a computational RNA biologist at Harvard, trying to understand the evolution of RNA/RNPs and codify this knowledge for future therapeutics!

Joined July 2009
SONATA BIS from the @NCN_PL ($1.2M) to launch a new RNA design lab to build AI models grounded in experimental data at the Centrum Nowych Technologii @UniWarszawski. Hiring: Experimental Postdoc (SELEX) & Bioinformatics / AI (postdoc and PhD) [email protected] #rna
3
4
15
492
MarcinMagnus 🦋 @mmagnus42.bsky.social retweeted
As we build the next generation of biomolecular OpenFold models, we are looking to increase our staffing on both the scientific and engineering fronts. I thought it'd be worthwhile to write down our philosophy and what we're offering, as well as what we're looking for. If this resonates with you, please apply at the link below. What we're offering: True open source: we are contractually obligated by our funding streams to open source everything we do, including our training code infrastructure and training data, which no other group in the space has done. All the results we publish are fully reproducible with no missing "training enhancements" that keep the recipes hidden. We will not become a startup and we will not pivot to an API model. We are doing this exclusively as a public good for the public commons. Of course, commercial companies can and are encouraged to build on top of our models, but you will be contributing to an ecosystem guaranteed to remain open source. Long horizon research: because we are not trying to turn a profit or satisfy investment trends, we can focus on hard problems that commercial labs are disincentivized to tackle. Our research vision spans years, not months, even while we release updates on a quarterly basis. This translates to problems spanning conformational ensembles, novel regions of chemical space, antibodies, nucleic acids, IDRs, macromolecular machines, and more. Reach for the frontier: the open source ecosystem currently lags the industrial frontier by a few years. We aim to eliminate this gap. The two big deltas are engineering expertise and compute resources. We're doing alright on the latter, but it is the former where we need to grow. To make this possible we offer salaries and compute resources competitive with industry. We are looking primarily for types of people, or the intersection of the two! Machine learning scientists and engineers: people who have built and trained models at scale, whose command of the literature extends to the latent developments in efficient diffusion, optimization, recurrence, and reasoning. Bioinformaticians and computational biologists: people who can assemble large and complex heterogeneous datasets, who write efficient data pipelines, and who deeply understand the structural biology domain. If this is of interest to your network, please reshare. And if this interests you directly, please apply using the link below. This link is a catch-all site and so the job description and salary range are generic. It's there to help us streamline collection and review of resumes. opportunities.columbia.edu/j…
4
20
2
71
7,659
Join us kn a talk on cutting edge RNA structure prediction! 💪
Don't miss our next RNA structure webinar featuring Peng Xiong from the top CASP15 team! Live only — no recording will be available. Zoom: 934 4593 5624 / 802843 Mailing list: groups.google.com/g/casp-rna… Full schedule: tinyurl.com/rna-sig-calendar
50
There is still time* to apply for a new MSc programme, Biological Therapeutics, developed through a collaboration between the University of Warsaw and the International Institute of Molecular and Cell Biology in Warsaw. We are convinced that this programme will be an excellent opportunity for students interested in modern biological and biomedical sciences. Key information: 👉 Tuition fees for the first edition of the programme have been waived.  👉 Applicants will be selected based on a qualifying interview conducted entirely in English. * The second round of the selection process is planned in September! medycyna.uw.edu.pl/rekrutacj…
1
74
MarcinMagnus 🦋 @mmagnus42.bsky.social retweeted
Two PhD positions available now! (1) Programme number: DSMBBC/2026/02 Title: RIBO-ICE: Ribosomes and Translation. Protein biosynthesis in cold, a study of Antarctic bacteria (2) Programme number: DSMBBC/2026/03 Title: Global pausing of translation during early sporulation in Bacillus subtilis – research on the role in translation regulation and mechanism of action. Apply now! ibb.edu.pl/en/phd-studies/re…
PostDoc and 2 PhD positions in two NCN grants available soon!
13
2
28
5,423
I'm thrilled to join over 1900+ global experts in oligos, peptides, and mRNA at #TIDESUSA! Learn more here: lnkd.in/e6KdVeN7 #rna #rnastructure
46
MarcinMagnus 🦋 @mmagnus42.bsky.social retweeted
Excited to have @edric_choi present his latest work on RNA chemical mapping at the CASP Nucleic Acids Reading Group! Thursday April 16 2026 on Zoom; Pacific Daylight Saving Time 8 am / Eastern Daylight Saving Time 11 am -- free to attend and full of interactive discussions.
2
13
868
Hi Nucleic Acid enthusiasts, #rna #rnastructure #rnadesign Tomorrow I will be speaking at the Institute of Genetics and Biotechnology seminar at the University of Warsaw about our work on OpenRNAFold and new research directions in the Magnus lab. The seminar will be held online (see link below). Eastern Daylight Saving Time 8:30 am / Central European Time: 1:30 pm OpenRNAFold: an end-to-end approach for RNA 3D structure prediction Abstract: RNA plays central roles in gene expression as messenger RNA and in many biological processes as structured non-coding RNAs. Understanding these functions requires knowledge of RNA tertiary structure, but experimental structure determination is slow and expensive, leading to a large gap between sequence and structure data. Inspired by advances in protein structure prediction, such as AlphaFold, RNA structure prediction has attracted growing interest. However, current deep learning models for RNA often report inflated accuracy due to structural overlap between training and test sets. Early benchmarks also indicate that AlphaFold3 remains inaccurate for RNA structures. Because RNA structures are scarce, we focus on two essentials: carefully curated training data to prevent data leakage (RNA3DB, Szikszai, et al., 2024), and high-quality sequence alignments (rnahub.org, Magnus, et al., 2025). Using these datasets and alignments, we are currently testing our own AlphaFold-based RNA model that explicitly emphasizes base pairing and RNA geometry. This work aims to improve RNA 3D structure prediction and is being evaluated in upcoming blind challenges such as CASP and RNA-Puzzles. It will also serve as a platform for further deep learning developments in RNA design and therapeutics in my Laboratory of RNA Design and Therapeutics at CeNT, University of Warsaw, scheduled to open in mid-2026. Thursday March 27 2026 on Google Meet lnkd.in/e6c2JrUv
4
77
We had a great session at our RNA CASP SIG featuring prof. Tiwary talking about his method that brings together deep learning, molecular dynamics, and statistical physics to understand structural ensembles of RNA, not just single structures. RNA function depends on dynamic 3D conformations, yet most approaches still focus on static predictions. RNAnneal addresses this by generating diverse structural ensembles from sequence, learning thermodynamic representations in a reduced latent space (PCA + SPIB), and scoring conformations via a probabilistic framework grounded in physics. This is a clear step toward physisc-aware RNA modeling, where capturing interactions, heterogeneity, and thermodynamics becomes central, especially for applications like RNA-targeted drug discovery and functional RNA design. #rna #casprnasig #rnastructure youtube.com/watch?v=OZQeE4J4…
2
79
MarcinMagnus 🦋 @mmagnus42.bsky.social retweeted
PostDoc and 2 PhD positions in two NCN grants available soon!
3
28
2
112
10,348
MarcinMagnus 🦋 @mmagnus42.bsky.social retweeted
Come learn about super interesting and cool DNA structure at our nucleic acid structure webinar by Cameron Mackereth "Unusual DNA architecture in a dopamine-bound aptamer complex" on March 5 Meeting ID: 934 4593 5624 Passcode: 802843 Mailing list: groups.google.com/g/casp-rna…
3
8
597
PyMOL4RNA: colorbyrmsd to spot differences between structures. It is especially useful for visually highlighting local and global deviations between reference RNAs and predicted models. #rnatools hashtag#rna hashtag#rnastructure github.com/mmagnus/rna-tools…
5
22
752
In ~20h Please join us for an exciting seminar by Dr Yun-Xing Wang, this Wednesday 26th November 8am Pacific. This seminar will not be recorded and is on Wednesday (not Thursday which is US thanksgiving) on zoom.
1
41
MarcinMagnus 🦋 @mmagnus42.bsky.social retweeted
Massive turnout for the BoltzGen seminar at MIT!
standing room for a research seminar in mit's largest lecture halls. ive never seen anything like it. congratulations to the boltz and boltzgen teams for this true tour de force.
4
10
1
146
15,679
Please join us for our next seminar, featuring Danny IncaRNAto, PhD: “Discovery of RNA regulatory structural switches via ensemble mapping” @incaRNAtolab #rna #casprnasig #rnastructure
1
6
1,134
Dear nucleic acid enthusiasts! Our next webinar this Thursday, October 2nd, by Prof. Debswapna Bhattacharya. This seminar will not be recorded. Title: RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation Join us!
2
40
Join is in 24h for a talk on RNA3D structure: EvryRNA tools with a special focus on RNAdvisor: an RNA structural quality assessment tool Thursday, September 18; Eastern Daylight Time 11 am #rna #casprnasig #rnastructure
1
7
554
Hehe join the team 😅 writing a grant for my lab at the University of Warsaw 🧬
It’s Sunday so I’m writing a grant due tomorrow. Meanwhile in an alternative universe:
3
90
MarcinMagnus 🦋 @mmagnus42.bsky.social retweeted
It’s Sunday so I’m writing a grant due tomorrow. Meanwhile in an alternative universe:
17
9
4
477
53,168