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<!DOCTYPE html>
<html lang="en-US">
<head>
<meta name="generator" content="Hugo 0.101.0" />
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
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<link rel="shortcut icon" href="https://blachlylab.github.io/img/favicon.ico" type="image/x-icon">
<link rel="canonical" href="https://blachlylab.github.io/">
<title>Blachly Lab</title>
</head>
<body>
<div class="home-anchor" id="home"></div>
<nav class="navbar navbar-default navbar-fixed-top" id="navbar-main">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<div class="navbar-brand">
<a class="logo" href="">
<img src="https://blachlylab.github.io/img/lab_logo.png" alt="University logo"></img>
</a>
<a href="">Blachly Lab</a>
</div>
</div>
<div class="collapse navbar-collapse" id="#navbar-collapse-1">
<ul class="nav navbar-nav navbar-right">
<li class="nav-item"><a data-scroll href="https://blachlylab.github.io/#top">Home</a></li>
<li class="nav-item"><a data-scroll href="https://blachlylab.github.io/research">Research</a></li>
<li class="nav-item"><a data-scroll href="https://blachlylab.github.io/#publications">Publications</a></li>
<li class="nav-item"><a data-scroll href="https://blachlylab.github.io/#projects">Projects</a></li>
<li class="nav-item"><a data-scroll href="https://blachlylab.github.io/#members">Members</a></li>
<li class="nav-item"><a data-scroll href="https://blachlylab.github.io/#posts">Blog</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Join us <span class="caret"></span></a>
<ul class="dropdown-menu">
<li><a href="">Internships</a></li>
<li><a href="">Vacancies</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Software <span class="caret"></span></a>
<ul class="dropdown-menu">
<li><a href="https://github.com/blachlylab/dhtslib">dhtslib</a></li>
<li><a href="https://github.com/blachlylab/fade">fade</a></li>
<li><a href="https://github.com/blachlylab/fishnet">fishnet</a></li>
<li><a href="https://github.com/blachlylab/maskerade">maskerade</a></li>
<li><a href="https://github.com/blachlylab/mucor3">mucor3</a></li>
<li><a href="https://github.com/blachlylab/nopilesum">nopilesum</a></li>
<li><a href="https://github.com/blachlylab/recontig">recontig</a></li>
<li><a href="https://github.com/blachlylab/SABER">SABER</a></li>
<li><a href="https://github.com/blachlylab/swiftover">swiftover</a></li>
</ul>
</li>
<li class="nav-item"><a data-scroll href="https://blachlylab.github.io/#contact">Contact</a></li>
</ul>
</div>
</div>
</nav>
<header class="space-below ">
<div class="header-content">
<div class="header-content-inner">
<h1>
<i class="img/lab_logo.png"></i>
BLACHLY LAB
</h1>
<p class="slogan-text">
Leverage emerging genome technologies to advance the understanding and treatment of leukemia
</p>
<div class="container-fluid">
<div class="row">
<div class="col-xs-12 col-md-4">
<h3>About</h3>
<p class="slogan-column">We pride ourselves on using the most cutting edge technologies to aid in research of leukemia. Our hope is the research we do directly impacts the understanding and treatment of leukemia, generating better outcomes for patients in the future. Checkout more about our tools on our GitHub or checkout what the lab has been up to in our Blog.</p>
</div>
<div class="col-xs-12 col-md-4">
<h3>Mission</h3>
<p class="slogan-column">The Blachly Lab’s mission is to advance research in understanding the role genetics and genomics play in the development, progression and treatment of blood cancers — especially acute myeloid leukemia (AML) and chronic lymphocytic leukemia (CLL) — and return that information back to the clinic, informing the design of future clinical trials to improve patient care.</p>
</div>
<div class="col-xs-12 col-md-4">
<h3>Approach</h3>
<p class="slogan-column">Members of the lab collaborate broadly with other scientists to help use bioinformatics and computational biology to answer important questions about cancer - a majority of this collaborative work also focused in leukemia. Software developed in the lab is broadly applicable in cancer research aiding in the lab’s own leukemia-focused work; we use our tools and those of the scientific community to examine functional genomic biomarkers from clinical trials to help inform contemporary treatment and guide the development of future therapeutics.</p>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-md-4">
<a href="https://blachlylab.github.io/about">Meet the team</a>
</div>
<div class="col-xs-12 col-md-4">
<a href="https://blachlylab.github.io/mission">Read more</a>
</div>
<div class="col-xs-12 col-md-4">
<a href="https://blachlylab.github.io/approach">Read more</a>
</div>
</div>
</div>
</div>
</div>
</header>
<section id="projects" class="home-section">
<div class="container">
<div class="row">
<div class="col-xs-12 col-md-12 section-heading">
<h1><a href="https://blachlylab.github.io/project/">Projects</a></h1>
</div>
</div>
<div class="row">
<div class="hidden-xs col-md-2">
<a href=https://blachlylab.github.io/project/tools/>
<div class="project-picture"></div>
</a>
</div>
<div class="visible-xs col-xs-5">
<a href=https://blachlylab.github.io/project/tools/>
<div class="project-picture"></div>
</a>
</div>
<div class="article-list-item">
<div class="col-xs-7 col-md-10">
</div>
<div class="col-xs-12 col-md-10">
<p class="article-style" itemprop="articleBody">
Assortment of tools developed in the Blachly Lab including (but not exlusive to) DHtslib, Fade, Swiftover, Mucor3, and Recontig
</p>
<p class="read-more">
<a href="https://blachlylab.github.io/project/tools/" class="btn btn-primary btn-outline">
Read more
</a>
</p>
</div>
</div>
</div>
<div class="row">
<div class="hidden-xs col-md-2">
<a href=https://blachlylab.github.io/project/finished/>
<div class="project-picture"></div>
</a>
</div>
<div class="visible-xs col-xs-5">
<a href=https://blachlylab.github.io/project/finished/>
<div class="project-picture"></div>
</a>
</div>
<div class="article-list-item">
<div class="col-xs-7 col-md-10">
</div>
<div class="col-xs-12 col-md-10">
<p class="article-style" itemprop="articleBody">
Finished Research Projects
</p>
<p class="read-more">
<a href="https://blachlylab.github.io/project/finished/" class="btn btn-primary btn-outline">
Read more
</a>
</p>
</div>
</div>
</div>
<div class="row">
<div class="hidden-xs col-md-2">
<a href=https://blachlylab.github.io/project/research/>
<div class="project-picture"></div>
</a>
</div>
<div class="visible-xs col-xs-5">
<a href=https://blachlylab.github.io/project/research/>
<div class="project-picture"></div>
</a>
</div>
<div class="article-list-item">
<div class="col-xs-7 col-md-10">
</div>
<div class="col-xs-12 col-md-10">
<p class="article-style" itemprop="articleBody">
Ongoing Projects and Collaborations
</p>
<p class="read-more">
<a href="https://blachlylab.github.io/project/research/" class="btn btn-primary btn-outline">
Read more
</a>
</p>
</div>
</div>
</div>
<div>
</div>
</div>
</section>
<section id="publications" class="home-section">
<div class="container">
<div class="row">
<div class="col-xs-12 col-md-4 section-heading">
<h1><a href="https://blachlylab.github.io/publication/">Publications</a></h1>
</div>
<div class="col-xs-12 col-md-8">
<div class="pub-list-item" itemscope itemtype="http://schema.org/CreativeWork">
<div class="row">
<div class="col-md-12">
<h3 class="article-title" itemprop="name">
<a href="https://blachlylab.github.io/publication/humu.24304/" itemprop="url">HOXD13 alterations in synpolydactyly</a>
</h3>
<div class="pub-authors" itemprop="author">
<div itemprop="author">
<span class="author-name">
Marilena Melas
</span>,
<span class="author-name">
Esko Kautto
</span>,
<span class="author-name">
Samuel J. Franklin
</span>,
<span class="author-name">
Mari Mori
</span>,
<span class="author-name">
Kim L. McBride
</span>,
<span class="author-name">
Theresa Mihalic Mosher
</span>,
<span class="author-name">
Ruthann B. Pfau
</span>,
<span class="author-name">
Maria Elena Hernandez‐Gonzalez
</span>,
<span class="author-name">
Sean D. McGrath
</span>,
<span class="author-name">
Peter White
</span>,
<span class="author-name">
Julie Balch Samora
</span>,
<span class="author-name">
Daniel C. Koboldt
</span>,
<span class="author-name">
Richard K. Wilson
</span>
</div>
</div>
<div class="pub-publication">
Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly
<div itemprop="datePublished">
November, 2021
</div>
</div>
<div class="pub-links">
<a class="btn btn-primary btn-outline btn-xs" href="https://blachlylab.github.io/publication/humu.24304/">Details</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://onlinelibrary.wiley.com/doi/epdf/10.1002/humu.24304">PDF</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://blachlylab.github.io/project/research">Project</a>
</div>
</div>
</div>
</div>
<div class="pub-list-item" itemscope itemtype="http://schema.org/CreativeWork">
<div class="row">
<div class="col-md-12">
<h3 class="article-title" itemprop="name">
<a href="https://blachlylab.github.io/publication/blood-2021-153812/" itemprop="url">VIP152 Is a Novel CDK9 Inhibitor with Efficacy in Chronic Lymphocytic Leukemia</a>
</h3>
<div class="pub-authors" itemprop="author">
<div itemprop="author">
<span class="author-name">
Steven Sher
</span>,
<span class="author-name">
Larry Beaver
</span>,
<span class="author-name">
Katie Williams
</span>,
<span class="author-name">
Shelley Orwick
</span>,
<span class="author-name">
Brandi R. Walker
</span>,
<span class="author-name">
Charles Thomas Gregory
</span>,
<span class="author-name">
Matthew Purcell
</span>,
<span class="author-name">
Alexander Pan
</span>,
<span class="author-name">
Pearlly S. Yan
</span>,
<span class="author-name">
Amy J. Johnson
</span>,
<span class="author-name">
Melanie M. Frigault
</span>,
<span class="author-name">
Joy M. Greer
</span>,
<span class="author-name">
Ahmed Hamdy
</span>,
<span class="author-name">
Raquel Izumi
</span>,
<span class="author-name">
Stuart Hwang
</span>,
<span class="author-name">
James S. Blachly
</span>,
<span class="author-name">
John C. Byrd
</span>,
<span class="author-name">
Rosa Lapalombella
</span>
</div>
</div>
<div class="pub-publication">
VIP152 Is a Novel CDK9 Inhibitor with Efficacy in Chronic Lymphocytic Leukemia
<div itemprop="datePublished">
November, 2021
</div>
</div>
<div class="pub-links">
<a class="btn btn-primary btn-outline btn-xs" href="https://blachlylab.github.io/publication/blood-2021-153812/">Details</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://ashpublications.org/blood/article/138/Supplement%201/270/479541/VIP152-Is-a-Novel-CDK9-Inhibitor-with-Efficacy-in">PDF</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://blachlylab.github.io/project/research">Project</a>
</div>
</div>
</div>
</div>
<div class="pub-list-item" itemscope itemtype="http://schema.org/CreativeWork">
<div class="row">
<div class="col-md-12">
<h3 class="article-title" itemprop="name">
<a href="https://blachlylab.github.io/publication/40478-021-01164-z/" itemprop="url">Molecular classification of a complex structural rearrangement of the RB1 locus</a>
</h3>
<div class="pub-authors" itemprop="author">
<div itemprop="author">
<span class="author-name">
Kathleen M. Schieffer
</span>,
<span class="author-name">
Alexander Z. Feldman
</span>,
<span class="author-name">
Esko A. Kautto
</span>,
<span class="author-name">
Sean McGrath
</span>,
<span class="author-name">
Anthony R. Miller
</span>,
<span class="author-name">
Maria Elena Hernandez-Gonzalez
</span>,
<span class="author-name">
Stephanie LaHaye
</span>,
<span class="author-name">
Katherine E. Miller
</span>,
<span class="author-name">
Daniel C. Koboldt
</span>,
<span class="author-name">
Patrick Brennan
</span>,
<span class="author-name">
Benjamin Kelly
</span>,
<span class="author-name">
Amy Wetzel
</span>,
<span class="author-name">
Vibhuti Agarwal
</span>,
<span class="author-name">
Margaret Shatara
</span>,
<span class="author-name">
Suzanne Conley
</span>,
<span class="author-name">
Diana P. Rodriguez
</span>,
<span class="author-name">
Rolla Abu-Arja
</span>,
<span class="author-name">
Ala Shaikhkhalil
</span>,
<span class="author-name">
Matija Snuderl
</span>,
<span class="author-name">
Brent A. Orr
</span>,
<span class="author-name">
Jonathan L. Finlay
</span>,
<span class="author-name">
Diana S. Osorio
</span>,
<span class="author-name">
Annie I. Drapeau
</span>,
<span class="author-name">
Jeffrey R. Leonard
</span>,
<span class="author-name">
Christopher R. Pierson
</span>,
<span class="author-name">
Peter White
</span>,
<span class="author-name">
Vincent Magrini
</span>,
<span class="author-name">
Elaine R. Mardis
</span>,
<span class="author-name">
Richard K. Wilson
</span>,
<span class="author-name">
Catherine E. Cottrell
</span>,
<span class="author-name">
Daniel R. Boué
</span>
</div>
</div>
<div class="pub-publication">
Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly
<div itemprop="datePublished">
April, 2021
</div>
</div>
<div class="pub-links">
<a class="btn btn-primary btn-outline btn-xs" href="https://blachlylab.github.io/publication/40478-021-01164-z/">Details</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://actaneurocomms.biomedcentral.com/track/pdf/10.1186/s40478-021-01164-z.pdf">PDF</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://blachlylab.github.io/project/research">Project</a>
</div>
</div>
</div>
</div>
<div class="pub-list-item" itemscope itemtype="http://schema.org/CreativeWork">
<div class="row">
<div class="col-md-12">
<h3 class="article-title" itemprop="name">
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</h3>