Bradford Taylor
@bradfordptaylor.bsky.social
Infectious disease modeler. Interested in: social drivers of infectious disease, evolution of abx resistance, math models. He/him.
Reposted by Bradford Taylor
This November, like every November, I am teaching basic research proposal writing to the new phd cohort at my institute. Here is the 2 page template we start with and adapt. Link to LaTeX github.com/rmcelreath/P...
![\title[PhD Plan for CANDIDATE]{Department of \mbox{Full Luxury Galactic Metascience}\\PhD Plan for CANDIDATE}
% list committee members
\author[]{Committee:\\
Prof.~MEMBER1\\
Dr.~MEMBER2\\
Dr.~MEMBER3}
\date{\today}
\begin{document}
\maketitle% this prints the handout title, author, and date
\begin{marginfigure}[-5.2cm]
\includegraphics[width=3.5cm]{Minerva.pdf}
\end{marginfigure}
\section{Phenomenon}
The subject matter to be addressed. What is the question? Citation for background are useful, but don't do a full lit review (yet).\cite{HenrichMcElreath:2003} Additional references can be included at the end bibliography by using \verb|\nocite|. \nocite{NBGA2005}
\section{Theoretical Perspective}
The framework for explaining the phenomenon. What are the implications of theory? If more than one theory is relevant, how do the implications differ? What are the current holes in the theory or theories?
\section{Approach}
Modeling and empirical research approach to address the theory/ies nominated above. Important thing is to \emph{justify} the approach in terms of theory.
\section{Specifics of Approach}
Outline any special skills, equipment, or techniques that will be required. This includes, in the case of field research, a paragraph on the background of the field location. Data analysis approach needs a sketch. Can use citation\cite{Merowetal2014} for further detail.
\section{Expected Products}
A list of the (usually 3) articles expected for completion of the PhD. Think of each as a fantasy abstract.
\begin{enumerate}
\item \emph{The Evolution of Human Uniqueness.} There is wide agreement that humans are unique. But it is rarely asked: Have they always been unique? In this paper, we derive a general uniqueness theorem that states that any unique species must have been less unique at some point in the past. This theorem has implications for the achievement of world peace.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ta2whs6wjtpljvpqgs5leu36/bafkreihnoflhyf2lajrvcsovawt3xr47qlm76jfhzet5lqumkabtzufvoe@jpeg)
November 3, 2025 at 7:45 AM
This November, like every November, I am teaching basic research proposal writing to the new phd cohort at my institute. Here is the 2 page template we start with and adapt. Link to LaTeX github.com/rmcelreath/P...
Reposted by Bradford Taylor
Current and former members of the NIH community have valuable personal perspectives to share about the devastation that is happening to US biomedical research, our federal agencies, and our democracy. This starter pack is a great way to hear what they have to say and what you can do about it.
🧪🧬🧠🥼🇺🇸
🧪🧬🧠🥼🇺🇸
August 28, 2025 at 2:57 AM
Current and former members of the NIH community have valuable personal perspectives to share about the devastation that is happening to US biomedical research, our federal agencies, and our democracy. This starter pack is a great way to hear what they have to say and what you can do about it.
🧪🧬🧠🥼🇺🇸
🧪🧬🧠🥼🇺🇸
Reposted by Bradford Taylor
Got a number in mind?
A new pre-print by @lshtm.bsky.social colleagues surveyed 13,000 participants, and found it's about 9 per day in the current era.
It also looks at how social mixing varies with age, ethnicity and social economic status. Link to paper:
A new pre-print by @lshtm.bsky.social colleagues surveyed 13,000 participants, and found it's about 9 per day in the current era.
It also looks at how social mixing varies with age, ethnicity and social economic status. Link to paper:
Post-pandemic social contact patterns in the United Kingdom: the Connect survey
Close-contact and respiratory infectious diseases are spread through social interactions, which were affected by the COVID-19 pandemic and wider demographic and cultural changes. To estimate post-pand...
www.medrxiv.org
August 19, 2025 at 5:41 PM
Got a number in mind?
A new pre-print by @lshtm.bsky.social colleagues surveyed 13,000 participants, and found it's about 9 per day in the current era.
It also looks at how social mixing varies with age, ethnicity and social economic status. Link to paper:
A new pre-print by @lshtm.bsky.social colleagues surveyed 13,000 participants, and found it's about 9 per day in the current era.
It also looks at how social mixing varies with age, ethnicity and social economic status. Link to paper:
Reposted by Bradford Taylor
⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10]
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Comparing Strategies to Introduce Two New Antibiotics for Gonorrhea: A Modeling Study
Introduction Drug resistance in Neisseria gonorrhoeae is an urgent public health threat. The anticipated approval of two new antimicrobials for gonorrhea prompts the need for evidence-based rollout st...
www.medrxiv.org
July 3, 2025 at 3:29 PM
⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10]
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Bradford Taylor
THIS. Immigrants are the backbone of US Science. 60% of Postdoc researchers at NIH are Visiting Fellows. Zooming out, 19% of all STEM workers and 43% of doctorate-level scientists and engineers in the US are foreign born.
American science runs on immigrant labor.
🌍Global brains, 🇺🇸American gains🧪
American science runs on immigrant labor.
🌍Global brains, 🇺🇸American gains🧪
This is true in science too. There are white Americans doing science, advancing the frontier of union knowledge. But there are many, many, immigrants.
Hard work is the core of science. People work 80 hrs a week; pour all of themselves into it. And it takes a diverse workforce to get the work done.
Hard work is the core of science. People work 80 hrs a week; pour all of themselves into it. And it takes a diverse workforce to get the work done.
Spot on. This is the clearest explanation I’ve seen. It ‘s relatable, and humanizes the issue in a way everyone can understand.
June 28, 2025 at 3:38 PM
THIS. Immigrants are the backbone of US Science. 60% of Postdoc researchers at NIH are Visiting Fellows. Zooming out, 19% of all STEM workers and 43% of doctorate-level scientists and engineers in the US are foreign born.
American science runs on immigrant labor.
🌍Global brains, 🇺🇸American gains🧪
American science runs on immigrant labor.
🌍Global brains, 🇺🇸American gains🧪
Reposted by Bradford Taylor
Sang Woo (Daniel) Park and I are excited to share a new preprint, "Susceptible host dynamics explain pathogen resilience to perturbations" [1/8]
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
June 23, 2025 at 9:07 PM
Sang Woo (Daniel) Park and I are excited to share a new preprint, "Susceptible host dynamics explain pathogen resilience to perturbations" [1/8]
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Bradford Taylor
I’m thrilled to share our latest preprint! We analyzed >130,000 SARS-CoV-2 genomes from MA to investigate complex transmission dynamics—from statewide patterns, within specific facilities, and at the individual level 🦠🧬
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes
Despite intensive study, gaps remain in our understanding of SARS-CoV-2 transmission patterns during the COVID-19 pandemic, in part due to limited contextual metadata accompanying most large genomic s...
www.medrxiv.org
April 9, 2025 at 7:11 PM
I’m thrilled to share our latest preprint! We analyzed >130,000 SARS-CoV-2 genomes from MA to investigate complex transmission dynamics—from statewide patterns, within specific facilities, and at the individual level 🦠🧬
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Reposted by Bradford Taylor
Working with an interdisciplinary team, we have developed a website to communicate how the White House's proposed cuts to health research would cause losses of $16B and 68,500 jobs.
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
March 28, 2025 at 2:15 AM
Working with an interdisciplinary team, we have developed a website to communicate how the White House's proposed cuts to health research would cause losses of $16B and 68,500 jobs.
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
Reposted by Bradford Taylor
So glad to share this work by @bradfordptaylor.bsky.social from his time working with us. It's a simple but elegant tweak to some of the established ID epi models. Among other things it helps explain why the great majority of 'variants' did not become dominant
elifesciences.org/reviewed-pre...
elifesciences.org/reviewed-pre...
Founder effects arising from gathering dynamics systematically bias emerging pathogen surveillance
important: Findings that have theoretical or practical implications beyond a single subfield
elifesciences.org
March 13, 2025 at 1:49 PM
So glad to share this work by @bradfordptaylor.bsky.social from his time working with us. It's a simple but elegant tweak to some of the established ID epi models. Among other things it helps explain why the great majority of 'variants' did not become dominant
elifesciences.org/reviewed-pre...
elifesciences.org/reviewed-pre...
Reposted by Bradford Taylor
"No one is coming out of the sky to give you your grant money. Your citation portfolio won’t survive this market crash. Your credentials mean nothing. Everything is going to change."
New for @undark.org
undark.org/2025/03/06/o...
New for @undark.org
undark.org/2025/03/06/o...
How Science Can Adapt to a New Normal
Opinion | In the wake of attacks on the research enterprise, scientists need to focus on protecting its fragile infrastructure.
undark.org
March 6, 2025 at 2:35 PM
"No one is coming out of the sky to give you your grant money. Your citation portfolio won’t survive this market crash. Your credentials mean nothing. Everything is going to change."
New for @undark.org
undark.org/2025/03/06/o...
New for @undark.org
undark.org/2025/03/06/o...
@npr.org is contributing to misinformation by not contextualizing Musk’s statements with 1) all feds responded to prior required DOGE emails (existence proof) and 2) that some agencies notified their employees of security dangers in responding to the non-mandatory 5 bullet email
President Trump warned federal workers who did not reply to recent emails asking them to describe "five things" they accomplished are "on the bubble" suggesting they are at risk of losing their jobs.
Musk says federal workers should expect another round of 'pulse check' emails
President Trump warned federal workers who did not reply to recent emails asking them to describe "five things" they accomplished are "on the bubble" suggesting they are at risk of losing their jobs.
www.npr.org
February 26, 2025 at 11:36 PM
@npr.org is contributing to misinformation by not contextualizing Musk’s statements with 1) all feds responded to prior required DOGE emails (existence proof) and 2) that some agencies notified their employees of security dangers in responding to the non-mandatory 5 bullet email
Reposted by Bradford Taylor
Should I stay or should I go? 🎵
In a new opinion piece, Claudia Igler, Andrina Bernhard and I discuss how conjugative plasmids and temperate bacteriophages balance vertical and horizontal transmission: ecoevorxiv.org/repository/v...
Our framework sheds light on many aspects of MGE biology (1/7)
In a new opinion piece, Claudia Igler, Andrina Bernhard and I discuss how conjugative plasmids and temperate bacteriophages balance vertical and horizontal transmission: ecoevorxiv.org/repository/v...
Our framework sheds light on many aspects of MGE biology (1/7)
Should I stay or should I go: Transmission trade-offs in mobile genetic elements
ecoevorxiv.org
October 22, 2024 at 2:52 PM
Should I stay or should I go? 🎵
In a new opinion piece, Claudia Igler, Andrina Bernhard and I discuss how conjugative plasmids and temperate bacteriophages balance vertical and horizontal transmission: ecoevorxiv.org/repository/v...
Our framework sheds light on many aspects of MGE biology (1/7)
In a new opinion piece, Claudia Igler, Andrina Bernhard and I discuss how conjugative plasmids and temperate bacteriophages balance vertical and horizontal transmission: ecoevorxiv.org/repository/v...
Our framework sheds light on many aspects of MGE biology (1/7)
Reposted by Bradford Taylor
It's real.
Asymptomatic: The Silent Spread of COVID-19 and the Future of Pandemics
Pre-order in advance of 10/22 release by Johns Hopkins University Press.
bit.ly/asymptomatic...
More soon on events and interactions to come.
.
Asymptomatic: The Silent Spread of COVID-19 and the Future of Pandemics
Pre-order in advance of 10/22 release by Johns Hopkins University Press.
bit.ly/asymptomatic...
More soon on events and interactions to come.
.
August 27, 2024 at 11:26 PM
It's real.
Asymptomatic: The Silent Spread of COVID-19 and the Future of Pandemics
Pre-order in advance of 10/22 release by Johns Hopkins University Press.
bit.ly/asymptomatic...
More soon on events and interactions to come.
.
Asymptomatic: The Silent Spread of COVID-19 and the Future of Pandemics
Pre-order in advance of 10/22 release by Johns Hopkins University Press.
bit.ly/asymptomatic...
More soon on events and interactions to come.
.
Reposted by Bradford Taylor
There is now a cover. Asymptomatic is available for pre-order, forthcoming from JHU Press on October 22, 2024.
www.amazon.com/Asymptomatic...
www.amazon.com/Asymptomatic...
April 23, 2024 at 5:45 PM
There is now a cover. Asymptomatic is available for pre-order, forthcoming from JHU Press on October 22, 2024.
www.amazon.com/Asymptomatic...
www.amazon.com/Asymptomatic...
Reposted by Bradford Taylor
Cool work from friends & mentors: "we deployed a high-throughput combinatorial screening platform, DropArray, to evaluate the interactions of over 30,000 compounds with up to 22 antibiotics and 6 strains of Gram-negative ESKAPE pathogens, totaling to over 1.3 million unique combinations"
Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens https://www.biorxiv.org/content/10.1101/2024.03.26.586803v1
Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens https://www.biorxiv.org/content/10.1101/2024.03.26.586803v1
Antibiotic resistance, especially in multidrug-resistant ESKAPE pathogens, remains a worldwide probl
www.biorxiv.org
March 27, 2024 at 9:52 AM
Cool work from friends & mentors: "we deployed a high-throughput combinatorial screening platform, DropArray, to evaluate the interactions of over 30,000 compounds with up to 22 antibiotics and 6 strains of Gram-negative ESKAPE pathogens, totaling to over 1.3 million unique combinations"
Reposted by Bradford Taylor
New @biorxiv-microbiol.bsky.social preprint on optimizing experiments to infer multiphasic decay of infectious viruses, led by Jeremy Seurat w/Justin Meyer & team, we leverage synthetic sims to design, implement, & identify a hidden majority of rapidly decaying phage
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 28, 2024 at 2:57 PM
New @biorxiv-microbiol.bsky.social preprint on optimizing experiments to infer multiphasic decay of infectious viruses, led by Jeremy Seurat w/Justin Meyer & team, we leverage synthetic sims to design, implement, & identify a hidden majority of rapidly decaying phage
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Bradford Taylor
A thread on using 'Quantitative Biosciences: Dynamics Across Cells, Organisms, and Populations' & the computational guides in Python, R or MATLAB in a classroom setting (release 3/5/24 via @princetonupress.bsky.social).
The central point for students: you can do it!
bit.ly/qbios_book
The central point for students: you can do it!
bit.ly/qbios_book
February 21, 2024 at 5:22 PM
A thread on using 'Quantitative Biosciences: Dynamics Across Cells, Organisms, and Populations' & the computational guides in Python, R or MATLAB in a classroom setting (release 3/5/24 via @princetonupress.bsky.social).
The central point for students: you can do it!
bit.ly/qbios_book
The central point for students: you can do it!
bit.ly/qbios_book
Reposted by Bradford Taylor
After nearly 10 years in development, delighted to share news that 'Quantitative Biosciences: Dynamics across Cells, Organisms, and Populations' is available for pre-order from Princeton University Press:
press.princeton.edu/books/paperb...
press.princeton.edu/books/paperb...
February 7, 2024 at 7:27 PM
After nearly 10 years in development, delighted to share news that 'Quantitative Biosciences: Dynamics across Cells, Organisms, and Populations' is available for pre-order from Princeton University Press:
press.princeton.edu/books/paperb...
press.princeton.edu/books/paperb...
Reposted by Bradford Taylor
Ross McInnes, a post-doc in my group, will sadly be leaving in Spring 2024 as we reach the end of a grant.
He is now looking for a job. Ross is excellent and has a skill set that includes molecular biology, functional and comparative genomics, and microbiome research: rosssmcinnes.github.io
He is now looking for a job. Ross is excellent and has a skill set that includes molecular biology, functional and comparative genomics, and microbiome research: rosssmcinnes.github.io
Ross S McInnes
rosssmcinnes.github.io
January 11, 2024 at 3:06 PM
Ross McInnes, a post-doc in my group, will sadly be leaving in Spring 2024 as we reach the end of a grant.
He is now looking for a job. Ross is excellent and has a skill set that includes molecular biology, functional and comparative genomics, and microbiome research: rosssmcinnes.github.io
He is now looking for a job. Ross is excellent and has a skill set that includes molecular biology, functional and comparative genomics, and microbiome research: rosssmcinnes.github.io
Are you an undergrad and love math modeling (or tolerate it and want to know more)? One week left to apply for the Workshop to Increase Diversity in Mathematical Modeling & Public Health! March 4-5, 2024 in Boston. #episky #idsky
ccdd.hsph.harvard.edu/increase-div...
ccdd.hsph.harvard.edu/increase-div...
November 13, 2023 at 8:16 PM
Are you an undergrad and love math modeling (or tolerate it and want to know more)? One week left to apply for the Workshop to Increase Diversity in Mathematical Modeling & Public Health! March 4-5, 2024 in Boston. #episky #idsky
ccdd.hsph.harvard.edu/increase-div...
ccdd.hsph.harvard.edu/increase-div...
Reposted by Bradford Taylor
1/ New paper! “Gender and retention patterns among U.S. faculty” w/ N Laberge KH Wapman @samzhang AC Morgan M Galesic BK Fosdick @danlarremore @aaronclauset: www.science.org/doi/10.1126/...
A systematic study of gendered rates & reasons for faculty attrition in US academia 🧵
A systematic study of gendered rates & reasons for faculty attrition in US academia 🧵
October 20, 2023 at 6:36 PM
1/ New paper! “Gender and retention patterns among U.S. faculty” w/ N Laberge KH Wapman @samzhang AC Morgan M Galesic BK Fosdick @danlarremore @aaronclauset: www.science.org/doi/10.1126/...
A systematic study of gendered rates & reasons for faculty attrition in US academia 🧵
A systematic study of gendered rates & reasons for faculty attrition in US academia 🧵
Reposted by Bradford Taylor
I like to read *real* microbial ecology research periodically to remind me that opportunistic pathogens and model systems exhibit only a narrow range of possible interactions. For example, this makes our fascination with surface-sensing seem small:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Chemotaxis shapes the microscale organization of the ocean’s microbiome - Nature
In situ experiments have demonstrated chemotaxis of marine bacteria and archaea towards specific phytoplankton-derived dissolved organic matter, which leads to microscale partitioning of biogeoch...
www.nature.com
October 13, 2023 at 6:50 PM
I like to read *real* microbial ecology research periodically to remind me that opportunistic pathogens and model systems exhibit only a narrow range of possible interactions. For example, this makes our fascination with surface-sensing seem small:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Bradford Taylor
“The more uncomfortable truth is that academic science has never been a trade that selects for or supports the best scientific minds in the world.”
https://www.scientificamerican.com/article/nobel-prize-debate-misses-the-mark-on-the-real-culprits-ignoring-scientific-merit/
https://www.scientificamerican.com/article/nobel-prize-debate-misses-the-mark-on-the-real-culprits-ignoring-scientific-merit/
Nobel Prize Debate Misses the Mark on the Real Culprits Ignoring Scientific Merit
The furor over a Nobel Prize winner’s derailed career lets scientists off the hook for their own responsibilities to fix a broken academic reward system
www.scientificamerican.com
October 5, 2023 at 7:58 PM
“The more uncomfortable truth is that academic science has never been a trade that selects for or supports the best scientific minds in the world.”
https://www.scientificamerican.com/article/nobel-prize-debate-misses-the-mark-on-the-real-culprits-ignoring-scientific-merit/
https://www.scientificamerican.com/article/nobel-prize-debate-misses-the-mark-on-the-real-culprits-ignoring-scientific-merit/
Reposted by Bradford Taylor
I'm excited to share our most theoretical work yet, led by 3rd year PhD student Paul Torrillo.
We revisit the old observation that dN/dS depends on the distance between compared sequences.
We arrive at a radically different conclusion than current prevailing theory.
www.biorxiv.org/content/10.1...
We revisit the old observation that dN/dS depends on the distance between compared sequences.
We arrive at a radically different conclusion than current prevailing theory.
www.biorxiv.org/content/10.1...
September 18, 2023 at 2:57 AM
I'm excited to share our most theoretical work yet, led by 3rd year PhD student Paul Torrillo.
We revisit the old observation that dN/dS depends on the distance between compared sequences.
We arrive at a radically different conclusion than current prevailing theory.
www.biorxiv.org/content/10.1...
We revisit the old observation that dN/dS depends on the distance between compared sequences.
We arrive at a radically different conclusion than current prevailing theory.
www.biorxiv.org/content/10.1...
Caught an interesting wnyc bit on the “enshittification” of the internet. Why things like fbook, amazon, twitter etc start off too good to be true and inevitably get worse over time. www.wnycstudios.org/podcasts/otm...
September 3, 2023 at 10:18 PM
Caught an interesting wnyc bit on the “enshittification” of the internet. Why things like fbook, amazon, twitter etc start off too good to be true and inevitably get worse over time. www.wnycstudios.org/podcasts/otm...