| RepeatModeler2 for automated genomic discovery of transposable element families JM Flynn, R Hubley, C Goubert, J Rosen, AG Clark, C Feschotte, AF Smit Proceedings of the National Academy of Sciences 117 (17), 9451-9457, 2020 | 1688 | 2020 |
| Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods JM Flynn, EA Brown, FJJ Chain, HJ MacIsaac, ME Cristescu Ecology and evolution 5 (11), 2252-2266, 2015 | 149 | 2015 |
| Spontaneous Mutation Accumulation in Daphnia pulex in Selection-Free vs. Competitive Environments JM Flynn, FJJ Chain, DJ Schoen, ME Cristescu Molecular biology and evolution 34 (1), 160-173, 2017 | 71 | 2017 |
| Selection constrains high rates of tandem repetitive DNA mutation in Daphnia pulex JM Flynn, I Caldas, ME Cristescu, AG Clark Genetics 207 (2), 697-710, 2017 | 29 | 2017 |
| Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads C Mérot, KSR Stenløkk, C Venney, M Laporte, M Moser, E Normandeau, ... Molecular Ecology, https://doi.org/10.1111/mec.16468, 2022 | 27 | 2022 |
| Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis JM Flynn, M Long, RA Wing, AG Clark Molecular Biology and Evolution 37 (5), 1362-1375, 2020 | 27 | 2020 |
| Accelerated rates of large-scale mutations in the presence of copper and nickel FJJ Chain, JM Flynn, JK Bull, ME Cristescu Genome research 29 (1), 64-73, 2019 | 18* | 2019 |
| Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii JM Flynn, SE Lower, DA Barbash, AG Clark Genome biology and evolution 10 (7), 1673-1686, 2018 | 18 | 2018 |
| Fitness and genomic consequences of chronic exposure to low levels of copper and nickel in Daphnia pulex mutation accumulation lines JK Bull, JM Flynn, FJJ Chain, ME Cristescu G3: Genes, Genomes, Genetics 9 (1), 61-71, 2019 | 9 | 2019 |
| Three recent sex chromosome-to-autosome fusions in a Drosophila virilis strain with high satellite DNA content JM Flynn, KB Hu, AG Clark Genetics, https://doi.org/10.1093/genetics/iyad062, 2023 | 6* | 2023 |
| Copy number evolution in simple and complex tandem repeats across the C57BL/6 and C57BL/10 inbred mouse lines JM Flynn, EJ Brown, AG Clark G3 11 (8), jkab184, 2021 | 5 | 2021 |
| The implications of satellite DNA instability on cellular function and evolution JM Flynn, YM Yamashita Seminars in Cell & Developmental Biology, 2023 | 3 | 2023 |
| High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the Drosophila virilis sub-group JM Flynn, YH Ahmed-Braimah, M Long, RA Wing, AG Clark Genome Biology and Evolution 16 (https://doi.org/10.1093/gbe/evad238), 2023 | 1 | 2023 |
| The implications of satellite DNA instability on cellular function and evolution YM Flynn, Jullien M., Yamashita OSF Preprints, https://osf.io/yfkhm/, 2023 | | 2023 |
| Evolution of Repetitive DNA: Methodologies, Expansions, and Constraints JM Flynn Cornell University, 2021 | | 2021 |
| Spontaneous mutation rates and spectra with and without the influence of natural selection in Daphnia pulex J Flynn McGill University Libraries, 2016 | | 2016 |
