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Publications.html
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<li><a href="index.html">Homepage</a></li>
<li><a href="Research.html">Research</a></li>
<li><a href="Team.html">Team</a></li>
<li class="active"><a href="Publications.html">Publications</a></li>
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<h2><BR></h2>
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<ul class="style">
<li>
<p class="posted">April 2019</p>
<img src="images/Karen.cover.tif.jpg" alt="" width="141" height="184" />
<p class="text">Chromatin landscape of butterfly wing metamorphosis.</p>
</li>
<li>
<p class="posted">October 2015</p>
<img src="images/Kurpios.cover.tif_covlowres.png" alt="" width="141" height="184" />
<p class="text">CTCF- and Pitx2-dependent asymmetry mirrors embryonic gut laterality.</p>
</li>
<li>
<p class="posted">April 2013</p>
<img src="images/S1097276513X00097_covlowres.jpg" alt="" width="141" height="184" />
<p class="text">Measuring elongation rates using GRO-seq.</p>
</li>
<li>
<p class="posted">June 2012</p>
<img src="images/eva.cover_jvc.gif" alt="" width="141" height="184" />
<p class="text">Ultrastructural changes in canine ARVC heart tissue.</p>
</li>
<li>
<p class="posted">February 2010</p>
<img src="images/kb1.cover_nature.jpg" alt="" width="141" height="184" />
<p class="text">Khoisan and Bantu genome sequencing and analysis.</p>
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<header>
<h2>Publications</h2>
<p><strong>Publications (<strong>* denotes equal contribution</strong>)(Danko lab members <span class="cgd">underlined</span>.)</strong> <a title="Pubmed" href="https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D&sort=date">[Pubmed]</a><a title="Google Scholar" href="http://scholar.google.com/citations?user=OQAuVuoAAAAJ&hl=en">[Google Scholar]</a></p>
</header>
<ul class="publist">
<li>
<span class="date"> Preprints </span>
<br>
<span class="papers">
<strong>Evolution of promoter-proximal pausing enabled a new layer of transcription control.</strong> <br>
<span class="cgd">Chivu AG</span>, Abuhashem A, <span class="cgd">Barshad G</span>, <span class="cgd">Rice EJ</span>, Leger MA, Vill AC, Wong W, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, <span class="cgd">Lewis JJ</span>, <span class="cgd">Danko CG</span>.<br>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2023.02.19.529146v1">bioRxiv.</a>
<BR><BR>
<strong>CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters.</strong> <br>
Marks BG, <span class="cgd">Choate LA</span>, Sams K, <span class="cgd">Zhu L</span>, <span class="cgd">Waidyaratne G</span>, <span class="cgd">Danko CG</span>, Coonrod SA.<br>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2022.08.22.504845v1">bioRxiv.</a>
<BR><BR>
<strong>The Long Noncoding RNA Playrr Regulates Pitx2 Dosage and Protects Against Cardiac Arrhythmias.</strong> <br>
Chen FL, Oxford EM, <span class="cgd">Chou SP</span>, Li N, Leach JP, Perry SK, Sanketi BD, Cong C, Kupiec-Weglinski SA, Dubowitz R, Daugherity E, Martin JF, <span class="cgd">Danko CG</span>, Kurpios NA.<br>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2022.09.20.508562v1">bioRxiv.</a>
<BR><BR>
<strong>RNA polymerase II and PARP1 shape enhancer-promoter contacts.</strong> <br>
<span class="cgd">Barshad G</span>, <span class="cgd">Lewis JJ</span>, <span class="cgd">Chivu AG</span>, Abuhashem A, Krietenstein N, <span class="cgd">Rice EJ</span>, Rando OJ, Hadjantonakis AK, <span class="cgd">Danko CG</span>.<br>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2022.07.07.499190v1">bioRxiv.</a>
<BR><BR>
<strong>Run-on sequencing reveals nascent transcriptomics of the human microbiome.</strong> <br>
Vill AC, <span class="cgd">Rice EJ</span>, De Vlaminck I, <span class="cgd">Danko CG</span>, Brito IL.<br>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2022.04.22.489220v1">bioRxiv.</a>
<BR><BR>
<strong>A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq).</strong> <br>
Judd J, Wojenski LA, Wainman LM, Tippens ND, <span class="cgd">Rice EJ</span>, Dziubek A, Villafano GJ, Wissink EW, Versluis P, Bagepalli L, Shah SR, Mahat DB, Tome JM, <span class="cgd">Danko CG</span>, Lis JT, Core LJ.<br>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/2020.05.18.102277">bioRxiv.</a>
<BR><BR>
</span>
</li>
<li>
<span class="date"> 2023 </span>
<br>
<span class="papers">
<strong>A-MYB and BRDT-dependent RNA Polymerase II pause release orchestrates transcriptional regulation in mammalian meiosis.</strong> <br>
<span class="cgd">Alexander AK</span>, <span class="cgd">Rice EJ</span>, Lujic J, Simon LE, Tanis S, <span class="cgd">Barshad G</span>, <span class="cgd">Zhu L</span>, <span class="cgd">Lama J</span>, Cohen PE, <span class="cgd">Danko CG</span>.<br>
<a title="[Nature Communications]" href="https://www.nature.com/articles/s41467-023-37408-w">Nature Communications.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2022.08.19.504615v2">bioRxiv.</a>
<BR><BR>
<strong>GDNF-RET signaling and EGR1 form a positive feedback loop that promotes tamoxifen resistance via cyclin D1.</strong> <br>
Marks BA, Pipia IM, Mukai C, Horibata S, <span class="cgd">Rice EJ</span>, <span class="cgd">Danko CG</span>, Coonrod SA.<br>
<a title="[BMC Cancer]" href="https://bmccancer.biomedcentral.com/articles/10.1186/s12885-023-10559-1">BMC Cancer.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2022.05.31.492660v1">bioRxiv.</a>
<BR><BR>
<strong>Mapping Transcription Regulation with Run-on and Sequencing Data Using the Web-Based tfTarget Gateway.</strong> <br>
Wang N, Wang Z, <span class="cgd">Danko CG</span>, Chu T.<br>
<a title="[Methods Mol Biol.]" href="https://link.springer.com/protocol/10.1007/978-1-0716-2847-8_15">Methods Mol Biol.</a>
<BR><BR>
</li>
<li>
<span class="date"> 2022 </span>
<br>
<span class="papers">
<strong>Comprehensive microRNA analysis across genome-edited colorectal cancer organoid models reveals miR-24 as a candidate regulator of cell survival.</strong> <br>
<span class="cgd">Villanueva JW</span>, Kwong L, Han T, Martinez SA, Shanahan MT, Kanke M, Dow LE, <span class="cgd">Danko CG</span>, Sethupathy P.<br>
<a title="[BMC Genomics]" href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-09018-1">BMC Genomics.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2021.12.13.472432v1">bioRxiv.</a>
<BR><BR>
<strong>RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription.</strong> <br>
Abuhashem A, <span class="cgd">Chivu AG</span>, Zhao Y, <span class="cgd">Rice EJ</span>, Siepel A, <span class="cgd">Danko CG</span>, Hadjantonakis AK.<br>
<a title="[G&D]" href="http://genesdev.cshlp.org/content/36/13-14/770.abstract">Genes & Development.</a>
<BR><BR>
<strong>Genetic Dissection of the RNA Polymerase II Transcription Cycle.</strong> <br>
<span class="cgd">Chou SP</span>, <span class="cgd">Alexander AK</span>, <span class="cgd">Rice EJ</span>, <span class="cgd">Choate LA</span>, <span class="cgd">Danko CG</span>.<br>
<a title="[eLife]" href="https://elifesciences.org/articles/78458">eLife.</a>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/2021.05.23.445279">bioRxiv.</a>
<BR><BR>
<strong>Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology.</strong> <br>
<span class="cgd">Chu T</span>, <span class="cgd">Wang Z</span>, Pe'er D, <span class="cgd">Danko CG</span>.<br>
<a title="[Nature Cancer]" href="https://www.nature.com/articles/s43018-022-00356-3">Nature Cancer.</a>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/2020.01.07.897900">bioRxiv.</a>
<BR><BR>
<strong>SETD2 haploinsufficiency enhances germinal center-associated AICDA somatic hypermutation to drive B cell lymphomagenesis.</strong> <br>
Leung W, Teater M, Durmaz C, Meydan C, <span class="cgd">Chivu AG</span>, Chadburn A, <span class="cgd">Rice EJ</span>, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, <span class="cgd">Danko CG</span>, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM.<br>
<a title="[Cancer Discovery]" href="https://aacrjournals.org/cancerdiscovery/article-abstract/doi/10.1158/2159-8290.CD-21-1514/694637/SETD2-haploinsufficiency-enhances-germinal-center?redirectedFrom=fulltext">Cancer Discovery.</a>
<BR><BR>
<strong>Prediction of histone post-translational modification patterns based on nascent transcription data.</strong> <br>
<span class="cgd">Wang Z</span>, <span class="cgd">Chivu AG</span>, <span class="cgd">Choate LA</span>, <span class="cgd">Rice EJ</span>, Miller DC, <span class="cgd">Chu T</span>, <span class="cgd">Chou S</span>, Kingsley NB, Petersen JL, Finno CJ, Bellone RR, Antczak DF, Lis JT, <span class="cgd">Danko CG</span>.<br>
<a title="[Nature Genetics]" href="https://www.nature.com/articles/s41588-022-01026-x">Nature Genetics.</a>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/2020.04.08.032730">bioRxiv.</a>
<BR><BR>
<strong>E-Protein Inhibition in ILC2 Development Shapes the Function of Mature ILC2s during Allergic Airway Inflammation.</strong> <br>
<span class="cgd">Barshad G</span>, Webb LM, Ting HA, Oyesola OO, Onyekwere OG, Lewis JJ, Rice EJ, Matheson MK, Sun XH, von Moltke J, <span class="cgd">Danko CG</span>, Tait Wojno ED.<br>
<a title="[Journal of Immunology]" href="https://www.jimmunol.org/content/208/5/1007.long">Journal of Immunology.</a>
<BR><BR>
<strong>Darwinian genomics and diversity in the tree of life.</strong> <br>
Stephan T, Burgess SM, Cheng H, <span class="cgd">Danko CG</span>, Gill CA, Jarvis ED, Koepfli KP, Koltes JE, Lyons E, Ronald P, Ryder OA, Schriml LM, Soltis P, VandeWoude S, Zhou H, Ostrander EA, Karlsson EK.<br>
<a title="[PNAS]" href="https://www.pnas.org/content/119/4/e2115644119.long">Proc Natl Acad Sci U S A.</a>
<BR><BR>
</span>
</li>
<li>
<span class="date"> 2021 </span>
<br>
<span class="papers">
<strong>Multiple stages of evolutionary change in anthrax toxin receptor expression in humans.</strong> <br>
<span class="cgd">Choate LA</span>, <span class="cgd">Barshad G</span>, <span class="cgd">McMahon PW</span>, <span class="cgd">Said I</span>, <span class="cgd">Rice EJ</span>, <span class="cgd">Munn PR</span>, <span class="cgd">Lewis JJ</span>, <span class="cgd">Danko CG</span>.<br>
<a title="[Nature Communications]" href="https://www.nature.com/articles/s41467-021-26854-z">Nature Communications.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2020.07.29.227660v1">bioRxiv.</a>
<BR><BR>
<strong>Identification and prediction of developmental enhancers in sea urchin embryos.</strong> <br>
Arenas-Mena C, Miljovska S, <span class="cgd">Rice EJ</span>, Gurges J, Shashikant T, Ercan S, <span class="cgd">Danko CG</span>.<br>
<a title="[BMC Genomics]" href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07936-0">BMC Genomics.</a>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/2021.03.26.436886">bioRxiv.</a>
<BR><BR>
<strong>Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells.</strong> <br>
Zhao Y, Dukler N, <span class="cgd">Barshad G</span>, Toneyan S, <span class="cgd">Danko CG</span>, Siepel A.<br>
<a title="[Bioinformatics]" href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab582/6348164">Bioinformatics.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/2021.03.16.435537v1">bioRxiv.</a>
<BR><BR>
<strong>Chromosome fusion affects genetic diversity and evolutionary turnover of functional loci, but consistently depends on chromosome size.</strong> <br>
Cicconardi F, <span class="cgd">Lewis JJ</span>, Martin SH, Reed RD, <span class="cgd">Danko CG</span>, Montgomery SH.<br>
<a title="[MBE]" href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab185/6306414">Molecular Biology and Evolution.</a>
<BR><BR>
<strong>The Dryas iulia genome supports multiple gains of a W chromosome from a B chromosome in butterflies.</strong> <br>
<span class="cgd">Lewis JJ</span>, Cicconardi F, Martin SH, Reed RD, <span class="cgd">Danko CG</span>, Montgomery SH.<br>
<a title="[GBE]" href="https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evab128/6297255">Genome Biology and Evolution.</a>
<BR><BR>
<strong>Uncovering Transcriptional Dark Matter via Gene Annotation Independent Single-Cell RNA Sequencing Analysis.</strong> <br>
Wang MFZ, Mantri M, <span class="cgd">Chou SP</span>, Scuderi GJ, McKellar D, Butcher JT, <span class="cgd">Danko CG</span>, De Vlaminck I.<br>
<a title="[Nature Communications]" href="https://www.nature.com/articles/s41467-021-22496-3">Nature Communications.</a>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/2020.07.31.229575">bioRxiv.</a>
<BR><BR>
<strong>Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data.</strong> <br>
Blumberg A, Zhao Y, Huang YF, Dukler N, <span class="cgd">Rice EJ</span>, <span class="cgd">Chivu AG</span>, Krumholz K, <span class="cgd">Danko CG</span>, Siepel A.<br>
<a title="[BMC Biology]" href="https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-00949-x">BMC Biology.</a>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/690644">bioRxiv.</a>
<BR><BR>
<strong>GLP-1 receptor signaling increases PCSK1 and β cell features in human α cells.</strong> <br>
<span class="cgd">Saikia M</span>, Holter MM, Donahue LR, Lee IS, Zheng QC, Wise JL, Todero JE, Phuong DJ, Garibay D, Coch R, Sloop KW, Garcia-Ocana A, <span class="cgd">Danko CG</span>, Cummings BP.<br>
<a title="[JCI Insight]" href="https://insight.jci.org/articles/view/141851">JCI Insight.</a>
</span>
</li>
<li>
<span class="date"> 2020 </span>
<br>
<span class="papers">
<strong>Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone.</strong> <br>
<span class="cgd">Lewis JJ</span>, Van Belleghem SM, Papa R, <span class="cgd">Danko CG</span>, Reed RD. <br>
<a title="[Science Advances]" href="https://advances.sciencemag.org/content/6/39/eabb8617">Science Advances.</a>
<BR><BR>
<strong>The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in Pancreatic Ductal Adenocarcinoma.</strong> <br>
Wan YCE, Liu J, Zhu L, Kang TZE, Zhu X, Ramakrishnan S, Tai SK, Yang D, Chan SY, Chan LL, Li Q, Lis J, Ishibashi T, Han J, <span class="cgd">Danko CG</span>, Wang X, Chan KM. <br>
<a title="[Signal Transduction and Targeted Therapy]" href="https://www.nature.com/articles/s41392-020-00219-2">Signal Transduction and Targeted Therapy.</a>
<BR><BR>
<strong>Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance.</strong> <br>
Mukai C, Choi E, Sams KL, Klampen EZ, Anguish L, Marks BA, <span class="cgd">Rice EJ</span>, <span class="cgd">Wang Z</span>, <span class="cgd">Choate LA</span>, <span class="cgd">Chou SP</span>, Kato Y, Miller AD, <span class="cgd">Danko CG</span>, Coonrod SA. <br>
<a title="[BMC Vet Res]" href="https://rdcu.be/b463Q">BMC Veterinary Research.</a>
<BR><BR>
<strong>Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance.</strong> <br>
Dinh TA, Sritharan R, Smith FD, Francisco AB, Ma RK, Bunaciu RP, Kanke M, <span class="cgd">Danko CG</span>, Massa AP, Scott JD, Sethupathy P.<br>
<a title="[Cell Reports]" href="https://www.sciencedirect.com/science/article/pii/S2211124720303995">Cell Reports.</a>
Preprint: <a title="[bioRxiv]" href="https://doi.org/10.1101/2020.01.18.911297">bioRxiv.</a>
<BR><BR>
<strong>Elevated circulating Th2 but not group 2 innate lymphoid cell responses characterize canine atopic dermatitis.</strong> <br>
Früh SP, <span class="cgd">Saikia M</span>, Eule J, Mazulis CA, Miller JE, Cowulich JM, Oyesola OO, Webb LM, Peng SA, Cubitt RL, <span class="cgd">Danko CG</span>, Miller WH, Tait Wojno ED.<br>
<a title="[Vet Immunol Immunopathol]" href="https://www.sciencedirect.com/science/article/abs/pii/S0165242719303435?via%3Dihub">Vet Immunol Immunopathol.</a>
</span>
</li>
<li>
<span class="date"> 2019 </span>
<br>
<span class="papers">
<strong>Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry.</strong> <br>
<span class="cgd">Lewis JJ</span>, Geltman RC, Pollak PC, Rondem KE, Van Belleghem SM, Hubisz MJ, <span class="cgd">Munn PR</span>, Zhang L, Benson C, Mazo-Vargas A, <span class="cgd">Danko CG</span>, Counterman BA, Papa R, Reed RD.<br>
<a title="[PNAS]" href="https://www.pnas.org/content/early/2019/11/05/1907068116.long">Proc Natl Acad Sci U S A.</a>
<BR><BR>
<strong>Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.</strong> <br>
Ray J, <span class="cgd">Munn PR</span>, Vihervaara A, <span class="cgd">Lewis JJ</span>, Ozer A, <span class="cgd">Danko CG</span>, Lis JT.<br>
<a title="[PNAS]" href="https://www.pnas.org/content/early/2019/09/09/1901244116.long">Proc Natl Acad Sci U S A.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/10.1101/527838v1">bioRxiv.</a>
<BR><BR>
<strong>Physical confinement induces malignant transformation in mammary epithelial cells.</strong> <br>
Lu YC, <span class="cgd">Chu T</span>, Hall MS, Fu DJ, Shi Q, Chiu A, An D, Wang L, Pardo Y, Southard T, <span class="cgd">Danko CG</span>, Liphardt J, Nikitin AY, Wu M, Fischbach C, Coonrod S, Ma M.<br>
<a title="[Biomaterials]" href="https://www.sciencedirect.com/science/article/pii/S0142961219304065?via%3Dihub">Biomaterials.</a>
<BR><BR>
<strong>Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis.</strong> <br>
van der Burg KRL, Lewis JJ, Martin A, Nijhout HF, <span class="cgd">Danko CG</span>, Reed RD.<br>
<a title="[Cell Reports]" href="https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30431-0">Cell Reports.</a>
<BR><BR>
<strong>The Notch signaling pathway promotes basophil responses during helminth-induced type 2 inflammation.</strong> <br>
Webb LM, Oyesola OO, Früh SP, Kamynina E, Still KM, Patel RK, Peng SA, Cubitt RL, Grimson A, Grenier JK, Harris TH, <span class="cgd">Danko CG</span>, Tait Wojno ED.<br>
<a title="[J Exp Med]" href="http://jem.rupress.org/content/early/2019/04/11/jem.20180131">J Exp Med.</a>
<BR><BR>
<strong>AlleleHMM: a data-driven method to identify allele-specific differences in distributed functional genomic marks.</strong> <br>
<span class="cgd">Chou S</span>, <span class="cgd">Danko CG.</span><br>
<a title="[Nucleic Acids Research]" href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz176/5421125">Nucleic Acids Research.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/early/2018/08/10/389262">bioRxiv.</a>
<BR><BR>
<strong>Identification of regulatory elements from nascent transcription using dREG.</strong> <br>
<span class="cgd">Wang Z</span>, <span class="cgd">Chu T</span>, <span class="cgd">Choate LA</span>, <span class="cgd">Danko CG.</span><br>
<a title="[Genome Research]" href="https://genome.cshlp.org/content/29/2/293.short">Genome Research.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/early/2018/11/17/321539">bioRxiv.</a>
<BR><BR>
<strong>Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells.</strong> <br>
<span class="cgd">Saikia M</span>, Burnham P, Keshavjee SH, Wang MFZ, Moral-Lopez P, Hinchman MM, <span class="cgd">Danko CG,</span> Parker JSL, De Vlaminck I<br>
<a title="[Nature Methods]" href="https://www.nature.com/articles/s41592-018-0259-9">Nature Methods.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/early/2018/11/13/328328">bioRxiv.</a>
<em>
<span style="color: #993300;">Featured in </span><a title="Lacadie & Ohler" href="https://prelights.biologists.com/highlights/simultaneous-multiplexed-amplicon-sequencing-transcriptome-profiling-single-cells-high-throughput-targeted-long-read-single-cell-sequencing-reveals-clonal-transcriptional-landscape/">preLights.</a>
</em>
</span>
</li>
<li>
<span class="date"> 2018 </span>
<span class="papers">
<strong>Discovering Transcriptional Regulatory Elements From Run‐On and Sequencing Data Using the Web-Based dREG Gateway.</strong> <br>
<span class="cgd">Chu T</span>, <span class="cgd">Wang Z</span>, <span class="cgd">Chou S</span>, <span class="cgd">Danko CG.</span><br>
<a title="[Current Protocols in Bioinformatics]" href="https://rdcu.be/bew8W">Current Protocols in Bioinformatics.</a>
<BR><BR>
<strong>Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme.</strong> <br>
<span class="cgd">Chu T</span>, <span class="cgd">Rice EJ</span>, Booth GT, Salamanca HH, <span class="cgd">Wang Z</span>, Core LJ, Longo SL, Corona RJ, Chin LS, List JT, Kwak H, <span class="cgd">Danko CG</span>.<br>
<a title="[Nature Genetics]" href="https://www.nature.com/articles/s41588-018-0244-3">Nature Genetics.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/early/2018/05/13/185991">bioRxiv.</a>
<BR><BR>
<strong>Building a Science Gateway for processing and modeling sequencing data via Apache Airavata.</strong> <br>
<span class="cgd">Wang Z</span>, Christie M, Abeysinghe E, <span class="cgd">Chu T</span>, Marru S, Pierce M, <span class="cgd">Danko CG.</span><br>
<a title="[PEARC '18]" href="https://dl.acm.org/citation.cfm?id=3219141">Proceedings of the Practice and Experience on Advanced Research Computing Article No. 39.</a>
<BR><BR>
<strong>A common pattern of DNase-I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization.</strong> <br>
<span class="cgd">Blumberg A</span>, <span class="cgd">Danko CG</span>, Kundaje A, Mishmar D.<br>
<a title="[Genome Research]" href="https://genome.cshlp.org/content/early/2018/07/12/gr.230409.117">Genome Research.</a>
Preprint: <a title="[bioRxiv]" href="https://www.biorxiv.org/content/early/2017/09/23/193037">bioRxiv.</a>
<BR><BR>
<strong>A bi-stable feedback loop between GDNF, EGR1, and ERα contribute to endocrine resistant breast cancer.</strong> <br>
Horibata S, <span class="cgd">Rice EJ</span>, Zheng H, Mukai C, <span class="cgd">Chu T</span>, Marks BA, Coonrod SA, <span class="cgd">Danko CG</span>.<br>
<a title="[Full text]" href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194522">PLoS One.</a>
<BR><BR>
<strong>ER-positive breast cancer cells are poised for RET-mediated endocrine resistance.</strong> <br>
Horibata S, <span class="cgd">Rice EJ</span>, Mukai C, Marks BA, Sams K, Zheng H, Anguish LJ, Coonrod SA, <span class="cgd">Danko CG</span>.<br>
<a title="[Full text]" href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194023">PLoS One.</a>
<BR><BR>
<strong>Herpes Simplex Virus 1 Dramatically Alters Loading and Positioning of RNA Polymerase II on Host Genes Early in Infection.</strong> <br>
Birkenheuer CH, <span class="cgd">Danko CG</span>, Baines JD.<br>
<a title="[Full text]" href="http://jvi.asm.org/content/early/2018/02/01/JVI.02184-17">J Virology.</a>
<BR><BR>
<strong>Dynamic evolution of regulatory element ensembles in primate CD4+ T cells.</strong> <br>
<span class="cgd">Danko CG</span>, <span class="cgd">Choate LA</span>, Marks BA, <span class="cgd">Rice EJ</span>, <span class="cgd">Wang Z</span>, <span class="cgd">Chu T</span>, Martins AL, Dukler N, Coonrod SA, Tait-Wojno E, List JT, Kraus WL, Siepel A.<br>
<a title="[Full text]" href="https://www.nature.com/articles/s41559-017-0447-5">Nature Ecology & Evolution.</a>
Preprint: <a title="[bioRxiv]" href="http://www.biorxiv.org/content/early/2017/07/16/083212">bioRxiv.</a>
<em>
<span style="color: #993300;">Featured in a </span><a title="Lacadie & Ohler" href="https://www.nature.com/articles/s41559-018-0479-5">perspective piece</a>.
</em>
</li>
<li>
<span class="date"> 2017 </span>
<span class="papers">
<strong>XX Disorder of Sex Development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris).</strong> <br>
Meyers-Wallen VN, Boyko AR, <span class="cgd">Danko CG</span>, Grenier JK, Mezey JG, Hayward JJ, Shannon LM, Gao C, Shafquat A, <span class="cgd">Rice EJ</span>, Pujar S, Eggers S, Ohnesorg T, Sinclair AH.<br>
<a title="[Full text]" href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186331">PLoS One.</a>
<BR><BR>
<strong>Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.</strong> <br>
Dukler N, Booth GT, Huang YF, Tippens N, <span class="cgd">Danko CG</span>, Lis JT, Siepel A.<br>
<a title="[Full text]" href="http://genome.cshlp.org/content/early/2017/10/12/gr.222935.117.abstract">Genome Research.</a> Preprint: <a title="[bioRxiv]" href="http://biorxiv.org/content/early/2017/03/16/117689">bioRxiv.</a>
<BR><BR>
<strong>Transcriptional response to stress is pre-wired by promoter and enhancer architecture.</strong> <br>
Vihervaara A, Mahat DB, Guertin MJ, <span class="cgd">Chu T</span>, <span class="cgd">Danko CG</span>, Lis JT, Sistonen L.<br>
<a title="[Full text]" href="https://www.nature.com/articles/s41467-017-00151-0">Nature Communications.</a>
<BR><BR>
<strong>Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution.</strong> <br>
Blumberg A, <span class="cgd">Rice EJ</span>, Kundaje A, <span class="cgd">Danko CG</span>, Mishmar D.<br>
<a title="[Full text]" href="http://genome.cshlp.org/content/early/2017/01/03/gr.209924.116">Genome Research.</a> Preprint: <a title="[bioRxiv]" href="http://biorxiv.org/content/early/2016/05/18/054031">bioRxiv.</a>
<BR><BR>
<strong>Rgtsvm: Support Vector Machines on a GPU in R.</strong> <br>
<span class="cgd">Wang Z</span>, <span class="cgd">Chu T</span>, <span class="cgd">Choate LA</span>, <span class="cgd">Danko CG.</span><br>
Preprint: <a title="[arXiv]" href="https://arxiv.org/abs/1706.05544">arXiv.</a>
</span>
</li>
<li>
<span class="date"> 2016 </span>
<span class="papers">
<strong>Poised for development.</strong> <br>
<span class="cgd">Choate LA</span>, <span class="cgd">Danko CG</span>.<br>
<a title="[Full text]" href="http://rdcu.be/jt2A">Nature Genetics.</a> Our News and Views article on: <a title="[Full text]" href="http://www.nature.com/ng/journal/v48/n8/full/ng.3591.html">Lesch et. al. (2016). Nature Genetics.</a>
<BR><BR>
<strong>Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq).</strong> <br>
Mahat DB, Kwak H, Booth GT, Jonkers IH, <span class="cgd">Danko CG</span>, Patel RK, Waters CT, Munson K, Core LJ, Lis JT.<br>
<a title="[Full text]" href="http://www.nature.com/nprot/journal/v11/n8/full/nprot.2016.086.html">Nature Protocols.</a>
<BR><BR>
<strong>RTFBSDB: an integrated framework for transcription factor binding site analysis.</strong> <br>
<span class="cgd">Wang Z</span>, <span class="cgd">Martins AL</span>, <span class="cgd">Danko CG</span>.<br>
<a title="[Full text]" href="http://bioinformatics.oxfordjournals.org/content/32/19/3024">Bioinformatics.</a> Preprint: <a title="[bioRxiv]" href="http://biorxiv.org/content/early/2016/01/05/036053.abstract">bioRxiv.</a> Software: <a title="[Github]" href="https://github.com/Danko-Lab/rtfbs_db">Github.</a>
<BR><BR>
<strong>Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation.</strong> <br>
Mahat DB, Salamanca H, Duarte FM, <span class="cgd">Danko CG</span>, Lis JT.<br>
<a title="[Full text]" href="http://www.sciencedirect.com/science/article/pii/S1097276516001362">Molecular Cell.</a>
</span>
</li>
<li>
<span class="date"> 2015 </span>
<span class="papers">
<strong>Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality.</strong> <br>
Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, <span class="cgd">Danko CG</span>, Lis JT, Zhang M, Martin JF, Kurpios NA.<br>
<a title="[Full text]" href="http://www.sciencedirect.com/science/article/pii/S2211124715009882">Cell Reports.</a>
<em><span style="color: #993300;">Cover Article.</span></em>
<BR><BR>
<strong>groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data.</strong> <br>
Chae M, <span class="cgd">Danko CG</span>, Kraus WL.<br>
<a title="[Full text]" href="http://www.biomedcentral.com/1471-2105/16/222">BMC Bioinformatics.</a> <em><span style="color: #800000;">Highly accessed.</span></em>
<BR><BR>
<strong>A unified architecture of transcriptional regulatory elements.</strong> <br>
Andersson R, Sandelin A, <span class="cgd">Danko CG</span>.<br>
<a title="[Full text]" href="http://www.sciencedirect.com/science/article/pii/S0168952515001043">Trends in Genetics.</a> Preprint: <a title="[bioRxiv]" href="http://www.biorxiv.org/content/early/2015/05/26/019844">bioRxiv.</a>
<BR><BR>
<strong>GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters.</strong> <br>
Fuda NJ, Guertin MJ, Sharma S, <span class="cgd">Danko CG</span>, Martins AL, Siepel A, Lis JT.<br>
<a title="[Full text]" href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005108">PLoS Genetics.</a>
<BR><BR>
<strong>Identification of active transcriptional regulatory elements from GRO-seq data. </strong> <br>
<span class="cgd">Danko CG</span>, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, and Siepel A. <br>
<a title="[Full text]" href="https://www.nature.com/articles/nmeth.3329">Nature Methods.</a> Preprint: <a title="[bioRxiv]" href="http://www.biorxiv.org/content/early/2014/11/12/011353">bioRxiv.</a> Software: <a title="[Github]" href="https://github.com/Danko-Lab/dREG">Github.</a> Data: <a title="UCSC Track Hub" href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://charlesdanko.com/hub/dreg/hub.txt">UCSC Track hub.</a>
</span>
</li>
<li>
<span class="date"> 2014 </span>
<span class="papers">
<strong>Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. </strong> <br>
Core LJ, Martins AL, <span class="cgd">Danko CG</span>, Waters CT, Siepel A, Lis JT. <br>
<a title="[Full text]" href="http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3142.html">Nature Genetics.</a>
<em><span style="color: #800000;">Featured in NG </span> <a title="Weingarten-Gabbay & Segal" href="http://www.nature.com/ng/journal/v46/n12/full/ng.3152.html">News and Views</a>.</em>
<BR><BR>
<strong>Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFalpha signaling revealed by integrated genomic analyses. </strong> <br>
Luo X, Chae M, Krishnakumar R, <span class="cgd">Danko CG</span>, Kraus WL. <br>
<a title="[Full text]" href="http://www.biomedcentral.com/1471-2164/15/155">BMC Genomics.</a>
<BR><BR>
<strong>Change in ß-Catenin Localization Suggests Involvement of the Canonical Wnt Pathway in Boxer Dogs with Arrhythmogenic Right Ventricular Cardiomyopathy.</strong> <br>
Oxford EM, <span class="cgd">Danko CG</span>, Fox PR, Kornreich BG, Moïse NS. <br>
<a title="[Full text]" href="http://onlinelibrary.wiley.com/doi/10.1111/jvim.12238/abstract">Journal of Veterinary Internal Medicine.</a>
</span>
</li>
<li>
<span class="date"> 2013 </span>
<span class="papers">
<strong> Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites. </strong> <br>
Hah N, Murakami S, Nagari A, <span class="cgd">Danko CG</span>, Kraus WL. <br>
<a title="[Full text]" href="http://genome.cshlp.org/content/23/8/1210.full?sid=7bee3c94-089b-4072-ac85-925894b50fd1">Genome Research.</a>
<BR><BR>
<strong>Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans. </strong><br>
Zeng L, Sang Chul C, <span class="cgd">Danko CG</span>, Siepel A, Stanhope MJ, Burne RA. <br>
<a title="[Link]." href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060465">PLoS ONE.</a>
<BR><BR>
<strong>Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells.</strong> <br>
<span class="cgd">Danko CG</span>, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. <br>
<a title="Link" href="http://www.sciencedirect.com/science/article/pii/S1097276513001718">Molecular Cell.</a>
<em>
<span style="color: #993300;">Featured in a </span><a title="Henriques & Adelman" href="http://www.sciencedirect.com/science/article/pii/S1097276513002906">perspective piece</a>.
<span style="color: #993300;">Cover Article.</span>
<span style="color: #993300;">Recommended by F1000.</span>
</em>
<BR>
</span>
</li>
<li>
<span class="date"> 2011 </span>
<span class="papers">
<strong>Bayesian inference of ancient human demography from individual genome sequences.</strong> <br>
Gronau I, Hubisz MJ, Gulko B, <span class="cgd">Danko CG</span>, Siepel A.<br>
<a href="http://www.nature.com/ng/journal/v43/n10/full/ng.937.html">Nature Genetics.</a>
<BR><BR>
<strong>Ultrastructural changes in cardiac myocytes from Boxer dogs with arrhythmogenic right ventricular cardiomyopathy.</strong> <br>
Oxford EM, <span class="cgd">Danko CG</span>, Kornreich BG, Maass K, Hemsley SA, Raskolnikov D, Fox PR, Delmar M, Moïse NS. <br>
<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142699/">Journal of Veterinary Cardiology.</a>
<em><span style="color: #993300;">Cover Article.</span></em>
<BR><BR>
<strong>A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.</strong> <br>
Hah N*, <span class="cgd">Danko CG*</span>, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. <br>
<a href="http://www.cell.com/abstract/S0092-8674%2811%2900376-X">Cell.</a>
<em><span style="color: #800000;">Featured in a</span> <a title="Prokesch & Lazar" href="http://www.cell.com/abstract/S0092-8674(11)00474-0">perspective piece</a>.</em>
</span>
</li>
<li>
<span class="date"> 2010- </span>
<span class="papers">
<strong>Complete Khoisan and Bantu genomes from southern Africa. </strong><br>
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, <span class="cgd">Danko CG</span>, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. <br>
<a href="http://www.nature.com/nature/journal/v463/n7283/full/nature08795.html">Nature.</a>
<em><span style="color: #800000;">Cover Article.</span></em>
<BR><BR>
<strong>Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. </strong> <br>
<span class="cgd">Danko CG</span>, Pertsov AM. <br>
<a href="http://www.biomedcentral.com/1755-8794/2/31">BMC Medical Genomics.</a>
<BR><BR>
<strong>Bioinformatic identification of novel putative photoreceptor specific cis-elements.</strong> <br>
<span class="cgd">Danko CG</span>, McIlvain VA, Qin M, Knox BE, Pertsov AM. <br>
<a href="http://www.biomedcentral.com/1471-2105/8/407">BMC Bioinformatics.</a>
<BR><BR>
<strong>MeCP2 expression in human cerebral cortex and lymphoid cells: immunochemical characterization of a novel higher-molecular-weight form. </strong> <br>
Jarrar MH, <span class="cgd">Danko CG</span>, Reddy S, Lee YJ, Bibat G, Kaufmann WE. <br>
<a href="http://jcn.sagepub.com/content/18/10/675.long">Journal of Child Neurology.</a>
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<b>In the news:</b>
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<p class="posted">May 2022</p>
<p class="text"><a href="https://www.genomeweb.com/informatics/researchers-develop-model-infer-cell-type-composition-gene-expression-bulk-rna-seq-data">Cell type, Gene Expression Inference.</a> GenomeWeb covers Tinyi's BayesPrism paper on inferring cell types and gene expression from bulk RNA-seq data.</p>
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<li>
<p class="posted">March 2022</p>
<p class="text"><a href="https://www.nature.com/articles/s41588-021-01004-9">Nascent transcription as a predictor and driver of histone modifications.</a> News & Views of Alex and Zhong's histone imputation paper by Karen Adelman.</p>
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<li>
<p class="posted">March 2022</p>
<p class="text"><a href="https://news.cornell.edu/stories/2022/03/new-technique-yields-insight-genome">Histone imputation yields insight into genome.</a> Cornell Chronicle, Phys.org, others cover Zhong and Alex's paper on histone imputation.</p>
</li>
<li>
<p class="posted">Nov 2018</p>
<p class="text"><a href="https://www.thenakedscientists.com/podcasts/short/glioblastomas-effect-genes">Glioblastoma's Effect on Genes.</a> The Naked Scientist podcast interviewed Charles about the ChRO-seq paper.</p>
</li>
<li>
<p class="posted">Oct 2018</p>
<p class="text"><a href="http://news.cornell.edu/stories/2018/10/new-tool-gives-deeper-understanding-glioblastoma">Understanding glioblastoma.</a> Chornell Chronicle article about our paper describing the use of ChRO-seq in glioblastoma.</p>
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<li>
<p class="posted">Jan 2018</p>
<p class="text"><a href="https://www.nature.com/articles/s41559-018-0479-5">Redundant regulation.</a> News & Views on our paper describing evolutionary changes in nascent transcription in primate CD4+ T-cells.</p>
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<p class="posted">Jan 2018</p>
<p class="text"><a href="http://news.cornell.edu/stories/2018/02/what-makes-us-human-isnt-just-our-genes-how-we-regulate-them">What makes us human?</a> Cornell Chronicle article about our recent paper on nascent transcription in primates.</p>
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<li>
<p class="posted">Dec 2015</p>
<p class="text"><a href="http://www.nature.com/news/should-dna-donors-see-their-genomic-data-1.18939?WT.mc_id=TWT_NatureNews">Returning data to research participants.</a> Should research participants who donate DNA or other material see their raw data?</p>
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<li>
<p class="posted">Nov 2014</p>
<p class="text"><a href="http://www.nature.com/ng/journal/v46/n12/full/ng.3142.html">Shared Architecture</a>. News & Views on our work describing a shared regulatory architecture at promoters and enhancers.</p>
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<p class="posted">April 2013</p>
<p class="text"><a href="http://www.cell.com/molecular-cell/abstract/S1097-2765%2813%2900290-6">Catching the Waves</a>. Perspective on our work measuring Pol II elongation rates.</p>
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<p class="posted">May 2011</p>
<p class="text"><a href="http://www.cell.com/abstract/S0092-8674%2811%2900474-0">A Hormone IMs the Genome</a>. Perspective on our profiling the targets of E2 signaling in breast cancer cells.</p>
</li>
<li>
<p class="posted">February 2010</p>
<p class="text"><a href="http://www.nytimes.com/2010/02/18/science/18genome.html">New York Times</a> and <a href="http://www.nature.com/news/2010/100217/full/463857a.html">Nature News</a> pieces on our work sequencing the Khoisan and Bantu genomes.</p>
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<li><a href="http://www.vet.cornell.edu/">College of Veterinary Medicine</a></li>
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<h2>Join the lab!</h2>
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<span>E-mail a 1 page cover letter, a curriculum vitae, and 3 letters of reference to Charles Danko.</span>
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<span>Apply through the graduate fields of <a href="http://www.cb.cornell.edu/">Computational Biology</a> or <a href="http://www.gendev.cornell.edu/">Genetics, Genomics & Development</a>.</span>
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