Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
Isha Walawalkar, MPH
@walawalki.bsky.social
I’m just a girl in an RNA world [alternative splicing] MD-PhD student | NIH F30 Fellow @jax.org, @uconnresearch.bsky.social
A combination of drugs restores stem-cell function in mouse models of sickle-cell disease go.nature.com/4w8xMVH
Sickle-cell disease linked to prematurely aged stem cells in mice
A combination of drugs restores stem-cell function in mouse models of the blood disorder.
go.nature.com
Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
nature.com
www.nature.com/articles/s41... how cool!
Intestinal stem cells count self-renewal divisions to switch multipotency - Nature
In Drosophila, cell fate switching in adult intestinal stem cells is determined through an epigenetic mechanism in which these cells count divisions, switching from producing enterocytes to producing ...
nature.com
Frank Grosveld, born in 1948, passed away last Friday. He was a colossal scientist in the transcriptional control of gene expression during development and helped us understand the complex regulation of beta-globin genes. His work will remain as a reference. May he rest in peace.
Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates
Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...
Nitric oxide drives proteomic diversity through alternative splicing
Nitric oxide drives proteomic diversity through alternative splicing
Schindler et al. report that RNA-binding proteins undergo widespread S-nitrosylation at evolutionarily conserved sites. S-nitrosylation of the master splicing regulator PTBP1 alters RNA-binding properties to reprogram the transcriptome and proteome. Nitric oxide thereby coordinates gene and protein regulation in cellular physiology and disease.
dlvr.it
How can a splicing factor bind to thousands of exons but regulate only a few of them? In our new preprint, we show that SRSF6 resolves this paradox through two distinct binding modes. @lab-nmr.bsky.social & @julianvonehr.bsky.social. Check it out: www.researchsquare.com/article/rs-9...
Check out our latest research, just published in Nature @nature.com @molbiolau.bsky.social @au.dk Molecular basis of polyadenylated RNA fate determination in the nucleus www.nature.com/articles/s41...
Molecular basis of polyadenylated RNA fate determination in the nucleus - Nature
Biochemical, structural and cell biological analyses reveal that UAP56 (DDX39B) assembles with a TREX-2–like module that redirects non-functional polyadenylated RNAs from export to degradati...
nature.com
Nature research paper: A natural depsipeptide antibiotic binds the E-site of the bacterial ribosome go.nature.com/3RMNwPW
A natural depsipeptide antibiotic binds the E-site of the bacterial ribosome - Nature
Improved fractionation strategies can identify antibiotics with previously unseen scaffolds and mechanisms, exemplified by manikomycin from Streptomyces rimosus, which acts by targeting the E-site of the bacterial large ribosomal subunit.
go.nature.com
Review | Best Practices in Demographic Data Collection for Equity, Diversity, and Inclusion in Rare Disease Research: A Systematic Review www.gimjournal.org/article/S109...
Best Practices in Demographic Data Collection for Equity, Diversity, and Inclusion in Rare Disease Research: A Systematic Review
Rare diseases affect small, dispersed populations and are often studied through multisite designs where equity-relevant demographic data are essential for inclusive recruitment and accurate interpreta...
gimjournal.org
Review | Genotype before phenotype? Reversing the diagnostic odyssey in genomic medicine www.sciencedirect.com/science/arti...
Genotype before phenotype? Reversing the diagnostic odyssey in genomic medicine
For decades, the diagnosis of rare genetic disorders has relied on a phenotype-driven approach, often resulting in a prolonged “diagnostic odyssey.” T…
sciencedirect.com
In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging
In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging
In vivo single-cell ribosome profiling reveals cell-type-specific translational landscapes across the epidermis and uncovers selective reprogramming of AP-1 subunit translation in aged stem cells, linking translational deregulation to stem cell aging.
dlvr.it
Messenger RNA technology vaccinations work to help the body's T cells identify the tumor and kill it. Of course, HHS secretary, a lawyer, RFK Jr is opposed to it and canceled $500 million in research funds. www.belfercenter.org/research-ana... www.nbcnews.com/health/cance...
Pancreatic cancer mRNA vaccine shows lasting results in an early trial
Scientists caution that more research is needed, but nearly all of the patients who responded to the personalized vaccine are still alive six years later.
nbcnews.com
Great science and fun reunion of Krainer Lab F1 and others #RNA2026 @rnasociety.bsky.social @chaolinzhang.bsky.social @hastingslab.bsky.social @walawalki.bsky.social
Grateful for the opportunity to present a glimpse of my thesis work on #poisonexons in pluripotent stem cells @rnasociety.bsky.social @jrrnascientists.bsky.social @jax.org #AnczukowLab #RNA2026
Presenting her work on #poisonexons #RNA @walawalki.bsky.social @rnasociety.bsky.social @jax.org
@jrrnascientists.bsky.social @rnasociety.bsky.social R-N-A pins to give my tRNA pin some company ! #RNA2026
Spatial maps of gene expression in whole human embryos across several weeks of early development offer insights into the molecular programs that drive organogenesis. go.nature.com/3S5QqPG
Organ formation in early human embryos captured in spatial cell atlas
Spatial maps of gene expression in whole human embryos across several weeks of early development offer insights into the molecular programs that drive organogenesis.
go.nature.com
Check out this article about the latest publication from our lab, highlighting our new method, KATMAP, for understanding and predicting gene splicing news.mit.edu/2025/katmap-...
A new way to understand and predict gene splicing
The KATMAP model, developed by researchers in the Department of Biology, can predict alternative cell splicing, which allows cells to create endless diversity from the same sets of genetic blueprints.
news.mit.edu
1\ Excited to finally share some of my PhD work: OpenSplice! We measured how >590,000 mutations affect exon inclusion across 600 human exons, creating a resource to study splicing regulation, benchmark variant effect predictors, and support variant interpretation.
OpenSplice: the impact of half a million mutations on the alternative splicing of 600 human exons https://www.biorxiv.org/content/10.64898/2026.05.22.727141v1
Keynote by Nahum Sonenberg on the history of the study of the 5’ mRNA cap #RNA2026 @rnasociety.bsky.social @jrrnascientists.bsky.social
OpenSplice: the impact of half a million mutations on the alternative splicing of 600 human exons Gioia Quarantani et al. www.biorxiv.org/content/10.6...
biorxiv.org
What is the role of #poison-exon in regulating splicing factors in stem cells and development? Check out new work from Nathan Leclair and Mattia Brugiolo and many others in my lab @jax.org #RNA #splicing www.biorxiv.org/content/10.6...
Online Now: Nitric oxide drives proteomic diversity through alternative splicing Online now:
Nitric oxide drives proteomic diversity through alternative splicing
Schindler et al. report that RNA-binding proteins undergo widespread S-nitrosylation at evolutionarily conserved sites. S-nitrosylation of the master splicing regulator PTBP1 alters RNA-binding properties to reprogram the transcriptome and proteome. Nitric oxide thereby coordinates gene and protein regulation in cellular physiology and disease.
dlvr.it
Splicing of ultraconserved poison exons controls mitotic fidelity and stem cell viability https://www.biorxiv.org/content/10.64898/2026.05.19.726407v1
A very exciting NMD story 🤩Congratulations to the team!
How are faulty #RNA degraded? New mechanistic insight into NMD: 1️⃣SMG5 & SMG6 PIN domains form a composite endonuclease (cPIN) 2️⃣ SMG5 completes the SMG6 active site, enabling efficient mRNA cleavage Fantastic collaboration with @labconti.bsky.social 🙏 👉 www.nature.com/articles/s41... 1/n
Excited to share our @natgenet.nature.com study showing that epigenetically rewired transposable elements control AML leukemia stem cell properties and patient outcome. Grateful to the team & collaborators. www.nature.com/articles/s41...
Transposable elements shape stemness in normal and leukemic hematopoiesis - Nature Genetics
This study identifies distinct transposable element subfamilies as genetic determinants of stemness properties in normal and leukemic stem populations with clinical implications for patients with acut...
nature.com