James Dewar
@jamesmdewar.bsky.social
Assistant Professor, @VUbasicsciences.bsky.social. DNA replication & repair | Biochemistry | Agentic bioinformatics | AI for Biomedical Education & Research Training | https://orcid.org/0000-0003-4153-3818
Excited to speak later this month at the ORISE week-long online symposium on AI Opportunities in STEM. It’s free, open to all, and designed for faculty and trainees. orisesymposium2026.vfairs.com Timing feels perfect: I’ve seen a real uptick in interest in this topic over the past few weeks.
Excited to share my piece in @nature.com Careers on why scientists are already trained for AI, plus ten places to start. 🧑🔬🤖 www.nature.com/articles/d41... Hope it helps! 🙏 Incredibly grateful to editors Jack Leeming and @jperkel.bsky.social for the opportunity and collaboration.
Want to get more from AI? Treat every prompt like an experiment
Taking a scientific approach to artificial-intelligence queries makes every output a result to be checked, says James Dewar. Here are ten tips for doing it right.
nature.com
Excited to see this published and to be able to read the whole story! Exciting science and a tour de force. www.nature.com/articles/s41... Ragini also gave a phenomenal talk on this at GS-Connect (gs-connect.us).
Centromeric footprints preserve telomere integrity in ALT cancers - Nature
Centromeric DNA repeat insertions and CENP-A chromatin assembly are identified as genomic signatures that preserve telomere integrity in ALT cancer cells.
nature.com
🧬 ⛓️💥 Our paper is now out in @natsmb.nature.com ! We examined the fate of replication forks that collapse at single-strand DNA breaks (SSBs) in vertebrates 🐸, comparing the consequences of collapse at single vs convergent forks. www.nature.com/articles/s41...
Distinct repair outcomes from single and convergent replication fork collapse - Nature Structural & Molecular Biology
Here the authors show that collapse of single replication forks causes recombination, end fusions or degradation but does not restart DNA synthesis. In contrast, collapse of convergent forks completes...
nature.com
Excited to share a preprint of my review: "How Topoisomerases Relax and Disentangle the Genome During DNA Replication" 🧬🪢🧵✂️🙏 papers.ssrn.com/sol3/papers....
How Topoisomerases Relax and Disentangle the Genome During DNA Replication
DNA replication generates topological stress that must be relaxed and molecular entanglements that must be resolved. Unwinding of the parental duplex creates po
papers.ssrn.com
Happy to share our new review in @annualreviews.bsky.social on abasic sites and their impact on DNA replication written by @angelotaglialatela.bsky.social. www.annualreviews.org/content/jour...
Endogenous Sources of Abasic Sites and Implications for DNA Replication: Mechanisms of Fork Stalling and Recovery
Apurinic/apyrimidinic (AP) sites, also known as abasic sites, are among the most frequent DNA lesions, arising spontaneously or as intermediates in base excision repair. Their structural impediment to...
annualreviews.org
Congratulations to all of the new members of the National Academy of Sciences! We are proud to see ACS Professor Dr. Johannes Walter recognized among these new members for his important work on DNA replication and repair. #CanSky #OncoSky 🧪
National Academy of Sciences@nasonline.org · 3mo agoWe are thrilled to announce the election of 120 members and 25 international members to the National Academy of Sciences in recognition of their distinguished and continued achievements in original research. Congratulations to our new #NASmembers and welcome to the Academy! 🎊
What are the genetic and molecular determinants underpinning the repair of bidirectional replication fork collapse in bacteria? PhD position open in my lab in collaboration with the brilliant @heathmurraylab.bsky.social. Please share and contact me if interested: www.findaphd.com/phds/project...
Identifying bacterial DNA repair requirements enabling stable genetic inheritance during bidirectional replication fork collapse at Newcastle University on FindAPhD.com
PhD Project - Identifying bacterial DNA repair requirements enabling stable genetic inheritance during bidirectional replication fork collapse at Newcastle University, listed on FindAPhD.com
findaphd.com
Updated the genome stability feed. Should be comprehensive but please let me know if relevant topics are missed.
Now widely sharing two AI preprints: 1. A practical guide to using LLMs in science and research: zenodo.org/records/1917... 2. A framework for integrating LLMs into education, with Madhvi Venkatesh: osf.io/preprints/ed... These are living documents, openly licensed for re-use.
Excited to finally see read story from Marta Markiewicz-Potoczny and Eros Lazzerini Denchi! www.nature.com/articles/s41...
Nonsense-mediated mRNA decay safeguards telomeres in pluripotent stem cells - Nature Cell Biology
Markiewicz-Potoczny et al. report that the nonsense-mediated mRNA decay pathway protects telomeres in the absence of core Shelterin component TRF2 by regulating the stability and abundance of TRF1 at ...
nature.com
Awesome resource and super proud of Dewar lab alum tatakavlashvili.bsky.social who co-led the work.
Tata Kavlashvili (@tatakavlashvili.bsky.social)
@DamonRunyon.org Timmerman Traverse Fellow w Agnel Sfeir at MSK • PhD in Dewar lab @vanderbilt.edu • from Tbilisi, Georgia 🇬🇪 basic scientist fascinated by mtDNA+🏔️⛷️🎭🗽
tatakavlashvili.bsky.social
Agnel Sfeir@agnelsfeir.bsky.social · last yr.Combining bacterial end joining with programmable nucleases, we induced mtDNA deletions in human cells at varying heteroplasmy and examined their metabolic and cellular effects. Simple tool to apply across any cell type and engineer pathogenic mtDNA deletions. www.sciencedirect.com/science/arti...
🧬⛓️ Our latest preprint examines the fate of collapsed forks in vertebrates 🐸 and our colleagues in @heathmurraylab.bsky.social asked similar questions in bacteria 🦠 to reveal how evolution shapes the response to fork collapse (see🧵) www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...
Resolution of collapsed forks is separate from completion of DNA synthesis
Replication fork collapse at single-strand DNA breaks (SSBs) poses a serious threat to genome stability. Using Xenopus egg extracts, we show that a replication fork encountering an SSB on either the l...
biorxiv.org
In our latest preprint we analyzed how abasic (AP) sites affect DNA replication: - AP sites stall DNA synthesis ⛓️💥 - Leading APs stall replisomes but lagging APs don’t 🛑/✅ - TLS is crucial for bypass of both leading and lagging strand AP sites 🛠️🧬 www.biorxiv.org/content/10.1...
Leading and lagging strand abasic sites differentially affect vertebrate replisome progression but involve analogous bypass mechanisms
Abasic sites are one of the most frequent forms of DNA damage that interfere with DNA replication. However, abasic sites exhibit complex effects because they can be processed into other types of DNA d...
biorxiv.org