Lab of Environmental Microbiology @RockefellerUniv

New York, NY
Joined January 2009
2026 Lab Retreat / NYLittle 2.0 with labs of @KarnaVGowda (OSU), Darcy McRose (MIT), and Jane Lucas (Cary). Special guests @hdkgeo and @nishantnaraya15
1
9
232
Avi Flamholz retweeted
Why is glutathione, rather than cysteine, the major cellular thiol? Our new work by @ToshiNakamura51 suggests unlike other amino acids, excess cysteine is intrinsically toxic to mammalian cells via mitochondrial iron accumulation. @RockefellerUniv nature.com/articles/s42255-0…
10
88
3
310
20,981
Avi Flamholz retweeted
This one is really special to me! As someone who probably spends more time on @uniprot than on Google, I’m incredibly proud that SeqHub search is now integrated with UniProt, bringing together UniProt’s rich protein annotations with SeqHub’s view of native genomic context across diverse microbial lineages. This gives researchers a more complete picture of proteins of interest, connecting what we know about their function with the genomic neighborhoods and evolutionary contexts in which they occur.
Replying to @uniprot
@uniprot is where most researchers start when they want to understand a protein. As of today, prokaryotic entries there will show something new: genomic context, powered by SeqHub, right in the Sequence section of the page.
4
20
1
117
9,350
Thrilled to share that I’ll be starting as an Assistant Professor in Mechanical Engineering at UC Berkeley in January 2027! I’ll be launching the Deep Lab for Microbial Biomechanics. 🧵 1/7 @Cal_Engineer
39
30
4
610
41,853
My limited experience with LLMs so far has only emphasized the importance of human knowledge, judgment, and wisdom.
5
119
Avi Flamholz retweeted
Horizyn-1 is now available via public API. Give it a chemical reaction, get back a ranked list of candidate enzymes, screened against ~7M representative sequences. Free to try, no setup: 💻 github.com/dayhofflabs/horiz… 📄 Paper (@PNASNews): pnas.org/doi/abs/10.1073/pna…
2
10
1
57
3,336
How can a defined liquid medium could simulate a porous dehydrated environment on another planet?! Isn't the whole enterprise of "defined liquid medium like X" a bit ... silly?
How do we simulate Mars here on Earth? We scrutinized Mars rover data so you don’t have to. 😛 Here’s what it tells us about how to simulate Mars on Earth, and which organisms could grow on Mars! 📄 Report: biorxiv.org/content/10.64898…
1
6
398
1/ We need new ways of producing foods and fuels to minimise our impact on our planet. Our new paper now in @NatureBiotech examines whether microbes hold the key to producing foods and fuels in the future Open access: rdcu.be/eiIUu nature.com/articles/s41587-0…
1
9
1
24
6,786
Every synthetic biologist, every biochemist, when they dream, will sometimes hear a voice calling A whisper on the wind, as impossible as infinity, as sweet as the ambrosia of the very Gods "Engineer RuBisCo" And this paper takes us one step closer nature.com/articles/s41586-0…
14
123
14
675
46,321
Reflects a wider neglect of pedestrian life throughout @PasadenaGov. A true shame for such an intrinsically walkable spot with so many families and young children. Transformative change could be achieved with simple adjustments, eg more time to cross the street @PasadenaCSC
As I leave Pasadena, I have special obscenity to offer @PasadenaGov regarding the intersection of Del Mar and Michigan, which was planned to get a traffic light 3 yrs ago and still doesn’t have one.
2
304
As I leave Pasadena, I have special obscenity to offer @PasadenaGov regarding the intersection of Del Mar and Michigan, which was planned to get a traffic light 3 yrs ago and still doesn’t have one.
2
1
6
667
really pleased to be moving HOME to an NYC with CONGESTION PRICING, even if the price is too low
1
4
374