Reposted by Joanna AchingerAntonio Scialdone @antonio-scialdone.bsky.social · 03/03/2026Transposable elements are increasingly studied in single-cell data, but how reliable are current locus-level quantification methods in short-read scRNA-seq data? If you work with single-cell RNA-seq or TEs, we hope this is a useful resource — feedback very welcome! 1146
Reposted by Joanna AchingerAndrew Deans @genomestability.bsky.social · 15/05/2025I'm super excited to announce that registrations are now open for the 19th Australian Cell Cycle, DNA Repair and Telomere Workshop. Awesome international speaker line-up, with plenty of locals being invited! Book now to secure your earlybird rate. www.australiancellcycle.org 11710
Reposted by Joanna AchingerRichard Sever @richardsever.bsky.social · 19/06/2025“In all my discussions with scientists across every sector, exactly zero think the journal system works well.” Some will disagree with aspects of Seemay’s analysis but this point is undoubtedly true open.substack.com/pub/asterain...?open.substack.comScientific Publishing: Enough is EnoughWhy we're no longer funding journal publications 88727
Reposted by Joanna AchingerAlexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 10/06/20252nd Meeting on Epigenetics & Epigenomics - 24th - 26th September, Brussels 🇧🇪 Speakers Line-up looks fantastic including @adelmanlab.bsky.social @kjarmache.bsky.social @mariekeoudelaar.bsky.social @tinekelenstra.bsky.social @lucianodicroce.bsky.social www.xcellsconferences.com/epigenetics2...xcellsconferences.comEpigenetics 2025 | Xcells Conferences 0116
Reposted by Joanna AchingerAxel Visel @axelvisel.bsky.social · 18/06/2025Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22 216479
Reposted by Joanna AchingerEmadden @emadden.bsky.social · 18/06/2025🧬🧪Fiber-seq was developed and originally published by Andrew Stergachis (now at @uwdeptmedicine.bsky.social) in 2020. It's a very cool method for adding chromatin accessibility data to native LRS experiments. You should definitely check out the original paper: www.science.org/doi/10.1126/...science.orgSingle-molecule regulatory architectures captured by chromatin fiber sequencingFiber-seq translates single-molecule chromatin stencils into a readout of the primary architecture of chromatin. 093
Reposted by Joanna AchingerWaggoner Lab @labwaggoner.bsky.social · 17/06/2025STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social www.cell.com/cell/fulltex... 01911
Reposted by Joanna AchingerThomas R. Cox @trcox.matrixandmetastasis.com · 04/06/2025New review paper written by Jess Chitty in the team just out in Trends in Cancer (@cp-trendscancer.bsky.social) (OpenAccess) The extracellular matrix in cancer: from understanding to targeting | → www.sciencedirect.com/science/arti... ← |sciencedirect.comThe extracellular matrix in cancer: from understanding to targetingSignificant advances in matrix biology research have enhanced our understanding of individual matrix components and extracellular matrix (ECM) signall… 0115
Reposted by Joanna AchingerDelilah Hendriks @delilahhendriks.bsky.social · 28/05/2025Fun writing this piece with @bartegiani.bsky.social! 164
Reposted by Joanna AchingerVictor Javier @vjsanchez.bsky.social · 25/05/2025Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...github.comGitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain types of data visualization - What are they and why are they bad.Friends don't let friends make certain types of data visualization - What are they and why are they bad. - GitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain ty... 23815
Reposted by Joanna AchingerFrancesca Mattiroli @fmattiroli.bsky.social · 07/05/2025This is very interesting! 062
Reposted by Joanna AchingerAnders Sejr Hansen @andersshansen.bsky.social · 07/05/2025(1/n) New preprint from @claricehongky.bsky.social Fan Fang Varshini Ramanathan in collab w Jie Liu. Q: How do we get ultra-high-res 3D genome maps? A: New deep learning model, Cleopatra. Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution. 36523
Reposted by Joanna AchingerEric Miska Lab @miskalab.bsky.social · 06/05/2025@fxquah.bsky.social 's paper is finally out @genomeresearch.bsky.social and we made the cover!! This was only possible due to the brilliant illustration by @sonhita.bsky.social Paper here: genome.cshlp.org/content/35/5... See below for more details 🧵 13512
Reposted by Joanna AchingerTransposon and Cancer Epigenetics Group @deniz-lab.bsky.social · 06/05/2025I am excited to share our lab's first review out with in Blood Cancer Journal. We discuss the impact of transposable elements on genome regulation and variation in both normal haematopoietic processes and haematological cancers. www.nature.com/articles/s41...nature.comTransposable elements as genome regulators in normal and malignant haematopoiesis - Blood Cancer JournalBlood Cancer Journal - Transposable elements as genome regulators in normal and malignant haematopoiesis 02710
Reposted by Joanna AchingerGamze Gürsoy @gamzeandgursoy.bsky.social · 14/04/2025Super excited to share the first 3D genome paper from my lab @narjournal.bsky.social , led by my smart and hardworking student Carlos (joint with @LuLaboratory) with assists from a brilliant summer intern Narjis. (1/n) academic.oup.com/nar/article/...academic.oup.compC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C dataAbstract. The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughpu 173
Reposted by Joanna AchingerHannah Long @hannahlong.bsky.social · 15/04/2025📣 A reminder about an open postdoctoral position in our group! 🧫 Are you interested in mechanisms of gene regulation, human facial development and disease? How our DNA shapes the way we look? Do you love chromatin and enhancers? 🧬 If so, reach out for an informal chat! 💬 longlab.co.ukelxw.fa.em3.oraclecloud.comPostdoctoral ResearcherOur research is focused on understanding how genetic changes in the non-coding genome can impact gene regulatory mechanisms, alter developmental processes and ultimately affect human craniofacial shap... 0818
Reposted by Joanna AchingerJuliane Glaser @julianeg.bsky.social · 15/04/2025A beautiful example of how cautious interpretation of an artifact leads to important results for the scientific community👇Congrats @konrad-chudzik.bsky.social @drmrobson.bsky.social and all authors! 071
Reposted by Joanna AchingerChris Saunders @ctsa.bsky.social · 10/04/2025Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n) doi.org/10.1093/bioi...doi.orgSawfish: Improving long-read structural variant discovery and genotyping with local haplotype modelingAbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu 24324
Reposted by Joanna AchingerMark Peifer (He, him) @peiferlabunc.bsky.social · 07/04/2025Colossal is back with their totally BS claims. They reverse engineered snps into 14 GENES and claim they changed a grey wolf into a dire wolf. 1/n time.com/7274542/colo...time.comThe Return of the Dire WolfColossal Biosciences has genetically engineered the first dire wolf to live in over 10,000 years. Here's what that means for other extinct species. 46719
Reposted by Joanna AchingerJacob Schreiber @jmschreiber91.bsky.social · 31/03/2025Interesting paper on using long-read sequencing to consider accessibility at repetitive elements. Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2 www.science.org/doi/full/10....science.org 1122
Reposted by Joanna AchingerKevin Mitchell @wiringthebrain.bsky.social · 01/03/2025Good Lord. EWAS w/ n's in the tens? This nonsense has to stop. Trauma leaves marks across generations but they're not epigenetic. 712126
Reposted by Joanna AchingerJohn Greally @greally.bsky.social · 01/03/2025I can't believe we're still allowing completely inadequate and uninterpretable Epigenome-Wide Association Studies (EWAS) to be published. I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria. www.nature.com/articles/s41...nature.comEpigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees - Scientific ReportsScientific Reports - Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees 47932
Reposted by Joanna AchingerPaul Noth @paulnoth.bsky.social · 12/03/2025Mine in today’s @newyorker.com 231177386
Reposted by Joanna AchingerLuca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 29/03/2025Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth 615059
Reposted by Joanna AchingerPradeepa Madapura @pradeepmadapura.bsky.social · 26/03/2025Check out our preprint "De-repression of Transposable Elements by Histone Hyperacetylation Leads to Sterile Inflammation in Preeclampsia" www.researchsquare.com/article/rs-6... 24315
Reposted by Joanna AchingerMaya Voichek @mayavoichek.bsky.social · 17/03/20251/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇 12547259
Reposted by Joanna AchingerSeth Cheetham @sethcheetham.bsky.social · 06/03/2025#mRNA meets Tardigrades! Delivery of an mRNA encoding a protein from the famously tough animal can protect healthy tissue from damaging radiation. Very creative! #RNAsky www.nature.com/articles/s41...nature.comRadioprotection of healthy tissue via nanoparticle-delivered mRNA encoding for a damage-suppressor protein found in tardigrades - Nature Biomedical EngineeringRadiation-therapy-induced DNA damage in oral and rectal epithelial cells can be reduced via the nanoparticle-mediated local delivery of messenger RNA encoding for a damage-suppressor protein found in ... 0127
Reposted by Joanna AchingerJoe Peters Lab @joepeterslab.bsky.social · 06/03/2025Telomeric transposons are pervasive in linear bacterial genomes | Science www.science.org/doi/10.1126/...science.orgTelomeric transposons are pervasive in linear bacterial genomesEukaryotes have linear DNA and their telomeres are hotspots for transposons, which in some cases took over telomere maintenance. Here we identify several families of independently evolved telomeric tr... 614375
Reposted by Joanna AchingerGeorge Ghanim @automnenine.bsky.social · 07/03/2025Did you know that two jumping sequences (LINE-1 and Alu) make up nearly 30% of our genomes? Ever wonder how they jump into new genomic sites? We have some exciting discoveries to share new in @science.org on the structural mechanisms of LINE-1 retrotransposition (aka jumping 🧬➡️🧬) 🧪 #ScienceResearch 611143
Reposted by Joanna AchingerTony Cesare @thecesarelab.bsky.social · 04/03/2025Review from our lab out today: "Roles for the 3D Genome In the cell cycle, DNA replication, and double strand break repair." Written by @scientistkate.bsky.social, with her co-supervisor @piptaberlay.bsky.social and collaborator Mat Jones. www.frontiersin.org/journals/cel... 05716
Reposted by Joanna AchingerPedro Rocha @pedroprocha.bsky.social · 26/02/2025Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development. Loss of a single CTCF motif is sufficient to cause embryonic lethality. www.sciencedirect.com/science/arti...sciencedirect.comDeletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic developmentChromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr… 813440
Reposted by Joanna AchingerArnaud Krebs @arnaudkr.bsky.social · 21/02/2025Program is out for our first EMBL #singlemolecule gene regulation meeting! Check out the dedicated panel sessions on single molecule genomics, single molecule imaging and theory where we would like to brainstorm the future of the field: Registration is open! 👇 www.embl.org/about/info/c...embl.orgGene regulation: one molecule at a time 0129
Reposted by Joanna AchingerME Torres-Padilla @metorrespadilla.bsky.social · 21/02/2025Paper out !!🥳big thanks to all authors @marliesoomen.bsky.social @diego-rt.bsky.social @kaessmannlab.bsky.social @jonathangoeke.bsky.social @lorenzamottes.bsky.social & 'bluesky-less' Lots of interesting new TE (& genes) biology Data fully browsable💻 👉 embryo.helmholtz-munich.de/shiny_embryo/ 814153
Reposted by Joanna AchingerKate Quinlan @katequinlan.bsky.social · 14/02/2025I have created a Bsky account just in time for #LorneGenome25 so that I can post from (and about) the meeting. I am very proud of the program that the Organising Committee has pulled together (www.lornegenome.org) and can't wait to see you all on Sunday! Looking forward to some science by the beach! 1227
Reposted by Joanna AchingerStefano Mangiola @stemang.bsky.social · 11/02/2025📢 An exciting #Postdoc position opened in our laboratory for a junior #Bioinformatician! Developing #Bioinformatic and #AI tools to advance precision oncology using the available #singlecell / #spatial data universe. careers.adelaide.edu.au/cw/en/job/51... Pls share! 🙏 #postdocposition 096
Reposted by Joanna AchingerAlistair Forrest @alforrest.bsky.social · 12/02/2025Heading to #lornegenome25 #LorneCancerConference ? Looking for a computational postdoc to work on spatial and single nuclei transcriptomics of poor prognosis cancers, please DM me or see me at Lorne. We will be advertising soon. @ozsinglecell.bsky.social #LorneCancer2025 #Lorne2025bsky.app 11012
Reposted by Joanna AchingerJackson Hoffman @jxhoffman.bsky.social · 12/02/2025Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that: 1) active histone mods occur independently of transcription 2) transcription coordinates histone deacetylation at active promoters www.science.org/doi/10.1126/...science.orgRNA polymerase II coordinates histone deacetylation at active promotersTranscription initiation limits histone acetylation and H2AZ incorporation at promoters. 511641
Reposted by Joanna AchingerThe Groth lab @grothlab.bsky.social · 12/02/2025🚨𝐌𝐚𝐣𝐨𝐫 𝐉𝐨𝐛 𝐀𝐥𝐞𝐫𝐭!🚨The Groth @groth-anja.bsky.social, Mailand, Nilsson @nilssonlab.bsky.social & Krietenstein @nilskrietenstein.bsky.social labs are hiring 𝟔 𝐏𝐡𝐃&𝐩𝐨𝐬𝐭𝐝𝐨𝐜𝐬 to join the new Center for Epigenetic Cell Memory (EpiC) in Copenhagen, Denmark. Apply here: tinyurl.com/yvd93na2 & please share!tinyurl.com6 Postdoctoral and PhD positions in Center for Epigenetic Cell Memory (EpiC)The Center for Epigenetic Cell Memory (EpiC) is a new Center of Excellence that will be established based on funding by the Danish National Research Foundation. 24545
Reposted by Joanna AchingerHore Lab @epiotago.bsky.social · 26/01/2025Delighted to share our 'Androgen clock' paper in #PNAS ow.ly/Guts50ULghF - the first way to predict long-term androgen exposure using DNA alone. We so much more than the sequence we are born with! Stellar work (and animation - SOUND ON) by Dr Victoria Sugrue youtu.be/GL55yjMalIIyoutu.bePredicting ‘male-time’ with the Androgen ClockYouTube video by Epigenetics Otago 083
Reposted by Joanna AchingerMel Eckersley-Maslin @meleckmas.bsky.social · 30/01/2025We're #hiring a #postdoc to join our lab 🧪 in Melbourne 🇦🇺🦘 in #StemCell and #Cancer #Epigenetics. Great opportunity to lead a research project within the broader vision of the lab, with plenty of scope to develop as an independent leader 👩🔬🔬 Apply by 27 Feb careers.petermac.org/job/MELBOURN...careers.petermac.orgPostdoctoral Researcher - Eckersley Maslin LabPostdoctoral Researcher - Eckersley Maslin Lab 01713
Reposted by Joanna AchingerDarko Barisic @darkobar.bsky.social · 30/01/2025Long-read sequencing just got an upgrade. 📢 Genome, methylome, epigenome & transcriptome in one go—haplotype-resolved & at single-molecule resolution. 🔥 062
Reposted by Joanna AchingerStephen Turner @stephenturner.us · 27/01/2025Genetic coupling of enhancer activity and connectivity in gene expression control www.nature.com/articles/s41467-025-… 🧬🖥️🧪 ...beautiful plots made with #Rstats plotgardner phanstiellab.github.io/plotgardener 2194
Reposted by Joanna AchingerRoman Barth @romanbarth.bsky.social · 27/01/2025CTCF stall DNA 🧬 loop ➰ extrusion by cohesin - but exactly how it pulls this off is a 'mechanistic mystery' (to cite @andersshansen.bsky.social, Nucleus, 2020). We just preprinted 📜 a new study @biorxivpreprint.bsky.social that provides some answers to this enigma: www.biorxiv.org/content/10.1... 53812
Reposted by Joanna AchingerTeif lab @teiflab.bsky.social · 23/01/2025Multiscale footprints reveal the organization of cis-regulatory elements www.nature.com/articles/s41... ▶️Footprints of DNA–protein interactions from bulk & single-cell ATAC-seq ⤵️ ▶️Deep learning to infer transcription factor and nucleosome binding ▶️Age-associated reduction of nucleosome footprints 0167
Reposted by Joanna AchingerOded Rechavi @odedrechavi.bsky.social · 18/01/2025If there's something we don't understand I assume transposons are responsible unless proven otherwise 1612829
Reposted by Joanna AchingerLucas Waltzer @lucaswaltzer.bsky.social · 19/01/2025An interesting link between 5mC and m6A; when #epigenetics meets #epitranscriptomics! www.cell.com/cell/abstrac...cell.comFine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiationBeyond its role as RNA m6A writer, METTL3-METTL14 can mediate 5mC deposition on DNA by recruiting the DNA methyltransferase DNMT1 to chromatin. The two marks co-orchestrate the expression of key genes... 0117
Reposted by Joanna AchingerThe Lonely Pipette @lonelypipette.bsky.social · 16/01/2025[📢 BIG ANNOUNCEMENT] We're partnering with @network-alba.bsky.social for their season 2. Worried about going from post-doc to group leader? In this new mini-series, we'll dive into this critical career stage with stories and experts 💌Subscribe to their newsletter : www.alba.network/diversity-po... 154
Reposted by Joanna Achinger@PhysGenCenter @physgencenter.bsky.social · 14/01/2025There’s a lot to unpack in our recent Science Advances paper - come check it out! Here’s a thread on what we found. #chromatin #genomics #biophotonics #dna #epigenetics #imaging #northwestern #science #biology #aging #longevity #biomedicine #cpge www.science.org/doi/10.1126/...science.orgChromatin conformation, gene transcription, and nucleosome remodeling as an emergent systemGene transcription is an emergent phenomenon of packing domain geometry in situ. 11911
Reposted by Joanna AchingerMing Tommy Tang @tommytang.bsky.social · 14/01/2025I promised to write an end-to-end tutorial to replicate this genomics figure during the holidays. Now it is ready 👇 1266
Reposted by Joanna AchingerRan Blekhman @blekhman.bsky.social · 14/01/2025Yes, they can hallucinate papers that don't exist, discuss results that seem to be imaginary, and can be confusing and inconsistent. But talking to tenured professors may still be helpful 14744167