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118 119 var css = 'html { -webkit-transition: margin-top 1s; transition: margin-top 1s; } /* 9001 */ html { margin-top: 46px !important; } * html body { margin-top: 46px !important; } @media screen and ( max-width: 660px ) { html { margin-top: 71px !important; } * html body { margin-top: 71px !important; } #wpcom_request_access_iframe { display: block; height: 71px !important; } } #wpcom_request_access_iframe { border: 0px; height: 46px; position: fixed; top: 0; left: 0; width: 100%; min-width: 100%; z-index: 99999; background: #23282d; } '; 120 121 var style = document.createElement( 'style' ); 122 style.type = 'text/css'; 123 style.id = 'wpcom_request_access_styles'; 124 style.appendChild( document.createTextNode( css ) ); 125 document.body.appendChild( style ); 126 127 document.body.appendChild( iframe ); 128 } 129 130 if ( data.msg === 'DONE' ) { 131 wpcom_remote_login_final_cleanup(); 132 } 133 } 134}, false ); 135 136// Inject the remote login iframe after the page has had a chance to load 137// more critical resources 138window.addEventListener( "DOMContentLoaded", function( e ) { 139 var iframe = document.createElement( "iframe" );
140 iframe.style.display = "none"; 141 iframe.setAttribute( "scrolling", "no" ); 142 iframe.setAttribute( "id", "wpcom_remote_login_key" ); 143 iframe.src = "https://r-login.wordpress.com/remote-login.php" 144 + "?wpcom_remote_login=key" 145 + "&origin=aHR0cHM6Ly9icnVua2xhYi5vcmc%3D" 146 + "&wpcomid=60109915" 147 + "&time=" + Math.floor( Date.now() / 1000 ); 148 document.body.appendChild( iframe ); 149}, false ); 150</script>
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411 </div></nav> 412 413 414<div class="wp-block-media-text alignfull has-media-on-the-right is-stacked-on-mobile a8c-section has-background-light-background-color has-background" style="grid-template-columns:auto 22%"><div class="wp-block-media-text__content"> 415<div class="wp-block-jetpack-layout-grid alignfull column1-desktop-grid__span-9 column1-desktop-grid__start-2 column1-desktop-grid__row-1 column1-tablet-grid__span-8 column1-tablet-grid__row-1 column1-mobile-grid__span-4 column1-mobile-grid__row-1"> 416<div class="wp-block-jetpack-layout-grid-column wp-block-jetpack-layout-grid__padding-none"> 417<h2 class="wp-block-heading a8c-section-title">Welcome to the Brunk Lab!</h2> 418 419 420 421<p class="a8c-section-text wp-block-paragraph">Iâm Liz Brunk, a computational chemist turned genome scientist and AI enthusiast. Here you can learn about my scientific journey, research program, and the broader community and educational efforts that shape my work.</p> 422 423 424 425<h6 class="wp-block-heading a8c-section-link-text"><em>First time to the site? <a href="https://brunklab.org/">Start here</a></em></h6> 426</div> 427</div> 428</div><figure class="wp-block-media-text__media"><a href="https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg"><img data-attachment-id="1443" data-permalink="https://brunklab.org/team/img_1645/" data-orig-file="https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg" data-orig-size="686,1044" data-comments-opened="0" data-image-meta="{"orientation":"1"}" data-image-title="img_1645" data-image-description="" data-image-caption="" data-large-file="https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg?w=673" width="673" height="1024" src="https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg?w=673" alt="" class="wp-image-1443 size-full" srcset="https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg?w=673 673w, https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg?w=99 99w, https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg?w=197 197w, https://brunklab.org/wp-content/uploads/2023/01/img_1645.jpg 686w" sizes="(max-width: 673px) 100vw, 673px" /></a></figure></div> 429 430 431 432<div style="height:32px" aria-hidden="true" class="wp-block-spacer"></div> 433 434 435 436<div class="wp-block-media-text alignfull is-stacked-on-mobile a8c-section has-background-light-background-color has-background" style="grid-template-columns:38% auto"><figure class="wp-block-media-text__media"><a href="https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg"><img data-attachment-id="1734" data-permalink="https://brunklab.org/team/img_2269/" data-orig-file="https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg" data-orig-size="1098,834" data-comments-opened="0" data-image-meta="{"orientation":"1"}" data-image-title="img_2269" data-image-description="" data-image-caption="" data-large-file="https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg?w=750" width="750" height="569" src="https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg?w=750" alt="" class="wp-image-1734 size-full" srcset="https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg?w=750 750w, https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg?w=150 150w, https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg?w=300 300w, https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg?w=768 768w, https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg?w=1024 1024w, https://brunklab.org/wp-content/uploads/2023/12/img_2269.jpg 1098w" sizes="(max-width: 750px) 100vw, 750px" /></a></figure><div class="wp-block-media-text__content"> 437<div class="wp-block-jetpack-layout-grid alignfull column1-desktop-grid__span-9 column1-desktop-grid__start-2 column1-desktop-grid__row-1 column1-tablet-grid__span-8 column1-tablet-grid__row-1 column1-mobile-grid__span-4 column1-mobile-grid__row-1"> 438<div class="wp-block-jetpack-layout-grid-column wp-block-jetpack-layout-grid__padding-none"> 439<h4 class="wp-block-heading a8c-section-title">Educational Path</h4> 440 441 442 443<p class="wp-block-paragraph">Liz earned her <strong>B.S. in Chemistry from the University of Michigan, Ann Arbor</strong>, followed by a <strong>Masterâs in Physical Chemistry from Ãcole Normale Supérieure </strong> and a <strong>Ph.D. from EPFL</strong>. She completed postdoctoral training at UC Berkeley and <strong>UC San Diego</strong>, working in the laboratories of <strong>Jay Keasling</strong>,<strong> Bernhard Palsson</strong> and <strong>Pablo Tamayo</strong> in systems genomics. She also gained industry research experience at <strong>Celgene (now Bristol Myers Squibb)</strong>.</p> 444 445 446 447<h4 class="wp-block-heading a8c-section-subtitle">Find me on:</h4> 448 449 450 451<ul class="wp-block-social-links is-content-justification-center is-layout-flex wp-container-core-social-links-is-layout-3e41869c wp-block-social-links-is-layout-flex">
451<li class="wp-social-link wp-social-link-linkedin wp-block-social-link"><a href="https://www.linkedin.com/in/elizabeth-brunk-0527511b/" class="wp-block-social-link-anchor"><svg width="24" height="24" viewBox="0 0 24 24" version="1.1" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" focusable="false"><path d="M19.7,3H4.3C3.582,3,3,3.582,3,4.3v15.4C3,20.418,3.582,21,4.3,21h15.4c0.718,0,1.3-0.582,1.3-1.3V4.3 C21,3.582,20.418,3,19.7,3z M8.339,18.338H5.667v-8.59h2.672V18.338z M7.004,8.574c-0.857,0-1.549-0.694-1.549-1.548 c0-0.855,0.691-1.548,1.549-1.548c0.854,0,1.547,0.694,1.547,1.548C8.551,7.881,7.858,8.574,7.004,8.574z M18.339,18.338h-2.669 v-4.177c0-0.996-0.017-2.278-1.387-2.278c-1.389,0-1.601,1.086-1.601,2.206v4.249h-2.667v-8.59h2.559v1.174h0.037 c0.356-0.675,1.227-1.387,2.526-1.387c2.703,0,3.203,1.779,3.203,4.092V18.338z"></path></svg><span class="wp-block-social-link-label screen-reader-text">LinkedIn</span></a></li> 452 453<li class="wp-social-link wp-social-link-bluesky wp-block-social-link"><a href="https://@brunklab.bsky.social" class="wp-block-social-link-anchor"><svg width="24" height="24" viewBox="0 0 24 24" version="1.1" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" focusable="false"><path d="M6.3,4.2c2.3,1.7,4.8,5.3,5.7,7.2.9-1.9,3.4-5.4,5.7-7.2,1.7-1.3,4.3-2.2,4.3.9s-.4,5.2-.6,5.9c-.7,2.6-3.3,3.2-5.6,2.8,4,.7,5.1,3,2.9,5.3-5,5.2-6.7-2.8-6.7-2.8,0,0-1.7,8-6.7,2.8-2.2-2.3-1.2-4.6,2.9-5.3-2.3.4-4.9-.3-5.6-2.8-.2-.7-.6-5.3-.6-5.9,0-3.1,2.7-2.1,4.3-.9h0Z"></path></svg><span class="wp-block-social-link-label screen-reader-text">Bluesky</span></a></li></ul> 454</div> 455</div> 456</div></div> 457 458 459 460<p class="wp-block-paragraph">My research program is centered on the development of computational and experimental frameworks that integrate molecular measurements across biological scales. I was trained first in quantitative modeling and theoretical chemistry with Ursula Roethlisberger, where all-atom simulations rooted in classical Newtonian mechanics gave me a foundation in biophysics, mechanistic biochemistry, and the use of models to explain how molecular structure gives rise to biological function. This training shaped the way I approach biology: not as isolated measurements, but as systems whose behavior emerges from interacting molecular layers that can be modeled, tested, and refined through experiment.</p> 461 462 463 464<p class="wp-block-paragraph">My postdoctoral training expanded this perspective from molecules to cells and systems. In the laboratories of Bernhard Palsson and Jay Keasling, I worked in bacterial systems biology, using multi-omic measurements to understand how engineered cells regulate metabolism and adapt across conditions. I later moved into human genomics and systems biology with Pablo Tamayo, and scientific interactions with Jill Mesirov and the Broad/CCLE ecosystem, where I focused on integrating genomic, transcriptomic, proteomic, and functional datasets to understand how cells rewire in response to perturbation. During this period, I helped develop Recon3D (Nature Biotechnology 2018), which linked genomic variation, transcriptomic and proteomic data, metabolomics, and protein structural information within a human metabolic modeling framework. Across these projects, the central idea was vertical integration: connecting DNA, RNA, protein, metabolism, structure, and phenotype to build more coherent and mechanistic models of cellular behavior.</p> 465 466 467 468<p class="wp-block-paragraph">This training prepared me to recognize both the promise and the limitations of large-scale multi-omic datasets. As a T32 trainee at the Moores Cancer Center and through work with large public and private datasets, I became immersed in the depth of available molecular data across cell lines, perturbations, time points, and therapeutic conditions. My subsequent work as an industry consultant further reinforced this view. I worked with teams generating thousands of samples across DNA, RNA, proteomic, and functional assays, where the central challenge was not data generation, but interpretation: how to integrate heterogeneous measurements in a way that revealed how cells were changing state, adapting to stress, or rewiring regulatory programs. These experiences convinced me that the next major advance in the field would require frameworks that connect modalities rather than analyze them separately.</p> 469 470 471 472<p class="wp-block-paragraph">As an independent investigator, I have built my laboratory around this problem. My group develops computational and experimental approaches for integrating single-cell sequencing, imaging, and cytogenetic measurements to understand how genome structure and molecular regulation coordinate to shape cell state. We have focused on experimentally tractable human cell line systems in which individual cells from the same population exhibit measurable differences in gene dosage, chromosome structure, RNA expression, protein abundance, protein localization, and morphology. Although many of these systems contain extrachromosomal DNA, the central focus of my work is broader: to use structured within-population variation as a biological anchor for building multimodal models of cell behavior. Over the first years of my faculty position, my laboratory has deeply characterized these systems, generated single-cell multi-omic and imaging datasets across multiple scales, and developed the experimental expertise needed to validate computational predictions with orthogonal measurements. </p> 473 474 475 476<p class="wp-block-paragraph">Teaching and mentorship are also central to my scientific program. Over the past four years, I have developed interactive, Jupyter-based âlearn-by-doingâ workflows that teach coding, data literacy, and omics analysis through real biological datasets. These materials have been incorporated into UNCâs large-enrollment undergraduate biochemistry course and have reached more than 3,500 undergraduates, many with
476no prior coding experience. My recently awarded NSF CAREER project will allow my group to expand these efforts into a broader AI + BIO educational program that trains students to use machine learning, multi-omics data, and biological reasoning together. The next generation of biomedical scientists will need to understand both experimental biology and computational modeling to make sense of increasingly multimodal data.</p> 477 478 479 480<h2 class="wp-block-heading">Previous posts for the academic community:</h2> 481 482 483 484<div style="height:32px" aria-hidden="true" class="wp-block-spacer"></div> 485 486 487 488<div class="wp-block-jetpack-layout-grid alignfull column1-desktop-grid__span-12 column1-desktop-grid__row-1 column1-tablet-grid__span-8 column1-tablet-grid__row-1 column1-mobile-grid__span-4 column1-mobile-grid__row-1"> 489<div class="wp-block-jetpack-layout-grid-column wp-block-jetpack-layout-grid__padding-none"> <div 490 class="wp-block-newspack-blocks-homepage-articles alignfull wpnbha is-grid columns-3 colgap-3 show-image image-aligntop ts-4 is-3 is-square " 491 style="" 492 > 493 <div data-posts data-current-post-id="1341"> 494 495 <article data-post-id="1163" 496 class="category-uncategorized type-post" 497 > 498 499 <div class="entry-wrapper"> 500 <h2 class="entry-title"><a href="https://brunklab.org/2019/10/07/faculty-application-materials/" rel="bookmark">FACULTY APPLICATION MATERIALS</a></h2> <div class="entry-meta"> 501 <time class="entry-date published" datetime="2019-10-07T19:01:21+00:00">October 7, 2019</time><time class="updated" datetime="2021-03-16T15:27:08+00:00">March 16, 2021</time> </div><!-- .entry-meta --> 502 </div><!-- .entry-wrapper --> 503 </article> 504 505 506 <article data-post-id="351" 507 class="tag-grant-writing tag-k99 tag-nih tag-research-proposal tag-timeline tag-tips category-blog-posts type-post" 508 > 509 510 <div class="entry-wrapper"> 511 <h2 class="entry-title"><a href="https://brunklab.org/2016/02/12/k99-grant-advice/" rel="bookmark">Structured timeline for the K99/R00 award</a></h2> <div class="entry-meta"> 512 <time class="entry-date published" datetime="2016-02-12T06:06:15+00:00">February 12, 2016</time><time class="updated" datetime="2019-08-08T06:12:10+00:00">August 8, 2019</time> </div><!-- .entry-meta --> 513 </div><!-- .entry-wrapper --> 514 </article> 515 516 </div> 517 518 </div> 519 </div> 520</div> 521 522 523 524<div class="wp-block-cover alignfull has-parallax a8c-background" style="min-height:100vh;aspect-ratio:unset;"><div class="wp-block-cover__image-background wp-image-1380 size-large has-parallax" style="background-position:50% 50%;background-image:url(https://brunklab.org/wp-content/uploads/2021/03/pexels-photo-2080963.jpeg?w=750)"></div><span aria-hidden="true" class="wp-block-cover__background has-background-dim" style="background-color:#7c5d44"></span><div class="wp-block-cover__inner-container is-layout-flow wp-block-cover-is-layout-flow"> 525<h2 class="wp-block-heading a8c-text-title">New posts in your inbox</h2> 526 527 528 <div class="wp-block-jetpack-subscriptions__supports-newline wp-block-jetpack-subscriptions"> 529 <div class="wp-block-jetpack-subscriptions__container is-not-subscriber"> 530 <form 531 action="https://wordpress.com/email-subscriptions" 532 method="post" 533 accept-charset="utf-8" 534 data-blog="60109915" 535 data-post_access_level="everybody" 536 data-subscriber_email="" 537 id="subscribe-blog" 538 > 539 <div class="wp-block-jetpack-subscriptions__form-elements"> 540 <p id="subscribe-email"> 541 <label 542 id="subscribe-field-label" 543 for="subscribe-field" 544 class="screen-reader-text" 545 > 546 Enter your email address </label> 547 <input 548 required="required" 549 type="email" 550 name="email" 551 autocomplete="email" 552 class="no-border-radius has-undefinedpx-font-size " 553 style="font-size: undefinedpx;padding: 15px 23px 15px 23px;border-radius: 0px;border-width: 1px;border-color: #010101; 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