Patryk Kalinowski 🇪🇺
@KalinowskiSTEMChemBio PhD Student @BUChemistry ‘24 - ‘?? | Fulbright Scholar @UChicagoBMB ‘22 - ‘24
Check out this wonderful Perspective piece in @ScienceMagazine by Christina Theodoris @UCSF @GladstoneInst: science.org/doi/10.1126/sc…
The study focuses on Evo, a genomic foundation model trained on 2.7 million evolutionarily diverse prokaryotic and phage genomes. The goal is to learn the fundamental grammar of DNA, which can then be used for various sequence modeling, prediction, and design tasks. The Evo…
Today we report Evo, a generalist foundation model for biology, on the cover of @ScienceMagazine Trained on billions of DNA nucleotides, Evo was designed to capture two key aspects of biology: the multi-modality of the central dogma and the multi-scale nature of evolution.
A new Science study presents “Evo”—a machine learning model capable of decoding and designing DNA, RNA, and protein sequences, from molecular to genome scale, with unparalleled accuracy. Evo’s ability to predict, generate, and engineer entire genomic sequences could change the…
Circular RNAs are prevalent, mysterious and fascinating, but their study requires great care go.nature.com/4fEj5C8
Here is the interpolation along the other diagonal, where GINN learned some "mirror anti-symmetry". 👇
Proud of our Geometry-Informed Neural Net (GINN🍸) which generates diverse shapes without training data. Paper: arxiv.org/abs/2402.14009 Great work and thanks to my amazing team mates and supervisors @artuursberzins @e_volkmann @SebSanokowski @HochreiterSepp @jo_brandstetter
2.5 years in the making, and today, we are so proud to drop this absolute banger!
Latest work from our group @Esoftbio @NCBS_Bangalore, led by Sree @padmanabh97, is out today in @NatureComms! In colab with @DeepaAgashe @c_kurzthaler we report that the physical confinement acts as a selective pressure on bacterial growth in 3D! [1/16] tinyurl.com/mvbdm3ue
Lynn Steger Strong writes about the climate-fuelled increase in hurricanes and how she views it through the lens of Shakespeare’s “King Lear.” “One of the gifts of ‘Lear,’‘ to me, is that the play doesn’t give hope. Instead, it grounds you,” she notes. nyer.cm/zBE5qnk
For readers interested in derivatization with fatty acids in peptide and protein drug discovery, as used in products such as Ozempic and Wegovy, here's a comprehensive review nature.com/articles/s4157… rdcu.be/dZAsu
Why did South Africa revise its health-research ethics guidelines to include a new section on heritable human genome editing? We've asked @HealthZA No response as yet. Here is the excellent @sarahemilywild for @Nature on what we know so far: nature.com/articles/d4158…
My latest: british physicist Mark Thomson of @STFC_Matters willbe @CERN ‘s next director general nature.com/articles/d4158…
Tools such as Rosetta and AlphaFold have redefined the protein-engineering landscape. But some problems remain out of reach — for now go.nature.com/3YT7zgN
Hi TED! 👋 Out now in @ScienceMagazine , we are finally ready to make our classification of all domains in AFDB v4 available to all! A joint effort of @CATH_Gene3D and the Jones group (@psipred), here's a link to the article science.org/doi/10.1126/sc… 1/5 🧵⤵️
For readers interested in antibody-drug conjugates in oncology, here's a comprehensive review nature.com/articles/s4157… rdcu.be/dYACI
TED: The Encyclopedia of Domains now published in @ScienceMagazine discovering and annotating 314 MILLION protein domains in the AlphaFold database. joint work of @CATH_Gene3D and @psipred here at UCL.
For the first time, researchers have accelerated muons — the heavier, unstable cousins of electrons — into a tightly controlled beam, bringing the vision of a muon collider a step closer to reality go.nature.com/3YEUpnv
Nature research paper: Parallel molecular data storage by printing epigenetic bits on DNA go.nature.com/3Ujwvv0
A new approach from @_Murphy_Lab @zoliviapg @FilipPetegem and colleagues enables elemental mapping in macromolecular complexes, by combining electron energy-loss spectroscopy with single-particle cryo-EM image processing tools. nature.com/articles/s4159…
Elsevier is one of the largest, most hated and most influential academic publishing companies in the world. How it started & how it's going A thread🧵
Many new machine learning tools for protein engineering have popped up in the last year. In these early days, it might be unclear how to actually use them for real molecular design tasks in industry. We demonstrate how to engineer a cholesterol drug and plastic degrading…
GlycoShape, a web-based platform, supplements 3D glycoprotein structures with missing structural information about glycans. @ElisaTelisa nature.com/articles/s4159…
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