I did not see accuracy validation, only benchmarks on one high-end GPU, and it requires bgzip to get the full efficiency advantage. Most software produce either uncompressed or gzip-compressed FASTQ. bgzip is standard for BAM/CRAM/VCF. Would be good to see this fleshed out a bit more.
To differentiate old-school bots from AI ones?
π
resolving proteins on polyacrylamide gels by electrophoresis in SDS? 250k-500k citations?
AlphaFold protein interaction modeling tutorial and workshop thenode.biologists.com/https-www-yo...
I have a set of 5M designed proteins against one target. What is the best way computationally to identify clusters and assess the diversity of target epitopes on this scale? I wrote a little script that performs contact-set Jaccard-similarity clustering but I wonder if Foldeseek is a better solution
PDB 7jsn colored by DAQ scores of fit in cryoEM map.
The ChimeraX DAQplugin computes DAQ scores showing the agreement between atomic models and cryoEM maps. Available from ChimeraX menu Tools / More Tools. cxtoolshed.rbvi.ucsf.edu/apps/chimera...
How to discovery new regulators of cell migration using a high-throughout assay?
Make use of our new label-free deep learning-based automated tracking assay DeepBIT.
To appear in Science Advances.
Read about DeepBIT here: www.biorxiv.org/content/10.1...
Last but not least, NIH is an equal opportunity employer, and candidates will be evaluated on their skills, experience, and potential, with these factors interpreted in the context of their training environment.
To apply, please send (i) a CV, (ii) a brief statement of research interests and relevant cryo-EM
experience, and (iii) contact information for 2β3 references to eugene.valkov@nih.gov
The position may be extended for up to 5 years. Relocation assistance is available subject to eligibility.
We are supported by robust core funding; external support (e.g., individual fellowships) is encouraged and actively mentored but not required. NIH offers highly competitive postdoctoral compensation, visa support, and a variety of benefits: www.training.nih.gov/researchtrai....
β’ Modern, centrally supported high-performance computing for cryo-EM processing
β’ Strong in-house capabilities in protein/RNP biochemistry and cell-based assays
β’ Exceptional opportunities to build networks with clinicians and translational scientists
Full access to on-campus high-quality cryo-EM workflows and instrumentation:
ccr.cancer.gov/center-for-s...
NIH provides an outstanding environment for mentorship, collaboration, and professional development. The fellow will have opportunities to lead high-impact projects with clear, well supported publication pathways while building a profile at the interface of cryo-EM, RNA regulation, and cancer.
A required qualification for this position is a PhD (or equivalent) in structural biology, biophysics, biochemistry, or a related field as well as a demonstrated proficiency in single-particle cryo-EM workflow.
A panel of such tools is already available and characterized, with scope to expand. As part of the project, there will be opportunities to use these tools to advance ex vivo structural biology with clinically derived samples, thereby bridging mechanistic discovery and translational application.
We will use binder-enabled mechanistic cryo-EM, with nanobodies isolated from immunized alpacas and computationally designed binders to stabilize complexes,
trap specific conformational states, map functional epitopes, and interrogate (and ultimately target)
disease-relevant interfaces.
We are looking for a postdoc to work on mechanisms of #RNA decay in cancer using #cryoEM with #nanobodies and #minibinders! Please RT
We are thrilled to share our latest work uncovering the mechanistic basis of target-directed microRNA degradation (TDMD). This work was driven by @jakobfarnung.bsky.social and @elenaslo.bsky.social in a fantastic collaboration with Brenda Schulman's lab. tinyurl.com/E3TDMD (1/5)
Check our latest collaboration with the Kleaveland Lab (kleavelandlab.org), led by Joanna Stefano and Lara Elcavage: academic.oup.com/nar/article/... (1/2)
New preprint from the lab π: Ξ³-tubulin is a novel target of the tubulin autoregulation pathway! Previously thought to exclusively target Ξ±- and Ξ²-tubulin mRNAs, we show that the TTC5βSCAPERβCNOT11 axis also degrades Ξ³-tubulin mRNA, expanding the scope of this fundamental regulatory mechanism.
Super proud of Joe - he's done fantastic work in the Ingolia lab. His paper last summer was a tour de force dissecting real functional constraints on disordered protein regions. A yeast paper, with just two authors, in Nature!
Thatβs terrifying
Gold is for the mistress β silver for the maid" β
Copper for the craftsman cunning at his trade!"
"Good!" said the Baron, sitting in his hall,
But Iron β Cold Iron β is master of them all." Kipling, 1910.
Check out the latest paper from the Gonatopoulos-Pournatzis lab using CRASP-seq, an RNA-coupled #CRISPR screening platform, to uncover novel #splicing regulators.
AI based framework for RNA modif detection using nanopore #RNAbiology
π₯ THIS IS HUGE!
Horizon is the worldβs science programme, hosted by the EU. It just got bigger.
Other non-European countries associated to the programme (ie paying in) include Korea, New Zealand, Canada.
However, after publishing, his H-index did not grow and he became an administrator.
#1 movie when you were ten is how your 2026 going to go
