Samuel Sledzieski
LightNews LightNews
banner
samsl.io
Samuel Sledzieski
@samsl.io
730 followers 230 following 56 posts
Research Fellow @flatironinstitute.org @simonsfoundation.org

Formerly @csail.mit.edu @msftresearch.bsky.social @uconn.bsky.social

Computational systems x structure biology | he/him | https://samsl.io | 👨🏼‍💻
Posts Replies Media Videos
Pinned
samsl.io
Samuel Sledzieski @samsl.io · Jun 23
New preprint 🚨--protein language models + MD training ➡️ allosteric networks!

@sonyahanson.bsky.social and I are developing RocketSHP 🚀 for rapid genome-scale inference of local+correlated fluctuations + structure token distributions!

📄: www.biorxiv.org/content/10.1...
💻: github.com/flatironinst...
www.biorxiv.org
Reposted by Samuel Sledzieski
minhuanli.bsky.social
Check our new preprint smoothing rugged Cryo-EM landscapes: shorturl.at/gYs9U

We tackle practical hurdles of Optimal Transport (OT) loss—differentiability, cost & noise sensitivity—make it a feasible inference workhorse.
W/ G. Woollard, D. Herreros, @pilarcossio.bsky.social, K. Dao Duc 🧵👇 (1/9)
January 2, 2026 at 4:03 PM
samsl.io
🌿 MINT is out now in Nature Communications!

📄: www.nature.com/articles/s41...
💻: github.com/VarunUllanat...
January 7, 2026 at 5:29 PM
Reposted by Samuel Sledzieski
rodger.bsky.social
Terrifying headline if you don’t realize they are sports teams.
Rockets owners expand talks to buy, move Sun
December 19, 2025 at 4:37 PM
Reposted by Samuel Sledzieski
haysconun.bsky.social
The Center for Computational Biology at the Flatiron Institute is accepting applications for summer intern positions. CCB is a great place to work, and the intern program is excellent. Please check out the Computer Vision and Developmental Dynamics groups in particular. apply.interfolio.com/177779
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
December 11, 2025 at 3:29 PM
samsl.io
We're recruiting summer interns at all levels (Bachelors, Masters, PhD) and across all groups at @flatironinstitute.org Center for Computational Biology. Come work with us in New York City! (Full-time paid, June 1-August 14 2026, applications close January 16 2026)

apply.interfolio.com/177779
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
December 1, 2025 at 8:32 PM
Reposted by Samuel Sledzieski
sonyahanson.bsky.social
Announcing cryo-EM heterogeneity challenge #2, now dubbed the 2025 Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA)! Join us for a webinar next Friday (Nov 14th) to learn more. Datasets already posted here: heterogeneity.notion.site/challenge #cryoem
CAHRA 2025: Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms
A community-wide data processing challenge for cryo-electron microscopy.
heterogeneity.notion.site
November 7, 2025 at 10:45 PM
Reposted by Samuel Sledzieski
pilarcossio.bsky.social
**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: pcossio@flatironinstitute.org
October 22, 2025 at 2:55 PM
samsl.io
D-SCRIPT + BMPI is out today in Bioinformatics!
academic.oup.com/bioinformati...
October 12, 2025 at 5:20 PM
Reposted by Samuel Sledzieski
lindorfflarsen.bsky.social
Integrative modelling of biomolecular dynamics

Time-dependent and -resolved experiments combined with computation provide a view on molecular dynamics beyond that available from static, ensemble-averaged experiments

Review w @dariagusew.bsky.social & Carl G Henning Hansen
doi.org/10.48550/arX...
Figure 1 from the review. Caption: Comparison of a schematic example showing static, time-dependent, and time-resolved experiments illustrated by a protein folding process. (a) A static experiment measuring the observable O$_{\text{exp}}$ is shown, which can be modelled as a distribution of simulated values, O$_{\text{calc}}$, representing a conformational ensemble of folded and unfolded states. (b) Shows a time-dependent experiment, where the equilibrium dynamics of reversible folding gives rise to measured transition times $\tau_1$ and $\tau_2$. These can be modelled as equilibrium dynamics, illustrated by a free energy (FE) surface along a chosen degree of freedom (D.O.F.) (c) A time-resolved experiment probes a non-equilibrium process, where the system begins at $t_{0}$ in the folded state. During the observation time $t$ the protein unfolds until $t_{\text{max}}$. At each time point, a distinct ensemble average, O$_{\text{exp}}$, can be observed, reflecting the proteins changing structure. This evolution can be modelled as distributions of O$_{\text{calc}}$ at each time point. These are shown together with a FE surface.
October 2, 2025 at 7:54 AM
Reposted by Samuel Sledzieski
rodger.bsky.social
These are the quarterbacks since 2010 who complete passes at roughly the rate Microsoft Excel’s AI mode accurately edits spreadsheets
Jake Locker Davis Webb Tom Savage Rex Grossman Garrett Gilbert Kellen Clemens Mark Sanchez Logan Woodside Zach Wilson David Blough Derek Anderson Johnny Manziel
October 2, 2025 at 12:26 AM
Reposted by Samuel Sledzieski
pilarcossio.bsky.social
*Job Alert*: postdoc positions available @flatironinstitute.org in Computational Mathematics: apply.interfolio.com/173401
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
September 19, 2025 at 10:40 AM
Reposted by Samuel Sledzieski
ekimb.bsky.social
Happy (a^2, b^2, c^2)!

www.npr.org/2025/09/16/n...
On 9/16/25, celebrate a date of mathematical beauty
Pythagorean Triple Square Day, as one man affectionately calls 9/16/25, is a day like no other this century.
www.npr.org
September 16, 2025 at 4:48 PM
Reposted by Samuel Sledzieski
davidaknowles.bsky.social
YouTube link for MLCB2025 is up! Starting in 30 min. www.youtube.com/live/19I7xTh...
Machine Learning in Computational Biology 2025
YouTube video by Machine Learning in Computational Biology
www.youtube.com
September 10, 2025 at 1:01 PM
samsl.io
I’ll be at MLCB today and tomorrow, and talking about our latest work on modeling protein dynamics 🚀 tomorrow afternoon!
pkoo562.bsky.social Peter Koo @pkoo562.bsky.social · Sep 10
2025 Machine Learning in Computational Biology (#MLCB) meeting starts TODAY (9/10) at 9:30a (EST) at the NY Genome Center in NYC!

We have a great lineup of keynotes, contributed talks, and posters today and tomorrow

Schedule: mlcb.org/schedule

Join for free via livestream: m.youtube.com/@mlcbconf
MLCB - Schedule
The in-person component will be held at the New York Genome Center, 101 6th Ave, New York, NY 10013. All times below are Eastern Time.
mlcb.org
September 10, 2025 at 1:04 PM
Reposted by Samuel Sledzieski
pkoo562.bsky.social
2025 Machine Learning in Computational Biology (#MLCB) meeting starts TODAY (9/10) at 9:30a (EST) at the NY Genome Center in NYC!

We have a great lineup of keynotes, contributed talks, and posters today and tomorrow

Schedule: mlcb.org/schedule

Join for free via livestream: m.youtube.com/@mlcbconf
MLCB - Schedule
The in-person component will be held at the New York Genome Center, 101 6th Ave, New York, NY 10013. All times below are Eastern Time.
mlcb.org
September 10, 2025 at 11:42 AM
Reposted by Samuel Sledzieski
bergerlab.bsky.social
Excited to share our recent work: Sparse autoencoders uncover biologically interpretable features in protein language model representations now in PNAS. Thread below 🧵
September 3, 2025 at 4:50 PM
Reposted by Samuel Sledzieski
diffuseproject.bsky.social
Announcing the Diffuse Project! We're unlocking protein dynamics through diffuse X-ray scattering - the overlooked signal that could revolutionize how we understand protein motion. seemay.substack.com/p/from-syste...
From systems operators to systems architects
Going up a level from data generation to think about the data systems we design and embed
seemay.substack.com
August 12, 2025 at 4:21 PM
Reposted by Samuel Sledzieski
iscb.bsky.social
The results of the ISCB Leadership vote are in! 

Terms for the ISCB President-Elect and ISCB Vice President will start on January 21, 2026.
August 13, 2025 at 1:08 PM
Reposted by Samuel Sledzieski
drglam.bsky.social
I just got the notice that all the FlyBase people at Harvard, including me, will be laid off on October 12. I'm devastated.
August 11, 2025 at 6:12 PM
Reposted by Samuel Sledzieski
vkmulligan.bsky.social
We have a new preprint out on the Masala software suite, a free and open-source platform for easy biomolecular modelling methods development. www.biorxiv.org/content/10.1...
The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design
Although canonical protein design has benefited from machine learning methods trained on databases of protein sequences and structures, synthetic heteropolymer design still relies heavily on physics-b...
www.biorxiv.org
July 14, 2025 at 1:07 PM
Reposted by Samuel Sledzieski
yoakiyama.bsky.social
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
Reposted by Samuel Sledzieski
ksdrew.bsky.social
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.

www.biorxiv.org/content/10.1...
DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments
Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...
www.biorxiv.org
July 29, 2025 at 8:58 PM
Reposted by Samuel Sledzieski
workshopmlsb.bsky.social
Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!
ginaelnesr.bsky.social Gina El Nesr @ginaelnesr.bsky.social · Jul 28
The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬

Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟
July 28, 2025 at 3:41 PM
Reposted by Samuel Sledzieski
miroastore.bsky.social
That's a wrap! The results of the first #cryoEM heterogeneity challenge are up on biorxiv!
biorxiv.org/content/10.110
biorxiv.org
July 23, 2025 at 9:43 PM