Qi Chen @qichen-lab.bsky.social · 12/09/2026Hearty congratulations to Xudong on receiving an NIH K99 — one of our wishes during our lab anniversary trip has come true. Wishing you a golden future ahead! 001
Reposted by Qi ChenAaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208... 183101
Reposted by Qi ChenQi Chen @qichen-lab.bsky.social · 20/07/2026A tRNA/rRNA can be cleaved into different small RNAs with distinct functions depending on the cut site, yet abundance-based small RNA analysis is blind to it. Tong Zhou & us built a tool to read that hidden layer. Meet qMAP & the 'RNA fragmentome' @molsystbiol.org link.springer.com/article/10.1...link.springer.comqMAP decodes RNA fragmentation dynamics in development and disease - Molecular Systems BiologyNoncanonical small RNAs, such as tRNA-derived (tsRNAs) and rRNA-derived (rsRNAs) fragments, are more abundant than microRNAs and arise from selective cleavage events rather than random degradation. Wh... 063
Qi Chen @qichen-lab.bsky.social · 26/07/2026Adding to the intriguing story of Vault structures & their component Vault RNAs, we highlighted that Vault RNA-derived small RNAs (vtsRNAs) also bear biological functions: nature.com/articles/s41... It's Fascinating to see how nature always repurposes molecules for new functions! ♾ 050
Qi Chen @qichen-lab.bsky.social · 20/07/2026A tRNA/rRNA can be cleaved into different small RNAs with distinct functions depending on the cut site, yet abundance-based small RNA analysis is blind to it. Tong Zhou & us built a tool to read that hidden layer. Meet qMAP & the 'RNA fragmentome' @molsystbiol.org link.springer.com/article/10.1...link.springer.comqMAP decodes RNA fragmentation dynamics in development and disease - Molecular Systems BiologyNoncanonical small RNAs, such as tRNA-derived (tsRNAs) and rRNA-derived (rsRNAs) fragments, are more abundant than microRNAs and arise from selective cleavage events rather than random degradation. Wh... 063
Reposted by Qi ChenNature Biotechnology @natbiotech.nature.com · 15/07/2026This Perspective positions cellular self-organization as a foundational principle for the origin of multicellular life and discusses how decoding this concept with stem cell-based models will advance biological engineering go.nature.com/4e1m3Br rdcu.be/ftZeLgo.nature.comDecoding the origins of cellular self-organization for engineered biology - Nature BiotechnologyThis Perspective positions cellular self-organization as a foundational principle for the origin of multicellular life and discusses how decoding this concept with stem cell-based models will advance ... 0125
Qi Chen @qichen-lab.bsky.social · 02/06/2026After years of crystallization, in @natbiotech.nature.com, @zernickagoetz.bsky.social and I discuss the evolutionary origins of multicellularity & how physical constraints inevitably drive cellular self-organization. Harnessing these rules may help us better understand & engineer life rdcu.be/flTKa 0123
Reposted by Qi ChenNature Biotechnology @natbiotech.nature.com · 01/06/2026Decoding the origins of cellular self-organization for engineered biology - @qichen-lab.bsky.social @zernickagoetz.bsky.social go.nature.com/4e1m3Brgo.nature.comDecoding the origins of cellular self-organization for engineered biology - Nature BiotechnologyThis Perspective positions cellular self-organization as a foundational principle for the origin of multicellular life and discusses how decoding this concept with stem cell-based models will advance ... 1166
Reposted by Qi ChenQi Chen @qichen-lab.bsky.social · 20/01/2026Perhaps the most puzzling part: We see a paradox: the rsRNA length shift is progressive⏳yet the global RNA profile shows an "Aging Cliff"📉. Cliff or Progression? Maybe the gradual shift is the forerunner—accumulating silently until it triggers the cliff. bsky.app/profile/qich... 074
Reposted by Qi ChenScience X / Phys.org @sciencex.bsky.social · 20/01/2026A molecular "aging clock" has been identified in human sperm RNA, showing progressive changes with age that may influence offspring health and metabolism. doi.org/hbkmvfphys.orgScientists discover a hidden RNA 'aging clock' in human spermIncreasing paternal age has been linked to elevated health risks for the next generation, including higher risks of obesity and stillbirth. 054
Reposted by Qi ChenJulie Kiefer @julieckiefer.bsky.social · 21/01/2026Fascinating research! Qi Chen and colleagues have identified a potential "aging cliff" in sperm RNA (rsRNA) that is associated with the increased health risks for the next generation that accompany advancing paternal age. Read on uofuhealth.utah.edu/newsroom/new...uofuhealth.utah.eduScientists Discover a Hidden RNA “Aging Clock” in Human SpermThe molecular contents of sperm go through similar shifts over time in both mice and humans, which may lead to a rapid, dramatic shift at mid-life. 021
Reposted by Qi ChenThe EMBO Journal @embojournal.org · 20/01/2026What underlies the impact of sperm aging on fertility and offspring health? small ncRNA profiling by Kenneth Aston, Tong Zhou, @qichen-lab.bsky.social and colleagues reveals a drastic shift in RNA complements able to affect recipient cell metabolism link.springer.com/article/10.1...link.springer.comConserved shifts in sperm small non-coding RNA profiles during mouse and human aging - The EMBO JournalSperm aging impacts male fertility and offspring health, highlighting the need for reliable aging biomarkers to guide reproductive decisions. However, the molecular determinants of sperm fitness durin... 054
Qi Chen @qichen-lab.bsky.social · 20/01/2026Perhaps the most puzzling part: We see a paradox: the rsRNA length shift is progressive⏳yet the global RNA profile shows an "Aging Cliff"📉. Cliff or Progression? Maybe the gradual shift is the forerunner—accumulating silently until it triggers the cliff. bsky.app/profile/qich... 074
Qi Chen @qichen-lab.bsky.social · 20/01/20261/5 It took us some time to connect the dots...now in @embojournal.org we use PANDORA-seq to start decoding the 'sperm RNA code of aging' We find a conserved rsRNA length shift that reflects aging in both mouse & human sperm, and an 'aging cliff' at mid-life🧵 link.springer.com/article/10.1... 194
Qi Chen @qichen-lab.bsky.social · 25/12/2025A road trip to Monument Valley and the wonders of the west, as an anniversary of lab’s 10th year operation…look forward to the journey ahead… 000
Qi Chen @qichen-lab.bsky.social · 23/12/2025Glad to see this thoughtful piece in @quantamagazine.bsky.social on paternal epigenetic inheritance and the emerging 'Sperm RNA Code', featuring many active colleagues in the field. It’s a reminder that our actions may echo in the next generation(s) & there are immense unknowns to explore... 020
Reposted by Qi ChenBruno Di Stefano @distefanolab.bsky.social · 28/10/20251/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...nature.comSelective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature BiotechnologyStem cell differentiation is controlled by manipulating RNA condensates. 49437
Qi Chen @qichen-lab.bsky.social · 18/09/2025After developing PANDORA-seq to reveal hidden small RNAs (e.g., tsRNA, rsRNA) and SPORTS to annotate them, we now expand our toolchain with Tong Zhou lab: introducing FUSION, a tool that robustly interprets small RNA changes even in small or 1-on-1 datasets. academic.oup.com/bioinformati...academic.oup.comFUSION: a family-level integration approach for robust differential analysis of small non-coding RNAsAbstractMotivation. Beyond well-studied microRNAs, noncanonical small non-coding RNAs (sncRNAs) derived from longer parental templates such as tRNAs, rRNAs 020
Qi Chen @qichen-lab.bsky.social · 20/08/2025Perhaps our boldest hypothesis… we propose a model for RNA Structural Memory propagation in @natcellbio.nature.com where RNA conformation is reshaped by stress, locked by RBPs, copied prion-like in condensates & passed across generations—all without altering DNA rdcu.be/eBwPJ 182
Reposted by Qi ChenTrends in Biochemical Sciences @cp-trendsbiochem.bsky.social · 01/05/2025Our 🌷 May 🌷 issue is online with a broad range of article topics and formats! In their Opinion article (on the cover, too!), @qichen-lab.bsky.social and colleagues describe the interactions between small ncRNAs and Toll-like receptors. Find the issue here: www.cell.com/trends/bioch... 153
Qi Chen @qichen-lab.bsky.social · 01/05/2025Very glad to see our Sequential Activation Hypothesis highlighted on the cover @cp-trendsbiochem.bsky.social , linking small RNA-TLR interactions to autoimmune disease mechanisms. 042
Reposted by Qi ChenNature Protocols @natprot.nature.com · 08/04/2025#NewNProt for #genomewide characterization of a diverse set of #smallnoncodingRNAs in cells and tissuesbit.lyOptimized identification and characterization of small RNAs with PANDORA-seq - Nature ProtocolsThis Protocol describes optimized procedures for purification and sequencing of small noncoding RNAs from a variety of samples to characterize these diverse RNA species and map them to the parental RNAs from which they originate. 021
Qi Chen @qichen-lab.bsky.social · 04/04/2025We put together a step-by-step protocols for PANDORA-seq, now available in Nature Protocols @natprot.bsky.social , including the sample preparation for sperm, sperm heads; and the analyzing software SPORTS optimized for various types of small RNAs including tsRNAs, rsRNAs, and miRNAs. rdcu.be/egk1Z 041
Qi Chen @qichen-lab.bsky.social · 16/02/2025How can abnormal small RNA biogenesis spark autoimmune disease? Our opinion @cp-trendsbiochem.bsky.social discuss a novel two-stage activation hypothesis that may explain why autoimmunity hits women harder, via small RNA-TLR7/8 interactions & augmented by autoantibodies. www.cell.com/trends/bioch... 153
Reposted by Qi Chenericgreerlab.bsky.social @ericgreerlab.bsky.social · 05/12/2024go.bsky.app/QkSL6S5 031
Qi Chen @qichen-lab.bsky.social · 30/11/2024Starting this platform with the excursion to the historic village Shirakawa-go. #tRNA2024 conference at Kanazawa, Japan 150