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Gene Myers just released super fast whole genome aligner github.com/thegenemyers/F…. He and Chenxi Zhou and I have lots of ideas for downstream use.

FASTGA uses very efficient and flexible github.com/thegenemyers/O… file format/library we are now using for multiple purposes. Compressed, indexed, schema-containing binary files with record-based text equivalent. Single C file interface with no dependencies.

Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB arxiv.org/abs/2409.00613

Excited to share this new preprint with @spence_jeffrey_ and Doc Edge in which we developed a method to infer demographic history and mutation rates from millions of genomes, and applied it to gnomAD v4 data. Read on for a brief thread! biorxiv.org/content/10.110…

It was recently reported that Africans experienced a sharp, severe bottleneck around 900kya and that this signal is absent in non-Africans. Here, we present evidence to show why this is likely a statistical artifact: Rasmus Nielsen Yun S. Song biorxiv.org/content/10.110… 1/4

I'm looking to change my career path and am quite excited about exploring jobs in biotechs in the Bay Area (or remote). I'm very keen to start a career that offers stability so my partner and I can finally live in the same state. Does anyone know of organizations that are hiring?

Happy to share a new preprint: No association between FMR1 premutation and either ADHD or anxiety in 53,707 women undergoing genetic testing for family planning purposes medrxiv.org/content/10.110… Thread:🧵

יערי ויגדר הוא דוקטורנט בקבוצה שלי באוניברסיטת ת"א (ומילואימניק לוחם) שאיבד בשבוע שעבר את אשתו ענבר בפיגוע הרצחני ביפו. ליערי צפויה התמודדות קשה עם השכול והחיים בתור אב חד-הורי, בין היתר מהפן הכלכלי. אתם מוזמנים לתרום ולשתף את הפוסט. כל תרומה תעזור! giveback.co.il/project/80886

What is the most common type of mutations, causing cancer and genetic diseases? C to T mutations in CpGs: Signature 1. What is the best understood mutational signature? Signature 1. Or is it? Results of over 8 years of our work is finally out! 🧵1/ nature.com/articles/s4158…

Insufficient evidence for a severe bottleneck in humans during the Early to Middle Pleistocene transition biorxiv.org/cgi/content/sh… #biorxiv_genetic

Academic Twitter, I need access Journal Citation Reports for faculty job applications but I don't have one. Any ideas what to do...?

Excited to share our new preprint in which we address: (1) Accurate sequencing of sperm at scale (2) Positive selection of spermatogenesis driver mutations across the exome (3) Offspring disease risks from male reproductive aging [1/15] medrxiv.org/content/10.110…

The #1 question I got at ASHG was where is the IAMDGC 2.0: it's under review, but preprint is finally out! A brand new diverse ancestry analysis, two new loci, and a full TOPMed imputed dataset. I am equal first author and thrilled to see it live! 🧵 doi.org/10.1101/2024.1…

Our latest paper is out in NatureEcoEvo: Inferring DNA methylation in non-skeletal tissues of ancient specimens. A major challenge in studying DNA methylation in ancient samples is that it is tissue-specific. 1/11

Happy New Year! Our Twigstats paper is now out! nature.com/articles/s4158…

Latest in #GENETICS, Yilei Huang, Shai Carmi, and Harald Ringbauer developed a new tool, TTNE, that uses identity-by-descent tracts in large ancient DNA time-series for inferring effective population size trajectories. Read more: buff.ly/3QDRgzw

Super exciting to see the Penghu jaw confirmed as Denisovan— its features line up beautifully with what we predicted Denisovan mandibles to look like! More in the thread 🧵 pubmed.ncbi.nlm.nih.gov/31539495/

Our Nature paper (rdcu.be/ei1NM) deep sequencing a 4-generation, 28-member family using multiple sequencing technologies to study transmission of all classes of genetic variation is out! Evan Eichler UW Genome Sciences HHMI

🚨Preprint Alert!🚨 Cell classification is one of the most difficult tasks in analyzing spatial data. We present CellTune - a powerful toolkit for accelerating biological discovery in spatial proteomics. 📄 biorxiv.org/content/10.110… 👇🧵1/7

1/6 🧬📊 Curious about the buzz around NLP in biology? Feeling overwhelmed by the rapid developments? We've got you covered! Our review on NLP applications in genomics, by the wonderful Ella Rannon, is now out as a pre-print! #NLP #Bioinformatics arxiv.org/abs/2506.02212