Publications

“My Bibliography” from NCBI
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* Equal contribution
✉ Corresponding author

Preprints

• Shukla H.G., Chakrabroty M.✉, Emerson J.J.✉ (2024).
  Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome. bioRxiv 2024.06.11.598575.
  (pdf) (doi)

• Zhang X.✉, Emerson J.J.✉ (2019).
  Inferring the genetic architecture of expression variation from replicated high throughput allele-specific expression experiments. bioRxiv 699074.
  (pdf) (doi)

Published

• Chakraborty M., Lara A.G., Dang A., McCulloch K.J., Rainbow D., Carter D., Ngo L.T., Solares E.A., Said I., Corbett-Detig R., Gilbert L.E., Emerson J.J.✉, Briscoe A.✉ (2023).
  Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies. PNAS 120, e2301411120.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Zhao R.✉, Lukacsovich T., Gaut R., Emerson J.J.✉ (2023).
  FREQ-Seq²: a method for precise high-throughput combinatorial quantification of allele frequencies. G3: Genes, Genomes, Genetics jkad162.
  (pdf) (doi) (pmc) (supp) (gs)

• Liao Y.*, Wang J.*, Zhu Z., Liu Y., Chen J., Zhou Y., Liu F., Lei J., Gaut B.S., Cao B.✉, Emerson J.J.✉, Chen C.✉ (2022)
  The 3D architecture of the pepper genome and its relationship to function and evolution traits. Nature Communications 13 3479.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Durkin S.M., Chakraborty M., Abrieux A., Lewald K.M., Gadau A., Svetec N., Peng J., Kopyto M., Chiu J.C., Emerson J.J., Zhao L.✉ (2021).
  Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii. Mol. Biol. Evol. msab048.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Chakraborty M.*, Ramaiah A.*, Adolfi A., Halas P., Kaduskar B., Ngo L.T., Jayaprasad S., Paul K., Whadgar S., Srinivasan S., Subramani S., Bier E., James A.A., Emerson J.J.✉ (2021).
  Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biol 19 28.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Liao Y.✉, Zhang X., Chakraborty M., Emerson J.J.✉ (2021).
  Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. Genome Research 31: 397-410.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Chakraborty M.*, Chang C.-H.*, Khost D.E., Vedanayagam J., Adrion J.R., Liao Y., Montooth K., Meiklejohn C.D., Larracuente A.M.✉, Emerson J.J.✉ (2021).
  Evolution of genome structure in the Drosophila simulans species complex. Genome Research 31: 380-396.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Adolfi A., Gantz V.M., Jasinskiene N., Lee H.-F., Hwang K., Bulger E.A., Ramaiah A., Bennett J.B., Terradas G., Emerson J.J., Marshall J.M., Bier E., James A.A.✉ (2020).
  Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi. Nature Communications 11 5553.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Kou Y.*, Liao Y.*, Toivainen T., Lv Y., Tian X., Emerson J.J., Gaut B.S.✉, Zhou Y.✉ (2020).
  Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication. Mol. Biol. Evol. msaa185.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Heras J.✉, Chakraborty M., Emerson J.J., German D.P. (2020).
  Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. Proc. R. Soc. B. 287.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Chakraborty M.✉, Emerson J.J., Macdonald S.J., Long A.D.✉ (2019).
  Structural variants exhibit allelic heterogeneity and shape variation in complex traits. Nature Communications 10 4872.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Zhang X. and Emerson J.J.✉ (2019).
  Inferring Compensatory Evolution of cis- and trans-Regulatory Variation. Trends in Genetics 35 1-3.
  (pdf) (doi) (pmc) (supp) (gs)

• Solares E.A.*, Chakraborty M.*, Miller D.E., Kalsow S., Hall K.E., Perera A.G., Emerson J.J.✉, Hawley R.S.✉ (2018).
  Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing. G3: Genes, Genomes, Genetics 8 3143-3154.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Chakraborty M.✉, VanKuren N.W., Zhao R., Zhang X., Kalsow S., and Emerson J.J.✉ (2018).
  Hidden genetic variation shapes the structure of functional elements in Drosophila. Nature Genetics 50, 20-25.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Emerson J.J.✉ (2017).
  Evolution: A Paradigm Shift in Snake Sex Chromosome Genetics. Current Biology 27, R800–R803.
  (pdf) (doi) (gs)

• Long M.*✉ and Emerson J.J.*✉ (2017).
  Meiotic Sex Chromosome Inactivation: Compensation by Gene Traffic. Current Biology 27, R659–R661.
  (pdf) (doi) (gs)

• Chakraborty M., Baldwin-Brown J.G., Long A.D., and Emerson J.J.✉ (2016).
  Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res 44, e147–e147.
  (pdf) (doi) (pmc) (supp) (preprint) (gs)

• Schaefke B.*, Emerson J.J.*, Wang T.-Y., Lu M.-Y.J., Hsieh L.-C., and Li W.-H. (2013).
  Inheritance of Gene Expression Level and Selective Constraints on Trans- and Cis-Regulatory Changes in Yeast. Mol Biol Evol 30, 2121–2133.
  (pdf) (doi) (supp) (gs)

• Vicoso B.*, Emerson J.J.*, Zektser Y., Mahajan S., and Bachtrog D. (2013).
  Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation. PLoS Biology 11, e1001643.
  (pdf) (doi) (pmc) (supp) (gs)

• Pool J.E., Corbett-Detig R.B., Sugino R.P., Stevens K.A., Cardeno C.M., Crepeau M.W., Duchen P., Emerson J.J., Saelao P., Begun D.J., and Langley C.H. (2012).
  Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture. PLoS Genetics 8, e1003080.
  (pdf) (doi) (pmc) (supp) (gs)

• Cardoso-Moreira M., Emerson J.J., Clark A.G., and Long M. (2011).
  Drosophila Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome. PLoS Genetics 7, e1002340.
  (pdf) (doi) (pmc) (supp) (gs)

• Nikaido M., Sasaki T., Emerson J.J., Aibara M., Mzighani S.I., Budeba Y.L., Ngatunga B.P., Iwata M., Abe Y., Li W.-H., and Okada N. (2011).
  Genetically distinct coelacanth population off the northern Tanzanian coast. PNAS 108, 18009–18013.
  (pdf) (doi) (supp)

• Emerson J.J. and Li W.-H. (2010).
  The genetic basis of evolutionary change in gene expression levels. Philosophical Transactions of the Royal Society B: Biological Sciences 365, 2581–2590.
  (pdf) (doi) (pmc)

• Emerson J.J.*, Hsieh L.-C.*, Sung H.-M.*, Wang T.-Y.*, Huang C.-J., Lu H.H.-S., Lu M.-Y.J., Wu S.-H., and Li W.-H. (2010).
  Natural selection on cis and trans regulation in yeasts. Genome Research 20, 826–836.
  (pdf) (doi) (pmc) (supp)

• Emerson J.J.*✉, Cardoso-Moreira M.*✉, Borevitz J.O., and Long M. (2008).
  Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster. Science 320, 1629–1631.
  (pdf) (doi) (supp)

• Fan C., Emerson J.J., and Long M. (2007).
  The origin of new genes. In Evolutionary Genomics and Proteomics (Sunderland, Massachusetts: Sinauer Associates, Inc.), pp. 27–44.
  (pdf)

• Cowan A.T., Bowman G.R., Edwards K.F., Emerson J.J., and Turkewitz A.P. (2005).
  Genetic, Genomic, and Functional Analysis of the Granule Lattice Proteins in Tetrahymena Secretory Granules. Mol. Biol. Cell 16, 4046–4060.
  (pdf) (doi) (pmc)

• Chen Y.*✉, Emerson J.J.*✉, and Martin T.M.*✉ (2005).
  Evolutionary genomics: Codon volatility does not detect selection. Nature 433, E6–E7.
  (pdf) (doi)

• The International Chicken Genome Sequencing Consortium (2004).
  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716.
  (pdf) (doi) (supp)

• Betran E., Emerson J.J., Kaessmann H., and Long M. (2004).
  Sex Chromosomes and Male Functions: Where Do New Genes Go? Cell Cycle 3, 871–873.
  (pdf) (doi)

• Wang W., Thornton K., Emerson J.J., and Long M. (2004).
  Nucleotide Variation and Recombination Along the Fourth Chromosome in Drosophila simulans. Genetics 166, 1783–1794.
  (pdf) (doi) (pmc)

• Emerson J.J.*, Kaessmann H.*, Betrán E., and Long M. (2004).
  Extensive Gene Traffic on the Mammalian X Chromosome. Science 303, 537–540.
  (pdf) (doi) (supp)

• Strassmann J.E., Queller D.C., Emerson J.J., Stagi M., Cervo R., and Turillazzi S. (2004).
  Comparing the costs and benefits of grouping with non-relatives in the social amoeba Dictyostelium discoideum (Amoebazoa) and the social wasp Polistes dominulus (Hymenoptera Vespidae). Redia LXXXVII, 145–148.
  (pdf)

• Bergelson J., Dwyer G., and Emerson J.J. (2001).
  Models and Data on Plant-Enemy Coevolution. Annual Review of Genetics 35, 469–499.
  (pdf) (doi)