Shukla, Harsh G; Chakraborty, Mahul; Emerson, JJ

Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome Journal Article

In: bioRxiv, vol. 2024.06.11.598575, 2024.

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Chakraborty, Mahul; Lara, Angelica Gudalupe; Dang, Andrew; McCulloch, Kyle J; Rainbow, Dylan; Ngo, Luna Thanh; Solares, Edwin A; Said, Iskander; Corbett-Detig, Russell; Gilbert, Lawrence E; others,

Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies Journal Article

In: Proceedings of the National Academy of Sciences, vol. 120, no. 33, pp. e2301411120, 2023.

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Thakare, Aditi; Ghosh, Chaitali; Alalamath, Tejashwini; Kumar, Naveen; Narang, Himani; Whadgar, Saurabh; Paul, Kiran; Shrotri, Shweta; Kumar, Sampath; Soumya, M; others,

The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity Journal Article

In: Scientific reports, vol. 12, no. 1, pp. 1–16, 2022.

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Chakraborty*, Mahul; Ramaiah*, Arunachalam; Adolfi, Adriana; Halas, Paige; Kaduskar, Bhagyashree; Ngo, Luna Thanh; Jayaprasad, Suvratha; Paul, Kiran; Whadgar, Saurabh; Srinivasan, Subhashini; others,

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly Journal Article

In: BMC biology, vol. 19, no. 1, pp. 1–16, 2021.

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Durkin, Sylvia M; Chakraborty, Mahul; Abrieux, Antoine; Lewald, Kyle M; Gadau, Alice; Svetec, Nicolas; Peng, Junhui; Kopyto, Miriam; Langer, Christopher B; Chiu, Joanna C; others,

Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii Journal Article

In: Molecular biology and evolution, vol. 38, no. 6, pp. 2532–2546, 2021.



Liao, Yi; Zhang, Xinwen; Chakraborty, Mahul; Emerson, JJ

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila Journal Article

In: Genome research, vol. 31, no. 3, pp. 397–410, 2021.

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Chakraborty*, Mahul; Chang*, Ching-Ho; Khost, Danielle E; Vedanayagam, Jeffrey; Adrion, Jeffrey R; Liao, Yi; Montooth, Kristi L; Meiklejohn, Colin D; Larracuente, Amanda M; Emerson, JJ

Evolution of genome structure in the Drosophila simulans species complex Journal Article

In: Genome research, vol. 31, no. 3, pp. 380–396, 2021.

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Linder, Robert A; Majumder, Arundhati; Chakraborty, Mahul; Long, Anthony

Two synthetic 18-way outcrossed populations of diploid budding yeast with utility for complex trait dissection Journal Article

In: Genetics, vol. 215, no. 2, pp. 323–342, 2020.

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Heras, Joseph; Chakraborty, Mahul; Emerson, JJ; German, Donovan P

Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish Journal Article

In: Proceedings of the Royal Society B, vol. 287, no. 1921, pp. 20192327, 2020.

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Chakraborty, Mahul; Emerson, JJ; Macdonald, Stuart J; Long, Anthony D

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits Journal Article

In: Nature communications, vol. 10, no. 1, pp. 1–11, 2019.

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Solares*, Edwin A; Chakraborty*, Mahul; Miller, Danny E; Kalsow, Shannon; Hall, Kate; Perera, Anoja G; Emerson, JJ; Hawley, R Scott

Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing Journal Article

In: G3: Genes, Genomes, Genetics, vol. 8, no. 10, pp. 3143–3154, 2018.

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Chakraborty, Mahul; VanKuren, Nicholas W; Zhao, Roy; Zhang, Xinwen; Kalsow, Shannon; Emerson, JJ

Hidden genetic variation shapes the structure of functional elements in Drosophila Journal Article

In: Nature genetics, vol. 50, no. 1, pp. 20–25, 2018.

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Bhat, Ramray; Chakraborty, Mahul; Glimm, Tilmann; Stewart, Thomas A; Newman, Stuart A

Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation Journal Article

In: BMC evolutionary biology, vol. 16, no. 1, pp. 1–11, 2016.

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Chakraborty, Mahul; Baldwin-Brown, James G; Long, Anthony D; Emerson, JJ

Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage Journal Article

In: Nucleic acids research, vol. 44, no. 19, pp. e147–e147, 2016.

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Chakraborty, Mahul; Fry, James D

Evidence that environmental heterogeneity maintains a detoxifying enzyme polymorphism in Drosophila melanogaster Journal Article

In: Current Biology, vol. 26, no. 2, pp. 219–223, 2016.

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Chakraborty, Mahul; Fry, James D

Parallel functional changes in independent testis-specific duplicates of Aldehyde dehydrogenase in Drosophila Journal Article

In: Molecular biology and evolution, vol. 32, no. 4, pp. 1029–1038, 2015.

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Bhat, Ramray; Chakraborty, Mahul; Mian, IS; Newman, Stuart A

Structural divergence in vertebrate phylogeny of a duplicated prototype galectin Journal Article

In: Genome biology and evolution, vol. 6, no. 10, pp. 2721–2730, 2014.

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Chakraborty, Mahul; Fry, James D

Drosophila lacking a homologue of mammalian ALDH2 have multiple fitness defects Journal Article

In: Chemico-biological interactions, vol. 191, no. 1-3, pp. 296–302, 2011.

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