It’s been an honor to contribute to the annotation of the T2T Y chr! The preprint of the first truly complete human Y chromosome is now available! Big thank you to my amazing mentor Alaina Shumate, PhD and PI Steven Salzberg 💙💛 and of course everyone in the T2T consortium!!

Today's Topic: miRNA I don't know r u RNA?

Our paper describing our new, greatly improved human genome annotation is just out in preprint form, by Ales Varabyou Mihaela Pertea Markus Sommer Beril Erdogdu @IliaMinkin Kuan-Hao Chao Jakob Heinz Alaina Shumate, PhD @thesteinegger Sukhwan Park et al. biorxiv.org/content/10.110…

first paper of 2023 for us: a gap-free, fully annotated genome of a southern Han Chinese individual, led by Kuan-Hao Chao, with Aleksey Zimin and Mihaela Pertea. We used the #T2T CHM13 genome to fill gaps academic.oup.com/g3journal/adva…

Accurate DTU detection in complex diseases with SPIT by Beril Erdogdu,Stephanie Hicks, PhD,Steven Salzberg 💙💛,Mihaela Pertea! Findings include previously unreported DTU events in 6 genes associated with schizophrenia. Also available on Google Colab -> Learn more at biorxiv.org/content/10.110…

📢📢Dear friends, our new software, Splam, a deep learning-based splice junction predictor, is now officially released🎉If you do RNA-Seq data analysis or need a reliable tool to evaluate splice junctions/introns, Splam is the perfect fit for you 🔗 github.com/Kuanhao-Chao/s… (1/10)

Remarkable work led by Arang Rhie and Adam Phillippy, finishing the human Y chromosome. It might be small but its complex structure made it super-difficult to complete. Pleased that my former student Adam Phillippy included my lab members Alaina Shumate, PhD and Jakob Heinz in the work

Our paper on the human gene annotation catalog CHESS, which now includes all of MANE and a more rigorous definition of genes of all types. With Mihaela Pertea Ales Varabyou @thesteinegger Markus Sommer Beril Erdogdu @IliaMinkin and others: genomebiology.biomedcentral.com/articles/10.11…

Mystery disease decimating coral reefs off the coast of Florida? Sounds like a job for Jakob Heinz and novel metagenomics methods in the Steven Salzberg 💙💛 lab, with guidance from Stephanie Rosales & Lindsay Huebner! Check out the paper! biorxiv.org/content/10.110…

Congrats to @jakobheinz9 (formerly an undergrad in my lab, now a PhD student @harvard) and Markus Sommer for this intriguing investigation, just released as a preprint, into what microbe is causing coral reefs to die near the Florida coast

Excited to share our collaborative research on the Wheeler Graph Toolkit from Johns Hopkins and UC Berkeley EECS. Check out our new Wheeler graph recognition algorithm and findings in the JHU Computer Science post. Great collaboration with Pei Wei Chen, @BenLangmead, and Sanjit Seshia.

📢📢Dear friends, I'm thrilled to introduce LiftOn, our new homology-based annotation lift-over tool🚀 Join my talk at RECOMBseq Saturday April 27th at 2:50PM! Jakob Heinz Celine Alan Mao Alaina Shumate, PhD Mihaela Pertea Steven Salzberg 💙💛 🔗github.com/Kuanhao-Chao/L… (1/5)

SO excited to share our recent work! To better understand the molecular impacts of human genetic variation, we need models that offer access to MANY more cell types and cell states. Here, we’re using a system called heterogeneous differentiating cultures (HDCs) to do this (1/n)

Friends, we are introducing LiftOn, a homology-based genome annotator that uses a protein-centric algorithm, considering both DNA & protein alignments to improve genome annotation lift-over 1/9 Steven Salzberg 💙💛 Mihaela Pertea Jakob Heinz Alaina Shumate, PhD Celine Alan Mao

Friends, LiftOn is now published in Genome Research! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments Steven Salzberg 💙💛 Mihaela Pertea Jakob Heinz Alaina Shumate, PhD Celine Alan Mao doi.org/10.1101/gr.279…

Genome annotation is falling behind how fast genomes can be assembled—but Johns Hopkins researchers Kuan-Hao Chao, Steven Salzberg 💙💛, Mihaela Pertea, Alaina Shumate, PhD, Celine, & Alan Mao (+ Jakob Heinz) have created a tool that can change that: cs.jhu.edu/news/solving-t…

Excited to share our new preprint on detecting foldback artifacts in long reads with my advisors Matthew Meyerson and Heng Li! Stop by poster C-180 on Wednesday at ISMB/ECCB2025 to learn more and chat!