{"id":127,"date":"2022-10-18T16:44:00","date_gmt":"2022-10-18T16:44:00","guid":{"rendered":"http:\/\/schellackia.sickkids.ca\/wordpress\/?page_id=127"},"modified":"2026-04-10T19:46:12","modified_gmt":"2026-04-10T19:46:12","slug":"publications","status":"publish","type":"page","link":"https:\/\/compsysbio.org\/index.php\/publications\/","title":{"rendered":".\/publications"},"content":{"rendered":"\n<h2 class=\"wp-block-heading alignwide\">submitted<\/h2>\n\n\n\n<script async src=\"https:\/\/badge.dimensions.ai\/badge.js\" charset=\"utf-8\"><\/script>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<p>Phanse, S., Peng, H., Kotelnikov, S., Egbert, ME., Ofaim, S., <strong>Stevens, GC.,<\/strong> Saccon, T., Ignatov, M., Dutta, S., Istace, Z., Moutaoufik, MT., Aoki, H., Kewalramani, N., Sun, J., Gong, Y., Padhorny, D., Poda, G., Alekseenko, A., Porter, KA., Jones, G., Rodionova I., Guo H., Pogoutse, O., Datta, S., Saier, M., Crovella, M., Vajda, S., Moreno-Hagelsieb, G., <strong>Parkinson, J.,<\/strong> Segre, D., Babu, M., Kozakov, D. and Emili, A. Comprehensive pipeline for global identification and validation of protein\u2013metabolite interactions in E. coli. Submitted.<\/p>\n\n\n\n<p><strong>Utkina, I., <\/strong>Alizadeh, M., Sharif, S. and <strong>Parkinson, J. <\/strong> <a href=\"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.02.08.704450v2\">Multi-compartment spatiotemporal metabolic modeling of the chicken gut guides the design of dietary interventions.<\/a> BioArxiv 2026.02.08.704450<\/p>\n\n\n\n<p><strong>Carruthers-Lay, D.,<\/strong> Lam, J.,<strong> Jurga, E.,<\/strong> Gray-Owen, SD. and <strong>Parkinson, J.<\/strong> <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2025.02.28.640638v1\">Network-based population analysis of 31,595 gonococcal genomes reveals phase variability, genetic diversity and mobile element dynamics drive antimicrobial resistance and phenotypic diversity.<\/a> BioARxiv 2025.02.28.640638v1<\/p>\n\n\n\n<p><strong>Curran, DM.,<\/strong> Ng, D., <strong>Parkinson, J.,<\/strong> Moraes, T., Gray-Owen, S, and Fegan, JE <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.09.08.611914v1\">Phylogeny-based selection of representative variants with Navargator: Proof of principle using humoral cross-reactivity data from two immunization studies.<\/a> BioArxiv 2024.09.08.611914<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">2026<\/h2>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/S2214-109X(25)00539-X\" data-style=\"small_circle\"><\/span><\/code><script><\/script><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Syal, R., Alfv\u00e9n, T., Ashorn, P., Black, RE., Chersich, M., Das, JK., Maimela, G., Neufeld, L., Phillips, D., Portela, A., Rudan, I., Swaminathan, S., Gaffey, MF., Bhutta, ZA. for the Climate Change and Health Impacts on Women and Children in LMICs Research Priorities Group*. (2026) <a href=\"https:\/\/doi.org\/10.1016\/S2214-109X(25)00539-X\">Setting research priorities to understand and address the impact of climate change on the health of women and children in low-income and middle-income countries using the Child Health and Nutrition Research Initiative method.<\/a> Lancet Global Health. In press. <a href=\"https:\/\/doi.org\/10.1016\/S2214-109X(25)00539-X\">DOI: 10.1016\/S2214-109X(25)00539-X<\/a>. *Group author<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/S2214-109X(25)00539-X\" data-style=\"small_circle\"><\/span><\/code><script><\/script><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Binepal, G.,* <strong>Jurga, E., *, Carruthers-Lay, D., <\/strong>Kr\u00fcger, S., Zitterman, S., Alexander, D., Martin, I., Allen, V., <strong>Parkinson, J.<sup>#<\/sup><\/strong> and Gray-Owen, SD.<sup>#<\/sup>&nbsp;<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.09.08.611882v1\">Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada.<\/a>&nbsp;mSphere. In Press; *Both authors contributed equally to the work; <sup>#<\/sup>These authors are considered co-senior\/corresponding authors.<\/p>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\">2025<\/h2>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s40168-025-02241-4\" data-style=\"small_circle\"><\/span><\/code><script><\/script><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Utkina, I.,<\/strong> Fan, Y., Willing, BP., and <strong>Parkinson, J.<\/strong> (2025) <a href=\"https:\/\/link.springer.com\/article\/10.1186\/s40168-025-02241-4\">Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation<\/a>. Microbiome. 13. 248. DOI: 10.1186\/s40168-025-02241-4<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1017\/gmb.2025.10013\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Campisi, SC., Zhang F., Seo, M., Muha, J., Schumacher, A., DeLuca I., Bradley-Ridout G., Merriman K., <strong>Parkinson, J.,<\/strong> and Korczak, DJ. (2025) <a href=\"https:\/\/www.cambridge.org\/core\/journals\/gut-microbiome\/article\/gut-microbiome-and-child-and-adolescent-depression-and-anxiety-a-systematic-review-and-metaanalysis-with-youth-consultation\/8A09996A3C9839A2E30A7FF62D033B74\">The gut microbiome and child and adolescent depression and anxiety: A systematic review and meta-analysis with youth consultation<\/a>. Gut Microbiome. 6. e17, 1-18.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/s41597-025-04921-0\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Alves-Ferreira, EVC., Galac, MR., Lorenzi, HA., Ho, MCW., Tjhin, ET., <strong>Popovic, A., Parkinson, J.<\/strong> and Grigg, ME. (2025) <a href=\"https:\/\/www.nature.com\/articles\/s41597-025-04921-0\">Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice.<\/a> Scientific Data. 12. 590. DOI: <a href=\"https:\/\/doi.org\/10.1038\/s41597-025-04921-0\">10.1038\/s41597-025-04921-0<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.cell.2025.01.003\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Peng, H.,* Kotelnikov, S.*, Egbert, ME.*, Ofaim, S.,* <strong>Stevens, GC.,*<\/strong> Phanse, S.,* Saccon, T., Ignatov, M., Dutta, S., Istace, Z., Moutaoufik, MT., Aoki, H., Kewalramani, N., Sun, J., Gong, Y., Padhorny, D., Poda, G., Alekseenko, A., Jones, G., Rodionova I., Guo H., Pogoutse, O., Datta, S., Saier, M., Crovella, M., Vajda, S., Moreno-Hagelsieb, G., <strong>Parkinson, J.,<\/strong> Segre, D., Babu, M., Kozakov, D. and Emili, A. (2025) <a href=\"https:\/\/www.cell.com\/cell\/fulltext\/S0092-8674(25)00032-7\">Ligand interaction landscape of transcription factors and essential enzymes in <em>E.&nbsp;coli<\/em>.<\/a> Cell. 188(5):1441-1455.e15. DOI: <a href=\"https:\/\/doi.org\/10.1016\/j.cell.2025.01.003\" target=\"_blank\" rel=\"noreferrer noopener\">10.1016\/j.cell.2025.01.003<\/a> *These authors contributed equally to the work.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.chom.2025.02.008\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Winsor, NJ., Bayer, G., Singh, O., Chan, J., Foerster, E., Tsankov, B., <strong>Popovic, A., <\/strong>Lemire, P., Maughan, H., Tam, E., Streutker, C., Chen, L., Heaver, SL., Ley, RE., <strong>Parkinson, J.,<\/strong> Montenegro Burke, R., Birchenough, GMH., Philpott, DJ. and Girardin, SE. (2025) <a href=\"https:\/\/www.cell.com\/cell-host-microbe\/abstract\/S1931-3128(25)00056-3\">Cross-kingdom-mediated detection of intestinal protozoa through NLRP6.<\/a> Cell Host &amp; Microbe. 33(3):388-407.e9. DOI: <a href=\"https:\/\/doi.org\/10.1016\/j.cell.2025.01.003\" target=\"_blank\" rel=\"noreferrer noopener\"><\/a><a href=\"https:\/\/doi.org\/10.1016\/j.chom.2025.02.008\" target=\"_blank\" rel=\"noreferrer noopener\">10.1016\/j.chom.2025.02.008<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\">2024<\/h2>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1371\/journal.pcbi.1012208\" data-style=\"small_circle\"><\/span><script async=\"\" src=\"https:\/\/badge.dimensions.ai\/badge.js\" charset=\"utf-8\"><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Swapna, L.,* Stevens, G.,*<\/strong>&nbsp;Sardinha da Silva, A., Hu, LZ.,&nbsp;<strong>Brand, V., Fusca, DD., Xiong, X.,<\/strong>&nbsp;Boyle, JP., Grigg, ME., Emili, A. and&nbsp;<strong>Parkinson J.<\/strong>&nbsp;(2024) <a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1012208\">ToxoNet: A high confidence map of protein-protein interactions in <em>Toxoplasma gondii<\/em> reveals novel virulence factors implicated in host cell invasion.<\/a>&nbsp;PLoS Computational Biology. 20(6):e1012208. doi: 10.1371\/journal.pcbi.1012208. *Both authors contributed equally to the work.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1084\/jem.20221727\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Cao, EY., Burrows, K., Chiaranunt, P.,&nbsp;<strong>Popovic, A.,<\/strong>&nbsp;Zhou, X., Xie, C., Thakur, A., Britton, GJ., Spindler, MP., Ngai, L., Tai, SL., Dasoveanu, DC., Nguyen, A., Faith, JJ.,&nbsp;<strong>Parkinson, J.,&nbsp;<\/strong>Gommerman, J. and Mortha A.&nbsp;(2024) <a href=\"https:\/\/rupress.org\/jem\/article\/221\/12\/e20221727\/277079\/The-protozoan-commensal-Tritrichomonas-musculis-is\">The protozoan commensal Tritrichomonas musculis is a natural adjuvant for mucosal IgA.<\/a>&nbsp;Journal of Experimental Medicine. 221(12): e20221727.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1136\/bmjopen-2023-081629\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Wasan, Y., Baxter, JB., <strong>Spiegel-Feld, C.,<\/strong> Begum, K., Rizvi, A., Iqbal, J., Hulst, JM., Bandsma, R., Suleman, S., Soofi, SB., Parkinson, J.,<sup>#<\/sup> and Bhutta, ZA<sup>#<\/sup> (2024) <a href=\"https:\/\/bmjopen.bmj.com\/content\/14\/8\/e081629\">Elucidating the Dynamics and Impact of the Gut Microbiome on Maternal Nutritional Status During Pregnancy in Rural Pakistan. Study Protocol for a Prospective, Longitudinal Observational Study<\/a>. BMJ Open. 14(8):e081629. <sup>#<\/sup>These authors are considered co-senior authors (BMJ only include one corresponding author).<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1080\/19490976.2024.2356277\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Chieu, R.,*<\/strong> Hamilton, K.,* Ryan, PM., Copeland, J., Wang, PW., Retnakaran, R., Guttman, DS., <strong>Parkinson, J.<sup>#<\/sup> and<\/strong> Hamilton, J.<sup>#<\/sup> (2024) <a href=\"https:\/\/www.tandfonline.com\/doi\/full\/10.1080\/19490976.2024.2356277\">The impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient.<\/a> Gut Microbes. 16(1): 2356277. *Both authors contributed equally to the work; <sup>#<\/sup>These authors are considered co-senior\/corresponding authors.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1093\/ismejo\/wrae023\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Popovic, A.,<\/strong> Cao,&nbsp;E.Y., Han,&nbsp;J., <strong>Nursimulu,&nbsp;N.,<\/strong> Alves-Ferreira,&nbsp;E.V.C., Kennard,&nbsp;A., Alsmadi,&nbsp;N. Grigg,&nbsp;M.E., Mortha,&nbsp;A. and <strong>Parkinson, J.<\/strong> (2024)&nbsp;<a href=\"https:\/\/academic.oup.com\/ismej\/article\/18\/1\/wrae023\/7601004?login=false\">Commensal protist&nbsp;<em>Tritrichomonas musculus<\/em>&nbsp;exhibits a dynamic life cycle that induces B cell-modulated remodeling of the gut microbiota.<\/a>&nbsp;ISME J. 18(1): wrae023.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s12859-024-05739-0\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Chan, D.,* Cromar, GL.,* Taj, B. and Parkinson, J.<\/strong> (2024) <a href=\"https:\/\/link.springer.com\/article\/10.1186\/s12859-024-05739-0?utm_source=rct_congratemailt&amp;utm_medium=email&amp;utm_campaign=oa_20240321&amp;utm_content=10.1186\/s12859-024-05739-0\">Cell4D: A general purpose spatial stochastic simulator for cellular pathways.<\/a> BMC Bioinformatics. 25: 121. *Both authors contributed equally to the work<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1093\/bioadv\/vbae016\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Verma, B. and Parkinson, J.<\/strong> (2024) <a href=\"https:\/\/doi.org\/10.1093\/bioadv\/vbae016\">HiTaxon: A hierarchical ensemble framework for taxonomic classification of short reads<\/a>. Bioinformatics Advances. 4(1): vbae016.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1371\/journal.pone.0301110\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Kairmi, SH., Taha-Abdelaziz, K., Spahany, H., Astill J., Trott, D., Wang, B., Wang, A., <strong>Parkinson, J.<\/strong> and Sharif, S. (2024) <a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0301110\">Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens<\/a>. PLoS ONE. 19(4): e0301110.<\/p>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\">2023<\/h2>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1017\/gmb.2023.16\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Romano, K., Shah, AN., Schumacher, A., Zasowski, C., Zhang, T., Bradley-Ridout, G., Merriman, K., <strong>Parkinson, J.,<\/strong> Szatmari, P., Campisi, SC., and Korczak, DJ (2023) <a href=\"https:\/\/doi.org\/10.1017\/gmb.2023.16\">The gut microbiome in children with mood, anxiety, and neurodevelopmental disorders: An umbrella review.<\/a> Gut Microbiome. 4: e18<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s40168-023-01562-6\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Taj , B.,* Adeolu, M.,* Xiong, X., Nursimulu, N.,<\/strong>&nbsp;Ang, J. and&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;(2023) <a href=\"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-023-01562-6\">MetaPro: A scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities.<\/a>&nbsp;Microbiome. 11: 143. *Both authors contributed equally to the work<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">2022<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1371\/journal.pcbi.1010452\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Nursimulu, N.,<\/strong>&nbsp;Moses, AM. and&nbsp;<strong>Parkinson J.<\/strong>&nbsp;(2022)&nbsp;<a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1010452\">Architect: a tool for producing high-quality metabolic models through improved enzyme annotation.<\/a>&nbsp;PLoS Computational Biology. 18(9): e1010452.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s40168-022-01319-7\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Zou, A.*,<\/strong>&nbsp;Nadeau, K.*,&nbsp;<strong>Xiong, X.\u2020,<\/strong>&nbsp;Wang, PW., Copeland, JK., Lee, JY., St Pierre, J., Ty, M., Taj, B., Brumell, JH., Guttman, DS., Sharif, S., Korver, D. and&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;(2022)&nbsp;<a href=\"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-022-01319-7\">Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure.<\/a>&nbsp;Microbiome. 10:127. *These authors contributed equally<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1371\/journal.pntd.0010600\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Cromar, GL.,*<\/strong>&nbsp;Epp J.,*&nbsp;<strong>Popovic, A.,<\/strong>&nbsp;Gu, Y., Ha, V., Walters, B.,&nbsp;<strong>St. Pierre, J., Xiong, X.,<\/strong>&nbsp;Howland, J., Josselyn, S., Frankland, PW.* and&nbsp;<strong>Parkinson, J.*<\/strong>&nbsp;(2022)&nbsp;<a href=\"https:\/\/journals.plos.org\/plosntds\/article?id=10.1371\/journal.pntd.0010600\">Toxoplasma infection alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease.<\/a>&nbsp;PLoS Neglected Tropical Diseases. 16(7): e0010600. *These authors contributed equally; * These authors are considered co-senior\/corresponding authors<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s42523-021-00157-6\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Ty, M.,<\/strong>&nbsp;Taha-Abdelaziz, K., Demey, V., Castex, M., Sharif, S. and&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;(2022)&nbsp;<a href=\"https:\/\/animalmicrobiome.biomedcentral.com\/articles\/10.1186\/s42523-021-00157-6\">Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry.<\/a>&nbsp;Animal Microbiome. 4:2.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.psj.2022.101864\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Kairmi, SH., Taha-Abdelaziz, K., Yitbarek, A.. Sargolzaei, M., Spahany, H., Astill, J., Shojadoost, B., Alizadeh, M., Kulkarni, RR.,&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;and Sharif, S. (2022)&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35477134\/\">Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens.<\/a>&nbsp;Poultry Science. 101(6):101864.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">2021<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/s41467-021-27010-3\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Popovic, A.,<\/strong>&nbsp;Bourdon, C., Wang, PW., Guttman, DS., Soofi, S., Bhutta, ZA., Bandsma, RHJ.,&nbsp;<strong>Parkinson, J.*<\/strong>&nbsp;and Pell, LG. (2021)&nbsp;<a href=\"https:\/\/rdcu.be\/cBynd\">Micronutrient supplements with iron promote disruptive protozoan and fungal communities in the developing infant gut.<\/a>&nbsp;Nature Communications. 12(1):6729. *Senior corresponding author.&nbsp;<a href=\"https:\/\/www.nature.com\/collections\/jedgcgeija\">Editors Highlight.<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1080\/19490976.2021.1994832\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Dacquay, LC., Tsang, T.,&nbsp;<strong>Chan, D., Parkinson, J.,<\/strong>&nbsp;Philpott, DJ. and McMillen, DR. (2021)&nbsp;<a href=\"https:\/\/www.tandfonline.com\/doi\/full\/10.1080\/19490976.2021.1994832\">E. coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis.&nbsp;<\/a>Gut Microbes. 13(1): 1994832.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.stemcr.2021.09.020\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Jiang, JX., Wellhauser, L., Laselva, O.,&nbsp;<strong>Utkina, I.,&nbsp;<\/strong>Bozoky, Z., Gunawardena, T., Ngan, Z., Xia, S., Eckford, PDW., Ratjen, F., Moraes, TJ.,&nbsp;<strong>Parkinson, J.,<\/strong>Wong, AP. and Bear, CE. (2021)&nbsp;<a href=\"https:\/\/www.cell.com\/stem-cell-reports\/fulltext\/S2213-6711(21)00497-5\">A new platform for high-throughput therapy testing on iPSC-derived, immature airway from Cystic Fibrosis Patients.<\/a>&nbsp;Stem Cell Reports. 16:1\u201313<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1109\/TMECH.2020.3043454\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Shokrollahi, P., Lai, YP., Rash-Ahmadi, S., Stewart, V., Mohammadigheisar, M., Huber, L., Matsuura, N., Zavodni, A.,&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;and Diller, E. (2021)&nbsp;<a href=\"https:\/\/ieeexplore.ieee.org\/document\/9288996\">Blindly Controlled Magnetically Actuated Capsule for Noninvasive Sampling of the Gastrointestinal Microbiome.<\/a>&nbsp;IEEE\/ASME Transactions on Mechatronics. 26(5)&#8221; 2616-2628.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">2020<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.7554\/eLife.51850\n\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Curran, DM.,*<\/strong>&nbsp;Grote, A.,*&nbsp;<strong>Nursimulu, N.,<\/strong>&nbsp;Geber, A., Voronin, D., Jones, DR., Ghedin, E.# and&nbsp;<strong>Parkinson, J..#<\/strong>&nbsp;(2020)&nbsp;<a href=\"https:\/\/elifesciences.org\/articles\/51850\">Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets.<\/a>&nbsp;eLife. 9:e51850. *Both authors contributed equally to the work; #Co-corresponding authors&nbsp;<a href=\"https:\/\/elifesciences.org\/for-the-press\/9fd7d0ba\/modelling-parasitic-worm-metabolism-suggests-strategy-for-developing-new-drugs-against-infection\">eLife news release<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1371\/journal.pcbi.1007721\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Bundalovic-Torma, C.,<\/strong>&nbsp;Whitfield, GB., Marmont, LS., Howell, PL. and&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;(2020)&nbsp;<a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1007721\">A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries.<\/a>&nbsp;PLoS Computational Biology. 16(4): e1007721.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1371\/journal.ppat.1008281\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Whitfield, GB., Marmont, LS.,&nbsp;<strong>Bundalovic-Torma, C.,<\/strong>&nbsp;Razvi, E., Roach, EJ., Khursigara, CM.,&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;and Howell, PL. (2020)&nbsp;<a href=\"https:\/\/journals.plos.org\/plospathogens\/article?id=10.1371\/journal.ppat.1008281\">Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster.<\/a>&nbsp;PLoS Pathogens. 16(4): e1008281.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.cels.2020.03.003\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Pourhaghighi, R., Ash, PEA., Phanse, S., Goebels, F., Hu, LZM., Chen, S., Zhang, Y., Wierbowski, SD., Boudeau, S., Moutaoufik, MT., Malty, RH., Malolepsza, E., Tsafou, K., Nathan, A.,&nbsp;<strong>Cromar, G.,<\/strong>Guo, H., AlAbdullatif, A., Apicco, DJ., Becker, LA., Gitler, AD., Pulst, SM., Youssef, A., Hekman, R., Havugimana, PC., White, CA., Blum, BC., Ratti, A., Bryant, CD.,&nbsp;<strong>Parkinson, J.,&nbsp;<\/strong>Lage, K., Babu, M., Yu, H., Bader, GD., Wolozin, B. and Emili, A. (2020)&nbsp;<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2405471220301095\">BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain.&nbsp;<\/a>Cell Systems. 10: 333-350.e14<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s12863-020-0807-z\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Zou, A.,<\/strong>&nbsp;Nadeau, K., Wang, PW., Lee, JY., Guttman, DS., Sharif, S., Korver, D., Brumell, JH. and&nbsp;<strong>Parkinson, J..<\/strong>&nbsp;(2020)&nbsp;<a href=\"https:\/\/bmcgenet.biomedcentral.com\/articles\/10.1186\/s12863-020-0807-z\">Accumulation of genetic variants associated with immunity in the selective breeding of broilers.<\/a>&nbsp;BMC Genetics. 21: 5.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">2019<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.vaccine.2019.09.046\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Yitbarek, A., Astill, J., Hodgins, DC.,&nbsp;<strong>Parkinson, J.,<\/strong>Nagy, E. and Sharif, S. (2019)&nbsp;<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0264410X19312551?utm_campaign=STMJ_75273_AUTH_SERV_PPUB&amp;utm_medium=email&amp;utm_dgroup=Email1Publishing&amp;utm_acid=12383745&amp;SIS_ID=0&amp;dgcid=STMJ_75273_AUTH_SERV_PPUB&amp;CMX_ID=&amp;utm_in=DM587115&amp;utm_source=AC_30\">Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated influenza virus subtype H9N2.<\/a>&nbsp;Vaccine. 37(44):6640-6647.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1093\/gbe\/evz100\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Zhang, J. and Parkinson, J.<\/strong>&nbsp;(2019)&nbsp;<a href=\"https:\/\/academic.oup.com\/gbe\/article\/11\/7\/1730\/5490198?guestAccessKey=e119d9ed-7458-4542-b5bc-5570572c01ff\">PopNetD3 \u2013 A network based web resource for exploring population structure.<\/a>&nbsp;Genome Biology and Evolution. 11(7):1730-1735.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/s41588-018-0262-1\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>International Helminths Genome Consortium (2019)&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/s41588-018-0262-1\">Comparative genomics of the major parasitic worms.<\/a>&nbsp;Nature Genetics. 51(1):163-174.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">2018<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s40168-018-0612-3\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Popovic, A.,<\/strong>&nbsp;Bourdon, C., Wang, P., Guttmann, D., Voskuijl, W., Grigg, M., Bandsma, R. and&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;(2018)&nbsp;<a href=\"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-018-0612-3\">Design and application of a novel two-barcode approach for defining the eukaryotic microbiome.<\/a>&nbsp;Microbiome. 6(1):228.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/s41522-018-0070-5\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Zou, A.,<\/strong>&nbsp;Sharif, S. and&nbsp;<strong>Parkinson, J.<\/strong>&nbsp;(2018)&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/s41522-018-0070-5\">Lactobacillus elicits a \u201cMarmite effect\u201d on the chicken cecal microbiome.&nbsp;<\/a>NPJ Biofilms and Microbiome. 4: 27.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1007\/978-1-4939-8728-3_18 \" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Adeolu, M., Parkinson, J. and Xiong, X.<\/strong>&nbsp;(2018)&nbsp;<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/30298261\">Analyzing Metabolic Pathways in Microbiomes.<\/a>&nbsp;Methods Mol Biol. 1849:291-307.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1007\/978-1-4939-8728-3_3 \" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Popovic, A. and Parkinson, J.<\/strong>&nbsp;(2018)&nbsp;<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/30298246\">Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing.<\/a>&nbsp;Methods Mol Biol. 1849:29-48.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s13059-018-1498-x\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Swapna L.S.,<\/strong>&nbsp;Molinaro A.M., Lindsay-Mosher N., Pearson B.J.,#&nbsp;<strong>and Parkinson, J.#<\/strong> (2018).&nbsp;<a href=\"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-018-1498-x\">Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identifies major cell types and pathway conservation.&nbsp;<\/a>Genome Biology. 19:124. #jointly supervised this work<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/s41598-018-31613-0\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Yitbarek A., Taha-Abdelaziz K., Hodgins D.C., Read L., Nagy E., Weese J.S., Caswell J.L.,&nbsp;<strong>Parkinson J.,<\/strong>&nbsp;and Sharif S. (2018).&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/s41598-018-31613-0\">Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses.<\/a>&nbsp;Scientific Reports. 8(1):13189.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1093\/bioinformatics\/bty368\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Nursimulu N., Xu L.Y.,<\/strong>&nbsp;Wasmuth J.D., Krukov I.&nbsp;<strong>and Parkinson J.&nbsp;<\/strong>(2018).&nbsp;<a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/bty368\/4990828?guestAccessKey=e4504761-2def-4a2d-9041-5035ba34702b\">Improved enzyme annotation with EC-specific cutoffs using DETECT v2.<\/a>&nbsp;Bioinformatics. 34(19):3393-3395.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1093\/femsec\/fix165\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Yitbarek A., Weese J.S., Alkie T.,&nbsp;<strong>Parkinson J.<\/strong>&nbsp;and Sharif S. (2018)&nbsp;<a href=\"https:\/\/doi.org\/10.1093\/femsec\/fix165\">Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens.<\/a>&nbsp;FEMS Microbiology Ecology. 94(1): fix165<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/nbt.4024\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Babu M.*#,&nbsp;<strong>Bundalovic-Torma C.*<\/strong>, Calmettes C.,* Phanse S., Zhang Q.,&nbsp;<strong>Jiang Y.,<\/strong>&nbsp;Minic Z., Kim S., Mehla J., Gagarinova A., Rodionova I., Kumar A., Guo H., Kagan O., Pogoutse O., Aoki H., Deineko V., Caufield J. H., Holtzapple E., Zhang Z., Vastermark A., Pandya Y., Lai C.C., El Bakkouri M., Hooda Y., Shah M., Burnside D., Hooshyar M., Vlasblom J., Rajagopala S.V., Golshani A., Wuchty S., Greenblatt J.F., Saier M.,# Uetz P.,# Moraes T.F.,#<strong>&nbsp;Parkinson J.#<\/strong>&nbsp;and Emili A.# (2018)&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/nbt.4024?utm_source=feedburner&amp;utm_medium=feed&amp;utm_campaign=Feed%253A%2Bnbt%252Frss%252Fcurrent%2B%2528Nature%2BBiotechnology%2B-%2BIssue%2529&amp;error=cookies_not_supported&amp;code=18eafd44-a08a-4095-9899-9e7f35688663\">Global landscape of cell envelope protein complexes in Escherichia coli.<\/a>&nbsp;Nature Biotechnology. 36: 103-112. *contributed equally; #jointly supervised this work<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.3920\/BM2017.0088\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Yitbarek A., Alkie T., Taha-Abdelaziz K., Astill J., Rodriguez-Lecompte J.C.,&nbsp;<strong>Parkinson J.,&nbsp;<\/strong>Nagy E. and Sharif S. (2018)&nbsp;<a href=\"http:\/\/www.wageningenacademic.com\/doi\/10.3920\/BM2017.0088\">Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2.<\/a>&nbsp;Beneficial Microbes. 9: 417-427.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">2017<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.cels.2017.10.010\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Malty R.H., Aoki H., Kumar A., Phanse S., Amin S., Zhang Q., Minic Z., Goebels F., Musso G., Wu Z., Abou-tok H., Meyer M.J., Deineko V., Kassir S., Sidhu V., Jessulat M., Scott N.E.,&nbsp;<strong>Xiong X.,<\/strong>&nbsp;Vlasblom J., Prasad B., Foster L.J., Alberio T., Garavaglia B., Yu H., Bader G.D., Nakamura K.,&nbsp;<strong>Parkinson J.,<\/strong>&nbsp;and Babu M. (2017)&nbsp;<a href=\"http:\/\/www.cell.com\/cell-systems\/fulltext\/S2405-4712(17)30447-7\">A map of human mitochondrial protein interactions linked to neurodegeneration reveals new mechanisms of redox homeostasis and NF-kB signaling.<\/a>&nbsp;Cell Systems. 5(6):564-577.e12<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s40168-017-0327-x\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Xiong X.,<\/strong>&nbsp;Bales C.E., Ir D., Robertson C.E., McManaman J.L., Frank D.N.# and&nbsp;<strong>Parkinson J.#<\/strong>&nbsp;(2017)&nbsp;<a href=\"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-017-0327-x\">Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine.<\/a>&nbsp;Microbiome. 5:117. #jointly supervised this work<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1093\/molbev\/msx110\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Zhang J.,<\/strong>&nbsp;Khan A., Kennard A., Grigg M.E. and&nbsp;<strong>Parkinson J.<\/strong>&nbsp;(2017)&nbsp;<a href=\"https:\/\/academic.oup.com\/mbe\/article-lookup\/doi\/10.1093\/molbev\/msx110\">PopNet: A Markov Clustering Approach to Study Population Genetic Structure.<\/a>&nbsp;Molecular Biology and Evolution. 34(7):1799-1811.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1080\/10409238.2017.1290043\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Swapna L.S. and Parkinson J.&nbsp;<\/strong>(2017)&nbsp;<a href=\"http:\/\/www.tandfonline.com\/doi\/abs\/10.1080\/10409238.2017.1290043?journalCode=ibmg20\">Genomics of Apicomplexan Parasites.<\/a>&nbsp;Critical Reviews in Biochemistry and Molecular Biology. 52(3): 254-273<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.neuron.2017.03.037 \" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Vetere G., Kenney J.W., Tran L.M., Xia F., Steadman P.E.,&nbsp;<strong>Parkinson J.,<\/strong>&nbsp;Josselyn S.A. and Frankland P.W. (2017)&nbsp;<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28426969\">Chemogenetic interrogation of a brain-wide fear memory network in mice.<\/a>&nbsp;Neuron. 94: 363-374.e4<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/nmicrobiol.2017.33\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Bertschi N.L., Toenhake C.G.,&nbsp;<strong>Zou A.,<\/strong>&nbsp;Niederwieser I., Henderson R., Moes S., Jenoe P.,&nbsp;<strong>Parkinson J.,<\/strong>, Bartfai R. and Voss T.S. (2017)&nbsp;<a href=\"http:\/\/www.nature.com\/articles\/nmicrobiol201733\">Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA.<\/a>&nbsp;Nature Microbiology. 2:17033.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">2016<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/nmicrobiol.2016.216\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Cotton J.A., Bennuru S., Grote A., Harsha B., Tracey A., Beech R., Doyle S.R., Dunn M., Hotopp J.C.D., Holroyd N., Kikuchi T., Lambert O., Mhashilkar A., Mutowo P.,&nbsp;<strong>Nursimulu N.,<\/strong>&nbsp;Ribeiro J.M.C., Rogers M.B., Stanley E.,&nbsp;<strong>Swapna L.S.,<\/strong>&nbsp;Tsai I.J., Unnasch T.R., Voronin D.,&nbsp;<strong>Parkinson J.,<\/strong>&nbsp;Nutman T.B., Ghedin E., Berriman M. and Lusgman S. (2016)&nbsp;<a href=\"http:\/\/www.nature.com\/articles\/nmicrobiol2016216\">The genome of Onchocerca volvulus, agent of river blindness.<\/a>&nbsp;Nature Microbiology. 2:16216<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.3945\/jn.116.239145\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Di Giovanni V., Bourdon C., Wang D.,&nbsp;<strong>Swapna L.,<\/strong>&nbsp;Senga E., Versloot C., Voskuijl W., Semba R., Trehan I., Moaddel R., Ordiz M., Zhang L.,&nbsp;<strong>Parkinson J.,<\/strong>&nbsp;Manary M. and Bandsma R. (2016)&nbsp;<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5118769\/\">Metabolomic changes in serum of children with different clinical diagnoses of malnutrition.<\/a>&nbsp;The Journal of Nutrition. 146(12):2436-2444.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1093\/database\/baw013\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Cromar, GL., Zhao, A., Xiong, X., Swapna, LS., Loughran, N., Song, H. and Parkinson, J.<\/strong>(2016)&nbsp;<a href=\"http:\/\/database.oxfordjournals.org\/content\/2016\/baw013.full\">PhyloPro2.0: A database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.&nbsp;<\/a>Database. pii: baw013.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.dib.2015.11.062\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Phanse, S., Wan, C., Borgeson, B., Tu, F., Drew, K., Clark, G.,&nbsp;<strong>Xiong, X.,&nbsp;<\/strong>Kagan, O., Kwan, J., Berzginov, A.,&nbsp;<strong>Chessman, K.,&nbsp;<\/strong>Pal, S.,&nbsp;<strong>Cromar, G.,&nbsp;<\/strong>Papoulas, O., Ni, Z., Boutz, DR., Stoilova, S., Havugimana, P., Guo, X., Malty, R., Sarov, M., Greenblatt, J., Babu, M., Derry, WB., Tillier, E., Wallingford, J.,&nbsp;<strong>Parkinson, J.,&nbsp;<\/strong>Marcotte, E. and Emili, A. (2016).&nbsp;<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4738005\/\">Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.<\/a>&nbsp;Data in Brief. 6: 715\u2013721.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1186\/s40168-015-0146-x\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p><strong>Jiang, Y., Xiong, X.<\/strong>, Danska, J. and&nbsp;<strong>Parkinson, J.<\/strong>(2016)&nbsp;<a href=\"http:\/\/www.microbiomejournal.com\/content\/4\/1\/2\">Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.<\/a>&nbsp;Microbiome. 4:2<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1016\/j.celrep.2015.12.060\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Kumar, A.*, Beloglazova, N.*,&nbsp;<strong>Bundalovic-Torma, C.*,<\/strong>&nbsp;Phanse, S., Deineko, V., Gagarinova, A., Musso, G., Vlasblom, J., Lemak, S., Hooshyar, M., Minic, Z., Wagih, O., Mosca, R., Aloy, P., Golshani, A.,&nbsp;<strong>Parkinson, J.,*<\/strong>&nbsp;Emili A.*, Yakunin, A.*, and Babu, M.* (2016)&nbsp;<a href=\"http:\/\/www.cell.com\/cell-reports\/abstract\/S2211-1247%2815%2901501-6\">Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.<\/a>&nbsp;Cell Reports. pii: S2211-1247(15)01501-6.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:5%\">\n<p><code><span class=\"__dimensions_badge_embed__\" data-doi=\"10.1038\/ncomms10147\" data-style=\"small_circle\"><\/span><script><\/script><\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:90%\">\n<p>Lorenzi, H., Khan, A., Behnke, M., Namasivayam, S.,&nbsp;<strong>Swapna, LS.,<\/strong>&nbsp;Hadjithomas, M., Karamycheva, S., Pinney, D., Brunk, B., Ajioka, J., Ajzenberg, D., Boothroyd, J., Boyle, J., Darde, M., Diaz-Miranda, MA, Dubey, JP., Fritz, H., Gennari, SM., Gregory, B., Kim, K., Saeij, JPJ., Su, C., White, MW., Zhu, X-Q., Howe, DK., Rosenthal, BM., Grigg, ME.,&nbsp;<strong>Parkinson, J.,<\/strong>Liu, L., Kissinger, JC., Roos, DS. and Sibley, LD. (2016)&nbsp;<a href=\"http:\/\/www.nature.com\/ncomms\/2016\/160107\/ncomms10147\/full\/ncomms10147.html\">Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes.<\/a>&nbsp;Nature Communications. 7:10147<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading alignwide\">pre-2016<\/h2>\n\n\n\n<div class=\"wp-block-columns alignwide is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<p>Only recent publications are shown. For a full list of publications, <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/sites\/myncbi\/1d3iekkXjLGki\/bibliography\/40489775\/public\/?sort=date&amp;direction=descending\">click here<\/a>. <\/p>\n<\/div>\n<\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>submitted Phanse, S., Peng, H., Kotelnikov, S., Egbert, ME., Ofaim, S., Stevens, GC., Saccon, T., Ignatov, M., Dutta, S., Istace, Z., Moutaoufik, MT., Aoki, H., Kewalramani, N., Sun, J., Gong, Y., Padhorny, D., Poda, G., Alekseenko, A., Porter, KA., Jones, G., Rodionova I., Guo H., Pogoutse, O., Datta, S., Saier, M., Crovella, M., Vajda, S., [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-127","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages\/127","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/comments?post=127"}],"version-history":[{"count":102,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages\/127\/revisions"}],"predecessor-version":[{"id":614,"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/pages\/127\/revisions\/614"}],"wp:attachment":[{"href":"https:\/\/compsysbio.org\/index.php\/wp-json\/wp\/v2\/media?parent=127"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}