Great collaboration with Dr. Na Liu and Dr. Jun Ma's teams! It was a fun journey to expand our research footprint into cancer-associated microorganisms. Special thanks to @simonemozzachiodi.bsky.social for critically reading our manuscript and providing valuable feedback. 🧬🦠

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

Came back to US for the first time after my PhD to attend the @genetics-gsa.bsky.social #Yeast26 Genetics Meeting. Great to meet many colleagues from the North American yeast community, whose research I have followed through papers. Until next time~

Great to come back to Nice, an ever charming & cozy city that I’ve spent good five years of my life ! Had a lovely reunion with my postdoc advisor @litinice.bsky.social as well as both old & new friends at @ircan.bsky.social. Until next time, à bientôt ~

Proud to have played a part in this multi-lab collaboration! 😀

⏰ Only 2 DAYS left for early registration! Join us at #Yeast26 (June 13-17, Pacific Grove, CA) for cutting-edge research in #genetics, #genomics, #disease, #regulation, #systemsBiology, #cellBiology, #lifeCycle, #syntheticBiology, & more. Register by April 16 to save! 🧬 genetics-gsa.org/yeast-2026/

Such a big relief to see my much belated PhD project finally wrapped up, after so many years and so much ups and downs ... "It is a long way from amphioxus, but we all came from there" ~

very happy to have this work published in mbe @molbioevol.bsky.social can now use phyloHessian to get a (hopefully) improved div time & subs rate estimate, particularly for deep-time or fast‑evolving lineages github.com/evolbeginner... #julialang #iqtree #mcmctree #molecularclock

The abstract submission deadline for #Yeast26 has been extended to next week, March 12! 📣 GSA is committed to meeting the needs of our genetics community and supporting our scientists through challenging times. Join us at the stunning Asilomar. Submit your abstract now: buff.ly/XmP8Z2i

David Botstein, a titan within the scientific community, died last week. GSA mourns his passing and celebrates his legacy. Read more about his significance to our community in this thread ⬇️🧵

We are deeply saddened to share the news of the passing of David Botstein, a towering figure in modern #genetics and a foundational force behind SGD. www.yeastgenome.org/blog/in-memo... #yeast #modelOrganism

ANNOUNCEMENT: The webpage for the upcoming yeast meetings of 2026 has recently been updated. Have a look at it to find out which exciting #yeast #conferences are ahead!!! 😀 onlinelibrary.wiley.com/page/journal...

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on chromosome engineering in 8p syndrome, convergent evolution in arid rodents, and more! tinyurl.com/Genome-Res-3...

📢 It has been a few years since we updated LRSDAY last time, during which the downloading URLs of some of its dependencies have become inaccessible. I've just implemented a fix in GitHub make the automatic installation script work again. github.com/yjx1217/LRSDAY

Jia-Xing Yue (@iamphioxus.bsky.social), principal investigator at Sun Yat-sen University, is one of the new members of the GBE editorial board. He is an expert in evolutionary genomics, genome instability, telomeres, aneuploidy, cancer, and yeast. #societyjournal

Honored to serve @genomebiolevol.bsky.social and the greater @official-smbe.bsky.social community! 🫡

Honored to serve on the Yeast Genetics Meeting Program Committee of Evolution & Population Genetics. Welcome for meeting registration and abstract submission, especially on our Evolution & Population Genetics program! genetics-gsa.org/yeast-2026/ @genetics-gsa.bsky.social #Yeast26

SMBE is now on Weixin/WeChat! Stay up-to-date with the latest news, events, and articles published in @molbioevol.bsky.social and @genomebiolevol.bsky.social Follow the @officialSMBE account, or scan the QR code with the app. 🔗 academic.oup.com/smbejournals/pages/wechat #society

It is great to have @petrovadmitri.bsky.social here at Sun Yat-sen University Cancer Center to give us an highly inspiring talk on “Fitness landscape of tumor suppressor genes in lung cancer ”. Tour de force experiments, mind blowing results, and exciting bench-to-bed perspectives!

First #SMBE meeting for our lab！Definitely a memorable experience. Already looking forward to the next one! @official-smbe.bsky.social #SMBE2025

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Super honored to have chance to co-organize the #SMBE2025 Symposium on Experimental Evolution, together with @jingli-0512.bsky.social and Dao-Qiong Zheng. Thank @petrovadmitri.bsky.social for serving as our invited speaker. Also thank all the oral/poster presenters and audience. @OfficialSMBE

📣Our #SMBE 2025 Symposium (No. 3) on Experimental Evolution will be held today (7.22, Tuesday) at 10:30 in Room 4, Building No. 8. An associated poster session will be held at 14:00 (poster number: S3-P01~P16). Welcome to join! let's study evolution in action! 🥳 🎉 @official-smbe.bsky.social

📅 The day is today! #SMBE2025 in Beijing starts now, as the registration desk opens to all participants. Join us for five days full of the latest discoveries in molecular biology and evolution 🧬 We hope all attendees enjoy the many opportunities for discussion and networking among our community.

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Welcome to attend our SMBE2025 Symposium on Experimental Evolution. Co-organized by Dao-Qiong Zheng, @‪jingli-0512.bsky.social‬ and myself.

Very excited about this work by @mrazo.bsky.social in collaboration with www.madhavmani.com bsky.app/profile/mraz... I am so lucky to be able to collaborate with such brilliant people! Learned a lot. This is our first foray into ML approaches and I am quite taken with their power 1/n

Keynote talk from Steven McCarroll from last weeks Biology of Genomes conf. My favorite talk of the whole meeting! #bog25 youtu.be/BCRAlmFv7ag?...

📢 3 Postdoc positions available in @evomicslab.bsky.social targeting on genome instability evolution of both yeast and human genomes. Both computational genomics and experimental genomics backgrounds are welcome! 🧬🧑‍💻🧪 For more information, see evomicslab.org or send me a message!

Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. www.nature.com/articles/s41...

1/35 New paper out! @jamesTstroud and I dive into why long-term studies are crucial for understanding evolution. They reveal processes impossible to detect in short timescales and capture rare events that transform our understanding of evolutionary dynamics. www.nature.com/articles/s41...

We are looking for a postdoc in #EvolutionarySystemsBiology. Exciting science, amazing team, wonderful city! landrylab.ibis.ulaval.ca/research-opp... #evolution #synbio #systemsbiology #genomics

Glad to see the copy-edited version of our VRPG paper formally published in the latest issue of @genomeresearch.bsky.social ! We developed VRPG as a novel visualization framework for intuitively exploring pangenome graphs in a linear-reference-projected context. genome.cshlp.org/content/35/2...

The new issue of @genomeresearch.bsky.social is now live! Follow the link to new research on homeodomain–DNA cooperative dimerization in developmental defects, nucleic quasi-primes, and more! tinyurl.com/Genome-Res-3...

📢📢📢 The FINAL COUNT DOWN for the extended abstract submission deadline of #SMBE2025! Please submit your abstract by 23:59 (GMT +8) of February 15, 2025 [Saturday]! And shout out again for our symposium on Experimental Evolution ! 🎉🎉🎉 @OfficialSMBE #LTEE #ExperimentalEvolution

A very significant step forward for synthetic genomics www.nature.com/articles/s41...

📢📢📢 #SMBE2025 Abstract Submission EXTENDED to Saturday, February 15, 2025 We also invite you to register at www.smbe2025.org @SMBEmeetings

📢 #Yeast2025 News! Registration and abstract submission are NOW OPEN! Join us at the 32nd ICYGMB 📅 Save the Date: 21-24 July 2025 📍 Location: Paris @sorbonne-universite.fr 🔗 Submit: premc.org/yeast2025/su... 🕒 Register now to take advantage of the Early Bird fee premc.org/yeast2025/re...

The new issue of @genomeresearch.bsky.social is now live! Follow the link to new research on AI in cell-free DNA diagnostics, disease progression insights using single-cell/-nucleus genomics, and more! tinyurl.com/Genome-Res-3...

The last 10-day countdown for abstract submission! Welcome to spread the word and of course welcome to submit the abstract!!! 📢😃⏰

Cool paper on evolutionary constraints and trajectories shaping point centromere evolution in budding yeasts by @helsenjana.bsky.social @gautamdey.bsky.social @gsherloc.bsky.social www.biorxiv.org/content/10.1...

Introducing VRPG, our recent work on the pangenome graph visualization & interpretation @genomeresearch.bsky.social !We posted our initial idea years ago and continuously improved it with many added features. Appreciate the great suggestions from all 3 reviewers. It is so much better now!

📢 2nd-round abstract submission call for the 2025 @OfficialSMBE annual meeting in #Beijing . Where: smbe2025.scimeeting.cn/en/web/index... When: now - 2025/01/30. Welcome for all abstract submissions, especially for our Experimental Evolution Symposium !!!

You can use my webapp to identify similar, overlapping, and duplicate images in PDFs of scientific papers: sholtodavid.pythonanywhere.com

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1

📣 ⚠️👀Attn: The abstract submission for the #SMBE2025 meeting in Beijing @official-smbe.bsky.social is open now! Submission site: smbe2025.scimeeting.cn/en/web/index... Submission Deadline: 2025.01.30 Welcome for all abstract submissions, especially for our Experimental Evolution Symposium !!!

Glad to announce that our (with Dao-Qiong Zheng & Jing Li) proposed symposium on #ExperimentalEvolution has been selected for the @official-smbe.bsky.social 2025 conference in #Beijing! @petrovadmitri.bsky.social will be our invited speaker! Please save the date and consider joining our symposium!

The copy-edited version of our NanoTrans paper has been recently published @JGenetGenomics ! Here we developed an all-in-one pipeline for comprehensive data analysis for @nanoporetech.com direct-RNA sequencing (#DRS). www.sciencedirect.com/science/arti...

Excited to introduce the ScRAPdb work that we recently published at Nucleic Acids Research, in which we assembled a #pangenome x #multi-omics database for #yeast. This is one step forward for a pan-multi-omics understanding of genome & trait evolution. Read more > academic.oup.com/nar/advance-...