https://holtlab.net/group-members/https://holtlab.net/wp-content/uploads/2024/09/laura-1-e1725954838991.pngLaurahttps://holtlab.net/wp-content/uploads/2024/09/laura.pngLaurahttps://holtlab.net/wp-content/uploads/2024/09/shaojie.pngShaojiehttps://holtlab.net/wp-content/uploads/2024/09/screenshot-2024-09-09-at-12.41.54.pngScreenshot 2024-09-09 at 12.41.54https://holtlab.net/wp-content/uploads/2024/09/screenshot-2024-09-09-at-12.41.49.pngScreenshot 2024-09-09 at 12.41.49https://holtlab.net/wp-content/uploads/2023/12/profile_ltc.jpgprofile_ltchttps://holtlab.net/wp-content/uploads/2023/10/kat_crop_1000x1000.jpgkat_crop_1000x1000https://holtlab.net/wp-content/uploads/2023/10/profile_photo.jpgprofile_photohttps://holtlab.net/wp-content/uploads/2023/09/img-0042.jpgimg-0042https://holtlab.net/wp-content/uploads/2023/03/erkison.jpgerkison2025-10-07T12:26:04+00:00weekly0.6https://holtlab.net/software/https://holtlab.net/wp-content/uploads/2024/03/logo.pnglogohttps://holtlab.net/wp-content/uploads/2024/03/logo-typhinet-prod-2942293534-e1710921986468.pnglogo-typhinet-prodhttps://holtlab.net/wp-content/uploads/2021/10/logo_transparent.pnglogo_transparenthttps://holtlab.net/wp-content/uploads/2021/02/trycycler.pngtrycyclerhttps://holtlab.net/wp-content/uploads/2019/06/badread.pngbadreadhttps://holtlab.net/wp-content/uploads/2018/11/deepbinner.pngdeepbinnerhttps://holtlab.net/wp-content/uploads/2015/04/kleborate_logo.pngkleborate_logohttps://holtlab.net/wp-content/uploads/2015/04/reddog_logo.pngreddog_logohttps://holtlab.net/wp-content/uploads/2015/04/bandage_logo.pngbandage_logohttps://holtlab.net/wp-content/uploads/2015/04/unicycler_logo.pngunicycler_logo2025-02-09T11:05:58+00:00weekly0.6https://holtlab.net/publications/https://holtlab.net/wp-content/uploads/2024/02/scholar_wordcloud_5feb24.pngscholar_wordcloud_5Feb24https://holtlab.net/wp-content/uploads/2018/04/screen-shot-2018-04-17-at-7-18-42-am.pngScreen Shot 2018-04-17 at 7.18.42 amhttps://holtlab.net/wp-content/uploads/2014/12/screen-shot-2016-01-23-at-11-54-56-am.pngScreen Shot 2016-01-23 at 11.54.56 amhttps://holtlab.net/wp-content/uploads/2014/12/abstract_wordcloud.pngabstract_wordcloud2024-02-05T14:19:54+00:00weekly0.6https://holtlab.net/ismapper/2020-08-13T08:28:13+00:00weekly0.6https://holtlab.net/2020/04/15/how-to-make-a-new-covid-19-vaccine-starting-from-scratch/2020-04-29T08:34:56+00:00monthlyhttps://holtlab.net/2014/12/27/typhoid-in-kathmandu-and-open-biology-oa-journal/2019-02-21T21:11:43+00:00monthlyhttps://holtlab.net/2018/11/12/highlights-from-smbe-satellite-workshop-in-kyoto/https://holtlab.net/wp-content/uploads/2018/11/yamanaka.jpgyamanaka2018-11-13T09:26:09+00:00monthlyhttps://holtlab.net/2018/08/21/amr-distribution-in-intestinal-e-coli-from-children-in-asia-and-africa/https://holtlab.net/wp-content/uploads/2018/08/geno_pheno.pnggeno_phenohttps://holtlab.net/wp-content/uploads/2018/08/screen-shot-2018-08-21-at-1-00-28-pm.pngScreen Shot 2018-08-21 at 1.00.28 pmhttps://holtlab.net/wp-content/uploads/2018/08/screen-shot-2018-08-21-at-12-59-41-pm.pngScreen Shot 2018-08-21 at 12.59.41 pmhttps://holtlab.net/wp-content/uploads/2018/08/cipr-gyra-parc.pngcipR gyrA parChttps://holtlab.net/wp-content/uploads/2018/08/drug-res-and-usage.pngdrug res and usagea) Resistance phenotypes. b) Frequency of antimicrobials prescribed to children with watery diarrhoea. c) Frequency of antimicrobials prescribed to children with dysentery.https://holtlab.net/wp-content/uploads/2018/08/region-gene-prevalence.pngregion gene prevalencehttps://holtlab.net/wp-content/uploads/2018/08/region-dapc.pngregion DAPChttps://holtlab.net/wp-content/uploads/2018/08/clone-dapc.pngclone DAPChttps://holtlab.net/wp-content/uploads/2018/08/genewise-case-control.pnggenewise case controlhttps://holtlab.net/wp-content/uploads/2018/08/amr_classes.pngAMR_classes2018-08-21T03:13:37+00:00monthlyhttps://holtlab.net/2016/01/12/tracking-down-insertion-sequences-causing-polymixin-resistance-in-acinetobacter-baumannii/https://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-12-at-6-58-17-pm.pngScreen Shot 2016-01-12 at 6.58.17 pmhttps://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-12-at-6-56-45-pm.pngScreen Shot 2016-01-12 at 6.56.45 pmhttps://holtlab.net/wp-content/uploads/2016/01/genes.pnggeneshttps://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-12-at-6-34-49-pm.pngScreen Shot 2016-01-12 at 6.34.49 pmhttps://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-12-at-6-35-40-pm.pngScreen Shot 2016-01-12 at 6.35.40 pmhttps://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-12-at-6-15-35-pm.pngScreen Shot 2016-01-12 at 6.15.35 pmhttps://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-12-at-6-15-23-pm.pngScreen Shot 2016-01-12 at 6.15.23 pm2017-10-20T05:13:43+00:00monthlyhttps://holtlab.net/2014/12/26/clarifier-bacterial-populations-and-communities/2017-10-17T02:23:40+00:00monthlyhttps://holtlab.net/2016/03/19/elizabethkingia-anophelis/https://holtlab.net/wp-content/uploads/2016/03/species_tree_with_nctc10588.pngspecies_tree_with_NCTC10588https://holtlab.net/wp-content/uploads/2016/03/speciestree_outbreaktree2.pngSpeciesTree_OutbreakTree2https://holtlab.net/wp-content/uploads/2016/03/speciestree_outbreaktree1.pngSpeciesTree_OutbreakTreehttps://holtlab.net/wp-content/uploads/2016/03/speciestree_outbreaktree.pngSpeciesTree_OutbreakTreehttps://holtlab.net/wp-content/uploads/2016/03/srr3240412_reddogtree.pngSRR3240412_RedDogTreehttps://holtlab.net/wp-content/uploads/2016/03/speciestree_parsnp-midpoint.pngSpeciesTree_parsnp.midpointhttps://holtlab.net/wp-content/uploads/2016/03/scaffolds_resolved_blast2.pngscaffolds_resolved_blast2https://holtlab.net/wp-content/uploads/2016/03/screen-shot-2016-03-19-at-8-26-50-pm.pngScreen Shot 2016-03-19 at 8.26.50 pmhttps://holtlab.net/wp-content/uploads/2016/03/srr3240413_bandage_graph.pngSRR3240413_bandage_graphhttps://holtlab.net/wp-content/uploads/2016/03/screen-shot-2016-03-19-at-7-24-21-pm.pngScreen Shot 2016-03-19 at 7.24.21 pm2017-10-17T02:22:54+00:00monthlyhttps://holtlab.net/2015/06/10/a-global-picture-of-typhoid-bacteria/https://holtlab.net/wp-content/uploads/2015/06/mdr_summary_regionasring.pngMDR_summary_regionAsRinghttps://holtlab.net/wp-content/uploads/2015/06/pathogen_linear_regression_fullandh58.pngpathogen_linear_regression_fullANDh58https://holtlab.net/wp-content/uploads/2015/06/map.pngmaphttps://holtlab.net/wp-content/uploads/2015/06/collapsed_tree_timelines2.pngcollapsed_tree_timelines2https://holtlab.net/wp-content/uploads/2015/06/fig_cyaa_yida_inserts.pngAcquired multidrug resistance in Typhi H582017-10-17T02:21:32+00:00monthlyhttps://holtlab.net/2016/01/19/genomics-of-atypical-enteropathogenic-e-coli/https://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-19-at-9-50-41-am.pngScreen Shot 2016-01-19 at 9.50.41 amhttps://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-19-at-9-46-45-am.pngScreen Shot 2016-01-19 at 9.46.45 amhttps://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-19-at-9-42-43-am.pngScreen Shot 2016-01-19 at 9.42.43 amSupplementary Figure 1https://holtlab.net/wp-content/uploads/2016/01/aepec_tree_lee_subtypes1.pngaEPEC_tree_LEE_subtypeshttps://holtlab.net/wp-content/uploads/2016/01/aepec_tree_lee_subtypes.pngaEPEC_tree_LEE_subtypeshttps://holtlab.net/wp-content/uploads/2016/01/aepec_distribution.pngaEPEC_distributionhttps://holtlab.net/wp-content/uploads/2016/01/aepec_tree.pngaEPEC_tree2017-10-17T02:21:01+00:00monthlyhttps://holtlab.net/2016/10/12/global-picture-typhoid/https://holtlab.net/wp-content/uploads/2016/09/journal-pntd-0004781-g001.pngjournal-pntd-0004781-g001https://holtlab.net/wp-content/uploads/2016/08/screen-shot-2016-08-29-at-11-47-15-pm.pngScreen Shot 2016-08-29 at 11.47.15 pmhttps://holtlab.net/wp-content/uploads/2016/08/screen-shot-2016-08-29-at-11-32-21-pm.pngScreen Shot 2016-08-29 at 11.32.21 pmhttps://holtlab.net/wp-content/uploads/2016/08/tree.pngtreehttps://holtlab.net/wp-content/uploads/2016/08/map.pngmaphttps://holtlab.net/wp-content/uploads/2016/08/screen-shot-2016-08-29-at-11-29-53-pm.pngScreen Shot 2016-08-29 at 11.29.53 pmhttps://holtlab.net/wp-content/uploads/2016/08/fig1c_worldmap_pies_subclades.pngFig1c_worldmap_pies_subcladeshttps://holtlab.net/wp-content/uploads/2016/08/subcladerect.pngsubcladerecthttps://holtlab.net/wp-content/uploads/2016/08/fig1_noh58_clade_colours_subcladebg_190515_labelled_ed.pngFig1_noH58_clade_colours_subcladebg_190515_labelled_EDhttps://holtlab.net/wp-content/uploads/2016/08/figs1_globaltreecolouredbyhgroups1.pngFigS1_GlobalTreeColouredByHgroups2017-10-17T02:20:32+00:00monthlyhttps://holtlab.net/2014/12/27/bacterial-genomics-tutorial-2/2017-10-17T02:19:19+00:00monthlyhttps://holtlab.net/2014/12/27/behind-the-paper-srst2-for-short-read-sequence-typing-of-bacterial-pathogens/2017-10-17T02:18:41+00:00monthlyhttps://holtlab.net/2014/12/27/global-and-local-views-of-shigella-sonnei-population-genomics/https://holtlab.net/wp-content/uploads/2014/12/shigella-vietnam.jpgshigella-vietnamPhylogeny of Vietnamese S. sonnei and map of Vietnam, showing the inferred path of evolution and geographical spread.https://holtlab.net/wp-content/uploads/2014/12/globalsonnei.jpgglobalsonneiDissemination of S. sonnei lineages out of Europe. Reprinted by permission from Macmillan Publishers Ltd: Nature Genetics 44:1056, copyright 2012.2017-10-17T02:17:04+00:00monthlyhttps://holtlab.net/2016/01/17/microbial-genomics-methods/https://holtlab.net/wp-content/uploads/2016/01/screen-shot-2016-01-17-at-6-32-16-pm.pngScreen Shot 2016-01-17 at 6.32.16 pmhttps://holtlab.net/wp-content/uploads/2016/01/wordlecarobig.jpgWordleCaroBig2017-10-17T02:15:40+00:00monthlyhttps://holtlab.net/2017/07/01/update-to-comparative-bacterial-genomics-tutorial/2017-10-17T02:15:05+00:00monthlyhttps://holtlab.net/2015/02/25/bandage-view-and-navigate-assembly-graphs/2017-10-17T02:14:26+00:00monthlyhttps://holtlab.net/2015/02/25/tools-for-bacterial-comparative-genomics/2019-02-26T22:09:22+00:00monthlyhttps://holtlab.net/2015/05/08/r-code-to-infer-tree-from-andi-output/2016-01-17T23:17:29+00:00monthlyhttps://holtlab.net/2015/07/20/locating-drug-resistance-regions-in-short-reads-using-bandage-and-ismapper/https://holtlab.net/wp-content/uploads/2015/07/mdr_summary_regionasring.pngMDR_summary_regionAsRinghttps://holtlab.net/wp-content/uploads/2015/07/screen-shot-2015-07-20-at-3-45-54-pm.pngScreen Shot 2015-07-20 at 3.45.54 pmhttps://holtlab.net/wp-content/uploads/2015/07/screen-shot-2015-07-20-at-3-46-30-pm.pngScreen Shot 2015-07-20 at 3.46.30 pmhttps://holtlab.net/wp-content/uploads/2015/07/screen-shot-2015-07-20-at-3-47-05-pm.pngScreen Shot 2015-07-20 at 3.47.05 pmhttps://holtlab.net/wp-content/uploads/2015/07/10071_883_plasmid_res.png10071_8#83_plasmid_reshttps://holtlab.net/wp-content/uploads/2015/07/10060_654_plasmid_coloured.png10060_6#54_plasmid_colouredhttps://holtlab.net/wp-content/uploads/2015/07/screen-shot-2015-07-20-at-3-33-59-pm.pngScreen Shot 2015-07-20 at 3.33.59 pmhttps://holtlab.net/wp-content/uploads/2015/07/screen-shot-2015-07-20-at-3-32-26-pm.pngbandage IS1https://holtlab.net/wp-content/uploads/2015/07/chromosome_insert_10060_671.pngchromosome_insert_10060_6#71https://holtlab.net/wp-content/uploads/2015/07/screen-shot-2015-07-20-at-3-24-48-pm.pngtransposonMultidrug resistance locus in Salmonella Typhi2016-01-17T01:07:49+00:00monthlyhttps://holtlab.net/2015/10/03/plotting-trees-data/https://holtlab.net/wp-content/uploads/2015/10/screen-shot-2015-12-15-at-4-47-34-pm.pngScreen Shot 2015-12-15 at 4.47.34 pmhttps://holtlab.net/wp-content/uploads/2015/10/screen-shot-2015-12-15-at-4-43-05-pm1.pngScreen Shot 2015-12-15 at 4.43.05 pmhttps://holtlab.net/wp-content/uploads/2015/10/screen-shot-2015-12-15-at-4-43-05-pm.pngScreen Shot 2015-12-15 at 4.43.05 pmhttps://holtlab.net/wp-content/uploads/2015/10/pan.pngpan2015-12-15T06:15:13+00:00monthlyhttps://holtlab.net/2015/06/23/population-genomics-of-klebsiella/https://holtlab.net/wp-content/uploads/2015/06/resistance-virulence-axis-2.pngresistance-virulence-axis-2https://holtlab.net/wp-content/uploads/2015/06/klebsstringadamjenney.jpgKlebsStringAdamJenneyhttps://holtlab.net/wp-content/uploads/2015/06/kp_pan_genome.pngKp_pan_genomehttps://holtlab.net/wp-content/uploads/2015/06/kp_pop_network.pngKp_pop_networkhttps://holtlab.net/wp-content/uploads/2015/06/screen-shot-2015-06-18-at-5-12-24-pm.pngScreen Shot 2015-06-18 at 5.12.24 pmhttps://holtlab.net/wp-content/uploads/2015/06/siderophores_by_class.pngsiderophores_by_classhttps://holtlab.net/wp-content/uploads/2015/06/screen-shot-2015-06-18-at-4-23-39-pm1.pngScreen Shot 2015-06-18 at 4.23.39 pmhttps://holtlab.net/wp-content/uploads/2015/06/screen-shot-2015-06-18-at-4-23-39-pm.pngScreen Shot 2015-06-18 at 4.23.39 pmhttps://holtlab.net/wp-content/uploads/2015/06/screen-shot-2015-06-18-at-4-21-43-pm.pngScreen Shot 2015-06-18 at 4.21.43 pmhttps://holtlab.net/wp-content/uploads/2015/06/screen-shot-2015-06-18-at-4-09-33-pm.pngScreen Shot 2015-06-18 at 4.09.33 pm2015-07-14T15:49:00+00:00monthlyhttps://holtlab.net/2015/04/14/bacterial-colonization-of-the-airways-during-the-first-year-of-life/https://holtlab.net/wp-content/uploads/2015/04/strep_haem_morax.jpgstrep_haem_morax2015-06-10T03:15:51+00:00monthlyhttps://holtlab.net/2015/03/05/postdoc-jobs-available-in-the-holt-lab/2015-04-11T07:26:27+00:00monthlyhttps://holtlab.netdaily1.02025-10-07T12:26:04+00:00