Publications Other

Publications

  1. Irber, L., et al. 2024. sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. Journal of Open Source Software.
  2. Castellanos, F.X., D. Moreno-Santillán, G.M. Hughes, N.S. Paulat, N. Sipperly, A.M. Brown, K.R. Martin, G.M. Poterewicz, M.C.W. Lim, A.L. Russell, M.S. Moore, M.G. Johnson, A.P. Corthals, D.A. Ray, L.M. Dávalos. 2023. The evolution of antimicrobial peptides in Chiroptera. Frontiers in Immunology.
  3. Barreto, E., M.C.W. Lim, D. Rojas, L.M. Dávalos, R.O. Wüest, A. Machac, and C.H. Graham. 2023. Morphology and niche evolution influence hummingbird speciation rates. Proceedings of the Royal Society B: Biological Sciences.
  4. Seimon, T.A., M.C.W. Lim, B. Nightingale, S. Elvin, A. Elmore, and A. Seimon. 2022. First report of Pallas’s cat in Sagarmatha National Park - Mount Everest Region, Nepal. CATnews.
  5. Charbonneau, A.L., A. Brady, K. Czajkowski, J. Aluvathingal, S. Canchi, R. Carter, K. Chard, D.J.B. Clarke, J. Crabtree, H.H. Creasy, M. D’Arcy, V. Felix, M. Giglio, A. Gingrich, R.M. Harris, T.K. Hodges, O. Ifeonu, M. Jeon, E. Kropiwnicki, M.C.W. Lim, R.L. Liming, J. Lumian, A.A. Mahurkar, M. Mandal, J.B. Munro, S. Nadendla, R. Richter, C. Romano, P. Rocca-Serra, M. Schor, R.E. Schuler, H. Tangmunarunkit, A. Waldrop, C. Williams, K. Word, S. Sansone, A. Ma’ayan, R. Wagner, I. Foster, C. Kesselman, C.T. Brown, and O. White. 2022. Making Common Fund data more findable: catalyzing a data ecosystem. GigaScience.
  6. Parigi, A.*, M.C.W. Lim*, S. Canchi*, J. Sanchez, J. Walter, R.M. Harris, A. Charbonneau, and C.T. Brown. 2022. A virtual training module for introducing the use of Amazon Web Services. Journal of Open Source Education. *co-first authors
  7. Lim, M.C.W., A. Seimon, B. Nightingale, C.C.Y. Xu, S.R.P. Halloy, A.J. Solon, N.B. Dragone, S.K. Schmidt, A. Tait, S. Elvin, A.C. Elmore, and T.A. Seimon. 2022. Estimating biodiversity across the tree of life on Mount Everest’s southern flank with environmental DNA. iScience.
  8. Pomerantz, A., K. Sahlin, N. Vasiljevic, A. Seah, M.C.W. Lim, E. Humble, S. Kennedy, H. Krehenwinkel, S. Winter, R. Ogden and S. Prost. 2022. Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment. Nature Protocols.
  9. Lim, M.C.W.*, A. Parigi*, S. Canchi*, J. Sanchez, J. Walter, A. Charbonneau, and C.T. Brown. 2021. Virtual training on virtual environments: an online open-source introduction to conda. Journal of Open Source Education. *co-first authors
  10. Potter, J.H.T., R. Drinkwater, K.T.J. Davies, N. Nesi, M.C.W. Lim, L.R. Yohe, H. Chi, X. Zhang, I. Levantis, B.K. Lim, C.C. Witt, G. Tsagkogeorga, M. dos Reis, Y. Liu, W. Furey, M.J. Whitley, D. Aksentijevic, L.M. Dávalos, S.J. Rossiter. 2021. Nectar-feeding bats and birds show parallel molecular adaptations in sugar metabolism enzymes. Current Biology.
  11. Vasiljevic, N., M.C.W. Lim, E. Humble, A. Seah, A. Kratzer, N. Morf, S. Prost, and R. Ogden. 2021. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Science International: Genetics.
  12. Lim, M.C.W., K. Bi, C.C. Witt, C.H. Graham, and L.M. Dávalos. 2021. Pervasive genomic signatures of local adaptation to altitude across highland specialist Andean hummingbird populations. Journal of Heredity.
  13. Sahlin, K., M.C.W. Lim, and S. Prost. 2021. NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data. Ecology and Evolution.
  14. Seah, A*, M.C.W. Lim*, D. McAloose, S. Prost, T.A. Seimon. 2020. MinION-based DNA barcoding of preserved and non-invasively collected wildlife samples. Genes. *Contributed equally.
  15. Lim, M.C.W., C.C. Witt, C.H. Graham, and L.M. Dávalos. 2019. Parallel molecular evolution in pathways, genes, and sites in high-elevation hummingbirds revealed by comparative transcriptomics. Genome Biol Evol.
  16. Morelli, T.L., S. Maher, M.C.W. Lim, C. Kastely, L. Eastman, L. Flint, A. Flint, S. Beissinger, and C. Moritz. 2017. Climate change refugia and habitat connectivity promote species persistence. Climate Change Responses.
  17. Graham, C.H., S.R. Supp, D. Powers, P.A. Beck, M.C.W. Lim, A. Shankar, T. Cormier, S. Goetz, and S. Wethington. 2016. Winter conditions influence biological responses of migrating hummingbirds. Ecosphere.
  18. Conroy, C. J., J.L. Patton, M.C.W. Lim, M. Phuong, B. Parmenter, and S. Höhna. 2016. Following the rivers: historical reconstruction of California voles Microtus californicus (Rodentia: Muridae) in the deserts of eastern California. Biological Journal of the Linnean Society.
  19. Parmenter, B.E., M.C.W. Lim, Y. Chen, C.J. Conroy, and B.F.M. Olechnowski. 2015. Microsatellite variation in the Owens Valley vole: Microtus californicus vallicola. Southwestern Naturalist.
  20. Supp, S.R., F.A. La Sorte, T.A. Cormier, M.C.W. Lim, D. Powers, S. Wethington, S. Goetz, and C.H. Graham. 2015. Citizen science data provides new insight into annual and seasonal variation in migration patterns. Ecosphere.
  21. Phuong, M.A., M.C.W. Lim, D.R. Wait, K.C. Rowe, and C. Moritz. 2014. Delimiting species in the genus, Otospermophilus (Rodentia: Sciuridae) using genetics, ecology, and morphology. Biological Journal of the Linnean Society.
  22. Rubidge, E.M., J.L. Patton, M. Lim, A.C. Burton, J.S. Brashares, and C.C. Moritz. 2012. Climate-induced range shift drives genetic erosion in an alpine mammal. Nature Climate Change.

Other

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