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Xiang Ji - Publications

Affiliations: 
2020- Mathematics Tulane University, New Orleans, LA, United States 
Area:
Phylogenetics
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Gangavarapu K, Ji X, Baele G, Fourment M, Lemey P, Matsen FA, Suchard MA. Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinformatics (Oxford, England). 40. PMID 38243701 DOI: 10.1093/bioinformatics/btae030  0.484
2023 Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, ... ... Ji X, et al. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell. PMID 38101407 DOI: 10.1016/j.cell.2023.11.024  0.46
2023 Fisher AA, Ji X, Nishimura A, Baele G, Lemey P, Suchard MA. Shrinkage-based Random Local Clocks with Scalable Inference. Molecular Biology and Evolution. 40. PMID 37950885 DOI: 10.1093/molbev/msad242  0.471
2023 He WT, Li D, Baele G, Zhao J, Jiang Z, Ji X, Veit M, Suchard MA, Holmes EC, Lemey P, Boni MF, Su S. Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus Evolution. 9: vead051. PMID 37711483 DOI: 10.1093/ve/vead051  0.481
2023 Yang Y, Xu T, Conant G, Kishino H, Thorne JL, Ji X. Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization. Molecular Biology and Evolution. PMID 37675606 DOI: 10.1093/molbev/msad198  0.566
2023 Zhang Z, Nishimura A, Trovão NS, Cherry JL, Holbrook AJ, Ji X, Lemey P, Suchard MA. Accelerating Bayesian inference of dependency between mixed-type biological traits. Plos Computational Biology. 19: e1011419. PMID 37639445 DOI: 10.1371/journal.pcbi.1011419  0.488
2023 Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals. Trends in Microbiology. PMID 37541811 DOI: 10.1016/j.tim.2023.07.002  0.442
2023 Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, ... ... Ji X, et al. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science (New York, N.Y.). 381: 336-343. PMID 37471538 DOI: 10.1126/science.adg6605  0.476
2023 Ji X, Fisher AA, Su S, Thorne JL, Potter B, Lemey P, Baele G, Suchard MA. Scalable Bayesian divergence time estimation with ratio transformations. Systematic Biology. PMID 37458991 DOI: 10.1093/sysbio/syad039  0.67
2023 Fourment M, Swanepoel CJ, Galloway JG, Ji X, Gangavarapu K, Suchard MA, Matsen FA. Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation. Genome Biology and Evolution. PMID 37265233 DOI: 10.1093/gbe/evad099  0.499
2023 Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Iv FAM, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. Random-effects substitution models for phylogenetics via scalable gradient approximations. Arxiv. PMID 36994154  0.748
2023 Gangavarapu K, Ji X, Baele G, Fourment M, Lemey P, Iv FAM, Suchard MA. Many-core algorithms for high-dimensional gradients on phylogenetic trees. Arxiv. PMID 36945693  0.541
2022 Zhao J, Dellicour S, Yan Z, Veit M, Gill MS, He WT, Zhai X, Ji X, Suchard MA, Lemey P, Su S. Early Genomic Surveillance and Phylogeographic Analysis of Getah Virus, a Reemerging Arbovirus, in Livestock in China. Journal of Virology. e0109122. PMID 36475767 DOI: 10.1128/jvi.01091-22  0.568
2022 Holbrook AJ, Ji X, Suchard MA. BAYESIAN MITIGATION OF SPATIAL COARSENING FOR A HAWKES MODEL APPLIED TO GUNFIRE, WILDFIRE AND VIRAL CONTAGION. The Annals of Applied Statistics. 16: 573-595. PMID 36211254 DOI: 10.1214/21-aoas1517  0.538
2022 Fisher AA, Hassler GW, Ji X, Baele G, Suchard MA, Lemey P. Scalable Bayesian phylogenetics. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210242. PMID 35989603 DOI: 10.1098/rstb.2021.0242  0.521
2022 McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, ... Ji X, et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature. PMID 35952712 DOI: 10.1038/s41586-022-05200-3  0.483
2022 Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats. Cell Reports. 39: 110969. PMID 35679864 DOI: 10.1016/j.celrep.2022.110969  0.467
2022 He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, et al. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell. PMID 35298912 DOI: 10.1016/j.cell.2022.02.014  0.453
2022 Holbrook AJ, Ji X, Suchard MA. From viral evolution to spatial contagion: a biologically modulated Hawkes model. Bioinformatics (Oxford, England). PMID 35040956 DOI: 10.1093/bioinformatics/btac027  0.565
2021 McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, ... Ji X, et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Medrxiv : the Preprint Server For Health Sciences. PMID 34981069 DOI: 10.1101/2021.12.14.21267606  0.485
2021 Kraemer M, McCrone J, Hill V, Bajaj S, Evans-Pena R, Lambert B, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski A, Sadilek A, Wu N, ... ... Ji X, et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Research Square. PMID 34981043 DOI: 10.21203/rs.3.rs-1159614/v1  0.485
2021 He WT, Bollen N, Xu Y, Zhao J, Dellicour S, Yan Z, Gong W, Zhang C, Zhang L, Lu M, Lai A, Suchard MA, Ji X, Tu C, Lemey P, et al. Phylogeography reveals association between swine trade and the spread of porcine epidemic diarrhea virus in China and across the world. Molecular Biology and Evolution. PMID 34951645 DOI: 10.1093/molbev/msab364  0.485
2021 Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Oude Munnink BB, Koopmans M, Sadilek A, Lai S, Tatem AJ, Baele G, et al. Untangling introductions and persistence in COVID-19 resurgence in Europe. Nature. PMID 34192736 DOI: 10.1038/s41586-021-03754-2  0.6
2021 Landeros A, Ji X, Lange K, Stutz TC, Xu J, Sehl ME, Sinsheimer JS. An examination of school reopening strategies during the SARS-CoV-2 pandemic. Plos One. 16: e0251242. PMID 34014947 DOI: 10.1371/journal.pone.0251242  0.459
2021 Lemey P, Ruktanonchai N, Hong S, Colizza V, Poletto C, den Broeck FV, Gill M, Ji X, Levasseur A, Sadilek A, Lai S, Tatem A, Baele G, Suchard M, Dellicour S. SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data. Research Square. PMID 33594355 DOI: 10.21203/rs.3.rs-208849/v1  0.483
2020 Landeros A, Ji X, Lange KL, Stutz TC, Xu J, Sehl ME, Sinsheimer JS. An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic. Medrxiv : the Preprint Server For Health Sciences. PMID 32793918 DOI: 10.1101/2020.08.05.20169086  0.451
2020 Fisher AA, Ji X, Zhang Z, Lemey P, Suchard MA. Relaxed Random Walks at Scale. Systematic Biology. PMID 32687171 DOI: 10.1093/Sysbio/Syaa056  0.552
2020 Ji X, Zhang Z, Holbrook A, Nishimura A, Baele G, Rambaut A, Lemey P, Suchard MA. Gradients do grow on trees: a linear-time Molecular Biology and Evolution. PMID 32458974 DOI: 10.1093/Molbev/Msaa130  0.479
2020 He WT, Ji X, He W, Dellicour S, Wang S, Li G, Zhang L, Gilbert M, Zhu H, Xing G, Veit M, Huang Z, Han GZ, Huang Y, Suchard MA, et al. Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus. Molecular Biology and Evolution. PMID 32407507 DOI: 10.1093/Molbev/Msaa117  0.567
2020 Sun J, He WT, Wang L, Lai A, Ji X, Zhai X, Li G, Suchard MA, Tian J, Zhou J, Veit M, Su S. COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives. Trends in Molecular Medicine. 26: 483-495. PMID 32359479 DOI: 10.1016/J.Molmed.2020.02.008  0.507
2019 Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P. Divergence dating using mixed effects clock modelling: An application to HIV-1. Virus Evolution. 5: vez036. PMID 31720009 DOI: 10.1093/Ve/Vez036  0.53
2019 Li G, Zhang W, Wang R, Xing G, Wang S, Ji X, Wang N, Su S, Zhou J. Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus. International Journal of Molecular Sciences. 20. PMID 31200479 DOI: 10.3390/Ijms20122881  0.354
2018 Zhou W, Ji X, Obata S, Pais A, Dong Y, Peet R, Jenny Xiang QY. Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling. Molecular Phylogenetics and Evolution. PMID 29631052 DOI: 10.1016/J.Ympev.2018.04.001  0.334
2016 Ji X, Griffing A, Thorne JL. A phylogenetic approach finds abundant interlocus gene conversion in yeast. Molecular Biology and Evolution. PMID 27297467 DOI: 10.1093/Molbev/Msw114  0.622
2015 Wang K, Yu S, Ji X, Lakner C, Griffing A, Thorne JL. Roles of solvent accessibility and gene expression in modeling protein sequence evolution. Evolutionary Bioinformatics Online. 11: 85-96. PMID 25987828 DOI: 10.4137/Ebo.S22911  0.736
2014 Lin LH, Hua L, Qu YF, Gao JF, Ji X. The phylogeographical pattern and conservation of the Chinese cobra (Naja atra) across its range based on mitochondrial control region sequences. Plos One. 9: e106944. PMID 25184236 DOI: 10.1371/Journal.Pone.0106944  0.31
2013 Sun BJ, Li SR, Xu XF, Zhao WG, Luo LG, Ji X, Du WG. Different mechanisms lead to convergence of reproductive strategies in two lacertid lizards (Takydromus wolteri and Eremias argus). Oecologia. 172: 645-52. PMID 23152168 DOI: 10.1007/S00442-012-2524-4  0.304
2010 Lin LH, Ji X, Diong CH, Du Y, Lin CX. Phylogeography and population structure of the Reevese's Butterfly Lizard (Leiolepis reevesii) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution. 56: 601-7. PMID 20433932 DOI: 10.1016/J.Ympev.2010.04.032  0.321
2005 DU W, JI X, ZHANG Y, XU X, SHINE R. Identifying sources of variation in reproductive and life-history traits among five populations of a Chinese lizard (Takydromus septentrionalis, Lacertidae) Biological Journal of the Linnean Society. 85: 443-453. DOI: 10.1111/J.1095-8312.2005.00508.X  0.302
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