@SarahAlamdari

Interested in all things deep learning, biology, and molecular dynamics. @MSRNE #diversity & #representation matter (she/her)

 Cambridge, MA
sarahalamdari.com
Joined April 2019
  • Tweets1.4K
  • Following1.1K
  • Followers1.6K
76Media
I'm recruiting PhD interns for Summer 2027! If you’re excited about using generative protein language models to tackle real functional protein problems, please apply here!
Kevin K. Yang 楊凱筌@KevinKaichuangOct 14
Are you a PhD student interested in the intersection of machine learning and biology or healthcare? Come do an internship with the BioML Group at MSR! Make sure you submit a research statement! apply.careers.microsoft.com/…
9
15
159
23,145
Sarah Alamdari retweeted
Marta Skreta@martoskreto21h
Your molecule is really into your target protein. Unfortunately, it’s into other proteins too 💔 Introducing SelectBench: a benchmark for selectivity in generative structure-based drug design. We started out thinking about algorithms for selectivity, then ran into a question: how do we evaluate them at scale on pharmacologically relevant examples? So we took a side quest and built a benchmark 🛠️ SelectBench is our first step toward evaluating in silico selectivity more systematically. Turns out, getting models to be picky is really hard! Super proud of the entire team, especially Ella (@ERajaonson) and Yoon (@yololulu_) for leading the work. We can’t wait to present SelectBench in Sydney at NeurIPS 2026 as part of the Datasets and Benchmarks track. 🤗 Can your model design molecules with a type? 🧬 📄 Paper: arxiv.org/abs/2610.24124 💻 Code & benchmark: github.com/lovetaro/selectbe…

On the Selectivity of Generative Models in Structure-Based Drug Design

Designing small-molecule drugs that selectively bind to a target protein while avoiding unintended interactions with other proteins is essential for reducing side effects that contribute...

arxiv.org
Ella Rajaonson@ERajaonsonOct 24
A molecule can bind the right protein and still be the wrong drug. Why? Because it might also bind proteins we don't want it to, potentially causing serious side effects. 📄 Paper: arxiv.org/abs/2610.24124
4
19
105
4,136
Sarah Alamdari retweeted
Lester Mackey@LesterMackeyOct 22
If you'd like to come work with me and my amazing colleagues as a full-time researcher @MSFTResearch @MSRNE, please apply here: apply.careers.microsoft.com/… apply.careers.microsoft.com/…
2
18
5
134
14,223
Sarah Alamdari retweeted
Yunha Hwang
@Micro_YunhaOct 22
Great to see more groups are looking closer at microbial intergenic gold mine! Genomic context, again, is the critical information axis for discovery and interpretation.
Arc Institute
@arcinstituteOct 22
Much of the functional biology encoded in genomes remains hidden in noncoding DNA. In a preprint out today, @pdhsu and team introduce COMPASS, a genomic language model-based approach to systematically map this underexplored sequence space.
1
12
53
3,450
Sarah Alamdari retweeted
David Alvarez Melis@elmelisOct 22
We’re hiring Senior and Principal researchers in ML & Stats at Microsoft Research New England @MSRNE! Amazing colleagues, remarkable breadth and depth of expertise, and unbeatable views. Come join us! Questions about the roles or the group? DM me!
4
11
2
89
12,611
Sarah Alamdari retweeted
Nate Corley@nscorleyOct 21
1/n Crossover episode! We introduce RFD4-Proteina, our latest design model - and the result of a year-long collaboration between the Baker Lab and NVIDIA GenAIR (the name says it all…). I hope you’ll agree - the results are astonishing. 🌐 Website: rfd4-proteina.org/

RFD4-Proteina

Biomolecular design through latent reasoning with RFD4-Proteina.

rfd4-proteina.org
7
48
3
191
15,468
Kieran is having a generational protein design run this month 👀🔥
Kieran Didi
@DidiKieranOct 21
Avengers assemble: 1 year BakerLab + NVIDIA GenAIR = 🔥 rfd4-proteina.org Presenting RFD4-Proteina, our latest protein design model, significantly better and faster than everything we compared against, both in silico and in the lab! 1/30
2
1
21
915
Sarah Alamdari retweeted
Christian Dallago@sacdallagoOct 21
A step change in protein design: RFD4-Proteina is enables everyone today. We partenered with @huggingface to make available a free space. You can solve your hardest biology problem right now. No CS degree required: huggingface.co/blog/nvidia/r… More to come...

Protein Design with RFD4-Proteina and Hugging Face Spaces

A Blog post by NVIDIA on Hugging Face

huggingface.co
Kieran Didi
@DidiKieranOct 21
Avengers assemble: 1 year BakerLab + NVIDIA GenAIR = 🔥 rfd4-proteina.org Presenting RFD4-Proteina, our latest protein design model, significantly better and faster than everything we compared against, both in silico and in the lab! 1/30
1
11
31
1,947
Sarah Alamdari retweeted
Lester Mackey@LesterMackeyOct 14
If you're a PhD student interested in interning with me or one of my amazing colleagues at Microsoft Research New England (@MSRNE, @MSFTResearch) this summer, please apply here apply.careers.microsoft.com/…

Research Intern - Machine Learning and Statistics | Microsoft Careers

Research Interns put inquiry and theory into practice. Alongside fellow doctoral candidates and some of the world's best researchers, Research Interns learn, collaborate, and network for life....

apply.careers.microsoft.com
7
45
1
299
27,599
Sarah Alamdari retweeted
Kieran Didi
@DidiKieranOct 21
Avengers assemble: 1 year BakerLab + NVIDIA GenAIR = 🔥 rfd4-proteina.org Presenting RFD4-Proteina, our latest protein design model, significantly better and faster than everything we compared against, both in silico and in the lab! 1/30
27
202
43
660
63,505
Sarah Alamdari retweeted
MRehMan
@_Wienman_Oct 20
Finally got GROMACS molecular dynamics simulations live-streaming directly into Blender using Molecular Nodes! Done via Docker, IMDv3 1.44 picoseconds/72 frames, all-atom molecular dynamics simulation of lysozyme in water, 303.15 K/30°C #GROMACS #Blender3D #MolecularDynamics #MolecularNodes
3
8
1
70
4,876
During my PhD (not that long ago...) a single simulation on a single system could take weeks to months. It’s amazing to see that timeline collapsing so quickly! Congrats to the team, looking forward to playing around with this!
Frank Noe@FrankNoeBerlinOct 20
Replying to @FrankNoeBerlin
Dynamics: folding & binding of an intrinsically disordered peptide to its protein receptor via an intermediate state. A 5 milliseconds simulation would take >10 GPU years with MD simulation. At 5 microsecond steps, BioEmu2 needs 40 minutes on the same GPU – a >100,000 x speedup!
1
7
68
5,332
Sarah Alamdari retweeted
Yuanqi Du
@YuanqiDOct 20
Sharing a one-day workshop at the @MSRNE office on the frontier of AI for materials science during the @Materials_MRS fall meeting at Boston! Scan the QR code to sign-up for poster and contributed presentations!
1
2
17
1,213
Sarah Alamdari retweeted
Frank Noe@FrankNoeBerlinOct 20
Public preview of BioEmu2! @MSFTResearch AI for Science’s new foundation model for biomolecular structure, dynamics and function. Open weights, MIT license. github.com/microsoft/bioemu2 Movie: BioEmu2-simulated binding of intrinsically disordered peptide PUMA to MCL-1 receptor. 🧵⬇️
22
243
27
900
63,842
Deep sea gene editor is crazy
Ceron Lab@CeronLabOct 18
🧬🌊 New preprint from our lab: DO1 Cas9, the first Cas9 nuclease characterised from the deep ocean — recovered from a metagenome at 1,500 m in the Atlantic. ❄️Cold-adapted: it cuts DNA efficiently at low temperature, where mesophilic SpCas9 retains only residual activity. 🧵1/4
1
21
1,494
Sarah Alamdari retweeted
Noelia Ferruz@ferruz_noeliaOct 19
Continuing with with early life origins, Weiss et al. analyzed 6.1 million genes and found 355 protein families likely present in the last common universal ancestor, suggesting it was anaerobic, CO2-fixing, H2-dependent, N2-fixing, and thermophilic: nature.com/articles/nmicrobi…

The physiology and habitat of the last universal common ancestor

Nature Microbiology - A phylogenetic approach was used to illuminate the physiology of the last universal common ancestor, supporting the theory that LUCA was an H2-dependent autotroph in a...

nature.com
1
17
64
3,953
Sarah Alamdari retweeted
Ceron Lab@CeronLabOct 18
🧬🌊 New preprint from our lab: DO1 Cas9, the first Cas9 nuclease characterised from the deep ocean — recovered from a metagenome at 1,500 m in the Atlantic. ❄️Cold-adapted: it cuts DNA efficiently at low temperature, where mesophilic SpCas9 retains only residual activity. 🧵1/4
2
63
8
265
22,095
Sarah Alamdari retweeted
Magnus Bauer@kinasekidOct 18
Can we design proteins that cut other proteins? Our de novo cysteine protease paper is out in Nature! We designed new folds that cleave peptide backbones, with activity demonstrated in mammalian cells. Paper and code 👇 nature.com/articles/s41586-0…
3
55
6
319
21,635
Sarah Alamdari retweeted
Rohith Krishna@r_krishna3Oct 15
Today we're sharing an update on our diffusion method from last year, RFdiffusion3, in @ScienceMagazine. Notably, we show significant improvement in design of sequence specific proteases for amyloid sequences and metallohydrolases for pesticide degradation.
6
31
4
125
7,347
Sarah Alamdari retweeted
Jasper Butcher@butcher_jasperOct 15
Today, RFdiffusion3 is out in @ScienceMagazine! science.org/doi/10.1126/scie… We have many exciting updates to share! We're also releasing Chaperone, an agent harness for general bio-molecular design. 1/n
4
37
4
187
9,316
Calling graduate students 📣. Come work on AI x Bio @MSFTResearch 🎉! We are currently recruiting graduate student interns for summer 2027! Apply and come work with me on problems in regulatory genomics, epigenomics, biosecurity, and wearables!
Kevin K. Yang 楊凱筌@KevinKaichuangOct 14
Are you a PhD student interested in the intersection of machine learning and biology or healthcare? Come do an internship with the BioML Group at MSR! Make sure you submit a research statement! apply.careers.microsoft.com/…
8
44
4,134
Load more