John Didion, PhD

Contact


Education

   
2008 to 2014 Doctor of Philosophy, Bioinformatics and Computational Biology
  University of North Carolina, Chapel Hill, NC
1996 to 2001 Bachelor of Science, Computer Science
  Northwestern University, Evanston, IL


Research Experience

   
2014 to Present National Human Genome Research Institute, Bethesda, MD
  Postdoctoral Fellow, Laboratory of Dr. Francis S Collins
 
  • Leveraging a large, multi-omics dataset to investigate epigenetic mechanisms underlying regulatory variants implicated in type 2 diabetes.
  • Developing machine-learning approaches to imputation for multi-omics data.
  • Using single-cell gene expression and chromatin accessibility data to understand cell-to-cell variability in pancreatic islets, including responses to glucose perturbation.
  • Designed a novel sequencing assay for single-molecule resolution transcriptome analysis.
  • Developed Atropos, user-friendly software for QC and pre-processing of NGS reads.
  • Awarded six grants, including an American Diabetes Association fellowship and an NIH K22.
2009 to 2014 University of North Carolina at Chapel Hill, Chapel Hill, NC
  Research Assistant, Laboratory of Dr. Fernando Pardo-Manuel de Villena
 
  • Mapped a novel meiotic drive locus, *R2d2*, and multiple modifier loci responsible for extreme transmission distortion in the Collaborative Cross.
  • Conducted a GWAS of wild mice to identify genes associated with the accumulation of Robertsonian translocations.
  • Developed CLASP, a software tool for validation of cell lines used in research.
2007 to 2008 Institute for Systems Biology, Seattle, WA
  Computational Biology Software Engineer, Laboratory of Dr. Ruedi Aebersold
  Developed informatics software to support proteomics research. Created TIQAM, a work flow management system for MRM (Multiple Reaction Monitoring) experiments.


Industry Experience

   
2004 to 2007 Muze, Inc., Seattle, WA
  Software Development Engineer
2003 to 2004 Encyclopaedia Britannica, Online Services, Chicago, IL
  Software Developer
2001 to 2003 ThoughtWorks, LLC, Chicago, IL
  Software Developer/Consultant


Publications

Journal Articles

[1] Didion JP, Martin M,, and FS, Collins, “Atropos: specific, sensitive, and speedy trimming of sequencing reads,” Preprint, Submitted, 2017

[2] Varshneya A, Scott LJ, Welch R, Erdos MR, Chines PS, Narisu N, D’Oliveira RA, Orchard P, Wolford BN, Kursawee R, Vadlamudi S, Cannon ME, Didion JP, et al., “Genetic regulatory signatures underlying islet gene expression and type 2 diabetes,” Proc Nat Acad Sci USA, 2017

[3] Morgan AP, Didion JP, et al., “Genome report: whole genome sequence of two wild-derived \textit{Mus musculus domesticus} inbred strains, LEWES/EiJ and ZALENDE/EiJ, with different diploid numbers,” G3, 2016

[4] Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM-F, Didion JP, et al., “The many evolutionary fates of a large segmental duplication in mouse,” Genetics, 2016

[5] Scott LJ, Erdos MR, Huyghe JR, Welch RP, Beck AT, Wolford BN, Chines PS, Didion JP, et al., “The genetic regulatory signature of type 2 diabetes in human skeletal muscle,” Nature Communications, 2016

[6] Didion JP, Morgan AP, et al., “\textit{R2d2} drives selfish sweeps in the house mouse,” Molecular Biology and Evolution, 2016

[7] Morgan AP, Fu C-P, Kao C-Y, Welsh CE, Didion JP, et al., “The Mouse Universal Genotyping Array: from substrains to subspecies,” G3, 2015

[8] Crowley JJ, …13 others…, Didion JP, et al., “Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance,” Nature Genetics, 2015

[9] Didion JP, Morgan AP, Clayshulte AMF, et al., “A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2,” PLoS Genetics, 2015

[10] Chandler RL, Damrauer JS, Raab JR, Schisler JC, Wilkerson MD, Didion JP, et al., “Coexistent ARID1A–PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signaling,” Nature Communications, 2015

[11] Didion JP, Buus RJ, Naghashfar Z, et al., “SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy,” BMC Genomics, 2014

[12] Calaway JD, Lenarcic AB, Didion JP, et al., “Genetic architecture of skewed X inactivation in the laboratory mouse,” PLoS Genetics, 2013

[13] Consortium, Collaborative Cross, “The genome architecture of the Collaborative Cross mouse genetic reference population,” Genetics, 2012

[14] Didion JP, , and Villena F, Pardo-Manuel de, “Deconstructing \textit{Mus gemischus}: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse,” Mammalian Genome, 2013

[15] Didion JP, Yang H, Sheppard K, et al., “Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias,” BMC Genomics, 2012

[16] Aylor DL, …11 others…, Didion JP, et al., “Genetic analysis of complex traits in the emerging Collaborative Cross,” Genome Research, 2011

[17] Yang H, Wang JR, Didion JP, et al., “Subspecific origin and haplotype diversity in the laboratory mouse,” Nature Genetics, 2011

[18] Eisener-Dorman AF, Didion JP, Santos C, Calaway JD, “The 23rd International Mammalian Genome Conference meeting report,” Mammalian Genome, 2010

[19] Lange V, Malmstrom JA, Didion JP, et al., “Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring,” Molecular and Cellular Proteomics, 2008


Funding

   
2017 NIH 1 K22 ES028024-01 BD2K Career Transition Award
  A Big Data Approach to Learning the Type 2 Diabetes Regulome
  Career transition award with 3 years tenure-track funding
2017 American Diabetes Association Postdoctoral Fellowship
  The Type 2 Diabetes Epigenome: A Multi-Tissue and Multi-Omics Investigaton of a Complex Disease
  Postdoctoral fellowship with up to 3 years salary and research support
2016 NIH Intramural Sequencing Center Pilot Grant
  Transcriptome analysis at single-molecule resolution
  Institutional award with funding for sequencing services
2015 NIH Intramural Sequencing Center Pilot Grant
  Extending ATAC-Seq to archival frozen and fixed tissue samples
  Institutional award with funding for sequencing services
2015 NIH Intramural Sequencing Center Pilot Grant
  Identifying functional variants in T2D GWAS loci using CATCh-PET
  Institutional award with funding for sequencing services
2014 NIH Intramural Sequencing Center Pilot Grant
  Epigenomic regulation of glucose response in a human pancreatic islet Beta cell line
  Institutional award with funding for sequencing services
2014 Department of Health and Human Services Ignite
  LabGenius: The Smart Lab Notebook for Scientists
  3-month incubator program incubator program to fund innovative projects within HHS
2009 Bioinformatics and Computational Biology Training Grant
  NIH GM067553-04
  Institution-awarded fellowship; 1 year stipend support
2009 International Mammalian Genome Society Fellowship
  Travel grant


Honors & Awards

   
2014.12 Dean’s Distinguished Dissertation Award (Nominee)
  University of North Carolina at Chapel Hill
  Nominee from the Bioinformatics and Computational Biology program
2013.09 Verne Chapman Young Scientist Award
  International Mammalian Genome Society
  Best trainee talk at the International Mammalian Genome Conference
2013.05 Chicago Prize
  Complex Traits Consortium
  Best graduate student talk at the Complex Traits Consortium meeting
2010.10 Genome Research Award for Outstanding Poster
  International Mammalian Genome Society
  Outstanding poster at the International Mammalian Genome Conference


Conference Participation

     
2016.10 Biological Data Science Meeting, Cold Spring Harbor, NY  
2015.10 American Society of Human Genetics Conference, Baltimore, MD Poster
2015.05 Biology of Genomes Meeting, Cold Spring Harbor, NY Poster
2014.10 28th Intl. Mammalian Genome Conference Bar Harbor, ME Poster
2013.09 27th Intl. Mammalian Genome Conference, Salamanca, Spain Talk
2013.05 12th Annual Meeting of the Complex Traits Community, Madison, WI Talk
2012.09 16th Evolutionary Biology Meeting, Marseille, France Talk, Poster
2011.06 Genetics Society of America Mouse Genetics Washington D.C. Poster
2011.06 National Centers for Systems Biology Annual Meeting Duke University Poster
2010.10 24th Intl. Mammalian Genome Conference, Heraklion, Greece Talk
2010.05 9th Annual Meeting of the Complex Traits Community, Chicago, IL Talk
2009.09 23rd Intl. Mammalian Genome Conference, San Diego, CA Talk


Other Invited Talks

   
2017.04 NIAID Genomics and Immunology Speaker Series, Bethesda, MD
2017.01 NIH Data Science Interest Group, Bethesda, MD
2015.10 NIH Digital Summit, Bethesda, MD
2012.09 UNC Genetics Department Retreat, Myrtle Beach, SC


Teaching Experience

   
2016 to Present NIH
  Software Carpentry, Instructor
2016 to Present FAES (NIH)
  American Academy of Bioinformatics, Instructor (paid)
2015 to Present NHGRI
  Graduate and undergraduate students, Mentor
2013 to 2014 University of North Carolina at Chapel Hill
  Undergraduate senior research project, Mentor
2013 Fall University of North Carolina at Chapel Hill
  Genetic Analysis 2, Teaching Assistant


Professional Memberships & Service

   
2016 to Present Software Carpentry
  Certified Instructor
2016 to Present NHGRI Preprint Journal Club
  Organizer
2016 NCBI Hackathon (multiple dates)
  Team Lead
2013 to 2015 International Mammalian Genome Society
  Secretariat member (honorary)
2013 UNC Genetics Department Retreat
  Abstract Review Committee

source | Generated April 12, 2017.