Keith A Crandall

For a complete list of publications, see my Google Scholar Page at https://scholar.google.com/citations?hl=en&user=nccuYroAAAAJ&view_op=list_works&sortby=pubdate

De Grave S., Decock W., Dekeyzer S., Davie P.J.F., Fransen C.H.J.M., Boyko C.B., Poore G.C.B., Macpherson E., Ahyong S.T., Crandall K.A., de Mazancourt V., Osawa M., Chan T.-Y., Ng P.K.L., Lemaitre R., van der Meij S.E.T., Santos S. 2023. Benchmarking global biodiversity of decapod crustaceans (Crustacea: Decapoda). J. Crustacean Biol. 43:ruad042.

Odom A.R., Faits T., Castro-Nallar E., Crandall K.A., Johnson W.E. 2023. Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data. Sci. Rep. 13:13957.

Bernot J.P., Owen C.L., Wolfe J.M., Meland K., Olesen J., Crandall K.A. 2023. Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling. Mol. Biol. Evol. 40. msad175

Kanholm T., Rentia U., Hadley M., Karlow J.A., Cox O.L., Diab N., Bendall M.L., Dawson T., McDonald J.I., Xie W., Crandall K.A., Burns K.H., Baylin S.B., Easwaran H., Chiappinelli K.B. 2023. Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci. Cancer Res. 83:2584–2599.

Dawson T., Rentia U., Sanford J., Cruchaga C., Kauwe J.S.K., Crandall K.A. 2023. Locus specific endogenous retroviral expression associated with Alzheimer’s disease. Front. Aging Neurosci. 15:1186470.

Bernot J.P., Avdeyev P., Zamyatin A., Dreyer N., Alexeev N., Pérez-Losada M., Crandall K.A. 2022. Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. Gigascience. 11.

Suvorov A., Scornavacca C., Fujimoto M.S., Bodily P., Clement M., Crandall K.A., Whiting M.F., Schrider D.R., Bybee S.M. 2022. Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies. Syst. Biol. 71:526–546.

Knyazev S., Chhugani K., Sarwal V., Ayyala R., Singh H., Karthikeyan S., Deshpande D., Baykal P.I., Comarova Z., Lu A., Porozov Y., Vasylyeva T.I., Wertheim J.O., Tierney B.T., Chiu C.Y., Sun R., Wu A., Abedalthagafi M.S., Pak V.M., Nagaraj S.H., Smith A.L., Skums P., Pasaniuc B., Komissarov A., Mason C.E., Bortz E., Lemey P., Kondrashov F., Beerenwinkel N., Lam T.T.-Y., Wu N.C., Zelikovsky A., Knight R., Crandall K.A., Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat. Methods. 19:374–380.

Chow J.H., Rahnavard A., Gomberg-Maitland M., Chatterjee R., Patodi P., Yamane D.P., Levine A.R., Davison D., Hawkins K., Jackson A.M., Quintana M.T., Lankford A.S., Keneally R.J., Al-Mashat M., Fisher D., Williams J., Berger J.S., Mazzeffi M.A., Crandall K.A., N3C Consortium and ANCHOR Investigators. 2022. Association of Early Aspirin Use With In-Hospital Mortality in Patients With Moderate COVID-19. JAMA Netw Open. 5:e223890.

Lewin H.A., Richards S., Lieberman Aiden E., Allende M.L., Archibald J.M., Bálint M., Barker K.B., Baumgartner B., Belov K., Bertorelle G., Blaxter M.L., Cai J., Caperello N.D., Carlson K., Castilla-Rubio J.C., Chaw S.-M., Chen L., Childers A.K., Coddington J.A., Conde D.A., Corominas M., Crandall K.A., Crawford A.J., DiPalma F., Durbin R., Ebenezer T.E., Edwards S.V., Fedrigo O., Flicek P., Formenti G., Gibbs R.A., Gilbert M.T.P., Goldstein M.M., Graves J.M., Greely H.T., Grigoriev I.V., Hackett K.J., Hall N., Haussler D., Helgen K.M., Hogg C.J., Isobe S., Jakobsen K.S., Janke A., Jarvis E.D., Johnson W.E., Jones S.J.M., Karlsson E.K., Kersey P.J., Kim J.-H., Kress W.J., Kuraku S., Lawniczak M.K.N., Leebens-Mack J.H., Li X., Lindblad-Toh K., Liu X., Lopez J.V., Marques-Bonet T., Mazard S., Mazet J.A.K., Mazzoni C.J., Myers E.W., O’Neill R.J., Paez S., Park H., Robinson G.E., Roquet C., Ryder O.A., Sabir J.S.M., Shaffer H.B., Shank T.M., Sherkow J.S., Soltis P.S., Tang B., Tedersoo L., Uliano-Silva M., Wang K., Wei X., Wetzer R., Wilson J.L., Xu X., Yang H., Yoder A.D., Zhang G. 2022. The Earth BioGenome Project 2020: Starting the clock. Proc. Natl. Acad. Sci. U. S. A. 119.

Lawniczak M.K.N., Durbin R., Flicek P., Lindblad-Toh K., Wei X., Archibald J.M., Baker W.J., Belov K., Blaxter M.L., Marques Bonet T., Childers A.K., Coddington J.A., Crandall K.A., Crawford A.J., Davey R.P., Di Palma F., Fang Q., Haerty W., Hall N., Hoff K.J., Howe K., Jarvis E.D., Johnson W.E., Johnson R.N., Kersey P.J., Liu X., Lopez J.V., Myers E.W., Pettersson O.V., Phillippy A.M., Poelchau M.F., Pruitt K.D., Rhie A., Castilla-Rubio J.C., Sahu S.K., Salmon N.A., Soltis P.S., Swarbreck D., Thibaud-Nissen F., Wang S., Wegrzyn J.L., Zhang G., Zhang H., Lewin H.A., Richards S. 2022. Standards recommendations for the Earth BioGenome Project. Proc. Natl. Acad. Sci. U. S. A. 119.

Rahnavard A., Chatterjee S., Sayoldin B., Crandall K.A., Tekola-Ayele F., Mallick H. 2021. Omics community detection using multi-resolution clustering. Bioinformatics. 37:3588–3594.

Bendall M.L., Gibson K.M., Steiner M.C., Rentia U., Pérez-Losada M., Crandall K.A. 2021. HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations. Mol. Biol. Evol. 38:1677–1690.

Bendall M.L., de Mulder M., Iñiguez L.P., Lecanda-Sánchez A., Pérez-Losada M., Ostrowski M.A., Jones R.B., Mulder L.C.F., Reyes-Terán G., Crandall K.A., Ormsby C.E., Nixon D.F. 2019. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS Comput. Biol. 15:e1006453.

Hong C., Manimaran S., Shen Y., Perez-Rogers J.F., Byrd A.L., Castro-Nallar E., Crandall K.A., Johnson W.E. 2014. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome. 2:33.

Clement M., Posada D., Crandall K.A. 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9:1657–1659.

Posada D., Crandall K.A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14:817–818.