, Kruglyak L. 2009. Comprehensive polymorphism survey elucidates population structure ofSaccharomyces cerevisiae.
  Nature 458:342-345.

• Kohn MH, Shapiro JA, Wu C-I. 2008. Decoupled differentiation of gene expression and coding sequence among Drosophila populations.
  Genes & Genetic Systems 83:265-273.

• Shapiro JA, Huang W, Zhang C, Lu J, Turissini DA, Fang S, Wang H-Y, Hudson RR, Wu C-I. 2007. Adaptive genic evolution in the Drosophila genomes.
  Proceedings of the National Academy of Sciences USA 104:2271-2276.

• Lee S, Bao J, Zhou G, Shapiro JA, Xu J, Shi RZ, Lu X, Clark T, Johnson D, Kim YX, Wing C, Tseng C, Sun M, Lin W, Wang J, Yang H, Wang J, Du W, Wu C-I, Zhang X, Wang SM. 2005. Detecting novel low-abundant transcripts in Drosophila.
  RNA 11:939-946.

• Reddi PP, Shore AM, Shapiro JA, Anderson A, Stoler MH, Acharya KK. 2003. Spermatid specific promoter of the SP-10 gene function as a insulator in somatic cells.
  Developmental Biology 262:173-182.

*Equal authorship contribution

Honors & Awards

• Post Doctoral Poster Prize, Annual Meeting of the Society for Molecular Biology and Evolution 2009

• Howard Hughes Medical Institute Pre-Doctoral Fellowship in Biological Sciences 2001-2006

• NSF Graduate Research Fellowship (Declined) 2001

• Honorable Mention NSF Graduate Research Fellowship 1999

• Fulbright Award (U.S. Student Program) full grant to Australia 1998

• Erastus C Benedict First Prize in Biology, Williams College 1998

• Phi Beta Kappa, elected 1998

• Sigma Xi, elected 1998