A bit late to post this but...
I'm starting my own lab at UCSD!!
We'll be doing machine learning for enzymes and metabolism, both
It's a joint appointment between
@UCSDSkaggsSOP
and
@UCSDChemBiochem
.
Happy to share our new work in
@PNASNews
: A thermodynamic atlas of carbon redox chemical space
It's
#3
in our trilogy on thermodynamics of redox biochem. through quantum chemistry, and it took us into the realm of
#prebioticchemistry
#originoflife
Our Mtb TnSeq database preprint is up. Our goal is to help TB researchers more easily explore the data gold in ~20 yrs. worth of Mtb TnSeq data.
It was such a pleasure and honor to work with
@anisha_zaveri
and Michael deJesus.
We'll be uploading a bunch of new screens soon!
Our paper "Quantum chemistry reveals thermodynamic principles of redox biochemistry" - with the beautiful artwork by
@beangoben
- was selected for the cover of this coming month's issue of PLOS Computational Biology
@PLOSCompBiol
@A_Aspuru_Guzik
@flamholz
HHMI is excited to announce the selection of 15 exceptional early career scientists as 2019
#HannaGrayFellows
to support
#diversity
in biomedical research:
"The history of deforestation is a tragic one, in which we ... lost these wild and beautiful landscapes & the wildlife within them. But, the fact that forest transitions are possible should give us confidence that a positive future is possible"
Can't love
@OurWorldInData
enough!
Over last three centuries we've lost forest 1.5-times the size of the USA.
Deforestation peaked in the 1980s – in that decade we lost an area half the size of India.
It has fallen since, but we've got work to do to bring it to an end.
My latest article:
I messed up my English past tense and told the
@Agilent
repair tech that I had "shat" a blank sample into the LC-MS and was observing serious contamination peaks. The look on his face was priceless
Our July issue is out! Cover story by
@A_Aspuru_Guzik
& team
@chemuoft
@HarvardCCB
! A combination of quantum chemistry & machine learning predicts biochemical redox potentials of more than 300 000 reactions, revealing factors contributing to energetics!
yeah! our new paper is out on
@ACSCentSci
. This is part 2/3 of our "thermodynamics of redox biochemistry" trilogy. Gaussian processes are a powerful and way of calibrating quantum chem. predictions of biochemical redox potentials with the amazing
@A_Aspuru_Guzik
and
@beangoben
Read
#ASAP
research on how a combination of quantum chemistry & machine learning accurately predicts biochemical redox potentials of more than 300 000 reactions, revealing factors contributing to energetics by
@A_Aspuru_Guzik
& team
@chemuoft
@HarvardCCB
!
In terms of outreach , I plan to focus on strengthening the SoCal / Baja California chapter of the
@ClubesCienciaMx
program. And can't wait to get to know other NIH-FIRST program colleagues to team up and learn from them!
First batch of rotation students is coming in, and I'm super excited to recruit:
- wet lab folks who want to learn or strengthen their coding
- comp. folks who want to delve into experiments
- or those who are happy where they are and don't want to touch a pipette/script :)
Just out! Sabine Ehrt's, Dirk Schnappinger's and Kyu Rhee's review for Nature Reviews Microbiology Tuberculosis metabolism. May a deep understanding of metabolism contribute to tackling the
#1
infectious disease killer:
the phage-loaded microparticles, were deposited throughout the lung, and the phages were delivered in an active state. P. aeruginosa-infected wild-type mice treated with phage-loaded microparticles showed 100% survival over six days...
@chngin_the_wrld
According to this article, it looks like Mexico City will implement the 4-10 schedule of
@UriAlonWeizmann
and
@MiloLabWIS
et al. starting June 15th. Amazing :)
Dr. Kyu Rhee of
@WeillCornellGS
receives the Burroughs Wellcome Fund's (
@BWFUND
) Physician-Scientist Institutional Award!
"This grant provides an opportunity for medical students and physicians who enjoy science to pursue careers in lab investigation.”
Running a crazy intensive online Zoom course (Taller Ciencia para Jóvenes) for 13 Mexican high-school students on TB drug discovery.
We're using the open dataset from
@EachanJohnson
's awesome PROSPECT Nature paper.
And all the Python notebooks are taught/run in
@GoogleColab
"Enzyme Substrate Prediction from 3D Feature Representations Using Space-Filling Curves"
With my friend Dmitrij Rappoport, we explore space-filling curves (SFCs) as feature representations of protein structures for enzyme substrate prediction.
Our quantum chemistry approach predicts redox potentials with considerably higher accuracy than Group Contribution Method (GCM), and we can even detect experimental values in the literature that are very likely wrong
It's a joint appointment between
@UCSDSkaggsSOP
and
@UCSDChemBiochem
, two amazing places full of inspiring new colleagues.
I'm especially grateful to the UCSD NIH-FIRST program led by
@joann_trejo
and to the
@HHMINEWS
Hanna Gray Fellowship for its support.
Inspire young future scientists from Mexico this summer (virtual edition) with the
@ClubesCienciaMx
program! You'll have an awesome, meaningful experience, guaranteed.
Really delighted to share with the world our recent work 'Conversion of Escherichia coli to Generate All Biomass Carbon from CO2'. Great team effort with Roee Ben-Nissan,
@yinonbaron
and other current and former members of the Milo lab.
Want a **FREE** trip to a beautiful city in Mexico to share/teach the science you know and love with the coolest high school/early undergrad students you'll ever meet? Fill out the form for the
@ClubesCienciaMx
program!
Instructors call is open!🤩🇲🇽
Apply now as an instructor and win a grant to support your travel to Clubes de Ciencia México ✈️
Clubes de Ciencia México será presencial este año 🧪🙌 ¿Ya terminaste tu aplicación?
¡La ciencia es de quien la trabaja!
👉
Jose Reyes in the
@LoweLabMSKCC
&
@dana_peer
labs seeks to understand how cancer cells change over time, and how such remarkable ability to change allows them to survive the multiple challenges that they face during tumor initiation and in response to therapy.
#NPAW2020
🇲🇽
@joshmich
@NickKristof
The most interesting part is the intermittent social distancing (+other): "We show that intermittent social distancing ... may allow interventions to be relaxed temporarily in relative short time windows, but measures will need to be reintroduced if or when case numbers rebound"
📣
#OpenCall
📣
Do you want to be one of the SCI instructors to inspire the new generation of young Iberoamerican scientists👨🔬🌎👩🔬? Take part in our open call and change the lives of high school and college students in Iberoamérica ☝️🤓.
APPLY HERE👉:
after hearing (another) academic horror story about a PI in a nearby institute who treats their postdocs like s#!t, was thinking about strategies to discourage that kind of behaviour..
what about YELP-like review site for PI's from former (and current?) lab members?
📣𝐓𝐡𝐞 𝐜𝐚𝐥𝐥 𝐢𝐬 𝐨𝐩𝐞𝐧!📣
𝗪𝐞 𝐡𝐚𝐯𝐞 𝐠𝐫𝐞𝐚𝐭 𝐧𝐞𝐰𝐬 𝐟𝐨𝐫 𝐲𝐨𝐮! Science Clubs International is launching its first international 𝐒𝐜𝐢𝐞𝐧𝐜𝐞 𝐂𝐥𝐮𝐛 𝐨𝐧𝐥𝐢𝐧𝐞 𝐞𝐝𝐢𝐭𝐢𝐨𝐧👨💻.
Apply now 👉
If you're passionate about mentoring the next generation of scientists and want to connect with talented youth in beautiful Peru, apply to be an international instructor for
@CdeCPeru
, you will not regret it.
Although he's not smiling much in either of these pics, I know Arren *really* enjoyed this metabolism workshop (Maine, 2015). He was the heart of the meeting, both in terms of the science and because he had everyone bursting out laughing with his unique sense of humor.
We are hiring faculty! Please apply to join our vibrant, diverse, and growing department
@UCSF_BTS
. We are looking for folks who bridge fields anywhere in or between bio, tech dev, and ML/AI. As the newest hire I can say it is an amazing place to grow!
Dear Arren: We will miss you so so much. You were such an inspiration and a source of sharp wisdom and vision. Thank you for your mentorship and everything you taught so many of us, and for the amazing science you produced in your way-too-short life. RIP
Our lab has faced the greatest loss imaginable. To us Arren was a mentor, a supervisor, a friend and the head of a family. We are shocked and speechless. Our thoughts are with everyone who got to know this unique genius. He will be sorely missed.
PE/PPE proteins mediate nutrient transport across the outer membrane of M. tuberculosis
"Phthiocerol dimycocerosate determined the low permeability of the mycobacterial outer membrane, and the PE/PPE proteins apparently act as solute-specific channels."
highlight divertido del curso locochón parte del Taller Ciencia para Jóvenes:
Visualizar moléculas del paper de Nature de PROSPECT en 3D en
@GoogleColab
.
Está de huevos Google Colab para dar talleres remotos. Me encantó la experiencia y los estudiantes un placer!
¡Acompáñanos en esta edición especial del
#CdCMx
#podcast
!
En este episodio los fundadores nos hablan de la actualidad de CdeCMx y nos explican cómo el uso de herramientas informáticas fueron clave para realizar una edición novedosa de clubes.
👉
2 badass climate change/ CO_2 emissions papers out in Nature today:
- *Seasonal origin of the thermal maxima at the Holocene and the last interglacial*
- *Global and regional drivers of land-use emissions in 1961–2017*
Wow.
@scismic
is an "avenue for early-career researchers to anonymously share information about their experiences in labs" Here they were featured in Science. cool! thanks to
@JKamens
for pointing this out.
Awesome collaboration between TB scientists at
@WeillCornell
, U. Minnessota, Rutgers, Texas A&M out in Science Translational Medicine
@ScienceTM
today:
Targeting protein biotinylation enhances tuberculosis chemotherapy
from amazing
@janhjensen
and team :
"High throughput virtual screening of 230 billion (!!!!!!!) molecular solar heat battery candidates"
"...the main conclusion of this study is that there are no molecules among the 230 billion with a storage density approaching 1 kJ/g."
Updated preprint: High Throughput Virtual Screening of 230 Billion Molecular Solar Heat Battery Candidates
#compchem
Took > 1 year to update but
@MKoerstz
magnum opus is finally done! With
@AndersSChristen
&
@mogens_br
so excited, I have "The Rosie Result" in my hands. I also got this cool free bag when I bought it here at the University of Otago bookshop in Dunedin, NZ. Shoutout to my currently favorite fiction writer in the world,
@GraemeSimsion
. Thanks for writing!
This week on
#AviLovesYourPaper
I re-read
@champiDicty
's "A thermodynamic atlas of carbon redox chemical space" - a really pleasing application of recent advances in computational chemistry to probe the origin and structure of cellular metabolism 1/n
Today, HHMI is proud to announce the new
#HannaGrayFellows
, 21 early career researchers who are taking on some of the biggest challenges in the life sciences.
Latest work by the amazing
@Robert_S_Jansen
from Kyu Rhee's lab, in collaboration with Eric Rubin's
@ericrubinlab
lab and Sacchettini lab is out! congrats to all!
"Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis"
Our latest work using untargeted metabolomics to discover the function of a gene of unknown function in Mycobacterium tuberculosis has been published!
@SpringerNature
@NatureComms
We are only 10 days away from the Cornell FIRST Future Faculty Symposium! We're so excited to welcome participants to campus! Looking forward to meeting everyone!
HHMI is proud to announce the 2020
#GilliamFellows
! They’re bound by a shared passion for science and will join a growing and diverse community of graduate students and their advisers.
I'm enjoying reading this review just out in Cell by
@laoneill111
and Michael Murphy.
"Krebs Cycle Reimagined: The Emerging Roles of Succinate and Itaconate as Signal Transducers".
Succinate is my favorite molecule in the (visible) universe.
Wow — dean of University of Washington medical school is asking qualified graduate students to pause their research and instead help run COVID-19 lab tests.
Voluntary until compensation structure can be determined
awesome! "UCSD is now launching a clinical center to refine phage treatments and help companies bring them to market"
@chngin_the_wrld
is changing the world! :)
Kids selling drugs on street corners went to prison, but McKinsey profited by "turbocharging" opioid sales by Purdue Pharma, leading to far more overdoses. So send McKinsey executives to prison and make all the partners pay. End impunity.
Are you a
#postdoc
? Interested in
#phagetherapy
?
@IPATH
is the 1st dedicated
#phage
therapy center in North America and we are looking to hire our 1st postdoc for our
#microbiology
lab! Email us your CV, letter of interest and 3 references to IPATH
@ucsd
.edu . Go viral in 2019!
Awesome how in this piece Nick Kristof puts Trump, Stephen Miller, Kirstjen Nilsen, John Kelly et al. side to side with the slave owners and the Nazis with their family separation policy. They're up there with them in their cruelty.
Agree with
@MoAlQuraishi
that this is super cool. Especially exciting for us in the TB community to see that there's a ton of data in there for Mtb protein-protein interactions.
This looks great. I think it's an idea that's been in the ether for some time but getting it to work is an altogether different matter. Will be interesting to see if it can be translated to animals, especially mammals.
We did it,
@DaveZeevi
! Our paper is now published in
@ScienceMagazine
!
We present a data-driven, computational perspective on how selective pressures resulting from nutrient limitation shape microbial coding sequences. Thread below:
Fresh approaches to deep learning are going head-to-head race to crack one of biology’s grandest challenges: predicting the 3D structures of proteins from their amino-acid sequences.
Thrilled to announce I will be joining BioE and Genetics at
@Stanfordmed
and
@StanfordEng
as an Assistant Professor in 2022. My lab will be part of
@StanfordBioX
and
@czbiohub
and I look forward to joining such incredible communities of colleagues, trainees and new friends! 1/
The Anthropocene by the Numbers: A Quantitative Snapshot of Humanity's Influence on the Planet
"We quantify twelve dimensionless ratios which put the magnitude of human impacts in context, comparing the magnitude of anthropogenic processes to their natural analogues."
I'm thrilled to share our preprint "The Anthropocene by the Numbers" posted today on the arXiv. Here, we present a synthesis of the myriad ways that humans have drastically changed the face of the Earth. In many ways, we match or exceed forces of nature
"This disparity is compounded by scientific academic working life, which holds ‘macho’ expectations, such as long working hours and miles travelled, to demonstrate career success"
So I wrote a thing that I'm proud of. I think is important for science, and vital for society. We must encourage and support men to do their fair share as dads. We'll get more equal workplaces and better families.
@ChemistryWorld
Congratulations
@Education4S
on becoming a 2020
#WISEAwards
winner! 👏 This great initiative focuses on the power of play as a mechanism of dialogue between teachers & students. Here’s how they’re changing the way students learn:
#FutureofEducation
We generated 652 redox reactions from KEGG compounds, calculated their potentials, showing that NAD(P) optimally satisfies two constraints: reversibly reducing/oxidizing the majority of redox reactions in central metabolism while keeping the concentration of carbonyls in check
the synthetic TaCo (tartronyl-CoA) pathway:
"Here, we developed glycolyl-CoA carboxylase (GCC), a new-to-nature enzyme, by combining rational design, high-throughput microfluidics and microplate screens."
Arren lives on.
The synthetic TaCo pathway: a synthetic photo-respiration by-pass, which relies on a new-to-nature CO2-fixing enzyme (GCC). A key step towards synthetic metabolism!
In collaboration with
@erblabs
@BaretJc
@SchullerJm
, and finally out!
I'm starting a (weekly?) tweet-thread series
#AviLovesYourPaper
where I (wait for it) hype papers I love. I'm planning to kick it off next week with
@champiDicty
's recent PNAS masterpiece. Pls reply/DM/email suggestions to papers.
Este pequeño video de la historia de Cabo Pulmo, México, es la cosa más inspiradora y conmovedora que he visto en mucho tiempo.
This little video on Cabo Pulmo, Mexico, is the most inspiring and moving thing I've seen in a while.
When the local community in Cabo Pulmo, Mexico, observed that their fish population was declining, they took action. The creation of a no-take marine reserve transformed the reef from an underwater desert to a vibrant, biodiverse ecosystem in just 10 yrs.
Foreign students in the U.S. whose classes are taught completely online will have to transfer to another school with face-to-face instruction or leave the country
Every breath you take - the heme metabolite, dedication and the Shemin pathway & . David Shemin ingested isotopically labeled glycine to ultimately help decipher the biosynthesis of heme. Early biochemists were amazing.
Ref. implementation of RGNs is now available on GitHub (), along with 6 pre-trained models spanning CASP7 - 12. The code enables training quite a variety of RGN models, including ones I’ve never tried!
The amazing work of
@valeriasouzaccb
et al. in Cuatro Ciénegas, cover of Science!
favorite part from summary:
"The researchers have also enlisted local high school students to aid in the conservation of the pools and the microscopic life they host."
Subcellular antibiotic visualization reveals a dynamic drug reservoir in infected macrophages
"Lipid droplets help anti-TB drug efficacy: Greenwood et al. (...) showed that the antitubercular (anti-TB) drug bedaquiline accumulated in host lipid droplets."
"We find that Earth is exactly at the crossover point; in the year 2020 (± 6), the anthropogenic mass, which has recently doubled roughly every 20 years, will surpass all global living biomass."
"Impact on …
Protein structure prediction?
The core field has been blown to pieces; there’s just no sugar-coating it."
Like many others, I love reading
@MoAlQuraishi
's blog posts so much : )
Prof. Carl Nathan at WCM shared this on preparing face masks from cloth:
"In 2006, the CDC published recommendations. One simple method was based on boiling a cotton undershirt to shrink and sterilize it and then folding it appropriately."
Rao Lab:
Rapid and specific labeling of single live M. tuberculosis with a dual-targeting fluorogenic probe
"The probe could identify single live tuberculosis bacteria from nontuberculosis and dead bacteria, was compatible with patient sputum samples."