{"id":450,"date":"2014-01-13T20:33:53","date_gmt":"2014-01-13T20:33:53","guid":{"rendered":"http:\/\/www.hmc.edu\/biology\/?page_id=450"},"modified":"2026-07-13T09:38:52","modified_gmt":"2026-07-13T16:38:52","slug":"bush","status":"publish","type":"page","link":"https:\/\/www.hmc.edu\/biology\/faculty-staff\/bush\/","title":{"rendered":"Eliot C. Bush"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Professor of Biology<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">F.W. Olin Science Center, Room&nbsp;1240<br>301 Platt Blvd.<br>Claremont, CA 91711<br><a href=\"tel:+19096070653\" class=\"phone\">909.607.0653<\/a><br><a href=\"mailto:&#69;li&#111;t_&#66;&#117;sh&#64;h&#109;c&#46;e&#100;&#117;\">&#69;li&#111;&#116;&#95;Bu&#115;&#104;&#64;&#104;&#109;c&#46;&#101;&#100;u<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading clear\">Education and Professional Experience<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>AB, Harvard University<\/li>\n\n\n\n<li>PhD, California Institute of Technology<\/li>\n\n\n\n<li>Postdoctoral Fellow, University of Chicago<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Research Interests<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Our current work is in the area of microbial genome evolution. We&#8217;ve developed a computational approach to reconstructing the history of genomic island insertions in clades of closely related microbes (<a href=\"https:\/\/github.com\/ecbush\/xenoGI\">link to xenoGI site<\/a>). We are now improving various aspects of this method, and using it to study patterns of horizontal transfer across the tree of life. Additional information can be found at our <a title=\"Bush Lab\" href=\"https:\/\/sites.google.com\/a\/g.hmc.edu\/bushlab\/\">lab web site<\/a>.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">For a Wider Audience<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.scientificamerican.com\/article\/our-evolutionary-past-can-teach-us-about-ais-future\/\">Our Evolutionary Past Can Teach Us about AI&#8217;s Future<\/a> (Scientific American 11\/2023)<\/li>\n\n\n\n<li><a href=\"https:\/\/www.scientificamerican.com\/article\/the-meaning-of-time-in-the-place-where-humanitys-earliest-ancestors-arose\/\">The Meaning of Time in the Place where Humanity&#8217;s Earliest Ancestors Arose<\/a> (Scientific American 6\/2020)<\/li>\n\n\n\n<li>Video: <a href=\"https:\/\/youtu.be\/hFEnGanM2YE\">How do we know where the pandemic coronavirus came from?<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/eliotbush.com\/\">Website\/blog<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Teaching<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Bio 46: Introduction to biology<\/li>\n\n\n\n<li>CS5 Green: a biology themed introduction to computer science<\/li>\n\n\n\n<li>Bio 23: Biology laboratory<\/li>\n\n\n\n<li>Bio 118b: Introduction to computational biology<\/li>\n\n\n\n<li>Bio 188: Advanced computational biology<\/li>\n\n\n\n<li>Bio 129: Human evolution<\/li>\n\n\n\n<li>Writ 1: Introduction to Academic Writing<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Publications<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Books<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Momand J, and <strong>Bush E<\/strong>. <em><a href=\"https:\/\/global.oup.com\/ushe\/product\/concepts-in-bioinformatics-and-genomics-9780198882381?q=Concepts%20in%20Bioinformatics&amp;cc=us&amp;lang=en\" data-type=\"link\" data-id=\"https:\/\/global.oup.com\/ushe\/product\/concepts-in-bioinformatics-and-genomics-9780198882381?q=Concepts%20in%20Bioinformatics&amp;cc=us&amp;lang=en\">Concepts in Bioinformatics and Genomics<\/a><\/em>, 2nd ed. Oxford University Press. 2025.<\/li>\n\n\n\n<li>Libeskind-Hadas R, and <strong>Bush E<\/strong>. <em><a href=\"https:\/\/www.cambridge.org\/highereducation\/books\/computing-for-biologists\/5B08EEEE2AE8A602113A8F225E89F5FD\">Computing for Biologists: Python Programming and Principles<\/a>.<\/em> Cambridge University Press. 2014.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Selected Articles and Chapters<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>*Liu, N., *Gonzalez TA, *Fischer J, *Hong C, *Johnson M, Mawhorter R, *Mugnatto F, *Soh R, *Somji S, Wirth JS, Libeskind-Hadas R, and <strong>Bush EC<\/strong>. <a href=\"https:\/\/rdcu.be\/dhrBI\">xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes<\/a>. <em>BMC Bioinformatics.<\/em> 24(295). 2023.<\/li>\n\n\n\n<li>Wirth JS, <strong>Bush EC<\/strong>. <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkad196\">Automating microbial taxonomy workflows with PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes<\/a>. <em>Nucleic Acids Research<\/em>. 51(7). 2023.<\/li>\n\n\n\n<li>*Liu J, Mawhorter R, *Liu N, *Santichaivekin S, <strong>Bush E<\/strong>, Libeskind-Hadas R. <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8340394\/\">Maximum Parsimony Reconciliation in the DTLOR Model<\/a>. <em>BMC Bioinformatics<\/em>. 22(394). 2021.<\/li>\n\n\n\n<li><strong>Bush EC<\/strong>, Adolph SC, Donaldson-Matasci MC, Hur JH, and Schulz D. <a href=\"https:\/\/www.nsta.org\/journal-college-science-teaching\/journal-college-science-teaching-januaryfebruary-2021-1\">Incorporating Programming, Modeling and Data Analysis into an Introductory Biology Course.<\/a> Journal of College Science Teaching. 50(3). 2021. [<a aria-label=\"PDF of Incorporating Programming, Modeling and Data Analysis into an Introductory Biology Course\" href=\"https:\/\/drive.google.com\/file\/d\/1dmxpRaqp3jPHg-kvKaskGDl4jxTH58aK\/view?usp=sharing\">PDF<\/a>]<\/li>\n\n\n\n<li><strong>Bush EC<\/strong>, *Clark AE, *DeRanek CA, *Eng A, *Forman J, *Heath K, *Lee AB, Stoebel DM, *Wang Z, *Wilber M, *Wu H. <a href=\"https:\/\/doi.org\/10.1186\/s12859-018-2038-0\">xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria<\/a>.&nbsp;<em>BMC Bioinformatics.<\/em> 19(32). 2018. [<a aria-label=\"bioRxiv preprint of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria\" href=\"http:\/\/www.biorxiv.org\/content\/early\/2017\/09\/14\/188599\">bioRxiv preprint<\/a>]<\/li>\n\n\n\n<li>*Wong GT, Bonocora RP, *Schep AN, *Beeler SM, Fong AJ, *Shull LM, Batachari LE, *Dillon M, Evans C, *Becker CJ, <strong>Bush EC<\/strong>, Hardin J, Wade JT, and Stoebel DM. Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. <em>J Bacteriol<\/em>. 199:e00755-16. 2017.<\/li>\n\n\n\n<li>Drewell, RA, <strong>Bush EC<\/strong>, Remnant EJ, *Wong GT, *Beeler SM, *Stringham JL, Lim J, Gouldie F, and Oldroyd BP. The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera. <em>Development<\/em>. 141(13):2702-11. 2014.<\/li>\n\n\n\n<li>*Beeler, SM, *Wong GT, Zheng JM, <strong>Bush EC<\/strong>, Remnant EJ, Oldroyd BP, and Drewell RA. Whole Genome DNA Methylation Profile of the Jewel Wasp (Nasonia vitripennis). <em>G3: Genes Genomes Genetics<\/em>, g3-113. 2013.<\/li>\n\n\n\n<li><strong>Bush EC<\/strong>, Clark AE*, DeBoever CM*, Haynes LE*, Hussain S*, Ma S*, McDermott MM*, Novak AM*, Wentworth JS*. (2012) <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0048920\">Modeling the Role of Negative Cooperativity in Metabolic Regulation and Homeostasis<\/a>.&nbsp;<i>PLoS ONE <\/i><strong>7<\/strong>(11): e48920.<\/li>\n\n\n\n<li>Nevarez PA*, DeBoever CM*, Freeland B*J, Quitt MA* &amp;&nbsp;<strong>Bush EC<\/strong>. <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/11\/462\">Context dependent substitution biases vary within the human genome<\/a>.&nbsp;<i>BMC Bioinformatics<\/i>,&nbsp;<strong>11<\/strong>(462). 2010.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">* undergraduate author<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/scholar.google.com\/citations?user=wJVvfR8AAAAJ&amp;hl=en&amp;authuser=1\">Complete publication list<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Professor of Biology F.W. Olin Science Center, Room&nbsp;1240301 Platt Blvd.Claremont, CA 91711909.607.0653El&#105;o&#116;&#95;&#66;us&#104;&#64;&#104;mc&#46;&#101;&#100;u Education and Professional Experience Research Interests Our current [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":2119,"parent":8,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-450","page","type-page","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/pages\/450","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/comments?post=450"}],"version-history":[{"count":11,"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/pages\/450\/revisions"}],"predecessor-version":[{"id":2155,"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/pages\/450\/revisions\/2155"}],"up":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/pages\/8"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/media\/2119"}],"wp:attachment":[{"href":"https:\/\/www.hmc.edu\/biology\/wp-json\/wp\/v2\/media?parent=450"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}