Truly stoked to be a part of this journey. Working with 100+ QCRG and
@KroganLab
scientists, we identified the human host targets of
#SARSCoV2
viral proteins, mapped those to drugs/compounds, and evaluated their efficacy against live virus.
#COVID19
We in
@KroganLab
spent two weeks mapping
#SARSCoV2
-human protein-protein interactions. My favorite interactions were with DNA polymerase (why??), the nuclear pore, the centrosome, and mitochondrial complexes. The resemblance to cancer biology is striking. Why? Pls comment!
Postdoc Position in Virology
@UCLA
@MicrobioUcla
@UCLAQCBio
. We are looking for a postdoc with a background in virology & molecular biology, interested in adding proteomics and bioinformatics (no prior experience required) to their skillset!
Thrilled to join
@UCLA
@UCLAQCBio
@UCLAlifesci
@dgsomucla
as an Assistant Professor in February 2023! Rooted in quantitative systems biology, my lab will combine math modeling/bioinformatics and mass spectrometry proteomics to study signaling networks at the virus-host interface.
Feeling excited after my first day
@MicrobioUcla
and
@UCLAQCBio
. Such an incredible environment! My white boards are blank---anyone excited to come fill them with me? Hiring Research Associates and Postdocs! If interested, send me your cover letter and CV! (Profile below)
Hey
@UCSF
, how about free parking for trainees when the air quality is near toxic from fires + COVID-19? It would be a big help for us to continue our projects in the lab.
We are
#hiring
for Postdoc in Virology, Proteomics, and Systems Biology at UCLA. Message me if you're interested in joining our team. We are attending ASV 2023 if you would like to meet! - via
#Whova
event app
In this new article, we map global phosphorylation profiles induced by
#SARSCoV2
infection to kinase activities, identifying kinase inhibitors with potential to treat
#COVID19
. See thread for findings
Lab dog mascot Dr Walter made an appearance at work today, looking concerned at my desalting technique. He at least approves of applying proteomics to study post-translational modifications during viral infection⦠He was good and stayed outside the lab in his chair.
If you, or someone you know, would be interested in a postdoc position combining mass spectrometry phosphoproteomics, bioinformatics, and virology to study the virus:kinase signaling interface, come join me!
#TeamMassSpec
#postdocjobs
Friday morning experimental design meetings with these fantastic rotating PhD students is such a treat. The experiment seems solid! Thanks
@sarakamalei
, Erin, and Mohammad!
@MicrobioUcla
@UCLAQCBio
I am super excited about our paper out in
@Nature
today. It may be expected that viruses evolve to enhance innate immune suppression. What I didnβt expect is that Alpha upregulates specific viral proteins during infection which likely drive this phenotype.
We strive to create an active training environment for our 7 current undergrads, who support a lot of our research. Not to mention the stellar graduate students and postdocs that are invaluable mentors in this endeavorβthank you!
It's an amazing feeling to be able to genetically perturb every human gene in a single experiment. What would my ancestors think?? Performing pooled genome-wide CRISPR screen with fellow
@UCSF
postdoc Nan tonight! 90 15cm plates, here we go!
In awe of my trainees
@MicrobioUcla
@UCLAQCBio
! Bouhaddou lab had a stellar year-end undergrad symposium. Yaβll and the whole lab did great work this quarter πͺπ½
Super cool to give a keynote at the
@UCLAQCBio
retreat yesterday to talk about past research and to present some of the newest (few) findings from the new lab βοΈ
Check out a paper from my PhD co-trainee Charles Olwal, a collab. between
@WACCBIP_UG
@QBI_UCSF
,
@MicrobioUcla
, and
@UCLAQCBio
. HIV worsens cervical cancer, irrespective of ART. We used network modeling to find mechanisms of synergy between HIV and HPV.
Consider me amazed when I had a 15-minute conversation with my high-school intern to tell them: "Use alphafold2 to generate a structure of a Chikungunya protein" ... a day later, I get this. Great work Darryl Wong for figuring this out so quickly!
I am looking to hire a Staff Research Associate
@UCLAQCBio
@MicrobioUcla
to serve as a lab manager and perform wet lab experiments related to mass spectrometry proteomics, virology, and molecular biology. If interested, please apply:
Was incredible to visit the University of Hawaii Institute of Marine Biology Coral Resistance Lab!! Stellar group of scientists with deep biological knowledge, technology, and vision. Excited to do phosphoproteomics to decipher the coral-symbiont interaction during bleaching βοΈ
Doing phospho enrichment for PTM analysis of respiratory virus infection followed by a genome-wide CRISPR screen for cancer? Just a normal day in the
@KroganLab
!
Any summer students interested to volunteer in the lab this summer at UCLA? We are recruiting a student to perform wet lab experiments. If you are interested, please send me an email with your CV describing your background and research interests.
Excited to announce our recent publication from the
@CancerCellMap
team (CCMI), a collaborative effort between the Krogan and Ideker labs
@TreyIdeker
, describing how cancer driver protein-protein interactions are enriched for additional cancer drivers!
A small taste of what is to come very soon ... new fun (and scary?) publication out from
@KroganLab
,
@dlswaney
,
@pedrobeltrao
and many other collaborators. Stay tuned!: Inside the body, the coronavirus is even more sinister than scientists had realized
Excited to join the HARC center
@QBI_UCSF
with my
@MicrobioUcla
colleagues Maureen Su and Oliver Fregoso to study how
#HIV
viral accessory factors impact the nervous system (distal symmetric polyneuropathy or DSP). Lots to explore here!
Iβve spent the past 3 weeks pouring into the details of
#SARSCoV2
-human protein-protein interactions. I have to say, what an fascinating virus with incredible biology. Excited to see if our drug targets pan out....
#COVID19
, weβre catching up with you!
What an incredible adventure it has been collaborating with an international group of scientists here
@UCSF
,
@IcahnMountSinai
, and
@institutpasteur
on building a map of how
#SARSCoV2
hijacks our cellular machinery to cause
#COVID19
. Stay tuned for the map coming very soon...
We hosted a Bouhaddou lab undergraduate research symposium for undergraduate researchers in the lab. I was so impressed with their presentations! Great work everyone!
#happyPI
We are excited to be featured on the cover of
@CellCellPress
for our article: βThe Global Phosphorylation Landscape of SARS-CoV-2 Infectionβ. Thanks to our fantastic collaborators, with special mention of Elizabeth Fischer who took this electron microscopy image of SARS-CoV-2!
Happy to contribute to this manuscript from
@andreaspuschnik
lab
@czbiohub
in collab with
@TheOttLab
@GladstoneInst
. 3 genome-wide CRISPR screens on
#SARSCoV2
, OC43, and 229E, reveal pathways and drug targets shared by multiple coronaviruses. Our contribution: data integration!
Excited to share our new preprint! We identified host factors that are hijacked by SARS-CoV-2 and related common cold coronaviruses during infection.
Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses
We previously published a virus-human SARS-CoV-2 protein interaction map in
@nature
(Gordon et al., 2020a). In our
@ScienceMagazine
article out today, we compared these interactions to those from other lethal coronaviruses, SARS-CoV-1 and MERS-CoV. More @
Our paper is out on
@biorxivpreprint
describing our SARS CoV2-human protein-protein interaction map and drug predictions from the data. It was a honor to work with so many fantastic scientists around the world. -Nevan
For a drug to be approved, it must possess a therapeutic window, balancing efficacy and toxicity. This often depends on the dosing regimen. In this review, we discuss how pharmacokinetics/pharmacodynamics math models can help select the optimal regimen.
Great
@nytimes
article by
@carlzimmer
breaking down the science in our paper for everyone to understand. Discovering upregulation of specific subgenomic viral proteins (Orf9b, Orf6, and N) during B.1.1.7 infection was surprising for us! ππΎ
Using simple but effective computational tools, we found the levels of two proteinsβCaveolin-1 and Sox-2βcan predict, with good accuracy, response to the EGFR inhibitor cetuximab, which we validated using PDX mouse models and human clinical samples. Biomarkers save lives!
#Cancer
Cetuximab was the first FDA-approved targeted agent for HNSCC, but still has no reliable biomarkers to guide clinical use. In this issue of
@JCI_insight
, we present a robust protein signature for cetuximab response prediction in HNSCC
@DoctorBou
@UCSF_OHNS
Excited to contribute the integrative network analysis (Fig 2!) to this article spearheaded by
@andreaspuschnik
alongside
@TheOttLab
and, yours truly,
@KroganLab
. Some fascinating gene targets and drugs with antiviral efficacy against multiple coronaviruses, including
#SARSCoV2
.
One last reminder to apply to my Staff Research Associate II position at UCLA! The candidate will lead the generation of mass spectrometry proteomics data on a brand new instrument and shape the organization of a new lab. Join me!
#TeamMassSpec
Interested to learnβvia a cute animated clipβhow SARS-CoV-2 variants of concern have evolved to better antagonize innate immunity? Watch this awesome video by
@rmkaake
and
@LorenaZAlvarez
in
@KroganLab
@QBI_UCSF
about our recent publication linked in π§΅
On this last day of 2019, I reflect on all the amazing trainees who explored science in my lab over the last 2 decades. Some have gone on to establish their own labs, while others are at the forefront in medicine and biotech.
They are the legacy I leave as a PI.
Congratulations to the 3 finalists of the ECR Manuscript Competition: Mehdi Bouhaddou, Stacy Malaker and Yansheng Liu. They will present their publications on Nov. 17 at HUPO ReCONNECT 2021.
@DoctorBou
@StacyMalaker
@Yanshen73854711
#HUPOReConnect
Autoantibodies to Casein Kinase 2 (CK2) found in Multisystem Inflammatory Syndrome in Children (MIS-C). How exactly do these autoantibodies mechanistically contribute to this disease?? Exciting opportunity for future studies!
4/ A number of candidate autoantibodies found elevated in MIS-C patients. Notable examples involve Casein-Kinase family members given recent report by
@DoctorBou
et al
@KroganLab
on upregulation of CSKII in SARS-CoV-2 infected cells:
Excited to be a part of this cool work, check it out! All about how the SARS-CoV-2 B.1.1.7 UK variant antagonizes our innate immune response, which we hypothesize could increase transmissibility by lowering the threshold needed to establish infection. Awesome collaboration too!
In our new preprint, we show the B.1.1.7
#SARSCoV2
UK variant suppresses the innate immune response, which we hypothesize increases transmissibility. This work was done in a great collaboration between the
@towerslab
,
@jollylab
, and QCRG
@QBI_UCSF
.
Super excited to contribute to this study. Host-directed drugs appear to be good candidates for tackling the emergence of SARS-CoV-2 variants.
@akreuschl
and
@lucygthorne
worked days and nights hard to get this out in time -- super inspiring work.
In first functional study of full-length UK B.1.1.7
#SARSCoV2
variant virus, we find plitidepsin (aplidin), ralimetinib, and remdesivir to possess similar antiviral activity against both the early-lineage and B.1.1.7 variant coronaviruses.
@J_my_sci
For virus studies, we get an earlier readout of the ISG response from RNAseq. Protein comes later. The rna signature is useful and complete (you get all the genes you care about!). But, look, at the end of the day, itβs the protein that matters β¦
I processed bleached and unbleached coral samples for phosphoproteomics analysis today. Finding the mechanism behind coral bleaching may help us find a solution to prevent it.
#StopGlobalWarming
#coralreefs
As researchers, we are typically removed from immediate responses to epidemics and instead tend focus on longer-term solutions to problems. But, did you ask yourself what experiment or analysis you could do today to help stop the spread of
#2019_nCov
? Do it!
#CoronaOutbreak
ICYMI: There's a third case of
#2019nCoV
in the US, in Orange County, California.
Details still sparse but another traveler from Wuhan, outbreak epicenter:
More here:
In our new paper, we knocked-out 426 proteins that physically interact with
#HIV
using
#CRISPR
in primary human CD4+ T cells. Our systematic approach reveals host-pathogen protein interactions to be an enriched source of functional host factors.
If anyone is putting together a U01 for the Human Virome Program RFA-RM-23-017 [Characterization of functional interactions between viruses and human and microbial hosts] and are interested in proteomics / computational biology, I would be excited to contribute!
Why are we still faxing medical records in 2020?? Why did it take me 4 hours on the phone to initiate a transfer of my medical records by fax from
@UCSDHealth
to
@UCSFHospitals
?? We need an overhaul of medical records management.
Brand new podcast from
@QBI_UCSF
where I team up with
@rmkaake
and friends to discuss our recent
@CellCellPress
publication and science around the regulation of phosphorylation and signaling during
#SARSCoV2
infection. Informative for all audiences (we hope)!
Hive mind: Where do people typically buy computers for mass spectrometry searches? Looking for the 100+ core range, good processing power, high ram. You know the drill.
#TeamMassSpec
New preprint alert! We mapped a foundational protein-protein interaction (PPI) network involving 100 high-confidence (hc) autism spectrum disorder (ASD) risk genes, and leveraged AlphaFold2 to reveal a deeper mechanistic understanding of autism biologyπ§΅π
We are honored to lead the QCRG Pandemic Response Program, an AViDD center
@QBI_UCSF
@UCSF
funded by
@NIAIDFunding
@NIH
to develop antivirals against pathogens of pandemic concern. Iβm excited to see what our team will create in the years to come.
β97% percent of drug-indication pairs that are tested in clinical trials in oncology never advance to receive U.S. FDA approval.β
Wow. Weβve got to be misunderstanding something fundamental about cancer β this is an astronomical percentage!
#Cancer
π¨Looking for students, postdocs, and research associates! Mentoring and training the next generation is an important focus of mine, with an eye towards enhancing the visibility of minorities in science, including
#LBGTQ
, women, and people of color -- all are welcome here.
A few of our top athletes swam, biked and ran across finish lines at the 2022 Escape From Alcatraz Triathlon over the weekend! We commend their endurance and adventurous spirits, all while repping QBI.
Today in the halls of
@institutpasteur
Nevan Krogan
@KroganLab
received the Legion of Honour, Franceβs highest award to a civilian for his work on promoting international collaboration, especially between France and USA during the Covid crisis.
If youβre attending and looking for a postdoc position, let me know, we should connect during a break. You can message me here, through the Whova app, or email.
Learn about a recent paper from the lab using genetic interaction data to inform structure determination of protein complexes: A Genetic Shortcut to Help Visualize Proteins at Work via
@YouTube
@HannesBraberg
@ig_ech
@KroganLab
If it wasn't for my amazing PhD advisor
@BirtwistleLab
, I wouldn't know any math -- thanks for spending countless hours scribbling away on the white board during my early years! It helped! And thank you
@IcahnMountSinai
for cultivating my passion for biology!
Dear Donald Trump,
Do you think that if you had not been able to afford the medical care you received, that you would have been much more likely to die from COVID-19? I think yes.
And thanks for working to eliminate Medicare for all!
#sarcasm
Check out our new paper on how to scale drug efficacy predictions from cell culture models to in vivo mouse models. Yes to reducing animal usage!
#Roche
@BirtwistleLab
Using proteomics interaction data from
@KroganLab
,
@gingraslab1
, and
#BrianRaught
, we found that several of the top-ranked genes from our screen were previously shown to directly interact with SARS-CoV-2 viral proteins:
Tune in to QBI TV
@QBI_UCSF
tomorrow at 4pm PST to hear Robyn Kaake and me talk about working as part of the coronavirus research group (QCRG) during these coronavirus pandemic times! We will share our views, share recent research, and answer community questions from YouTube!
Tomorrow, June 18: QBI TV presents "Science in the Time of Corona", a live panel discussion on the ways that COVID-19 has impacted how scientists conduct research. Tune in for this half-hour premiere!
Find out more and register:
Also need to thank the co-first authors that carried a lot of the work:
@_b_meyer
,
@verorezelj
, Kris White,
@danishm20
, Miguel Marrero, Benjamin Polacco, Jim Melnyk, Svenja Ulferts, Robyn Kaake, and
@Jyoti71822796
!
@PSBROOKES
@benoitbruneau
@UCSF
@BicycleLobby
Totally great point from a climate point of view. I ride my bike everyday to work usually. But when air quality is around 200 US AQI, itβs kinda dodgy riding your bike around.