Paired-end mappability of transposable elements in the human genome (2019)

Sexton, Corinne E, and Han, Mira V. Mobile DNA, 10 (1), 29. doi: 10.1186/s13100-019-0172-5

Transcriptome analysis reveals negative correlation between transcripts of mitochondrial genes and L1HS, and positive correlation between KRAB-ZFPs and older LINE elements in normal somatic tissue (2018)

Chung, Nicky, Jonaid, GM, Quinton, Sophia, Ross, Austin, Alberto, Adrian, Clymer, Cody, Churchill, Daphnie, Leija, Omar Navarro, and Han, Mira V. bioRxiv, , 385062. doi: 10.1101/385062

Genome-wide analysis of starvation-selected Drosophila melanogaster—A genetic model of obesity (2017)

Hardy, Christopher M, Burke, Molly K, Everett, Logan J, Han, Mira V, Lantz, Kathryn M, and Gibbs, Allen G. Molecular biology and evolution, 35 (1), 50--65. doi: 10.1093/molbev/msx254

Genomics of parallel experimental evolution in Drosophila (2017)

Graves Jr, JL, Hertweck, KL, Phillips, MA, Han, MV, Cabral, LG, Barter, TT, Greer, LF, Burke, MK, Mueller, LD, and Rose, MR. Molecular biology and evolution, 34 (4), 831-842. doi: 10.1093/molbev/msw282

Measuring accelerated rates of insertions and deletions independent of rates of nucleotide substitution (2016)

Leija, Omar Navarro, Varghese, Sanju and Han, Mira V. Journal of molecular evolution, 83 (3-4), 137--146. doi: 10.1007/s00239-016-9761-9

Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes (2015)

Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arc{\`a Bruno, Arensburger, Peter, Artemov, Gleb, and others,. Science, 347 (6217), 1258522. doi: 10.1126/science.1258522

Estimating gene gain, loss rates in the presence of error in genome assembly, annotation using CAFE 3 (2013)

Han, Mira V, Thomas, Gregg WC, Lugo-Martinez, Jose, and Hahn, Matthew W. Molecular biology, evolution, 30 (8), 1987--1997. doi: 10.1093/molbev/mst100

Genome sequence of the model medicinal mushroom Ganoderma lucidum (2012)

Chen, Shilin, Xu, Jiang, Liu, Chang, Zhu, Yingjie, Nelson, David R, Zhou, Shiguo, Li, Chunfang, Wang, Lizhi, Guo, Xu, Sun, Yongzhen and others. Nature communications, 3 , 913. doi: 10.1038/ncomms1923

Characterizing gene movements between chromosomes in Drosophila (2012)

Han, Mira V. Fly, 6 (2), 121--125. doi:

Inferring the history of interchromosomal gene transposition in Drosophila using n-dimensional parsimony (2011)

Han, Mira V and Hahn, Matthew W. Genetics, 190 (2), 813-825. doi: 10.1534/genetics.111.135947

Developmental decoupling of alternative phenotypes: insights from the transcriptomes of horn-polyphenic beetles (2011)

Snell-Rood, Emilie C, Cash, Amy, Han, Mira V, Kijimoto, Teiya, Andrews, Justen, and Moczek, Armin P. Evolution, 65 (1), 231--245. doi: 10.1111/j.1558-5646.2010.01106.x

Metabolic flexibility revealed in the genome of the cyst-forming $\alpha$-1 proteobacterium Rhodospirillum centenum (2010)

Lu, Yih-Kuang, Marden, Jeremiah, Han, Mira, Swingley, Wesley D, Mastrian, Stephen D, Chowdhury, Sugata Roy, Hao, Jicheng, Helmy, Tamer, Kim, Sun, Kurdoglu, Ahmet A, and others. BMC genomics, 11 (1), 325. doi:

The contribution of gene movement to the "two rules of speciation" (2010)

Moyle, Leonie C, Muir, Christopher D, Han, Mira V, and Hahn, Matthew W. Evolution, 64 (6), 1541--1557. doi: 10.1111/j.1558-5646.2010.00990.x

Adaptive evolution of young gene duplicates in mammals (2009)

Han, Mira V, Demuth, Jeffery P, McGrath, Casey L, Casola, Claudio, and Hahn, Matthew W. Genome research, 19 (5), 859--867. doi: 10.1101/gr.085951.108

phyloXML: XML for evolutionary biology and comparative genomics (2009)

Han, Mira V and Zmasek, Christian M. BMC bioinformatics, 10 (1), 356. doi: 10.1186/1471-2105-10-356

A complex suite of forces drives gene traffic from Drosophila X chromosomes (2009)

Meisel, Richard P, Han, Mira V, and Hahn, Matthew W. Genome biology and evolution, 1 , 176--188. doi: 10.1093/gbe/evp018

Limitations of pseudogenes in identifying gene losses (2008)

Costello, James C, Han, Mira V, Hahn and Matthew W. , , 14--25. doi: 10.1007/978-3-540-87989-3_2


HAN, MIRA W and Hahn, Matthew W. , 14 , 114--125. doi:

Evolution of genes and genomes on the Drosophila phylogeny (2007)

Drosophila 12 Genomes Consortium and others. Nature, 450 (7167), 203. doi: 10.1038/nature06341

Gene family evolution across 12 Drosophila genomes (2007)

Hahn, Matthew W, Han, Mira V, Han, and Sang-Gook Han. PLoS genetics, 3 (11), e197. doi: 10.1371/journal.pgen.0030197

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007)

Stark, Alexander, Lin, Michael F, Kheradpour, Pouya, Pedersen, Jakob S, Parts, Leopold, Carlson, Joseph W, Crosby, Madeline A, Rasmussen, Matthew D, Roy, Sushmita, Deoras, Ameya N, and others. Nature, 450 (7167), 219. doi: 10.1038/nature06340