For a complete publication list, please visit Dr. Crandall's GoogleScholar page.
Posada, D., and K.A. Crandall. 2021. Felsenstein Phylogenetic Likelihood. Journal of Molecular Evolution https://doi.org/10.1007/s00239-020-09982-w.
Bendall, M.L., K.M. Gibson, M.C. Steiner, U. Retina, M. Pérez-Losada, and K.A. Crandall. 2021. HAPHPIPE: Haplotype reconstruction and phylodynamics for deep sequencing of intra-host viral populations. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msaa315
Alekseyenko, A., B. Hamidi, K.A. Crandall, J. Powers, S.L. Carroll, J.S. Obeid, and L.A. Lenert. 2021. Each patient is a research biorepository: Informatics-enabled reuse of surplus clinical specimens via the Living BioBank. Journal of the American Medical Informatics Association 28(1):138-143 https://doi.org/10.1093/jamia/ocaa236
Kolbe, A.R., M.L. Bendall, A.T. Pearson, D. Paul, D.F. Nixon, M. Pérez-Losada, and K.A. Crandall. 2020. Human endogenous retrovirus expression is associated with head and neck cancer and differential survival. Viruses 12(9):956. https://doi.org/10.3390/v12090956
Steiner, M.C., K.M. Gibson, and K.A. Crandall. 2020. Drug resistance prediction using deep learning techniques on HIV-1 sequence data. Viruses 12(5):560. https://doi.org/10.3390/v1205056
Mavian, C., S.K. Pond, S. Marini, B.R. Magalis, A-M. Vandamme, S. Dellicour, S.V. Scarpino, C. Houldcroft, J. Villabona-Arenas, T.K. Paisie, N.S. Trovão, C. Boucher, Y. Zhang, S.H. Scheuermann, O. Gascuel, T.T. Lam, M.A. Suchard, A. Abecasis, E. Wilkinson, T. de Oliveira, A.I. Bento, H.A. Schmidt, D. Martin, J. Hadfield, N. Faria, N.D. Grubaugh, R.A. Neher, G. Baele, P. Lemey, T. Stadler, J. Albert, K.A. Crandall, T. Leitner, A. Stamatakis, M. Prosperi, and M. Salemi. 2020. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-CoV-2 infections unreliable. Proceedings of the National Academy of Sciences, USA. https://doi.org/10.1073/pnas.2007295117
Gibson, K.M., K. Jair, A.D. Castel, M.L. Bendall, B. Wilbourn, J.A. Jordan, K.A. Crandall, M. Pérez-Losada, & the DC Cohort. 2020. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Scientific Reports 1989 (2020). https://doi.org/10.1038/s41598-020-58410-y
Xavier, JB, VB Young, J Skufca, F Ginty, T. Testerman, AT Pearson, P Macklin, A Mitchell, I Shumulevich, L Xie, JG Caporaso, KA Crandall, NL Simone, F. Godoy-Vitorino, TJ Griffin, KL Whiteson, HH Gustafson, DJ Slade, TM Schmidt, MRS Walther-Antonio, T Korem, B-J Webb-Robertson, MP Styczynski, WE Johnson, C Jobin, JM Ridlon, AY Koh, M Yu, L Kelly, JA Wargo. 2020. The Cancer Microbiome: Distinguishing direct and indirect effects requires a systemic view. Trends in Cancer 6(3):192-204. https://doi.org/10.1016/j.trecan.2020.01.004
Spurr, L, N Alomran, P Bousounis, D. Reece-Stremtan, NM Prashant, H. Liu, P Slowinski, J Li, Q Zhang, J Sein, G Asher, KA Crandall, K Tsaneva-Atanasova, and A Horvath. 2019. ReQTL: Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data. Bioinformatics 36(5):1351-1359. https://doi.org/10.1093/bioinformatics/btz750
Iñiguez, LP, M de Mulder Rougvie, N Stearrett, RB Jones, CE Ormsby, G Reyes-Terán, KA Crandall, DF Nixon, and ML Bendall. 2019. Potential sources of error in the transcriptomic analyses of human endogenous retroviruses in SLE. Proceedings of the National Academy of Sciences, USA 116(43):21350-21351. https://doi.org/10.1073/pnas.1907705116
Bendall, M.L., M. de Mulder, A. Lecanda-Sánchez, M. Pérez-Losada, M.A, Ostriowski, R.B. Jones, L.C.F. Mulder, G. Reyes-Terán, K.A. Crandall, C.E. Ormsby, and D.F. Nixon. 2019. TELESCOPE: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS Computational Biology 15(9):e1006453 https://doi.org/10.1371/journal.pcbi.1006453
Hourigan, S.K., M. Ahn, K. Gibson, M. Pérez-Losada, G. Felix, M. Weidner, I. Leibowitz, J.E. Niederhuber, C.L. Sears, K.A. Crandall, and M. Oliva-Hemker. 2019. Fecal transplant in children with Clostridioides difficile gives sustained reduction in antimicrobial resistance and pathogenic burden. Open Forum Infectious Diseases https://doi.org/10.1093/ofid/ofz379
King, C.H., H. Desai, A.C. Sylvetsky, J. LoTempio, S. Ayanyan, J. Carrie, K.A. Crandall, B.C. Fochtman, L. Gasparayan, N. Gulzar, P. Howell, N. Issa, K. Krampis, L. Mishra, H. Morizono, J.R. Pisegna, S. Rao, Y. Ren, V. Simonyan, K. Smith, S. VedBrat, M.D. Yao, and R. Mazumder. 2019. Baseline human gut microbiota profile in healthy people and standard reporting template. PLoS One 14(9), e0206484 https://doi.org/10.1371/journal.pone.0206484
Gibson, K.M., B.N. Nguyen, L.M. Neumann, M. Miller, P. Buss, S. Daniels, M.J. Ahn, K.A. Crandall, and B. Pukazhenthi. 2019. Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health. Scientific Reports 9:7570. https://www.nature.com/articles/s41598-019-43875-3
Kegerreis, B., A. Labonte, C. Zeng, N. Stearrett, K.A. Crandall, A. Grammer, and P. Lipsky. Accepted. Machine learning approaches to predict disease activity and treatment in lupus. Scientific Reports 9(1):9617. https://www.nature.com/articles/s41598-019-45989-0
Gibson KM, Steiner MC, Kassaye S, Maldarelli F, Grossman Z, Pérez-Losada M, Crandall KA. 2019. A 28-Year History of HIV-1 Drug Resistance and Transmission in Washington, DC. Frontiers in Microbiology 10:369. doi: 10.3389/fmicb.2019.00369
Stern, DB and KA Crandall. 2018. The evolution of gene expression underlying vision loss in cave animals. Molecular Biology and Evolution 35(8):2005-2014. doi:10.1093/molbev/msy106.
Pérez-Losada, M., K.J. Authelet, C.E. Hoptay, C. Kwak, K.A. Crandall, and R.J. Freishtat. 2018. Pedatric asthma comprises different phenotypic clusters with unique nasopharyngeal microbiotas. Microbiome 6(1):179. https://doi.org/10.1186/s40168-018-0564-7.
Hahn, A, ML Bendall, K Gibson, H Chaney, I Sami, GF Perez, AC Koumbourlis, TA McCaffrey, RJ Freishtat, and KA Crandall. 2018. Benchmark evaluation of true single molecular sequencing to determine cystic fibrosis airway microbiome diversity. Frontiers in Microbiology 9:1069. doi: 10.3389/fmicb.2018.01069.
Houzet, L, M Pérez-Losada, G Matusali, C Deleage, N Dereuddre-Bosquet, AP Satie, F Aubry, E Becker, B Jégou, R Le Grand, BF Keele, KA Crandall, and N Dejucq-Rainsford. 2018. Semen in SIV chronically-infected cynomolgus macaques is dominated by viruses originated from multiple genital organs. Journal of Virology 92:e00133-18. https://doi.org/10.1128/JVI.00133-18.
Stern, DB and KA Crandall. 2018. Phototransduction gene expression and evolution in cave and surface crayfish. Integrative and Comparative Biology 58(3):398-410. doi:10.1093/icb/icy029.
Lewin, H.A., G. Robinson, W.J. Kress, W. Baker, J. Coddington, K. Crandall, R. Durbin, S. Edwards, F. Forest, T. Gilbert, M. Goldstein, I. Grigoriev, K. Hackett, D. Haussler, E. Jarvis, W. Johnson, A. Patrinos, S. Richards, J.C. Castilla Rubio, M.A. van Sluys, P. Soltis, X. Xu, H. Yang, and G. Zhang. 2018. The Earth BioGenome Project: Sequencing Life for the Future of Life. Proceedings of the National Academy of Sciences 115(17):4325-4333. Doi/10.1073/pnas.1720115115
Pérez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, Maxwell T, Greenberg AE, Crandall KA. 2017. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS ONE 12(9): e0185644. https://doi.org/10.1371/journal.pone.0185644
Restrepo, P., M. Movassagh, N. Alomran, C. Miller, M. Li, C. Trenkov, Y. Manchev, S. Bahl, S. Warnken, L. Spurr, T. Apanasovich, K. Crandall, N. Edwards, and A. Horvath. 2017. Overexpressed somatic alleles are enriched in functional elements in Breast Cancer. Scientific Reports 7:8287. doi:10.1038/s41598-017-08416-w
Pérez-Losada M, Crandall K.A., Freishtat R.J. 2016. Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children. Microbiome 4:25 DOI: 10.1186/s40168-016-0170-5
Hilton SK, Castro-Nallar E, Perez-Losada M, Toma I, McCaffrey TA, Hoffman EP, Siegel MO, Simon GL, Johnson WE, Crandall KA. 2016. Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology. Frontiers in Microbiology, 7:484.
Hinchliff, C., S.A. Smith, J.F. Allman, J.G. Burleigh, R. Chaudhary, L.M. Coghill, K.A. Crandall, J. Deng, B.T. Drew, R. Gazis, K. Gude, D.S. Hibbett, L.A. Katz, H.D. Laughinghouse, E.J. McTavish, P.E. Midford, C.L. Owen, R. Ree, J.A. Rees, D.E. Soltis, T. Wiliams, and K.A. Cranston. 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, USA 112(41):12764-12769. doi: 10.1073/pnas.1423041112
Castro-Nallar, E., Y. Shen, R. J. Freishtat, M. Pérez-Losada, S. Manimaran, G. Liu, A. Spira, W. E. Johnson, K. A. Crandall. 2015. Integrating metagenomics and host gene expression to characterize asthma-associated microbial communities. BMC Medical Genomics 8:50, DOI 10.1186/s12920-015-0121-1.
Hong, C., S. Manimaran, Y. Shen, J.F. Perez-Rogers, A.L. Byrd, E. Castro-Nallar, K.A. Crandall, and W.E. Johnson. 2014. PathoScope 2.0: A complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome 2:33.
Faison, W.J., A. Rostovtsev, E. Castro-Nallar, K.A. Crandall, K. Chumakov, V. Simonyan, and R. Mazumder. 2014. Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial, and human genomes. Genomics 104(1):1-7
Byrd, A.L., J.F. Perez-Rogers, C. Hong, S. Manimaran, E. Castro-Nallar, I. Toma, T. McCaffrey, S. Siegel, G. Benson, K.A. Crandall, and W.E. Johnson. 2014. Clinical PathoScope: Rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC Bioinformatics 15:262.