Publications

@article{Samano2024stephensi,

title = {Genome structural variants shape adaptive success of an invasive urban malaria vector \emph{Anopheles stephensi}},

author = {Alejandra Samano and Naveen Kumar and Yi Liao and Farah Ishtiaq and Mahul Chakraborty},

url = {https://www.biorxiv.org/content/10.1101/2024.07.29.605641v2},

doi = {https://doi.org/10.1101/2024.07.29.605641},

year  = {2024},

date = {2024-07-30},

urldate = {2024-07-30},

journal = {bioRxiv},

volume = {2024.07.29.605641},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shukla2024array,

title = {Genetic variation in recalcitrant repetitive regions of the \emph{Drosophila melanogaster} genome},

author = {Harsh G Shukla and Mahul Chakraborty and JJ Emerson},

url = {https://www.biorxiv.org/content/10.1101/2024.06.11.598575v1},

doi = {https://doi.org/10.1101/2024.06.11.598575},

year  = {2024},

date = {2024-06-11},

urldate = {2024-06-11},

journal = {bioRxiv},

volume = {2024.06.11.598575},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2022sex,

title = {Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in \emph{Heliconius} butterflies},

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

url = {https://www.pnas.org/doi/abs/10.1073/pnas.2301411120},

doi = {https://doi.org/10.1073/pnas.2301411120},

year  = {2023},

date = {2023-08-08},

urldate = {2023-08-08},

journal = {Proceedings of the National Academy of Sciences},

volume = {120},

number = {33},

pages = {e2301411120},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{thakare2022genome,

title = {The genome trilogy of \emph{Anopheles stephensi}, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity},

author = {Aditi Thakare and Chaitali Ghosh and Tejashwini Alalamath and Naveen Kumar and Himani Narang and Saurabh Whadgar and Kiran Paul and Shweta Shrotri and Sampath Kumar and M Soumya and others},

url = {https://www.nature.com/articles/s41598-022-07462-3},

doi = {10.1038/s41598-022-07462-3},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Scientific reports},

volume = {12},

number = {1},

pages = {1--16},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2021hidden,

title = {Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly},

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

url = {https://link.springer.com/article/10.1186/s12915-021-00963-z},

doi = {10.1186/s12915-021-00963-z},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {BMC biology},

volume = {19},

number = {1},

pages = {1--16},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{durkin2021behavioral,

title = {Behavioral and genomic sensory adaptations underlying the pest activity of \emph{Drosophila suzukii}},

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

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Molecular biology and evolution},

volume = {38},

number = {6},

pages = {2532--2546},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{liao2021topologically,

title = {Topologically associating domains and their role in the evolution of genome structure and function in Drosophila},

author = {Yi Liao and Xinwen Zhang and Mahul Chakraborty and JJ Emerson},

url = {https://genome.cshlp.org/content/31/3/397.short},

doi = {10.1101/gr.266130.120},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Genome research},

volume = {31},

number = {3},

pages = {397--410},

publisher = {Cold Spring Harbor Lab},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2021evolution,

title = {Evolution of genome structure in the \emph{Drosophila simulans} species complex},

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

url = {https://genome.cshlp.org/content/31/3/380.short},

doi = {10.1101/gr.263442.120},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Genome research},

volume = {31},

number = {3},

pages = {380--396},

publisher = {Cold Spring Harbor Lab},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{linder2020two,

title = {Two synthetic 18-way outcrossed populations of diploid budding yeast with utility for complex trait dissection},

author = {Robert A Linder and Arundhati Majumder and Mahul Chakraborty and Anthony Long},

url = {https://academic.oup.com/genetics/article/215/2/323/5930408},

doi = {10.1534/genetics.120.303202},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Genetics},

volume = {215},

number = {2},

pages = {323--342},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{heras2020genomic,

title = {Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish},

author = {Joseph Heras and Mahul Chakraborty and JJ Emerson and Donovan P German},

url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2019.2327},

doi = {10.1098/rspb.2019.2327},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Proceedings of the Royal Society B},

volume = {287},

number = {1921},

pages = {20192327},

publisher = {The Royal Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2019structural,

title = {Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits},

author = {Mahul Chakraborty and JJ Emerson and Stuart J Macdonald and Anthony D Long},

url = {https://www.nature.com/articles/s41467-019-12884-1},

doi = {10.1038/s41467-019-12884-1},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Nature communications},

volume = {10},

number = {1},

pages = {1--11},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{solares2018rapid,

title = {Rapid low-cost assembly of the \emph{Drosophila melanogaster} reference genome using low-coverage, long-read sequencing},

author = {Edwin A Solares* and Mahul Chakraborty* and Danny E Miller and Shannon Kalsow and Kate Hall and Anoja G Perera and JJ Emerson and R Scott Hawley},

url = {https://academic.oup.com/g3journal/article/8/10/3143/6026978},

doi = {10.1534/g3.118.200162},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {G3: Genes, Genomes, Genetics},

volume = {8},

number = {10},

pages = {3143--3154},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2018hidden,

title = {Hidden genetic variation shapes the structure of functional elements in Drosophila},

author = {Mahul Chakraborty and Nicholas W VanKuren and Roy Zhao and Xinwen Zhang and Shannon Kalsow and JJ Emerson},

url = {https://www.nature.com/articles/s41588-017-0010-y},

doi = {10.1038/s41588-017-0010-y},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Nature genetics},

volume = {50},

number = {1},

pages = {20--25},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bhat2016deep,

title = {Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation},

author = {Ramray Bhat and Mahul Chakraborty and Tilmann Glimm and Thomas A Stewart and Stuart A Newman},

url = {https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-016-0729-6},

doi = {10.1186/s12862-016-0729-6},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {BMC evolutionary biology},

volume = {16},

number = {1},

pages = {1--11},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2016contiguous,

title = {Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage},

author = {Mahul Chakraborty and James G Baldwin-Brown and Anthony D Long and JJ Emerson},

url = {https://academic.oup.com/nar/article/44/19/e147/2468393},

doi = {10.1093/nar/gkw654},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Nucleic acids research},

volume = {44},

number = {19},

pages = {e147--e147},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2016evidence,

title = {Evidence that environmental heterogeneity maintains a detoxifying enzyme polymorphism in \emph{Drosophila melanogaster}},

author = {Mahul Chakraborty and James D Fry},

url = {https://www.sciencedirect.com/science/article/pii/S0960982215014888},

doi = {10.1016/j.cub.2015.11.049},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Current Biology},

volume = {26},

number = {2},

pages = {219--223},

publisher = {Cell Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2015parallel,

title = {Parallel functional changes in independent testis-specific duplicates of Aldehyde dehydrogenase in \emph{Drosophila}},

author = {Mahul Chakraborty and James D Fry},

url = {https://academic.oup.com/mbe/article/32/4/1029/1076625},

doi = {10.1093/molbev/msu407},

year  = {2015},

date = {2015-01-01},

urldate = {2015-01-01},

journal = {Molecular biology and evolution},

volume = {32},

number = {4},

pages = {1029--1038},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bhat2014structural,

title = {Structural divergence in vertebrate phylogeny of a duplicated prototype galectin},

author = {Ramray Bhat and Mahul Chakraborty and IS Mian and Stuart A Newman},

url = {https://academic.oup.com/gbe/article/6/10/2721/611707},

doi = {10.1093/gbe/evu215},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Genome biology and evolution},

volume = {6},

number = {10},

pages = {2721--2730},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty2011drosophila,

title = {Drosophila lacking a homologue of mammalian ALDH2 have multiple fitness defects},

author = {Mahul Chakraborty and James D Fry},

url = {https://www.sciencedirect.com/science/article/abs/pii/S000927971100055X},

doi = {10.1016/j.cbi.2011.01.031},

year  = {2011},

date = {2011-01-01},

urldate = {2011-01-01},

journal = {Chemico-biological interactions},

volume = {191},

number = {1-3},

pages = {296--302},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}