{"id":408,"date":"2020-01-09T14:38:31","date_gmt":"2020-01-09T14:38:31","guid":{"rendered":"https:\/\/josejimenezlab.com\/?page_id=408"},"modified":"2026-09-06T14:09:40","modified_gmt":"2026-09-06T14:09:40","slug":"join-us","status":"publish","type":"page","link":"https:\/\/josejimenezlab.com\/?page_id=408","title":{"rendered":"Publications"},"content":{"rendered":"<p><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 fusion-parallax-none nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-padding-bottom:60px;--awb-background-image:url(&quot;https:\/\/josejimenezlab.com\/wp-content\/uploads\/2020\/01\/Foto-header5.jpg&quot;);--awb-background-size:cover;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-bg-size:cover;--awb-margin-top:150px;--awb-margin-bottom:50px;\"><div class=\"fusion-column-wrapper fusion-column-has-shadow fusion-flex-column-wrapper-legacy\"><div class=\"fusion-title title fusion-title-1 fusion-sep-none fusion-title-text fusion-title-size-one\" style=\"--awb-margin-top-small:0px;--awb-margin-right-small:0px;--awb-margin-bottom-small:20px;--awb-margin-left-small:0px;\"><h1 class=\"fusion-title-heading title-heading-left fusion-responsive-typography-calculated\" style=\"margin:0;--fontSize:53;line-height:1.4;\"><h1 style=\"text-align: center;\"><span style=\"color: #ffffff;\">Publications<\/span><\/h1><\/h1><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-2 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-padding-top:100px;--awb-margin-top:-200px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-1 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-bg-color:#ffffff;--awb-bg-color-hover:#ffffff;--awb-bg-size:cover;\"><div class=\"fusion-column-wrapper fusion-column-has-shadow fusion-flex-column-wrapper-legacy\"><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:50PX;margin-bottom:50PX;width:100%;\"><\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-3 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-2 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-padding-right:5%;--awb-padding-left:5%;--awb-bg-size:cover;\"><div class=\"fusion-column-wrapper fusion-column-has-shadow fusion-flex-column-wrapper-legacy\"><div class=\"accordian fusion-accordian\" style=\"--awb-border-size:1px;--awb-icon-size:13px;--awb-content-font-size:16px;--awb-icon-alignment:left;--awb-hover-color:#f9f9f9;--awb-border-color:#cccccc;--awb-background-color:#ffffff;--awb-divider-color:#e0dede;--awb-divider-hover-color:#e0dede;--awb-icon-color:#ffffff;--awb-title-color:#03a9f4;--awb-content-color:#212121;--awb-icon-box-color:#d4d8e0;--awb-toggle-hover-accent-color:#002344;--awb-title-font-family:&quot;Mulish&quot;;--awb-title-font-weight:regular;--awb-title-font-style:normal;--awb-title-font-size:54px;--awb-title-line-height:1.5;--awb-content-font-family:&quot;Mulish&quot;;--awb-content-font-style:normal;--awb-content-font-weight:400;\"><div class=\"panel-group fusion-toggle-icon-boxed\" id=\"accordion-408-1\"><div class=\"fusion-panel panel-default panel-372113602d8b6251f fusion-toggle-has-divider\" style=\"--awb-title-color:#03a9f4;--awb-content-color:#212121;\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_372113602d8b6251f\"><a class=\"active\" aria-expanded=\"true\" aria-controls=\"372113602d8b6251f\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-408-1\" data-target=\"#372113602d8b6251f\" href=\"#372113602d8b6251f\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Journals<\/span><\/a><\/h4><\/div><div id=\"372113602d8b6251f\" class=\"panel-collapse collapse in\" aria-labelledby=\"toggle_372113602d8b6251f\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<ul>\n<li>Banks A.B., Abdulmutalib U., Wain B., Sonnendecker C., Doherty H., Zhang Z., Kim J., Bosomworth C., Brown S., Wei R., \u00c1lvarez C., Pomposiello P., Avignone-Rossa C., Larrouy-Maumus G., Zimmerman W. and Jim\u00e9nez J.I. Engineering environmental bacteria for whole-cell PET hydrolysis and assimilation (2026). <em>Accepted in Trends in Biotech. <\/em>(<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.09.24.614569v1\">preprint<\/a>) (<a href=\"https:\/\/www.cell.com\/trends\/biotechnology\/fulltext\/S0167-7799(26)00248-9\">link<\/a>)(<a href=\"https:\/\/www.cell.com\/action\/showPdf?pii=S0167-7799%2826%2900248-9\">pdf<\/a>)<\/li>\n<li>K\u00fctahya C., Crua\u00f1as P\u00e1niker C., Ly F., Jerath A., Little E., Young T., Gali R., Haimi M.Z.D., Bin Hj Abd Malek A.H., Muhamad K.B., Supian S.B., Lawrence S., Nee T.Y., Bell T., <strong>Jim\u00e9nez J.I.<\/strong> and Huynh F. Masterbatch-enabled acceleration of polyolefin biodegradation under open air terrestrial environmental conditions (2026). <em><u>Npj Mater. Deg. <\/u><\/em><u>10:90<\/u> (<a href=\"https:\/\/www.nature.com\/articles\/s41529-026-00817-5#citeas\">link)<\/a><\/li>\n<li>Oh J., <strong>Jim\u00e9nez J.I.<\/strong> and Kim J. Safe and resource-aware microbial design for food production (2026). <em><u>Curr. Opin. Biotechnol<\/u>. <\/em>100:103529 (link)<\/li>\n<li>Merali N., Chouari T., Sardar P., Suyama S., Bagwan I., Karanjia N.D., Kumar R., Lahiri R.P., Pencavel T.D., Platt E., Riga A., Worthington T.R., Relph K., <strong>Jim\u00e9nez J.I.<\/strong>, Velliou E., Sivakumar S., Demirkan A., Krell J., Rockall T.A, Bartlett D., Giovannetti E., Pedicord V., Annels N.E. and Frampton A.E.. The bile microbiome is a surrogate for the intratumoral microbiome in pancreatic ductal adenocarcinoma and is associated with oncological outcomes (2026). <em><u> J. Surg<\/u>. <\/em>112(8):13478-13492 (<a href=\"https:\/\/www.ovid.com\/jnls\/international-journal-of-surgery\/fulltext\/10.1097\/js9.0000000000005219~the-bile-microbiome-is-a-surrogate-for-the-intratumoral\">link<\/a>)<\/li>\n<li>Benton J., Crua\u00f1as-Paniker C. and Jim\u00e9nez J.I. Responsible Research and Innovation of Bio-based approaches to the management of plastic waste: a stakeholder perspective (2026). <span style=\"text-decoration: underline;\"><em>Nat. Comms.<\/em><\/span> 17:2281. (<a href=\"https:\/\/rdcu.be\/e7BcS\">link<\/a>)<\/li>\n<li>Jim\u00e9nez J.I., Crua\u00f1as P\u00e1niker C. and Wain B. Engineering whole-cell catalysts to use plastic waste as a feedstock (2026). <span style=\"text-decoration: underline;\"><em>Curr.<\/em> <em>Opin. Biotechnol. <\/em><\/span>97:103443 (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S095816692600008X\">link<\/a>)<\/li>\n<li>Molpeceres-Garcia F.J., Garcia-Miro A., Mateos E., Prieto A., Sanz D., Jim\u00e9nez J.I. and Barriuso J. <em>Pseudomonas putida<\/em> JM37 as a novel bacterial chassis for ethylene glycol upcycling<em>\u00a0<\/em>(2026)<em>. <span style=\"text-decoration: underline;\">Bioresour. Technol.<\/span> <\/em>443:133884 (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0960852425018516?via%3Dihub\">link)<\/a><\/li>\n<li>\n<div><span lang=\"EN-US\">Tom\u00e1s-Nery, E., Avignone-Rossa C., Sapienza L., McFadden J., Olaya-Castro A. and Jim\u00e9nez J.I. Directed evolution of LH2 complexes with altered energy transfer in purple non-sulfur bacteria (2025).<i>\u00a0<\/i>(<a href=\"https:\/\/doi.org\/10.1101\/2025.10.01.678743\">preprint<\/a>)<\/span><\/div>\n<\/li>\n<li>Kim J., Darlington A.P., Bates D.G. and Jimenez J.I. The interplay between growth rate and nutrient quality defines gene expression capacity (2025). <em><span style=\"text-decoration: underline;\">ACS Synth. Biol<\/span>. <\/em>14:2012\u20132029 (<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acssynbio.4c00828\">link<\/a>)(<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.04.02.438188v1\">preprint<\/a>)<\/li>\n<li><span style=\"font-family: var(--awb-content-font-family); font-size: var(--awb-content-font-size); font-style: var(--awb-content-font-style); letter-spacing: var(--awb-content-letter-spacing); text-transform: var(--awb-content-text-transform);\">Mehta H., Jim\u00e9nez J.I., Ledesma-Amaro R., Stan G-B.V. Investigating the potential of division of labour in synthetic bacterial communities for the production of violacein (2025). <\/span><span style=\"text-decoration: underline;\"><em style=\"font-family: var(--awb-content-font-family); font-size: var(--awb-content-font-size); letter-spacing: var(--awb-content-letter-spacing); text-transform: var(--awb-content-text-transform);\">ACS Synth. Biol<\/em><\/span><span style=\"font-family: var(--awb-content-font-family); font-size: var(--awb-content-font-size); font-style: var(--awb-content-font-style); letter-spacing: var(--awb-content-letter-spacing); text-transform: var(--awb-content-text-transform);\"><span style=\"text-decoration: underline;\">.<\/span>\u00a0<span class=\"cit-volume\">14:<\/span><span class=\"cit-pageRange\">2703\u20132709<\/span> (<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acssynbio.5c00120\">link<\/a>)(<\/span><a style=\"font-family: var(--awb-content-font-family); font-size: var(--awb-content-font-size); font-style: var(--awb-content-font-style); letter-spacing: var(--awb-content-letter-spacing); text-transform: var(--awb-content-text-transform);\" href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2025.01.07.631562v1\">preprint<\/a><span style=\"font-family: var(--awb-content-font-family); font-size: var(--awb-content-font-size); font-style: var(--awb-content-font-style); letter-spacing: var(--awb-content-letter-spacing); text-transform: var(--awb-content-text-transform);\">)<\/span><\/li>\n<li>Coimbra A.A.B., Prakash S., Jim\u00e9nez J.I. and Rios-Solis L.. Establishing <em>Halomonas<\/em> as a chassis for industrial biotechnology: Leveraging advanced synthetic biology tools and metabolic engineering strategies (2025). <em>Microb Cell Fact.\u00a0<\/em>24:133. (<a href=\"https:\/\/microbialcellfactories.biomedcentral.com\/articles\/10.1186\/s12934-025-02757-2#citeas\">link<\/a>)<\/li>\n<li>Banks A.B., Abdulmutalib U., Sonnendecker C., Kim J., Bosomworth C., Brown S., Wei R., \u00c1lvarez, C., Pomposiello P., Avignone-Rossa C., Larrouy-Maumus G., Zimmerman W. and Jim\u00e9nez J.I.. Degradation of PET plastic with engineered environmental bacteria (2024). <em>Submitted<\/em>. (<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.09.24.614569v1\">preprint<\/a>)<\/li>\n<li>Merali N., Chouari T., Terroire J., Suyama S., Jessel M.D., Wooldridge T., Liu D.S.H., Smith J.H., Dhillon T., Jimenez J.I., Krell J., Roberts K., Rockall T.A., Velliou E., Sivakumar S., Giovannetti E., Pedicord V.A., Demirkan A., Annels N.E. and Frampton A.E. Bile microbiome signatures as biomarkers for differentiating pancreatic ductal adenocarcinoma from benign disease: Discovery of novel microbial signatures in a UK pilot study (2023). <em><u>Int J Mol Sci<\/u>. <\/em>24:16888 (<a href=\"https:\/\/www.mdpi.com\/1422-0067\/24\/23\/16888\">link<\/a>)<\/li>\n<li>Avenda\u00f1o R., Mu\u00f1oz-Montero S., Rojas-G\u00e4tjens D., Fuentes P., Vieto S., Montenegro R., Salvador M., Frew R., Kim J., Chavarr\u00eda M. and Jimenez J.I. Production of selenium nanoparticles occurs through an interconnected pathway of sulfur metabolism and oxidative stress response in <em>Pseudomonas putida<\/em> KT2440 (2023). <em>Microb Biotechnol. <\/em>16:931-946 (<a href=\"https:\/\/ami-journals.onlinelibrary.wiley.com\/doi\/full\/10.1111\/1751-7915.14215\">link<\/a>)(<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.09.29.507446v1\">preprint<\/a>)<\/li>\n<li>Dvo\u0159\u00e1k P., Calcagno-Galv\u00e3o T., Pfl\u00fcger-Grau K., Banks A.M., de Lorenzo V. and Jimenez J.I. Water potential governs effector specificity of the transcriptional regulator XylR of <em>Pseudomonas putida<\/em> (2023)<em>. Environ Microbiol. <\/em>25:1041-1054 (<a href=\"https:\/\/ami-journals.onlinelibrary.wiley.com\/doi\/full\/10.1111\/1462-2920.16342\">link<\/a>)(<a href=\"https:\/\/ami-journals.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.16342\">pdf<\/a>)<\/li>\n<li>Fernandez-Gonzalez A., Cowen S., Kim J., Foy C.A., Jimenez J.I., Huggett J.F. and Whale A.S. Applicability of control materials to support gene promoter characterization and expression in engineered cells using digital PCR (2022). <em>Anal Chem.<\/em> 94:5566-5574 (<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.analchem.1c05134\">link<\/a>)(<a href=\"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.analchem.1c05134\">pdf<\/a>)<\/li>\n<li>Merali N., Chouari T., Kayani K., Rayner C.J., Jimenez J.I., Krell J., Giovannetti E., Bagwan I., Relph K., Rockall T.A., Dhillon T., Pandha H., Annels N.E. and Frampton A.E. A comprehensive review of the current and future role of the microbiome in pancreatic ductal adenocarcinoma (2022). <em>Cancers<\/em>. 14:1020 (<a href=\"https:\/\/www.mdpi.com\/2072-6694\/14\/4\/1020\/htm\">link<\/a>)<\/li>\n<li>Hidalgo D., Martinez-Ortiz C.A, Palsson B.O., Jimenez J.I. and Utrilla J. Regulatory perturbations of ribosome allocation results in a trade-off between fast growth and adaptation capacity (2022). <em>iScience. <\/em>25:103879 (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2589004222001493\">link<\/a>) (<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.08.01.454633v3\">preprint<\/a>)<\/li>\n<li>Vieto S., Rojas-G\u00e4tjens D., Jimenez J.I., Chavarria M. The potential of <em>Pseudomonas<\/em> for bioremediation of oxyanions (2021). <em>Environ Microbiol Rep<\/em>. 13:773-789 (<a href=\"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/abs\/10.1111\/1758-2229.12999\">link<\/a>)<\/li>\n<li>Narancic T., Salvador M., Hughes G., Beagan N., Kenny S.T., Wu H-H., O\u2019Connor K.E. and Jimenez J.I. Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: Production of PHA and PHB out of PET monomers. (2021) <em>Microb Biotechnol. <\/em>14:2463-2480 (<a href=\"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/abs\/10.1111\/1751-7915.13712\">link<\/a>)<\/li>\n<li>Gonzalez J, Salvador M, Ozkayab O, Spick M, Costa C, Bailey M.J., Avignone-Rossa C, Kummerli R and Jimenez J.I. Loss of a pyoverdine secondary receptor in <em>Pseudomonas aeruginosa<\/em> results in a fitter strain suitable for population invasion. (2021) <em>ISME J.<\/em> 15:1330-1343 (<a href=\"https:\/\/doi.org\/10.1038\/s41396-020-00853-2\">link<\/a>) (<a href=\"https:\/\/rdcu.be\/ccfxW\">pdf<\/a>) (<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.05.08.085159v1\">preprint<\/a>)<\/li>\n<li><span lang=\"ES-MX\">Lastiri-Pancardo G., Mercado-Hernandez J.S., Kim J., Jimenez J.I<\/span><span lang=\"ES-MX\">. and<\/span> <span lang=\"ES-MX\">Utrilla J.<\/span>A quantitative method for proteome reallocation using minimal regulatory interventions. (2020) <em>Nat Chem Biol<\/em>. 16:1026\u20131033 (<a href=\"https:\/\/www.nature.com\/articles\/s41589-020-0593-y?proof=t\">link<\/a>) (<a href=\"http:\/\/rdcu.be\/b5AwJ\">pdf<\/a>) (<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/733592v1\">preprint<\/a>)<\/li>\n<li>Kim J., Darlington A., Salvador M., Utrilla J. and Jimenez J.I. Tradeoffs between gene expression, growth and phenotypic diversity in microbial populations. (2020) <em>Curr Opin Biotechnol<\/em><em>. <\/em>62:29-37 (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0958166919300588\">link<\/a>) (<a title=\"1-s2.0-S0958166919300588-main\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2019\/10\/1-s2.0-s0958166919300588-main.pdf\">pdf<\/a>)<\/li>\n<li>Salvador M., Abdulmutalib U., Gonzalez J., Kim J., Smith A.A., Faulon J-L., Wei R., Zimmermann W. and Jimenez J.I. Microbial genes for a circular and sustainable bio-PET economy. (2019) <em>Genes<\/em>. 10:373 <a href=\"https:\/\/www.mdpi.com\/2073-4425\/10\/5\/373\">(link)<\/a> <a href=\"https:\/\/www.preprints.org\/manuscript\/201904.0284\/v1\">(preprint)<\/a><\/li>\n<li>Darlington A.P., Kim J., Jimenez J.I., Bates D.G. Engineering translational allocation controllers: Mechanistic models, design guidelines, and potential biological implementations. (2018)<em> ACS Synth Biol.<\/em>7:2485-2496 <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acssynbio.8b00029\">(link)<\/a> <a title=\"main-text-final-with-figures\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2018\/10\/main-text-final-with-figures.pdf\">(pdf)<\/a> <a title=\"supplementary-material-final\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2018\/10\/supplementary-material-final.pdf\">(SI)<\/a> <a href=\"http:\/\/engineering%20translational%20resource%20allocation%20controllers:%20Mechanistic%20Models,%20Design%20Guidelines,%20and%20Potential%20Biological%20Implementations\/\">(bioRxiv)<\/a><\/li>\n<li>Darlington A.P.\u00b9, Kim J.\u00b9, Jimenez J.I.\u00b2, Bates D.G.\u00b2 Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. (2018) <em> Nat Commun<\/em>. 9:695 (\u00b9equal contribution, \u00b2corresponding authors) <a href=\"https:\/\/www.biorxiv.org\/content\/early\/2017\/05\/16\/138362\">(bioRxiv)<\/a> <a href=\"https:\/\/www.nature.com\/articles\/s41467-018-02898-6.epdf?author_access_token=QJM9-AiIN1PeJe_Wn6tP3NRgN0jAjWel9jnR3ZoTv0MQuqhQhcUGRjq1HYJ0U2E3ya2OdaNM7nohA2YVyrJNYm3nzA7P2ITzCJ_hcoFv0aq8wX3BHncSXF9CLPN9WsSf-ghn6-1gRBJA1HKe1NU4VA%3D%3D\">(link)<\/a><\/li>\n<li>Cavaliere M., Fang S. Soyer O. and Jimenez J.I. Cooperation in microbial communities and their biotechnological applications. (2017)<em> Environ Microbiol.<\/em>19(8):2949-2963<em>. <\/em><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1462-2920.13767\/abstract?systemMessage=Wiley+Online+Library+is+migrating+to+a+new+platform+powered+by+Atypon%2C+the+leading+provider+of+scholarly+publishing+platforms.+The+new+Wiley+Online+Library+will+be+migrated+over+the+weekend+of+February+24+and+25+and+will+be+live+on+February+26%2C+2018.+For+more+information%2C+please+visit+our+migration+page%3Ahttp%3A%2F%2Fwww.wileyactual.com%2FWOLMigration%2F\">(link)<\/a> <a title=\"manuscript-eb-161130\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2015\/10\/manuscript-eb-170408_1.pdf\">(pdf)<\/a><\/li>\n<li>Qian Y., Huang HH., Jimenez J.I. and Del Vecchio D. Resource competition shapes the response of genetic circuits. <em>ACS Synth Biol. <\/em>6(7):1263-1272<em>. <\/em><a title=\"FinalMain\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2015\/10\/finalmain.pdf\">(pdf)<\/a> <a title=\"SI_rev\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2015\/10\/si_rev.pdf\">(SI)<\/a> <a href=\"http:\/\/biorxiv.org\/content\/early\/2016\/12\/03\/091306\">(bioRxiv<\/a><a href=\"http:\/\/biorxiv.org\/content\/early\/2016\/12\/03\/091306\">)<\/a> <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acssynbio.6b00361\">(link)<\/a><\/li>\n<li>Jimenez J.I. Shedding light on the black box models of the cell. (2017) <em>Microb Biotechnol<u>.<\/u><\/em> 10(1):43-45 <u><a title=\"jimenez-cb-161128\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2015\/10\/jimenez-cb-161128.pdf\">(pdf)<\/a><\/u> <u><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1751-7915.12489\/full\">(link)<\/a><\/u><\/li>\n<li>Kim J., Salvador M., Saunders E., Gutierrez J., Avignone-Rossa C. and Jimenez J.I. Properties of alternative microbial hosts used in Synthetic Biology: Towards the modular design of a chassis. (2016) <em>Essays Biochem<u>.<\/u> <\/em>60(4):303-313. <a href=\"http:\/\/essays.biochemistry.org\/content\/60\/4\/303\">(link)<\/a><\/li>\n<li>Avenda\u00f1o R., Chaves N., Fuentes P., Sanchez E., Jimenez J.I. and Chavarria M. Production of selenium nanoparticles in <em>Pseudomonas putida<\/em> (2016) <em><u>Sci Rep.<\/u> <\/em>6:37155 <a href=\"http:\/\/www.nature.com\/articles\/srep37155\">(link)<\/a><\/li>\n<li>Xulvi-Brunet R., Campbell G.W., Rajamani S., Jimenez I. and Chen I.A. Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments. (2016) <em>Methods<\/em>. 106:86-96. <a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1046202316301426\">(link)<\/a><\/li>\n<li>Jimenez J.I., Fraile S., Zafra O., de Lorenzo V. Phenotypic knockouts of selected metabolic pathways by targeting enzymes with camel derived nanobodies (VHHs). (2015) <em>Metab <\/em><em>Eng<\/em>. 30:40-48. <a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1096717615000464\">(link)<\/a><\/li>\n<li>Gyorgy A., Jimenez J.I., Yazbek J., Huang H.H., Chung H., Weiss R. and Del Vecchio D. Isocost lines describe the cellular economy of genetic circuits. (2015) <em>Biophys J. <\/em>109(3):639-646. <a href=\"http:\/\/www.cell.com\/biophysj\/comments\/S0006-3495(15)00617-7\">(link)<\/a><\/li>\n<li>Nilgiriwala K., Jimenez J.I., Rivera P.M. and Del Vecchio D. A synthetic tunable amplifying genetic circuit in <em>coli<\/em>. (2015) <em>ACS Synth Biol<\/em>. 4(5):577-84. <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb5002533\">(link)<\/a><\/li>\n<li>Freese P., Korolev K., Jimenez J.I. and Chen I.A. Genetic drift suppresses bacterial conjugation in spatially structured populations. (2014) <em>Biophys<\/em> <em>J. <\/em>106(4):944-54. <a href=\"http:\/\/www.cell.com\/biophysj\/abstract\/S0006-3495(14)00080-0\">(link)<\/a><\/li>\n<li>Jimenez J.I., Perez-Pantoja D., Chavarria M, Diaz E. and de Lorenzo V. A second chromosomal copy of the <em>catA <\/em>gene endows <em>Pseudomonas putida<\/em> mt-2 with an enzymatic safety valve for excess of catechol. (2014). <em>Environ<\/em><em> Microbiol.<\/em> 16(6):1767-78. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1462-2920.12361\/suppinfo\">(link)<\/a><\/li>\n<li>Jimenez J.I., Xulvi-Brunet R., Campbell G.W., Turk-McLeod R. and Chen I.A. Comprehensive experimental fitness landscape and evolutionary network for RNA. (2013) <em>PNAS. <\/em>110(37):14984-9<em>. <\/em><a href=\"http:\/\/www.pnas.org\/content\/110\/37\/14984.abstract\">(link)<\/a><\/li>\n<li>Fraile S., Jimenez J.I., Gutierrez C. and de Lorenzo V. NanoPad: an integrated platform for bacterial production of camel nanobodies aimed at detecting environmental biomarkers. (2013) <em>Proteomics<\/em>. 13(18-19):2766-75. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pmic.201300009\/abstract\">(link)<\/a><\/li>\n<li>Diaz E., Jimenez J.I. and Nogales J. Aerobic degradation of aromatic compounds. (2013) <em>Curr<\/em> <em>Opin Biotechnol.<\/em> 24:1-12.<\/li>\n<li>Lin A., Jimenez J.I., Derr J., Vera P., Manapat M.L., Esvelt K.M., Villanueva L., Liu D.R. and Chen I.A. Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model. (2011) <em>PLoS One<\/em>. 6(5):e19991. <a href=\"http:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0019991\">(link)<\/a><\/li>\n<li>Jimenez J.I., Juarez J.F., Garcia J.L. and Diaz E. A finely tuned regulatory circuit of the nicotinic acid degradation pathway in Pseudomonas putida. (2011) <em>Environ<\/em><em> Microbiol.<\/em> 13(7):1718-32. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1462-2920.2011.02471.x\/abstract\">(link)<\/a><\/li>\n<li>Zafra O., Fraile S., Gutierrez C., Haro A., Paez A.D., Jimenez J.I. and de Lorenzo V. Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins. (2011) <em>Environ<\/em><em> Microbiol.<\/em> 13(4):960-74. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1462-2920.2010.02401.x\/abstract;jsessionid=C0BF1209792AB718C20FFEF27531DF91.f04t03\">(link)<\/a><\/li>\n<li>Jimenez J.I., Acebron-Avalos I., Diaz E. and Manche\u00f1o. A preliminary crystallographic study of recombinant NicX, an Fe<sup>2+<\/sup>-dependent 2,5-dihydroxypyridine dioxygenase from <em>Pseudomonas putida<\/em> (2010) <em>Acta Crystallogr Sect F Struct Biol Cryst Commun.<\/em> 66(Pt 5):549-53. <a href=\"http:\/\/scripts.iucr.org\/cgi-bin\/paper?S174430911001119X\">(link)<\/a><\/li>\n<li>Jimenez J.I., Canales A., Jimenez-Barbero J., Ginalski K., Rychlewski L., Garcia J.L. and Diaz E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440. (2008) <em>PNAS<\/em>. 105(32):11329-34. <a href=\"http:\/\/www.pnas.org\/content\/105\/32\/11329.long\">(link)<\/a><\/li>\n<li>Yuste L., Hervas A.B., Canosa I., Tobes R., Jimenez J.I., Nogales J., Santero E., D\u00edaz E., Ramos J.L., de Lorenzo V. and Rojo F. Growth-phase dependent expression of the <em>Pseudomonas putida<\/em> KT2440 transcriptional machinery throughout the growth phase analyzed by means of a genome-wide microarray. (2006) <em>Environ<\/em><em> Microbiol.<\/em> 8(1):165-177. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1462-2920.2005.00890.x\/abstract\">(link)<\/a><\/li>\n<li>Jimenez J.I., Minambres B., Garcia J.L. and Diaz E. Genomic analysis of the aromatic catabolic pathways from <em>Pseudomonas putida<\/em> (2002) <em>Environ Microbiol.<\/em> 4(12):824-841. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1046\/j.1462-2920.2002.00370.x\/abstract\">(link)<\/a><\/li>\n<\/ul>\n<\/div><\/div><\/div><\/div><\/div><div class=\"accordian fusion-accordian\" style=\"--awb-border-size:1px;--awb-icon-size:13px;--awb-content-font-size:16px;--awb-icon-alignment:left;--awb-hover-color:#f9f9f9;--awb-border-color:#cccccc;--awb-background-color:#ffffff;--awb-divider-color:#e0dede;--awb-divider-hover-color:#e0dede;--awb-icon-color:#ffffff;--awb-title-color:#03a9f4;--awb-content-color:#212121;--awb-icon-box-color:#d4d8e0;--awb-toggle-hover-accent-color:#002344;--awb-title-font-family:&quot;Mulish&quot;;--awb-title-font-weight:regular;--awb-title-font-style:normal;--awb-title-font-size:54px;--awb-title-line-height:1.5;--awb-content-font-family:&quot;Mulish&quot;;--awb-content-font-style:normal;--awb-content-font-weight:400;\"><div class=\"panel-group fusion-toggle-icon-boxed\" id=\"accordion-408-2\"><div class=\"fusion-panel panel-default panel-3af5e760b73a84d7d fusion-toggle-has-divider\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_3af5e760b73a84d7d\"><a aria-expanded=\"false\" aria-controls=\"3af5e760b73a84d7d\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-408-2\" data-target=\"#3af5e760b73a84d7d\" href=\"#3af5e760b73a84d7d\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Book chapters<\/span><\/a><\/h4><\/div><div id=\"3af5e760b73a84d7d\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_3af5e760b73a84d7d\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<ul>\n<li>Wierckx N., Narancic T., Eberlein C., Wei R., Drzyzga O., Magnin A., Ballerstedt H., Kenny S.T., Pollet E., Av\u00e9rous L., O\u2019Connor K.E., Zimmermann W., Heipieper H.J., Prieto M.A., Jim\u00e9nez J.I. and Blank L.M. (2018) Plastic biodegradation: challenges and opportunities. Handbook of Hydrocarbon and Lipid Microbiology Consequences of Microbial Interaction with Hydrocarbons, Oils and Lipids Biodegradation and Bioremediation. 1-29. <a title=\"Wierckx_et_al_plastic biodegradation_authors_pre-print\" href=\"https:\/\/surreysynbio.files.wordpress.com\/2018\/03\/wierckx_et_al_plastic-biodegradation_authors_pre-print.pdf\">(pdf)<\/a><\/li>\n<li>Xulvi-Brunet R., Campbell G.W., Rajamani S., Jimenez J.I. and Chen I.A. Quantitative analysis of synthesized nucleic acid pools. (2016) In\u00a0<em>Non-linear events in Biology.\u00a0<\/em>Springer Publishers. 7:19-41<em>.\u00a0<\/em><a href=\"http:\/\/link.springer.com\/chapter\/10.1007%2F978-3-319-33054-9_2\">(link)<\/a><\/li>\n<li>de Lorenzo V., Fraile S. and Jimenez J.I. Emerging Systems and Synthetic Biology approaches to Hydrocarbon Biotechnology. (2009) In\u00a0<em>Handbook of Hydrocarbon and Lipid\u00a0<\/em><em>Microbiology<\/em>. Chapter 41, 1411-1435 Ed.: K. Timmis, Springer Publishers.\u00a0<a href=\"http:\/\/link.springer.com\/referenceworkentry\/10.1007%2F978-3-540-77587-4_97\">(link)<\/a><\/li>\n<li>Jimenez J.I., Nogales J., Garc\u00eda J.L. and Diaz E. A genomic view of the catabolism of aromatic compounds in Pseudomonas. (2009) In\u00a0<em>Handbook of Hydrocarbon and Lipid<\/em>\u00a0Chapter 35, 1297-1325 Ed.: K. Timmis, Springer Berlin Heidelberg Publishers.\u00a0<a href=\"http:\/\/link.springer.com\/referenceworkentry\/10.1007%2F978-3-540-77587-4_91\">(link)<\/a><\/li>\n<li>Jimenez J.I., Minambres B., Garcia J.L. and Diaz E. Genomic insights in the metabolism of\u00a0<em>Pseudomonas putida\u00a0<\/em>KT2440. (2004) In\u00a0<em>Pseudomonas<\/em>. Vol. 3, chapter 15, 425-462 Ed. J.L. Ramos. Kluwer Publishers.<\/li>\n<\/ul>\n<\/div><\/div><\/div><\/div><\/div><div class=\"accordian fusion-accordian\" style=\"--awb-border-size:1px;--awb-icon-size:13px;--awb-content-font-size:16px;--awb-icon-alignment:left;--awb-hover-color:#f9f9f9;--awb-border-color:#cccccc;--awb-background-color:#ffffff;--awb-divider-color:#e0dede;--awb-divider-hover-color:#e0dede;--awb-icon-color:#ffffff;--awb-title-color:#03a9f4;--awb-content-color:#212121;--awb-icon-box-color:#d4d8e0;--awb-toggle-hover-accent-color:#002344;--awb-title-font-family:&quot;Mulish&quot;;--awb-title-font-weight:regular;--awb-title-font-style:normal;--awb-title-font-size:54px;--awb-title-line-height:1.5;--awb-content-font-family:&quot;Mulish&quot;;--awb-content-font-style:normal;--awb-content-font-weight:400;\"><div class=\"panel-group fusion-toggle-icon-boxed\" id=\"accordion-408-3\"><div class=\"fusion-panel panel-default panel-c8d43d41d2bc6002f fusion-toggle-has-divider\" style=\"--awb-title-color:#03a9f4;--awb-content-color:#212121;\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_c8d43d41d2bc6002f\"><a aria-expanded=\"false\" aria-controls=\"c8d43d41d2bc6002f\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-408-3\" data-target=\"#c8d43d41d2bc6002f\" href=\"#c8d43d41d2bc6002f\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Briefing and Policy papers<\/span><\/a><\/h4><\/div><div id=\"c8d43d41d2bc6002f\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_c8d43d41d2bc6002f\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<ul>\n<li>Benton J, Jimenez J.I., Banks A., Romain C., Lee K.Y., Lee P.H., Wright S., Kakadellis S. and von Holstein I. Using microbes for the removal of microplastics from waste-water and sewage sludge. Institute of Molecular Science and Engineering (2024). (<a href=\"https:\/\/spiral.imperial.ac.uk\/handle\/10044\/1\/108242\">pdf<\/a>)<\/li>\n<\/ul>\n<\/div><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"100-width.php","meta":{"footnotes":""},"class_list":["post-408","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=\/wp\/v2\/pages\/408","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=408"}],"version-history":[{"count":27,"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=\/wp\/v2\/pages\/408\/revisions"}],"predecessor-version":[{"id":939,"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=\/wp\/v2\/pages\/408\/revisions\/939"}],"wp:attachment":[{"href":"https:\/\/josejimenezlab.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=408"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}