Adam Session, Ph.D
Education:
Ph.D., Molecular and Cell Biology. University of California, Berkeley. Berkeley, CA. (2015)
B.A., Genetics and Microbiology. Rutgers, The State University of New Jersey. New Brunswick, NJ. (2009)
Research Interests:
- Genome evolution, focus on polyploids
- Evolution of repetitive sequences, focus on retrotranspon phylogeny
- Differential expression and epigenetic evolution
Experience:
Postdoctoral research University of California, Berkeley
Mentor: Professor Daniel Rokhsar
Molecular and Cell Biology Department; (January 2020 – May 2021)
-Working on gene annotation and comparative analysis of Xenopus laevis and Xenopus borealis.
-Identified subgenomes of allooctoploid strawberry, Fragaria x ananassa
-Identification of allotetraploid goldfish subgenomes
-Disproved shared polyploidy of goldfish and carp
-Annotation and genetic analysis of Rana muscosa
Private Research Tiny Farms Inc.
Chief Scientist (April 2017 – December 2019).
-Awarded DARPA grant to establish genetic techniques in the non-model insect, Gryllodes sigillatus.
-Established EMS mutagenesis in G. sigillatus.
-Identified two novel mutants to aid in farming of G. sigillatus for protein production
-Optimizing production efficiency of cricket rearing
-Incorporating local waste stream sources into cricket feed while maintaining animal welfare
Postdoctoral research Joint Genome Institute, Department of Energy
Mentor: Professor Daniel Rokhsar
Eukaryotic Genomics Supergroup (June 2015 – September 2019).
-Working on gene annotation and comparative analysis of polyploid plant genomes, including Brachypodium hybridum and Panicum virgatum.
-Confirmed allopolyploid status of B. hybridum as a descendant of the hybridized ancestors of B. distachyon and B. stacei.
-Tested and proved allopolyploid status of P. virgatum by identifying and studying the distribution of chromosome-specific 15mers in the polyploid genome
-Identified low copy transposons and uncollapsed haplotypes as errors in the current P. virgatum assembly
-Identified a conservative set of orthologs between Panicum species to overcome the excess amount of low copy transposons in the annotations.
Ph.D. studies University of California, Berkeley
Mentor: Professor Daniel Rokhsar
Molecular and Cell Biology Department; Genetics, Genomics and Development Division.
-Worked on assembly and analysis of the allopolyploid frog Xenopus laevis by writing code to assess genome completeness, annotation quality and improvement, align GBS, RNA-seq, ChIP-seq, and Hi-C data sets.
– Worked with Xenbase on presenting/distributing the different versions of genome DNA and annotations to the Xenopus community of scientists prior to publication.
-Developed computational and wet lab experiments to prove the allotetraploid hypothesis in X. laevis, as well as study the effects of the whole genome duplication on genome evolution.
-Wrote code to analyze gene loss rate, evolution of expressed and pseudogene sequences, including t heir cis-regulatory elements.
-Built gene-coexpression networks to create a cartography of gene expression in Xenopus, as well as detail the subgenome-specific divergence to ancestral expression patterns.
-Helped study the relationship between gene expression and the differential evolution of epigenetic marks following polyploidy
-Mentored four undergraduate scientists in genome evolution, statistics, and basic coding (Unix, Perl, R). Additionally, helped one student develop and complete her honors thesis.
UC Berkeley Amgen Scholars Internship University of California, Berkeley-Rachel Brem, Ph.D
Molecular and Cell Biology . (May 2008 – August 2008)
-Generation of an interspecific Saccharomyces hybrid and optimization of RNA-seq library generation.
Duke University Genome Sciences Internship Duke University-Fred Dietrich, Ph.D
Institute for Genome Sciences and Policy. (May 2007 – August 2007)
-Studied the evolutionary history of the yeast biotin synthesis pathway by transformation of yeast.
Undergraduate research Rutgers University-Mary Konsolaki, Ph.D
Genetics and Microbiology. (January 2007 – May 2009)
-Design and optimization of a behavioral assay to assess the effect of amyloid-beta aggregation in Drosophila melanogaster.
Publications:
Chapman, J.A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A.M., Strnadova, V., Jenkins, J., Sehgal, S., Oliker, L. et al.: A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology 2015, 16(1):26.
Session, A.M., Uno, Y., Kwon, T., Chapman, J. A., Toyoda, A., Takahashi, S., … Rokhsar, D.S. (2016). Genome evolution in the allotetraploid frog Xenopus laevis. Nature, 538(7625), 336–343.
Mitros, T.*, Lyons, J.B.*, Session, A.M.*, et al. “A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.” Developmental biology 452 1 (2019): 8-20 .
Miller, K.E., Session, A.M., & Heald, R. (2019). Kif2a Scales Meiotic Spindle Size in Hymenochirus boettgeri. Current Biology, 29, 3720-3727.e5.
Gordon, S.P., Contreras-Moreira, B., Levy, J.J., Djamei, A., Czedik-Eysenberg, A., Tartaglio, V.S., Session, A.M., et al(2020). Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications, 11.
Mitros, T., Session, A.M., James, B.T. et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020).
Submitted Manuscripts:
Session, A.M, Rokhsar, D.S. Discovering subgenomes of the allooctoploid strawberry (in review Nature Genetics). bioRxiv 2020.11.04.330431; doi: https://doi.org/10.1101/2020.11.04.330431
Manuscripts in preparation:
Bredeson, Jessen, Session, A.M, et al. Evolution of chromosome sub compartments in allotetraploid Xenopus
Technical skills:
- High-throughput sequencing methods: Previous experience with shotgun sequencing and long-range scaffolding of frog genomes using jumping libraries and genetic maps. Currently using new long-read sequencing with Hi-C to rapidly form chromosome-scaled assemblies of complex vertebrates.
- Proficiency in genome assembly, genome annotation, population genetics, comparative genomics, bioinformatics, and phylogenetics.
- Includes and writing custom scripts/tools in Perl, Python, and R.
- Molecular biology and Xenopus developmental biology: embryo staging, in situ hybridization, and RNAseq. Creation of RNA DNA libraries for sequencing.
Presentations:
Genome Evolution following polyploidy in grasses San Diego, CA
Poster: Plant and Animal Genome Conference (January 2018)
Establishing EMS mutagenesis in the nonmodel insect, Gryllodes sigillatus San Diego, CA
Invited Speaker: Plant and Animal Genome Conference (January 2018)
EMS mutageneis reveals novel mutants in Gryllodes sigillatus Natick, MA
Invited Speaker: DARPA Insect Alliance PI meeting (July 2017)
Repetitive elements reveal the evolutionary history of polyploid genomes San Diego, CA
Invited Speaker: Plant and Animal Genome Conference (January 2017)
A survey of the evolutionary consequences of allopolyploidy in Xenopus laevis Woods Hole, MA
Invited speaker: Xenopus PI Meeting (October 2015)
Asymmetric subgenome evolution following polyploidy in Xenopus laevis Berkeley, CA
Invited Speaker: Molecular and Cell Biology Departmental Genetics Symposium (May 2015)
Asymmetric subgenome dynamics following allotetraploidy in Xenopus laevis Asilomar, CA
Invited Speaker: Molecular and Cell Biology Departmental Retreat (October 2014)
Asymmetric subgenome evolution in the allotetraploid frog, Xenopus laevis Asilomar, CA
Poster: International Xenopus Meeting (June 2014)
Asymmetric subgenome dynamics following allotetraploidy in Xenopus laevis San Juan, PR
Invited Speaker: Society for Molecular Biology and Evolution Conference (October 2014)
The genomic response to allotetraploidy in the frog, Xenopus laevis Asilomar, CA
Invited Speaker: Molecular and Cell Biology Departmental Retreat (October 2013)
Xenopus: A natural experiment in whole genome duplication Asilomar, CA
Invited Speaker: Molecular and Cell Biology Departmental Retreat (October 2012)
Initial genomic analysis of the allotetraploid frog, Xenopus laevis Asilomar, CA
Poster: Molecular and Cell Biology Departmental Retreat (October 2011)
Teaching experience:
Teaching Assistant. (2010 – 2011). University of California, Berkeley
Courses: (1) Genetics, Genomics, and Cell Biology. (2) Genes, Cells, and Organisms: Biology for non-majors
Amgen Scholars Graduate Assistant. (2010-2011). University of California, Berkeley
Mentoring visiting undergraduate researchers, giving presentations on graduate school applications, poster/oral presentation work. Generally advising visiting scholars on how to apply to graduate school
Grants:
- DARPA SBIR grant – Tiny Farms
Designed genetic screen for new cricket species and identified two morphological mutants to establish inbred lines for future genetic experiments
Session Lab @ Binghamton University 