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Joanna Achinger

@aachinger.bsky.social
612 followers 550 following 7 posts

Lab head in 3D chromatin organisation at SAiGENCI, University of Adelaide 🇦🇺 | Interested in 3D chromatin structure, gene regulation, transposable elements and cancer | website: achingerlab.com

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Reposted by Joanna Achinger
Antonio Scialdone @antonio-scialdone.bsky.social · 03/03/2026
Transposable 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!
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Andrew Deans @genomestability.bsky.social · 15/05/2025
I'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
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Richard 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.com
Scientific Publishing: Enough is Enough
Why we're no longer funding journal publications
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 10/06/2025
2nd 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.com
Epigenetics 2025 | Xcells Conferences
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Axel Visel @axelvisel.bsky.social · 18/06/2025
Textbooks: “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
A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.
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Emadden @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.org
Single-molecule regulatory architectures captured by chromatin fiber sequencing
Fiber-seq translates single-molecule chromatin stencils into a readout of the primary architecture of chromatin.
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Waggoner Lab @labwaggoner.bsky.social · 17/06/2025
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social www.cell.com/cell/fulltex...
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Reposted by Joanna Achinger
Thomas R. Cox @trcox.matrixandmetastasis.com · 04/06/2025
New 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.com
The extracellular matrix in cancer: from understanding to targeting
Significant advances in matrix biology research have enhanced our understanding of individual matrix components and extracellular matrix (ECM) signall…
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Reposted by Joanna Achinger
Delilah Hendriks @delilahhendriks.bsky.social · 28/05/2025
Fun writing this piece with @bartegiani.bsky.social!
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Victor Javier @vjsanchez.bsky.social · 25/05/2025
Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...
github.com
GitHub - 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...
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Francesca Mattiroli @fmattiroli.bsky.social · 07/05/2025
This is very interesting!
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Anders 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.
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Eric 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 🧵
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Transposon and Cancer Epigenetics Group @deniz-lab.bsky.social · 06/05/2025
I 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.com
Transposable elements as genome regulators in normal and malignant haematopoiesis - Blood Cancer Journal
Blood Cancer Journal - Transposable elements as genome regulators in normal and malignant haematopoiesis
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Gamze Gürsoy @gamzeandgursoy.bsky.social · 14/04/2025
Super 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.com
pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data
Abstract. The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughpu
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Hannah 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.uk
elxw.fa.em3.oraclecloud.com
Postdoctoral Researcher
Our 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...
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Juliane Glaser @julianeg.bsky.social · 15/04/2025
A 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!
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Chris Saunders @ctsa.bsky.social · 10/04/2025
Great 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.org
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling
AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 07/04/2025
Colossal 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.com
The Return of the Dire Wolf
Colossal Biosciences has genetically engineered the first dire wolf to live in over 10,000 years. Here's what that means for other extinct species.
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Jacob Schreiber @jmschreiber91.bsky.social · 31/03/2025
Interesting 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
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Kevin Mitchell @wiringthebrain.bsky.social · 01/03/2025
Good Lord. EWAS w/ n's in the tens? This nonsense has to stop. Trauma leaves marks across generations but they're not epigenetic.
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John Greally @greally.bsky.social · 01/03/2025
I 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.com
Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees - Scientific Reports
Scientific Reports - Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees
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Paul Noth @paulnoth.bsky.social · 12/03/2025
Mine in today’s @newyorker.com
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 29/03/2025
Celebrating 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
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Pradeepa Madapura @pradeepmadapura.bsky.social · 26/03/2025
Check out our preprint "De-repression of Transposable Elements by Histone Hyperacetylation Leads to Sterile Inflammation in Preeclampsia" www.researchsquare.com/article/rs-6...
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Maya Voichek @mayavoichek.bsky.social · 17/03/2025
1/ 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 🧵👇
Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte
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Seth 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.com
Radioprotection of healthy tissue via nanoparticle-delivered mRNA encoding for a damage-suppressor protein found in tardigrades - Nature Biomedical Engineering
Radiation-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 ...
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Joe Peters Lab @joepeterslab.bsky.social · 06/03/2025
Telomeric transposons are pervasive in linear bacterial genomes | Science www.science.org/doi/10.1126/...
science.org
Telomeric transposons are pervasive in linear bacterial genomes
Eukaryotes 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...
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George Ghanim @automnenine.bsky.social · 07/03/2025
Did 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
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Tony Cesare @thecesarelab.bsky.social · 04/03/2025
Review 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...
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Pedro Rocha @pedroprocha.bsky.social · 26/02/2025
Here 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.com
Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development
Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…
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Arnaud Krebs @arnaudkr.bsky.social · 21/02/2025
Program 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.org
Gene regulation: one molecule at a time
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ME Torres-Padilla @metorrespadilla.bsky.social · 21/02/2025
Paper 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/
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Kate Quinlan @katequinlan.bsky.social · 14/02/2025
I 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!
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Stefano 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
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Alistair Forrest @alforrest.bsky.social · 12/02/2025
Heading 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 #Lorne2025
bsky.app
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Jackson Hoffman @jxhoffman.bsky.social · 12/02/2025
Unpause! 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.org
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
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The 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.com
6 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.
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Hore Lab @epiotago.bsky.social · 26/01/2025
Delighted 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/GL55yjMalII
youtu.be
Predicting ‘male-time’ with the Androgen Clock
YouTube video by Epigenetics Otago
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Mel Eckersley-Maslin @meleckmas.bsky.social · 30/01/2025
We'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.org
Postdoctoral Researcher - Eckersley Maslin Lab
Postdoctoral Researcher - Eckersley Maslin Lab
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Darko Barisic @darkobar.bsky.social · 30/01/2025
Long-read sequencing just got an upgrade. 📢 Genome, methylome, epigenome & transcriptome in one go—haplotype-resolved & at single-molecule resolution. 🔥
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Stephen Turner @stephenturner.us · 27/01/2025
Genetic 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
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Roman Barth @romanbarth.bsky.social · 27/01/2025
CTCF 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...
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Teif lab @teiflab.bsky.social · 23/01/2025
Multiscale 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
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Oded Rechavi @odedrechavi.bsky.social · 18/01/2025
If there's something we don't understand I assume transposons are responsible unless proven otherwise
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Lucas Waltzer @lucaswaltzer.bsky.social · 19/01/2025
An interesting link between 5mC and m6A; when #epigenetics meets #epitranscriptomics! www.cell.com/cell/abstrac...
cell.com
Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation
Beyond 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...
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The 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...
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@PhysGenCenter @physgencenter.bsky.social · 14/01/2025
There’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.org
Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system
Gene transcription is an emergent phenomenon of packing domain geometry in situ.
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Ming Tommy Tang @tommytang.bsky.social · 14/01/2025
I promised to write an end-to-end tutorial to replicate this genomics figure during the holidays. Now it is ready 👇
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Ran Blekhman @blekhman.bsky.social · 14/01/2025
Yes, 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
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