Lab News
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2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011
2021
May
Tyler Starr discusses maximizing breadth and resistance to viral escape in antibodies to the SARS-CoV-2 receptor-binding domain for HHMI's Science of COVID Seminar Series.
April
Allie Greaney presents on mapping mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition at Basic Sciences' Friday Night Talks.
March
We've created an interactive website to visualize >100,000 experimental measurements of how mutations to SARS-CoV-2 receptor-binding domain affect binding by antibodies and sera: https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/ Explore it to examine a wealth of information about the antigenic effects of viral mutations.
Jesse gives a virtual talk on "Interpreting the Evolution of SARS-CoV-2" for HHMI's COVID-19 Seminar Series.
February
NIH Director, Dr. Francis Collins, discusses our study prospectively mapping which SARS-CoV-2 mutations escape lead clinical antibodies, on the NIH Director's Blog.
Karen Barnard receives a Life Sciences Research Foundation Postdoctoral Fellowship.
January
Our study mapping SARS-CoV-2 mutations that escape key therapeutic monoclonal antibodies is out in Science Magazine.
Our work led by Adam Dingens to compare the neutralizing and binding specificities of anti-HIV serum is out in eLife.
Our recent preprint on coronavirus antigenic evolution is featured on This Week in Virology (TWiV).
Allie Greaney talks to BCC about CoV mutations (@15:20).
2020
December
Our recent work is offering some insight into the tenets underlying SARS-CoV-2 evolution. What that means for new viral variants is covered in the New York Times.
November
Jesse gives a virtual talk on "Evolutionary Potential of the SARS-CoV-2 Receptor Binding Domain (RBD)" for HHMI's Science of COVID-19 Seminar Series.
October
Congratulations to two of our foundational members, who have moved on to industry jobs:
Sarah Hilton is now a Data Scientist at bluebird bio.
Adam Dingens is now a Scientist at Shape Therapeutics.
September
Lauren Gentles receives the Whiteley Fellowship.
August
Sarah Hilton's paper describing the dms-view visualization tool is published in JOSS.
One of our studies with work by Kate Crawford and Adam Dingens is covered in the Seattle Times and the New York Times.
A new study on flu-based SARS-CoV-2 vaccine led by Andrea Loes in our group receives coverage from News Medical.
Undergraduate Jon Mah departs to start graduate school at the UCLA bioinformatics program.
July
Bernadeta Dadonaite receives an EMBO postdoctoral fellowship.
Allie Greaney is appointed on the Viral Pathogenesis and Evolution Training Grant
June
Science Translational Medicine Blog posts about Tyler Starr and Allie Greaney's deep mutational scanning study of SARS-CoV-2 RBD.
MCB Graduate Students, Will Hannon and Frances Welsh, join the Lab.
May
The Seattle Times features an article on a study led by Adam Dingens and Kate Crawford of seroprevalence of SARS-CoV-2 in children in Seattle.
Sarah Hilton defends her PhD thesis.
Tal Einav receives a Damon Runyon postdoctoral fellowship in Quantitative Biology.
March
Karen Barnard joins the group as a postdoc.
February
Katherine's paper comparing the evolution of influenza within and between human hosts is published in Virus Evolution.
January
Bernadeta Dadonaite joins the group as a postdoc.
2019
December
Kate Crawford is lead author on a paper in the Journal of Open Source Software describing our new alignparse software package.
Kate Crawford is awarded a F30 from the NIAID.
Our collaboration with the Evans lab is the cover article for Journal of Virology.
October
Undergraduate Jon Mah receives as Washington Research Foundation Fellowship.
September
PNAS publishes a news article on our recent eLife paper examining how influenza virus can escape polyclonal human serum.
Jesse discusses influenza virus evolution and the lab's work in ASM's "Meet a Microbiologist" podcast.
First-year MCB grad students Frances Welsh and Ian Humphries start their rotations in the lab.
Our collaboration with the Evans lab to perform deep mutational scanning of Zika virus envelope is published in Journal of Virology.
July
Tyler Starr receives a Damon Runyon postdoctoral fellowship.
We hold our third annual joint-lab retreat at Sahalie Lodge--this year with the Neil King lab.
Tal Einav joins the lab as a postdoc. Tal is also a recipient of the Mahan Postdoctoral Fellowship in Computational Biology.
Undegrad Jon Mah is selected for the Herschel Roman Scholarship.
Juhye Lee's paper mapping how human sera exerts selection on influenza virus is published in eLife.
Postdoc Alistair Russell departs for a faculty position at UCSD.
June
Alistair Russell wraps up his postdoc and starts a faculty position at UC San Diego.
Keara Malone starts in our lab as a Research Technician.
A Nature News article on the "social lives of viruses" discusses Katherine Xue's research on influenza viruses that cooperate---but only in cell culture.
Liz Tseng at PacBio writes a blog post on Alistair Russell's single-cell virus sequencing of influenza infections.
May
Alistair's paper on single-cell virus sequencing of influenza infections that trigger innate immunity is published in Journal of Virology.
Adam's paper on mapping mutations that affect HIV sensitivity to the drug enfuvirtide is published in Viruses.
Juhye Lee defends her thesis!
Katherine Xue defends her thesis!
April
Shirleen's paper on comprehensive mapping of mutations that adapt avian flu polymerase to humans is published in eLife.
March
Andrea Loes joins as our new lab manager after completing her PhD in the Harms lab.
Adam Dingens receives the Weintraub Graduate Student award.
February
Immunity publishes a nice perspective piece highlighting our recent work led by Adam Dingens to completely map the functional epitopes of anti-HIV antibodies.
Katherine Xue's paper resolving the question of how much viral diversity is present in human influenza infections is published in Nature Genetics.
Alilstair Russell is a recipient of the Damon Runyon Dale F. Frey Award for Breakthrough Scientists.
January
Adam Dingens's antigenic atlas of HIV escape from antibodies is published in Immunity. See also the nice Hutch news story.
Heather Machkovech's ribosome profiling study of translation initiation in influenza-infected cells is published in PLoS Pathogens.
Katherine Xue receives a James S. McDonnell postdoctoral fellowship in understanding dynamic and multi-scale systems to support her work in her impending postdoc.
Rachel Eguia joins the lab as a Research Tech.
2018
December
Katherine Xue is selected as an awardee by the James F. Crow early-career scientist symposium.
Sarah Hilton presents a phyloseminar on her work developing phylogenetic substitution models informed by experiments.
Alistair Russell receives a K22 Career Transition Grant from the NIAID.
Jon Mah is awarded both a UW Microbiology Undergraduate Research Scholarship and UW Mary Gates Research Scholarship to support his undergrad research in our lab.
November
Sarah Hilton's paper examining how site-specific models affect phylogenetic estimates of divergence times is published in Virus Evolution.
October
Tyler Starr joins the lab as a postdoc supported by a WRF fellowship.
September
Sarah Hilton is one of a small number of graduate students worldwide who is invited to attend the Heidelberg Laureate Forum.
Hannah Itell joins the lab as a MCB rotation student.
August
Juhye Lee's paper (in collaboration with the Bedford lab) on using deep mutational scanning to understand the evolution of human influenza in nature is published in PNAS. The Hutch writes a nice news story about the work.
We hold our second annual joint-lab retreat at Sahalie Lodge. This year we are joined by the Harms lab, the Harris lab, and the Barber lab. Check out the group photo!
July
Our collaboration with the Vaccine Research Center (led by Adam Dingens) to functionally map vaccine-elicited antibodies to HIV is published in PLoS Pathogens.
June
MCB graduate student Caelan Radford joins the lab.
May
Katherine Xue receives the James F. Crow Early Career Award award at PEQG18.
Heather Machkovech defends her thesis!
Juhye Lee is awarded a F30 from the NIAID to support her thesis project "Comprehensive antigenic mapping of seasonal influenza viruses."
April
Sarah Hilton is selected to attend the 6th annual Heidelberg Laureate Forum.
Mike Doud and Juhye Lee's complete mapping of escape mutations to strain-specific and broadly neutralizing anti-H1 influenza hemagglutinin antibodies is published in Nature Communications.
Lauren Gentles receives a NSF Graduate Fellowship!
All the hard work on travel grant applications to conferences pays off! Lauren Gentles, Kate Dusenbury, Shirleen Soh, and Alistair Russell all receive travel grants to the ASV meeting. Sarah Hilton receives a SPAC travel grant to attend the SMBE meeting.
March
Hugh Haddox and Adam Dingens publish in eLife a comparative study of the effects of mutations to the Env proteins of two different HIV strains.
Katherine Xue receives the Weintraub Graduate Student Award!
Juhye Lee presents her work at the Influenza Epidemiology and Evolution workshop in Hanoi, Vietnam.
Undergrad Noah Cassidy is awarded a Mary Gates Scholarship for his work with Jeremy Roop in our lab and the lab of Julie Overbaugh.
Allie Greaney joins the lab as an MD/PhD student.
February
Alistair Russell's paper using single-cell mRNA sequencing to look at influenza-infected cells is published in eLife.
Katherine Xue's review on within-host evolution of human influenza is published in Trends in Microbiology. Check out the cool figures!
January
Katherine Xue's paper reporting an absence of cooperating flu viruses in clinical samples is published in mSphereDirect. See also the nice article by Rachel Tompa.
2017
December
Adam Dingens is selected to speak at the Norm Letvin Early Career Investigator Session of the CAVD meeting.
October
Jacob Kowalsky is awarded a Washington Research Foundation (WRF) Undergraduate Research Fellowship to support his work in the lab.
August
Jeremy Roop is awarded a Damon Runyon postdoctoral fellowship.
Hugh Haddox defends his thesis, giving a great seminar!
July
Sarah's paper describing the phydms software package is published in PeerJ.
Our lab holds a joint-lab retreat with the Bedford and Hensley labs at Sahalie Lodge. Lots of great talks and hiking!
June
Katherine's paper on influenza virus evolution within infected humans is published in eLife. She also wrote a broader-interest account of the work for The Conversation, and there is press coverage in The Atlantic and WIRED.
Adam's paper on comprehensively mapping HIV's escape from antibodies is published in Cell Host and Microbe. There is also a nice accompanying preview article.
We welcome three new lab members for the summer: Allie Greaney (rotation student), Alexandria Wilson (undergraduate), and Rachel Eguia (post-bac student in the UW PREP program).
The Baker lab's cool work on designing influenza-binding proteins is published in Nature Biotechnology. We helped out a tiny bit with this work.
April
Katherine gives a great public lecture on "How Flu Evolves in You" at the University of Washington's Engage Program.
March
Orr Ashenberg's paper on mapping sites in influenza nucleoprotein that affect sensitivity to MxA is published in PLoS Pathogens.
Mike Doud's paper on complete mapping of antibody escape is published in PLoS Pathogens on March 13 -- the same day that he defends his thesis. Congratulations Mike!
Jacob Kowalsky is awarded a Mary Gates Scholarship to support his undergraduate reserach in the lab. Congratulations to both Jacob and his mentor Alistair.
January
Jesse's paper on leveraging deep mutational scanning to improve the detection of positive selection in natural sequences is published in Biology Direct.
2016
December
Hugh Haddox's tour-de-force deep mutational scanning of HIV's envelope protein is published in PLoS Pathogens!
November
Adam Dingens receives a Young Investigator Scholarship to present at CROI 2017 the research that he has been performing in the Bloom and Overbaugh labs.
Jeremy Roop joins the lab as a postdoc. Jeremy is a joint-advised by the Overbaugh and Bloom labs. He completed his PhD at Berkeley, working with Rachel Brem.
September
Katherine Xue receives the Parker Travel Award for the best graduate student presentation at the Genome Sciences department retreat.
August
Mike Doud wins the award for the best abstract in virology and pathogenesis at the Options for Control of Influenza IX meeting.
July
Danny Lawrence (an MD/PhD student and Genome Sciences graduate student) joins the lab.
June
Our lab's research is featured in a news article on evolution in Science News.
Mike's paper on improved deep mutational scanning of influenza hemagglutinin is published in Viruses.
Sarah Hilton (a Genome Sciences graduate student) joins the lab.
Shirleen Soh has been awarded a Damon Runyon Foundation postdoc fellowship
March
Katherine's paper on cooperating influenza viruses is published in eLife. Her paper receives extra coverage here and here.
Sarah Hilton (a first-year Genome Sciences student) joins the lab for the next few months as a rotation student.
January
Jolie Carlisle (a first-year Genome Sciences student) joins the lab for the next few months as a rotation student.
2015
October
Shirleen Soh joins the lab as a postdoctoral fellow. Shirleen is supported by a Mahan Fellowship from the Computational Biology Program at the Hutch. She comes to the lab after completing her PhD with David Page.
Anja Ollodart (a first-year MCB student) joins the lab for the next few months as a rotation student.
August
Heather's paper demonstrating selection in CD8+ T-cell epitopes of human influenza nucleoprotein is published in the Journal of Virology.
July
Mike and Orr's paper that uses deep mutational scanning to compare the site-specific amino-acid preferences of two protein homologs is published in MBE.
We bid Alec Heckert farewell as he heads off to Berkeley to begin his PhD.
June
Katie Hooper defends her thesis, becoming the first Bloom lab PhD graduate!
Jai Padmakumar recieves a Microbiology Undergraduate Research Fellowship for his work in the lab (mentored by Orr Ashenberg)
Genome Sciences graduate student Katherine Xue joins the lab; she will be joint-advised by Josh Akey.
Jesse is named a Pew Scholar
Jesse is awarded a Burroughs Wellcome Young Investigator in the Pathogenesis of Infectious Diseases grant.
May
Congratulations to Alistair Russell, who has been awarded a Damon Runyon Foundation postdoc fellowship.
Congratulations to graduate student Hugh Haddox, who has been awarded a spot on the CMB Training Grant.
Congratulations to graduate student Heather Machkovech, who has been awarded a spot on the Viral Pathogenesis Training Grant.
Congratulations to Berkeley-bound Bloom lab undergraduate Alec Heckert, who has been awarded the University of Washington Chemistry Department's Award for Distinguished Research in Chemistry for work he did in the Gabriele Varani lab prior to joining the Bloom lab.
April
Congratulations to Genome Sciences rotation student Hannah Pliner, who has been awarded an NSF Graduate Research Fellowship.
Congratulations to Genome Sciences rotation student Katherine Xue, who has been awarded a Hertz Fellowship.
March
Congratulations to undergraduates Alec Heckert and Khrystyna Dilai, who have matriculated for graduate school at the Berkeley MCB and University of Washington Genome Sciences programs, respectively.
February
Jesse is awarded the 2015 Young Investigator Prize in Virology.
January
Katie Hooper's second paper on influenza viruses that use neuraminidase as the receptor-binding protein is published in the Journal of Virology.
Katie Hooper is selected as an invitee to present her work at the St. Jude National Graduate Student Symposium.
2014
November
We bid Bargavi Thyagarajan farewell as she heads to New York to begin work at the HIV Vaccine Enterprise after a very productive postdoc.
Our lab makes a small contribution to the Hensley lab's excellent study in PNAS showing how original antigenic sin might help explain the high rate of pdmH1N1 infections in middle-aged adults during the last flu seasion.
October
Our lab contributes to a perspective article in eLife on assessing influenza pandemic risk.
September
Alistair Russell joins the lab as a postdoc.
July
Bargavi's paper on using deep mutational scanning to profile the inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin is published in eLife.
Jesse's paper that applies experimentally informed evolutionary models to beta-lactamase is published in Molecular Biology and Evolution.
June
Every lab gets its 15 seconds of fame! The Bloom and Fowler labs take a joint trip to the ballpark. The Mariner's lose the game, but the labs get a shout-out on the scoreboard.
May
Mike is awarded a spot on the Viral Pathogenesis Training grant
Jesse's paper on experimentally determined evolutionary models in phylogenetics is published in Molecular Biology and Evolution
Ian's paper on epistasis and adaptation is published in PLoS Genetics
April
Katie's collaboration with Aeron Hurt's group is published in PLoS Pathogens
Adam is awarded an NSF Graduate Fellowship
Former Bloom Lab undergraduate Donna Leet is awarded a Goldwater Scholarship
2013
December
Orr receives PhRMA Foundation Post Doctoral Fellowship in Informatics
Orr, Ian, and Jesse's paper on the evolutionary conservation of mutational effects on protein stability is published in PNAS
September
Katie's paper on an influenza virus that uses neuraminidase to bind to cells is published in Journal of Virology
Center News | Researchers discover a new way that influenza can infect cells: Study may have implications for immunity against flu
August
Katie is named one of the top two TAs for the entire University of Washington School of Medicine for her TA-ing efforts in the Spring of 2013
Hugh is awarded a position on the Molecular Biophysics Training Grant
Ari and Donna present at the Summer Undergraduate Research Program Poster Session. Donna wins Best Poster Design Award.
July
Scientific American story on cryptic mutations discusses Bloom Lab's work
Mike Doud, a UW Genome Sciences graduate student, joins Bloom Lab
June
Hugh Haddox, a UW MCB graduate student, joins Bloom Lab
May
Katie is awarded a position on the Cell and Molecular Biology Training Grant
Orr and Hugh are awarded scholarships to attend the Summer Institute in Statistics and Modeling of Infectious Diseases
Bloom Lab publishes its first paper in eLife
April
Donna wins Amherst College's William C. Young prize, awarded annually to a single student from the Biology Department to undertake a summer course or research
February
Orr Ashenberg, a new post-doc, joins Bloom Lab
2012
September
Bloom Lab is awarded its first R01 grant (1R01GM102198-01)
July
Jesse is awarded a Creative and Novel Ideals in HIV Research (CNIHR) grant from the International AIDS Society. The CNIHR initiative, which totals $5 million, will fund 12 research projects for up to two years
June
Katie Hooper, a UW MCB graduate student, joins Bloom Lab
April
Jesse is named one of 15 Searle Scholars for 2012 and awarded $300,000 for the next three years
February
Jesse is awarded the 2012 Sloan Research Fellowship for early-career scientists and scholars of outstanding promise
2011
October
Bargavi Thyagarajan, a new post-doc, joins Bloom Lab
September
Ian wins program cover design competition for the 2011 Basic Sciences Retreat
July
Quick takes: Jesse Bloom
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