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fhalbritter committed May 7, 2024
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8 changes: 3 additions & 5 deletions index.html
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Expand Up @@ -74,8 +74,7 @@ <h4>We trace (aberrant) changes in cells during development.</h4>
<span><a href="https://doi.org/10.1016/j.stem.2016.10.019" title="DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation">Cell Stem Cell 2016</a>;</span>
<span><a href="https://doi.org/10.1126/science.aaf4238" title="Specification of tissue-resident macrophages during organogenesis">Science 2016</a>;</span>
<span><a href="https://doi.org/10.1158/2159-8290.CD-19-0138" title="Epigenomics and Single-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis">Cancer Discov. 2019</a></span>
</p>
<p>Now: Using <i>in vitro</i> differentiation to make sense of intra-tumor plasticity</p>
</p>
</div>
<div class="col-md-4 arr">
<img src="images/regepi.svg" onerror="this.src='images/regepi.png'">
Expand All @@ -86,7 +85,6 @@ <h4>We map regulatory networks that shape cell identity.</h4>
<span><a href="https://doi.org/10.7554/eLife.27746" title="Distinct SoxB1 networks are required for naïve and primed pluripotency">eLife 2017</a>;</span>
<span><a href="https://doi.org/10.15252/embj.201695476" title="Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation">EMBO J. 2018</a></span>
</p>
<p>Now: Dissecting effects of oncogenic mutations in key regulators</p>
</div>
<div class="col-md-4 arr">
<img src="images/intana.svg" onerror="this.src='images/intana.png'">
Expand All @@ -97,12 +95,12 @@ <h4>We develop tools that connect pieces of data into knowledge.</h4>
<span><a href="https://doi.org/10.1038/nbt.3605" title="Quantitative comparison of DNA methylation assays for biomarker development and clinical applications">Nat. Biotechnol. 2016</a>;</span>
<span><a href="https://doi.org/10.1016/j.stem.2018.06.014" title="Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells">Cell Stem Cell 2018</a></span>
</p>
<p>Now: Machine learning to translate complex data into simpler components</p>
</div>
<p>Now: Using <i>in vitro</i> differentiation to dissect the effect of oncogenic mutations on tumorigenesis and intra-tumor plasticity. <a href="https://doi.org/10.1038/s41467-024-47945-7" title="A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations">Nat. Commun. 2024</a></p>
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<hr/>
<p>
<strong><i class="fa fa-newspaper-o"></i> Check out our latest pre-prints and papers: <a href="https://doi.org/10.1101/2022.11.21.515753">Saldana, Montano, <i>et al.</i></a>, <a href="https://doi.org/10.1038/s41467-024-45802-1">Kirchberger, Shoeb, <i>et al.</i></a>, &amp; <a href="https://doi.org/10.1101/2023.03.28.534443">Hafemeister &amp; Halbritter</a></strong>
<strong><i class="fa fa-newspaper-o"></i> Check out our latest pre-prints and papers: <a href="https://doi.org/10.1038/s41467-024-47945-7">Saldana, Montano, <i>et al.</i></a>, <a href="https://doi.org/10.1038/s41467-024-45802-1">Kirchberger, Shoeb, <i>et al.</i></a>, &amp; <a href="https://doi.org/10.1101/2023.03.28.534443">Hafemeister &amp; Halbritter</a></strong>
</p>
<hr/>
<p><i class="fa fa-info-circle"></i> Find out <a href="research.html">more about our research here</a>! Do you have the know-how, creativity, and passion to join the quest? <a href="join.html">We'd like to hear from you!</a></p>
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4 changes: 2 additions & 2 deletions join.html
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Expand Up @@ -70,8 +70,8 @@ <h2 class="page-title">Join us!</h2>

<p>A list of all current vacancies is available here: <a href="https://www.ccri.at/job-openings/">https://www.ccri.at/job-openings/</a></p>

<p>No current vacancies? We are always open to reviewing applications from exceptionally motivated, creative computational biologists with a solid background in functional genomics data, programming skills, and the drive to take control of their own research.
Before you <a href="contact.html">get in touch</a>, please take a moment to think about what it is that attracts you to our group and what you would like to achieve by joining us. We appreciate informal requests and personal(ized) applications. Mass emails and off-the-shelf applications will be ignored.
<p>No current vacancies? We are always open to reviewing applications from exceptionally motivated, creative <strong>computational biologists</strong> with a solid background in functional genomics data, programming skills, and the drive to take control of their own research, or from <strong>stem cell and cancer biologists</strong> with innovative (and slightly crazy) ideas how to tackle open questions in pediatric cancer research.
Before you <a href="contact.html">get in touch</a>, please think carefully about what it is that attracts you to our group and what you would like to achieve by joining us. We appreciate informal requests and personal(ized) applications. Mass emails and off-the-shelf applications will be ignored.
</p>
</div>
<div class="row">
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21 changes: 12 additions & 9 deletions people.html
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Expand Up @@ -113,7 +113,7 @@ <h4>Christoph Hafemeister</h4>
<div class="col-md-3 post boxed-content">
<h4>Maud Plaschka</h4>
<div><img src="https://ccri.at/wp-content/uploads/2022/05/MaudPlaschka_NOVY6972-150x150.jpg"/></div>
<div>Postdoc (with <a href="https://www.meduniwien.ac.at/hp/dermatologie/wissenschaft-forschung/inimac-innate-immune-activation-lab-pi-matthias-farlik/">Farlik lab</a>)</div>
<div>Postdoc (<a href="https://ccri.at/fwfs-esprit-program-supports-research-on-%ce%b2-catenin-in-wilms-tumor/">FWF ESPRIT fellow</a>)</div>
<div>
<a href="https://github.com/maud-p"><i class="fa fa-github"></i></a>
<a href="https://www.linkedin.com/in/maud-plaschka-7913ba84"><i class="fa fa-linkedin"></i></a>
Expand All @@ -138,7 +138,8 @@ <h4>Your name here</h4>
</div>

<h2>Alumni:</h2>
<ul>
<ul>
<li>2024, Eszter Söjtöry (intern)</li>
<li>2019-20, Katja Nettermann (MSc thesis)</li>
<li>2019-20, Martin Koban (MSc thesis)</li>
<li>2019, Hanja Pisa</li>
Expand All @@ -151,7 +152,11 @@ <h2>Current &amp; long-term collaborators (alphabetical):</h2>

<li><a href="https://www.erasmusmc.nl/klinische_genetica/research/introduction/stefan-barakat/">Stefan Barakat</a> @ Erasmus, Clinical genetics</li>

<li><a href="https://www.maxperutzlabs.ac.at/research/research-groups/buecker">Christa Buecker</a> @ MFPL, Enhancers &amp; ESCs</li>
<li><a href="https://www.maxperutzlabs.ac.at/research/research-groups/buecker">Christa Buecker</a> @ MPL, Enhancers &amp; ESCs</li>

<li><a href="https://www.crcl.fr/en/tumor-escape-resistance-immunity-department/cancer-cell-plasticity-in-melanoma/">Julie Caramel</a> @ CRCL, Spatial imaging</li>

<li><a href="https://www.icr.ac.uk/our-research/researchers-and-groups/professor-louis-chesler">Louis Chesler</a> @ ICR, Mouse models</li>

<li><a href="https://science.ccri.at/research/research-areas/immunology/boztug/">Kaan Boztug</a> @ CCRI / LBI-RUD, Rare diseases</li>

Expand All @@ -167,16 +172,14 @@ <h2>Current &amp; long-term collaborators (alphabetical):</h2>

<li><a href="https://science.ccri.at/research/research-areas/solid-tumours/molecular-biology-of-solid-tumours/">Heinrich Kovar</a> @ CCRI, Sarcomas</li>

<li><a href="https://www.maxperutzlabs.ac.at/research/research-groups/leeb">Martin Leeb</a> @ MFPL, Embryonic stem cells</li>

<li><a href="https://science.ccri.at/research/research-areas/immunology/development-of-cellular-therapeutics/">Manfred Lehner</a> @ CCRI, CAR-T cells</li>

<li><a href="https://www.maxperutzlabs.ac.at/research/research-groups/leeb">Martin Leeb</a> @ MPL, Embryonic stem cells</li>

<li><a href="https://www.meduniwien.ac.at/hp/kinderchirurgie/wissenschaft-forschung/">Martin Metzelder</a> @ MedUni Vienna, Pediatric solid tumours</li>

<li><a href="https://moriggllab.com/neubauergroup/">Heidi Neubauer</a> @ VetMedUni Vienna, Mouse models</li>

<li><a href="https://science.ccri.at//research/research-areas/leukaemias/genetics-of-leukaemias/">Sabine Strehl</a> @ CCRI, Leukemias</li>

<li><a href="https://www.bdr.riken.jp/en/research/labs/takasato-m/index.html">Minoru Takasato</a> @ RIKEN, Developmental biology</li>

<li><a href="https://science.ccri.at/research/research-areas/solid-tumours/tumour-biology/">Sabine Taschner-Mandl</a> @ CCRI, Tumor biology</li>

<li><a href="https://www.sheffield.ac.uk/cscb/tsakiridis">Anestis Tsakiridis</a> @ University of Sheffield, Developmental biology</li>
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16 changes: 8 additions & 8 deletions pubs.html
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Expand Up @@ -79,19 +79,13 @@ <h2 class="page-title">Publications &amp; Resources</h2>

<p>Lab members <u>underlined</u>. *,# mark equal contributions.<p>

<h2 style="margin-top:2em">Current preprints:</h2>

<p>Saldana-Guerrero IM*, <u>Montano-Gutierrez LF*</u>, Boswell K, <u>Hafemeister C</u>, Poon E, Shaw LE, Stavish D, Lea RA, <u>Wernig-Zorc S</u>, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, <u>Shoeb MR</u>, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A<sup>#</sup>, <u>Halbritter F<sup>#</sup></u>. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. <b>bioRxiv</b>. 2022:2022.11.21.515753. <a href="https://doi.org/10.1101/2022.11.21.515753">https://doi.org/10.1101/2022.11.21.515753</a></p>
<p><u>Hafemeister C</u>, <u>Halbritter F</u>. Single-cell RNA-seq differential expression tests within a sample should use pseudo-bulk data of pseudo-replicates. <b>bioRxiv</b>. 2023:2023.03.28.534443. <a href="https://doi.org/10.1101/2023.03.28.534443">https://doi.org/10.1101/2023.03.28.534443</a></p>
<p>Buri MC, <u>Shoeb MR</u>, Bykov A, Repiscak P, Baik H, Dupanovic A, David FO, Kovacic B, Hall-Glenn F, Urbanus J, Sippl L, Stofner S, Emminger D, Cosgrove J, Lehner M, Perié L, Schumacher TN, Gotthardt D, <u>Halbritter F</u>, Putz EM. NK cells shape the clonal evolution of B-ALL cells by IFN-γ production. <b>bioRxiv</b>. 2023:2023.11.16.567430. <a href="https://doi.org/10.1101/2023.11.16.567430">https://doi.org/10.1101/2023.11.16.567430</a></p>




<p>&nbsp;</p>

<h2>Main contributions (first | last authorship):</h2>

<p>Saldana-Guerrero IM*, <u>Montano-Gutierrez LF*</u>, Boswell K, <u>Hafemeister C</u>, Poon E, Shaw LE, Stavish D, Lea RA, <u>Wernig-Zorc S</u>, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, <u>Shoeb MR</u>, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A<sup>#</sup>, <u>Halbritter F<sup>#</sup></u>. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. <b>Nat Commun</b>. 2024;15;3745. <a href="https://doi.org/10.1038/s41467-024-47945-7">https://doi.org/10.1038/s41467-024-47945-7</a> <i class="fa fa-star"></i> <a href="https://github.com/cancerbits/saldana_montano2024_ncnb">Code</a> | <a href="https://zenodo.org/records/10891507">Code Archive</a> | <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219153">Data: GSE219153</a> | <a href="http://r2platform.com/halbritter24/">Interactive Data @R2</a> </p>

<p>Kirchberger S*, <u>Shoeb MR*</u>, Lazic D, Wenninger-Weinzierl A, Fischer K, Shaw LE, Nogueira F, Rifatbegovic F, Bozsaky E, Ladenstein R, Bodenmiller B, Lion T, Traver D, Farlik M, Schöfer C, Taschner-Mandl S, <u>Halbritter F<sup>#</sup></u>, Distel M<sup>#</sup>. Cross-species analysis identifies conserved transcriptional mechanisms of neutrophil maturation. <b>Nat Commun</b>. 2024;15;1792. <a href="https://doi.org/10.1038/s41467-024-45802-1">https://doi.org/10.1038/s41467-024-45802-1</a> <i class="fa fa-star"></i> <a href="https://github.com/cancerbits/Kirchberger_Shoeb2024_neut">Code</a> | <a href="https://doi.org/10.5281/zenodo.10475407">Code Archive</a> | <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE252788">Data: GSE252788</a> </p>

<p>Santini L*, <u>Halbritter F*</u>, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <b>Nat Commun</b>. 2021;12:3804. <a href="https://doi.org/10.1038/s41467-021-23510-4">https://doi.org/10.1038/s41467-021-23510-4</a> <i class="fa fa-star"></i> <a href="https://github.com/cancerbits/santini2021_imprints">Code</a> | <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152106">Data: GSE152106</a> | <a href="https://www.ccri.at/2021/06/21/hot-off-the-press-a-new-role-for-histone-modifications-in-genomic-imprinting/">Press@CCRI</a> </p>
Expand All @@ -118,6 +112,12 @@ <h2>Main contributions (first | last authorship):</h2>

<p>&nbsp;</p>

<h2 style="margin-top:2em">Current preprints:</h2>

<p><u>Hafemeister C</u>, <u>Halbritter F</u>. Single-cell RNA-seq differential expression tests within a sample should use pseudo-bulk data of pseudo-replicates. <b>bioRxiv</b>. 2023:2023.03.28.534443. <a href="https://doi.org/10.1101/2023.03.28.534443">https://doi.org/10.1101/2023.03.28.534443</a></p>
<p>Buri MC, <u>Shoeb MR</u>, Bykov A, Repiscak P, Baik H, Dupanovic A, David FO, Kovacic B, Hall-Glenn F, Urbanus J, Sippl L, Stofner S, Emminger D, Cosgrove J, Lehner M, Perié L, Schumacher TN, Gotthardt D, <u>Halbritter F</u>, Putz EM. NK cells shape the clonal evolution of B-ALL cells by IFN-γ production. <b>bioRxiv</b>. 2023:2023.11.16.567430. <a href="https://doi.org/10.1101/2023.11.16.567430">https://doi.org/10.1101/2023.11.16.567430</a></p>

<p>&nbsp;</p>

<h2>Other contributions:</h2>

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