https://fabilab.org/2024-01-04T00:00:00+11:002024-01-04T00:00:00+11:002024-01-04T00:00:00+11:00Fabio Zaninitag:fabilab.org,2024-01-04:/approxpreprint2024.html

<p>Our manuscript on cell atlas approximations, a new way to analyse cell atlases fast and without coding skills, is on&nbsp;bioRxiv!</p> <p><a href="https://www.biorxiv.org/content/10.1101/2024.01.03.573994v1">https://www.biorxiv.org/content/10.1101/2024.01.03.573994v1</a></p> <p>Thanks to Ying and Joanna for their hard work on the&nbsp;project!</p>2023-07-29T00:00:00+10:002023-07-29T00:00:00+10:00Fabio Zaninitag:fabilab.org,2023-07-29:/priscilla2023.html

<p>Priscilla Boon has joined the lab as a bioinformatician,&nbsp;welcome!</p> <p>Priscilla received her PhD from National University of Singapore and is now leading our efforts on single cell multi-omics of myelodysplastic syndromes (<span class="caps">MDS</span>) in collaboration with the Pimanda lab at <span class="caps">UNSW</span>.</p>2023-05-29T00:00:00+10:002023-05-29T00:00:00+10:00Fabio Zaninitag:fabilab.org,2023-05-29:/deadlylearnersmay2023.html

<p>Today Catherine and Fabio had an awesome educational session with the Aberdeen public school children organised by <a href="https://deadlyscience.org.au/">Deadly Science</a>, an amazing organisation that broadcasts <span class="caps">STEM</span> materials and knowledge to rural and remote&nbsp;communities.</p> <p>It was great fun and to yes - microscopes are almost&nbsp;magic!</p>2023-04-15T00:00:00+10:002023-04-15T00:00:00+10:00Fabio Zaninitag:fabilab.org,2023-04-15:/czigrant2023.html

<p>The lab was awarded a <a href="https://chanzuckerberg.com/science/programs-resources/single-cell-biology/">single cell data insight grant</a> from the Chan-Zuckerberg&nbsp;Initiative!</p>2021-12-06T00:00:00+11:002021-12-06T00:00:00+11:00Fabio Zaninitag:fabilab.org,2021-12-06:/htseq2arxiv.html

<p>Our HTSeq 2.0 preprint is on&nbsp;arXiv!</p> <p><a href="https://arxiv.org/abs/2112.00939">https://arxiv.org/abs/2112.00939</a></p> <p>Congrats to Givanna and thanks to all authors for their&nbsp;contributions!</p> <p>(Fingers crossed with the&nbsp;submission)</p>2021-11-26T00:00:00+11:002021-11-26T00:00:00+11:00Fabio Zaninitag:fabilab.org,2021-11-26:/abacbsaward2021.html

<p>Fabio has won the 2021 Open Source Award from the <a href="https://www.abacbs.org/">Australian Bioinformatics and Computational Biology Society (<span class="caps">ABACBS</span>)</a> for his long standing committment to open source and open science and his work on <a href="https://igraph.org/">igraph</a> and <a href="https://github.com/htseq/htseq/">HTSeq 2.0</a>.</p> <p>Congrats!</p>2021-10-01T00:00:00+10:002021-10-01T00:00:00+10:00Fabio Zaninitag:fabilab.org,2021-10-01:/labpicnic2021.html

<p>Today core fabilab members met for a picnic at Moore&nbsp;Park!</p> <p>Everyone finally met Viraj in person, and we enjoyed the delicious food and drinks everyone&nbsp;brought.</p> <p>Hopefully we&#8217;ll have another one with a few more people once restrictions&nbsp;ease!</p>2021-08-04T00:00:00+10:002021-08-04T00:00:00+10:00Fabio Zaninitag:fabilab.org,2021-08-04:/openphdjellyfish2021.html

<p><img alt="opening" src="images/research/bluebottle.jpg"></p> <p>We are looking for a passionate and motivated student to work on a new collaboration with <a href="http://www.oceanography.unsw.edu.au/">Amandine Schaeffer</a> on <strong>gene stealing in bluebottle jellyfish</strong>. <a href="https://fabilab.org/images/bluebottle_single_cell_project.pdf">Project&nbsp;description</a></p> <p>If you are interested in evolution, single cell biology, and the sea, reach out and let&#8217;s have a&nbsp;chat.</p>2021-08-03T00:00:00+10:002021-08-03T00:00:00+10:00Fabio Zaninitag:fabilab.org,2021-08-03:/grantczi2021.html

<p><img alt="opening" src="images/blog/czi_plus_igraph.png"></p> <p>Our collaboration with Vincent Traag in the Netherlands and the other amazing <a href="https://igraph.org/">igraph</a> developers was awarded a second grant from the Chan Zuckerberg Initiative to improve network analysis tools in Python, R, and&nbsp;Mathematica.</p> <p>Congrats to&nbsp;all!</p>2021-04-30T00:00:00+10:002021-04-30T00:00:00+10:00Fabio Zaninitag:fabilab.org,2021-04-30:/preprintendo2021.html

<p>Our preprint on endothelial cell development in the neonatal lung is&nbsp;out!</p> <p><a href="https://www.biorxiv.org/content/10.1101/2021.04.27.441649v1">https://www.biorxiv.org/content/10.1101/2021.04.27.441649v1</a></p> <p>While many single cell papers describe all endothelial cells in their data set as a single cluster of &#8220;vasuclar&#8221; cells, we focused specifically on those cells in the context of the mammalian neonatal lung and - guess what! - we discovered an amazing degree of interesting&nbsp;diversity.</p> <p>Thank you to all authors for their amazing work, and special thanks to Cristina Alvira who did so much work on&nbsp;this!</p>2021-03-30T00:00:00+11:002021-03-30T00:00:00+11:00Fabio Zaninitag:fabilab.org,2021-03-30:/preprintveev2021.html

<p>Our paper on single cell sequencing of Venezuelan equine encephalitis virus is out in <span class="caps">PLOS</span> Neglected Tropical&nbsp;Diseases!</p> <p><a href="https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0009306">https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0009306</a></p> <p>Thank you to all authors for their amazing&nbsp;work!</p>2020-08-04T00:00:00+10:002020-08-04T00:00:00+10:00Fabio Zaninitag:fabilab.org,2020-08-04:/openpos_scimmunology.html

<p>We have an open, fully funded position for a PhD student in single cell immunology and live cell imaging. See the <a href="pages/jointhelab">join</a> page for&nbsp;details.</p> <p>To apply, write an email to Fabio with a half page research interest statement and a <span class="caps">CV</span>.</p>2020-05-28T00:00:00+10:002020-05-28T00:00:00+10:00Fabio Zaninitag:fabilab.org,2020-05-28:/czieoss_2020.html

<p><img alt="opening" src="images/blog/czi_plus_igraph.png"></p> <p>We have received an award by the Chan Zuckerberg Initiative to support our contribution to <a href="https://igraph.org/">igraph</a> as essential open software! Thank you to all other awardees for their amazing work on&nbsp;igraph.</p> <p>See the <a href="https://chanzuckerberg.com/newsroom/awards-3-8-million-open-source-software-projects-essential-science/"><span class="caps">CZI</span> press release</a> and <a href="https://chanzuckerberg.com/eoss/proposals/providing-a-solid-foundation-for-network-analysis/">project description</a>.</p> <p><a href="pages/people.html">Yasir</a> has been contributing to igraph recently, it&#8217;s great to see our work on free software is&nbsp;appreciated!</p>2020-05-27T00:00:00+10:002020-05-27T00:00:00+10:00Fabio Zaninitag:fabilab.org,2020-05-27:/paulaklavinainternship.html

<p><img alt="opening" src="images/people/paula_klavina.jpg"></p> <p>Paula Klavina has joined as a visiting student from Trinity College biochemistry for the Winter! She&#8217;ll be looking at single cell biology in the neonatal lung - not an easy task but so much to&nbsp;discover!</p>2020-03-24T00:00:00+11:002020-03-24T00:00:00+11:00Fabio Zaninitag:fabilab.org,2020-03-24:/grantcellulargenomics2020.html

<p><img alt="opening" src="images/blog/cellular_genomics.png"></p> <p>The lab has received a seed grant from the <a href="https://research.unsw.edu.au/unsw-cellular-genomics-futures-institute"><span class="caps">UNSW</span> Cellular Genomics Futures Institute</a> to study the molecular basis of complex immune cell&nbsp;behaviour.</p> <p>Let&#8217;s figure out what makes immune cells so&nbsp;special!</p>2020-02-12T00:00:00+11:002020-02-12T00:00:00+11:00Fabio Zaninitag:fabilab.org,2020-02-12:/preprintlungimmune2020.html

<p><img alt="opening" src="images/lung_immune.png"></p> <p>Our preprint with the Alvira and Cornfield labs is out! What happens to our lung immune cells when we inhale our first breath of air? Oxygen and&nbsp;pathogens!</p> <p><a href="https://biorxiv.org/content/10.1101/2020.02.10.942359v1">https://biorxiv.org/content/10.1101/2020.02.10.942359v1</a></p> <p>We discovered that <strong>right before birth</strong> the lung immune landscape in mice is dominated by a <strong>highly specific type of macrophage (Mac I)</strong> that is proliferative and expresses tissue remodeling genes over pathogen defense genes. These cells <strong>beautifully encircle small blood vessels</strong>.</p> <p>Fast forward to <strong>one day after birth</strong>, and <strong>a Pandora box has been opened</strong>! Four different kinds of macrophages with multiple subtypes within; three kinds of dendritic cells; B, T, <span class="caps">NK</span>, and innate lymphoid cells; basophils and mast cells, and a diverse set of&nbsp;neutrophils.</p> <p>Three weeks into air-breathing life and lung immunity starts looking like an adult tissue, with lots of lymphocytes and a gene expression that relates to pathogen&nbsp;protection.</p> <p>Thank you to all authors for their amazing work, and special thanks to Racquel Domingo-Gonzales (my co-first author), Xibing Che (soo many experiments!), and Michael Swift (the lymphocyte&nbsp;expert).</p>2020-01-11T00:00:00+11:002020-01-11T00:00:00+11:00Fabio Zaninitag:fabilab.org,2020-01-11:/postdocopening012020.html

<p><img alt="opening" src="images/blog/postdoc.jpg"></p> <p>We have an opening for a Postdoctoral Researcher in <strong>computational biology</strong>.</p> <p><strong>Topic</strong>: Identifying all cell types in the human&nbsp;body.</p> <p><strong>Time frame</strong>: 1 year, maybe longer. Starting&nbsp;anytime.</p> <p><strong>Requirements</strong>: Proficiency (PhD level) with computational analysis of biomedical data including&nbsp;coding.</p> <p><strong>+</strong>: Knowledge of Python and basic Javascript, linear algebra and stats will make your life&nbsp;easier.</p> <p><strong>++</strong>: Experience with single cell transcriptomic&nbsp;data.</p> <p>Just write to Fabio (see <a href="pages/contact.html">contact page</a>) for&nbsp;inquiries.</p>2019-12-11T00:00:00+11:002019-12-11T00:00:00+11:00Fabio Zaninitag:fabilab.org,2019-12-11:/abacbs2019.html

<p><a href="https://www.abacbs.org/conference2019/about"><img alt="ABACBS 2019" src="images/blog/ABACBS_2019.png"></a></p> <p>Fabio just came back from the 2019 <span class="caps">ABACBS</span> conference which was an amazing display of exciting bioinformatics from all over Australia and beyond! Thank you to the organisers for their fantastic&nbsp;work!</p>2019-10-24T00:00:00+11:002019-10-24T00:00:00+11:00Fabio Zaninitag:fabilab.org,2019-10-24:/firstpost.html

<p>First post to test the website&nbsp;generator.</p> <p><svg height=300 width=100 id='ciao'></svg></p>