Mehdi Bouhaddou, PhD
@DoctorBou
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649
Assist. Prof. @UCLAQCBio @MicrobioUcla . Postdoc @KroganLab . PhD @BirtwistleLab . Phosphoproteomics + Math Modeling + Viruses. 50% dry, 50% wet.🇺🇸🇫🇷🇲🇦🏳️🌈
San Francisco, CA
Joined March 2018
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Send us removal request.
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I am WAY too excited to get pipets in the lab, as lame as that may sound. So here is a pic of me with my first pipets 🤙🏽 Now we can do science!!
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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
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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!
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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!
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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.
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@microRNApro
@emartinez78987
@BGLTHMND
@AlumiLynn
@JNAlexandratos
@kidoctr
@Rectitude20
@USoA34805717
@LoriSan29894021
@WeAreVacInjured
@FTC
@doritmi
@mcfunny
I am the author of the paper you posted. What you’ve stated is not what the paper is about. In fact, it makes no sense at all.
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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)
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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.
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First set of virus infected samples going on the mass spec after so much optimization! Ouf!
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I feel lucky to have helped lead this truly collaborative project, illustrating how
#SARSCoV2
hijacks cellular signaling using time-course proteomics. Big thanks to
@pedrobeltrao
,
@dlswaney
,
@grosse_lab
,
@kevansf
, Elizabeth Fischer,
@VirusPathways
,
@VignuzziLab
and their labs!
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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.
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Too old to use BeReal, but it’s good to see our undergrads are enjoying their time in the lab 🫶🏽
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Thursday morning lab meetings are VERY fun with this stellar group! Feeling lucky.
@UCLAQCBio
@MicrobioUcla
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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
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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
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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 didn’t expect is that Alpha upregulates specific viral proteins during infection which likely drive this phenotype.
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Look at this beautiful
@UCLAQCBio
@MicrobioUcla
lab working hard 💪🏽
@Delgado_Yenn
@prashantk88
@armenkhaan
@sarakamalei
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Was exited to present at
#CROI2023
on our SARS-CoV-2 variants proteomics/bioinformatics work. And, it’s snowing in Seattle!
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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 endeavor—thank you!
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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!
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In awe of my trainees
@MicrobioUcla
@UCLAQCBio
! Bouhaddou lab had a stellar year-end undergrad symposium. Ya’ll and the whole lab did great work this quarter 💪🏽
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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 ⭐️
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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.
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Maybe nobody cares? But
#1
on PubMed trending for our paper is cool to me!
Delighted to see our paper trending on
@PubTrend
where we show enhanced innate immune evasion by SARS-CoV-2 Alpha variant. Nice work
@lucygthorne
,
@akreuschl
,
@LorenaZAlvarez
,
@jolly_lab
,
@KroganLab
,
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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!
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Looking for molecular biology and virology postdocs — please consider applying! See 🧵👇🏽
#virology
#postdoc
#TeamMassSpec
#molecularbiology
#postdocjobs
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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:
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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 ☀️
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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
!
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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.
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Great to have
@dschweppe1
visit
@dgsomucla
and give a great seminar. Love getting more proteomics talks at UCLA!
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Check out my most recent pub, a collaborative UCSF/UCSD effort. Are proteins that physically interact with commonly mutated cancer drivers also commonly mutated? It seems so!
@CancerCellMap
#cancer
#cellmap
#disease
#protein
#PrecisionMedicine
#genetics
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!
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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
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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!
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I’ve 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
, we’re 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...
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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
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Super excited to be on the cover!
We are excited to be featured on the cover of
@CellCellPress
for our article: “The Global Phosphorylation Landscape of SARS-CoV-2 Infection”. Thanks to our fantastic collaborators, with special mention of Elizabeth Fischer who took this electron microscopy image of SARS-CoV-2!
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My undergrad sent me an official LaTeX document of the equations we discussed during our meeting yesterday.
#impressed
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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
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My contribution to this awesome manuscript was in the PPI clustering and the development of the differential interaction score alongside
@TreyIdeker
and
@jp_jisoopark
. We also made/annotated the PPI maps alongside members of the
@KroganLab
.
@cytoscape
&
#adobeillustrator
, thanks!
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 @
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It’s out!! Such as pleasure to work with these incredible scientists.
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
1K
579
1K
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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.
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Thanks
@KroganLab
for wishing on the wishing tree for me. All PIs should do this for their trainees. C’mon NIAID!
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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! 👇🏾
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Great to be back with the
@QBI_UCSF
family in Chicago for the Systems Biology of Infectious Diseases Centers Meeting. What a great group!
@LisaMiorin
@Monita_M_Dhar
@KroganLab
@HultquistLab
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Incredible to see everyone out for our joint Bouhaddou lab -
@SchmidtLabHMS
@schmittwitt_
bonfire 🔥
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Using simple but effective computational tools, we found the levels of two proteins—Caveolin-1 and Sox-2—can 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
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@Saskajanet
@wendy_bickmore
YES, thank you. Editors, please step up to address this disparity.
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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
.
#Genome
-wide
#CRISPR
screens to identify host factors required for
#infection
by
#SARSCoV2
and the common
#cold
#coronaviruses
. Online Now!
For all
@CellPressNews
#coronavirus
research and commentary, visit
#COVID19
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#SoCalSystemsBio
@UCIrvine
is such a cool community — recommend anyone to check it out, especially if you are in Southern California ☀️
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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
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Interested to learn—via a cute animated clip—how 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 🧵
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What can I say, I got spoiled with rainin pipets and couldn’t change that
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#Queen
. What an inspiration you are
@VirusesImmunity
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.
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Thanks for the shout out!
#HUPOReConnect
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
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We should work to increase representation of LBGTQ people in science. It is OK to be gay and out and be a scientist. Try it!
#NationalComingOutDay
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On my way to
#ASV2023
: If you’re going this year, reach out, let’s connect! Looking forward to chatting about viruses all week 👏🏽
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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:
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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
.
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Look at our stellar
@UCLA
@MicrobioUcla
graduate students at the West Coast Retrovirus Meeting in Palm Springs ☀️ Here is the future folks:
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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.
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@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, it’s the protein that matters …
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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
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Great to finally meet Marco
@VignuzziLab
in person after a few years of working together!
#pandemicresearch
Great to have
@VignuzziLab
visit
@QBI_UCSF
and give a great seminar summarizing his last 20 years of work! Excited for what is next.
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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:
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Excited to contribute to this! Great paper with great people. HIV KO screen of HIV host complexes in primary human T cells.
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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!
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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.
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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)!
NEW EPISODE: Join us for an exciting discussion about how the
#SARSCOV2
virus hijacks host signaling networks. Listen in full here:
#b3
#sciencepodcast
#ucsf
#basicbiology
#qbiscience
#filopodia
#kinases
#cytoskeleton
#sciencemadesimpler
#newepisode
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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
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Protein-protein interactions meet AlphaFold meet Disease. Amazing!
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 biology🧵👇
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Very excited to see this funded! Some fantastic science in this!
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. I’m excited to see what our team will create in the years to come.
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“97% percent of drug-indication pairs that are tested in clinical trials in oncology never advance to receive U.S. FDA approval.”
Wow. We’ve got to be misunderstanding something fundamental about cancer — this is an astronomical percentage!
#Cancer
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🚨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.
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Just going through some Spike mutant sequences from
@GISAID
and I either found an error or a groundbreaking discovery. Guessing it’s the former.
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It’s amazing how many people love pipets! PhD students — please apply to my postdoc position!
Looking for molecular biology and virology postdocs — please consider applying! See 🧵👇🏽
#virology
#postdoc
#TeamMassSpec
#molecularbiology
#postdocjobs
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Postdoc-ing at one quantitative biosciences institute (
@QBI_UCSF
) and faculty-ing at another (
@UCLAQCBio
) is a dream come true.
@QBI_UCSF
,
@GladstoneInst
,
@KroganLab
, and
@dlswaney
have shaped me as a scientist and taught me how to collaborate. I feel lucky to have trained here.
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Very cool study! We are so intertwined with microbes, even in our development.
Bifidobacteria-mediated immune system imprinting early in life
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Proud to represent
@QBI_UCSF
!
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.
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It was a fantastic tutorial — excited to see what this can do to revolutionize the classroom !
Step Into Biology followed the science- right to
@UCLA
. We met with
@DoctorBou
and a team of Microscopists and Modellers to discuss how
@stpn2biology
can help scientists share, collaborate and inform through teaching and research.
#ScienceTech
#AugmentedReality
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Proud of you Nevan!
@KroganLab
Today in the halls of
@institutpasteur
Nevan Krogan
@KroganLab
received the Legion of Honour, France’s highest award to a civilian for his work on promoting international collaboration, especially between France and USA during the Covid crisis.
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Turns out that spending the week surfing is a great way to de-stress. Try it.
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If you’re 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.
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Watch this to further your education. Angela Davis: How Does Change Happen? AD is an
#inspiration
.
#BlackLivesMatter
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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
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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!
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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
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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
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Good to see some of our
@KroganLab
PPIs showing up in the genome wide CRISPR screens.
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:
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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:
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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
!
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Great way to visualize kinases regulated during infection as reported in our
#phosphoproteomics
analysis of
#SARSCoV2
:
Want to explore
#COVID19
#phosphoproteomics
#network
from recent
@CellCellPress
study by
@KroganLab
@pedrobeltrao
@VirusPathways
? Here is an interface for that! Feedback welcome as we develop the tool!
@SesmaLab
@florian_krammer
@MiriamMerad
@SinaiImmunol
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@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, it’s kinda dodgy riding your bike around.
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