Tien-Chi Huang @tienchihuang.bsky.social · 23/09/2026www.genetics.cuimc.columbia.edu/news/memoria... such a giant.genetics.cuimc.columbia.eduIn memoriam of Professor Timothy H. BestorIn memoriam: Professor Timothy H. Bestor 1952-2026 075
Tien-Chi Huang @tienchihuang.bsky.social · 11/09/2026www.nature.com/articles/s41... I hope we will get the answer in my lifetime. 😂nature.comPRC2–RNA interactions through the lens of bioinformatics pipeline choices - Nature Reviews Molecular Cell BiologyFour recent studies that have differently assessed PRC2–RNA interactions reveal key technical pitfalls underlying research in the field. 010
Reposted by Tien-Chi HuangReese Richardson @reeserichardson.bsky.social · 25/08/2026A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵 18455329
Reposted by Tien-Chi HuangCameron Thrash @jcamthrash.bsky.social · 18/08/2026As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles journals.asm.org/doi/full/10.... #jcampubs 77126
Reposted by Tien-Chi HuangDi Jiang @dijiang319.bsky.social · 30/07/2026Why is the X chromosome rich in L1 mobile elements? @science.org X-chromosome inactivation draws L1 mutagenesis to the human X chromosome | Science www.science.org/doi/10.1126/...science.orgX-chromosome inactivation draws L1 mutagenesis to the human X chromosomeX-chromosome inactivation (XCI) enables gene dosage compensation in XX eutherians. Long interspersed element-1 (LINE-1 or L1) retrotransposons are unusually abundant on the human X chromosome and are ... 16018
Reposted by Tien-Chi HuangKonrad Chudzik @konrad-chudzik.bsky.social · 30/06/2026My first PhD paper is out in Nucleic Acids Research! We describe "Ab-trapping" - an antibody artifact that distorts assays relying on antibody diffusion (microscopy, CUT&Tag, CUT&RUN). The revisions made the story much stronger. Check it out! doi.org/10.1093/nar/...doi.orgAntibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleusAbstract. Chromatin has a complex 3D structure and diverse binding proteins that coordinate the genome’s most essential functions. Many microscopy and geno 36130
Reposted by Tien-Chi HuangStephen Royle @steveroyle.bsky.social · 09/04/2026It's been a while... dusted off some old code to see what the current publication lag times are at cell bio journals. At the end of the post there's the poor paper with the longest delay in the dataset... Hold On Hope: publication lag times at cell biology journals quantixed.org/2026/04/09/h...quantixed.orgHold On Hope: publication lag times at cell biology journalsPublication lag times are still a frustration for researchers. Although preprints circumvent the delay in sharing science with others, publication is still king when it comes to evaluation. Contracts are short and publication delays can be long… 22611
Reposted by Tien-Chi HuangTobias Warnecke @tobiaswarnecke.bsky.social · 08/04/2026academic.oup.com/genetics/adv... Also thanks to Lyndall & @psarkies.bsky.social, @ahocher.bsky.social, and members of the lab for their comments and Francis Barr @oxfordbiochemistry.bsky.social for encouraging me to write down my thoughts. 2/2academic.oup.comActually, what is a gain-of-function mutation?Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien 24611
Tien-Chi Huang @tienchihuang.bsky.social · 22/02/2026Happy to share our latest paper. Our findings uncover a unique chromatin architecture and spatial chromosome arrangement in gonadal germ cells and document that alongside global DNA demethylation, the germline epigenetic reprogramming involves reorganisation of the 3D genome.nature.comGlobal reorganization of genome architecture at the transition to gametogenesis - Nature Structural & Molecular BiologyHuang, Rigau and colleagues observe major changes in how DNA is organized in early germ cells before they start developing into sperm or eggs. These results show that germline removes structural ‘memo... 22511
Reposted by Tien-Chi HuangeLife @elife.bsky.social · 11/02/20265/ Marthe Gautier played a crucial role in identifying trisomy 21 as the cause of Down syndrome. Working with minimal institutional support, she built a cytogenetics laboratory from scratch and produced the preparations that revealed an extra chromosome in affected children. 176
Reposted by Tien-Chi HuangRetraction Watch @retractionwatch.com · 14/01/2026Nature has retracted a paper after an investigation at a U.K. institution found the first author — then a doctoral student — manipulated data.retractionwatch.comNature retracts paper for data manipulation by Ph.D. studentNature has retracted a paper after an investigation at a U.K. institution found the first author — then a doctoral student — manipulated data. The paper, which looked at the sensitivity of lu… 1135
Reposted by Tien-Chi HuangElphege Nora Lab at UCSF @elphegenoralab.bsky.social · 27/11/2025Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇 49045
Tien-Chi Huang @tienchihuang.bsky.social · 18/11/2025Happy to share our latest preprint. We uncover a previously uncharacterised and evolutionarily conserved chromatin architecture in premeiotic gonadal germ cells, revealed through integrated cytological and high-resolution Hi-C approaches. www.biorxiv.org/content/10.1... Thread🧵🔽 1166
Reposted by Tien-Chi HuangGang Fang @gangfang.bsky.social · 20/11/2024[3] Navigating the pitfalls of mapping DNA and RNA modifications www.nature.com/articles/s41... [*] Please note the detection of exogeneous DNA mods is different from mapping natural endogenous DNA mods , because abundant exogeneous DNA mods are introduced (e.g. Fiber-seq, DiMeLo-seq, etc) n/n [END]nature.comNavigating the pitfalls of mapping DNA and RNA modifications - Nature Reviews GeneticsThe ability to map DNA and RNA modifications has improved our understanding of these marks, but in some cases inconsistent results have been problematic. Here, Kong et al. discuss how to recognize and... 0124
Reposted by Tien-Chi HuangMaxim Greenberg @maxvcg.bsky.social · 09/08/2025I believe that over the past ~ two decades, since the breakthrough papers on UHRF1, this is the first reported DNA methylation phenotype of its close paralog, UHRF2 (and not for lack of trying). Congrats to Ambre Bender and Michael Weber on this fantastic study! www.nature.com/articles/s41...nature.comUHRF2 mediates resistance to DNA methylation reprogramming in primordial germ cells - Nature CommunicationsDNA methylation in mouse primordial germ cells (PGCs) is restricted to transposable elements, but how this unique DNA methylome is established is poorly understood. Here, the authors identify UHRF2 as... 13310
Tien-Chi Huang @tienchihuang.bsky.social · 20/07/2025Reading published results is like looking at the distant star-everything you see happened in the deep past. Light years between a truly novel discovery and its communication within the scientific community. 020
Reposted by Tien-Chi HuangJuliane Glaser @julianeg.bsky.social · 09/07/2025Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5nature.comEnhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature GeneticsActivation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c... 15296128
Tien-Chi Huang @tienchihuang.bsky.social · 04/07/2025It was nice to hear this story in the GRC conference. Glad it’s out.cell.comGeneration of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free conditionUsing mouse pluripotent stem cells, Nosaka et al. created an ovarian somatic cell (OSC)-free system to induce an abundant number of oocyte-like cells at diplotene arrest, followed by their growth into... 030
Reposted by Tien-Chi HuangKonrad Chudzik @konrad-chudzik.bsky.social · 14/04/2025🚨 Preprint alert 🚨 Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇 doi.org/10.1101/2025...doi.orgAb-trapping - a peripheral staining artifact in antibody-based microscopy and genomicsAntibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra... 26841
Reposted by Tien-Chi HuangME 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 Tien-Chi HuangJeff Vierstra @jeffvierstra.bsky.social · 24/01/2025There has been a couple of manuscripts released regarding transcription factor footprinting - or digital genomic footprinting (DGF) as we call it. I would like to put some of the claims, results and conclusions in context, since I have worked and published on this for ~15 years. 1/n 24212
Reposted by Tien-Chi HuangAafke Gros @aafkegros.bsky.social · 15/01/2025Microscopy Nodes is now up on bioRxiv! 🚀 This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev). High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬 www.biorxiv.org/content/10.1... 9330124