Emma Doughty
@emmadoughty.bsky.social
Genomicist 🧬 at the intersection of bioinformatics 💻, epidemiology🫂 and global public health 🌍
Reposted by Emma Doughty
Genomic data is powerful only when reliable.
The 6Cs of quality—completeness, continuity, collinearity, correctness, contamination, concordance—show where things go wrong and how errors ripple downstream.
Check out our latest blog post to learn more:
The 6Cs of quality—completeness, continuity, collinearity, correctness, contamination, concordance—show where things go wrong and how errors ripple downstream.
Check out our latest blog post to learn more:
A Genomic Data Quality Framework: The 6Cs and Downstream Consequences
This Genomic Data Quality Framework provides a basis for genomic quality control and laboratory process improvement
tinyurl.com
October 1, 2025 at 9:00 AM
Genomic data is powerful only when reliable.
The 6Cs of quality—completeness, continuity, collinearity, correctness, contamination, concordance—show where things go wrong and how errors ripple downstream.
Check out our latest blog post to learn more:
The 6Cs of quality—completeness, continuity, collinearity, correctness, contamination, concordance—show where things go wrong and how errors ripple downstream.
Check out our latest blog post to learn more:
I’ve got something exciting to share. After years of working with labs around the world, I’m starting something new!
I’ve seen how many labs want to do more with genomics, but the path forward isn’t always clear. The process is complex, and without the right guidance, it’s easy to get stuck.
I’ve seen how many labs want to do more with genomics, but the path forward isn’t always clear. The process is complex, and without the right guidance, it’s easy to get stuck.
August 14, 2025 at 8:43 AM
I’ve got something exciting to share. After years of working with labs around the world, I’m starting something new!
I’ve seen how many labs want to do more with genomics, but the path forward isn’t always clear. The process is complex, and without the right guidance, it’s easy to get stuck.
I’ve seen how many labs want to do more with genomics, but the path forward isn’t always clear. The process is complex, and without the right guidance, it’s easy to get stuck.
Reposted by Emma Doughty
Since it is that time of year:
One of the most rewarding parts of being faculty is paying forward mentorship with students, residents+ fellows for their research projects. So far, as 4th year faculty, I’ve mentored ~40 trainee projects (17 completed). Here are what I talk about at 1st meeting:
One of the most rewarding parts of being faculty is paying forward mentorship with students, residents+ fellows for their research projects. So far, as 4th year faculty, I’ve mentored ~40 trainee projects (17 completed). Here are what I talk about at 1st meeting:
a man in a suit and bow tie stands in front of a table full of measuring cups and boxes that say in the name of science
ALT: a man in a suit and bow tie stands in front of a table full of measuring cups and boxes that say in the name of science
media.tenor.com
August 1, 2025 at 12:17 AM
Since it is that time of year:
One of the most rewarding parts of being faculty is paying forward mentorship with students, residents+ fellows for their research projects. So far, as 4th year faculty, I’ve mentored ~40 trainee projects (17 completed). Here are what I talk about at 1st meeting:
One of the most rewarding parts of being faculty is paying forward mentorship with students, residents+ fellows for their research projects. So far, as 4th year faculty, I’ve mentored ~40 trainee projects (17 completed). Here are what I talk about at 1st meeting:
Answer: Countries that are high on the Welcoming Countries Rankings and where logistics would be great for hosting conferences. 🙏
An immigration crackdown makes the United States less attractive. Where should you hold your next conference?
https://go.nature.com/3ZD4GAK
https://go.nature.com/3ZD4GAK
Where is the best place to hold a scientific conference right now?
Nature - An immigration crackdown makes the United States less attractive. These locations could steal its crown and make conferences more globally inclusive.
go.nature.com
June 23, 2025 at 12:23 PM
Answer: Countries that are high on the Welcoming Countries Rankings and where logistics would be great for hosting conferences. 🙏
Reposted by Emma Doughty
My Canadian university, Queen's, is offering TWENTY 4-year funded PhDs (40k CAD/yr) for a student of ANY citizenship who has been accepted at a top 100 US university but have had offer rescinded OR are reconsidering offer due to US policy.
Details found here👇
www.queensu.ca/grad-postdoc...
Details found here👇
www.queensu.ca/grad-postdoc...
Queen’s Special U.S. Doctoral Recruitment Initiative | School of Graduate Studies and Postdoctoral AffairsDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown...
Queen’s University is a globally engaged, research-intensive institution dedicated to attracting and supporting exceptional PhD students who will significantly advance our research mission.
www.queensu.ca
June 5, 2025 at 3:31 PM
My Canadian university, Queen's, is offering TWENTY 4-year funded PhDs (40k CAD/yr) for a student of ANY citizenship who has been accepted at a top 100 US university but have had offer rescinded OR are reconsidering offer due to US policy.
Details found here👇
www.queensu.ca/grad-postdoc...
Details found here👇
www.queensu.ca/grad-postdoc...
Reposted by Emma Doughty
Amazing work from our colleagues in Sierra Leone, Nigeria, and elsewhere, making the first sequences available from the ongoing Mpox epidemic in Sierra Leone.
More to come - for now, head over to @pathoplexus.org:
pathoplexus.org/seqsets/PP_S...
More to come - for now, head over to @pathoplexus.org:
pathoplexus.org/seqsets/PP_S...
Pathoplexus | SeqSets
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
pathoplexus.org
May 27, 2025 at 8:28 PM
Amazing work from our colleagues in Sierra Leone, Nigeria, and elsewhere, making the first sequences available from the ongoing Mpox epidemic in Sierra Leone.
More to come - for now, head over to @pathoplexus.org:
pathoplexus.org/seqsets/PP_S...
More to come - for now, head over to @pathoplexus.org:
pathoplexus.org/seqsets/PP_S...
Reposted by Emma Doughty
The spread of Mpox in Sierra Leone is unlike anything we have ever seen - and we have been keeping an eye on this bug in the region for >15 years.
Given geographical spread, 50/50 men vs women, this is no "sexual network".
This could be the next one.
clt.npha.gov.sl/outbreak.aspx
Given geographical spread, 50/50 men vs women, this is no "sexual network".
This could be the next one.
clt.npha.gov.sl/outbreak.aspx
May 22, 2025 at 9:56 PM
The spread of Mpox in Sierra Leone is unlike anything we have ever seen - and we have been keeping an eye on this bug in the region for >15 years.
Given geographical spread, 50/50 men vs women, this is no "sexual network".
This could be the next one.
clt.npha.gov.sl/outbreak.aspx
Given geographical spread, 50/50 men vs women, this is no "sexual network".
This could be the next one.
clt.npha.gov.sl/outbreak.aspx
Really pleased to see this! Helps to address such a critical question for genomic interpretation
Well done, @katholt.bsky.social et al!
Well done, @katholt.bsky.social et al!
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
May 22, 2025 at 10:19 AM
Really pleased to see this! Helps to address such a critical question for genomic interpretation
Well done, @katholt.bsky.social et al!
Well done, @katholt.bsky.social et al!
Reposted by Emma Doughty
It's official: the #PandemicAccord is officially adopted by the World Health Assembly!
My warmest congratulations to @who.int Member States for their commitment to keeping their people and the world safer.
What a moment in global health history. Together!
My warmest congratulations to @who.int Member States for their commitment to keeping their people and the world safer.
What a moment in global health history. Together!
May 20, 2025 at 8:19 AM
It's official: the #PandemicAccord is officially adopted by the World Health Assembly!
My warmest congratulations to @who.int Member States for their commitment to keeping their people and the world safer.
What a moment in global health history. Together!
My warmest congratulations to @who.int Member States for their commitment to keeping their people and the world safer.
What a moment in global health history. Together!
Reposted by Emma Doughty
Have said before that conference organisers when deciding on a host country should consider how easy it is for people to get visas (particularly for those from the Global South). For example, applying for a Canadian visa from the UK takes 344 days (www.canada.ca/en/immigrati...).
March 21, 2025 at 10:56 AM
Have said before that conference organisers when deciding on a host country should consider how easy it is for people to get visas (particularly for those from the Global South). For example, applying for a Canadian visa from the UK takes 344 days (www.canada.ca/en/immigrati...).
Reposted by Emma Doughty
Hello, I'm always trying to spread the word about the Academic Editing Circle, which organizes professional editors to volunteer time for Black and/or Indigenous scholars.
I can't promise that a volunteer can donate time for a whole book-length dissertation, but maybe we can help.
I can't promise that a volunteer can donate time for a whole book-length dissertation, but maybe we can help.
March 9, 2025 at 2:05 AM
Hello, I'm always trying to spread the word about the Academic Editing Circle, which organizes professional editors to volunteer time for Black and/or Indigenous scholars.
I can't promise that a volunteer can donate time for a whole book-length dissertation, but maybe we can help.
I can't promise that a volunteer can donate time for a whole book-length dissertation, but maybe we can help.
A must-read for anyone doing Global North-South work: Ways to level the highly unequal playing field
"the African academic is spending
their precious time contributing to your success. How are you contributing to theirs?"
"the African academic is spending
their precious time contributing to your success. How are you contributing to theirs?"
Fantastic read.A compelling behind the scenes look of realities that scholars based in Africa face when collaborating w colleagues based in the Global North. Also offers advice on building more ethical collaborations.
For everyone in global collaborative research.
www.tandfonline.com/doi/full/10....
For everyone in global collaborative research.
www.tandfonline.com/doi/full/10....
“My Flight Arrives at 5 am, Can You Pick Me Up?”: The Gatekeeping Burden of the African Academic
Over the past decade, there has been increased awareness and discourse around the inequalities which structure North–South academic collaboration. The purpose of this discussion is to look at the o...
www.tandfonline.com
March 1, 2025 at 11:25 AM
A must-read for anyone doing Global North-South work: Ways to level the highly unequal playing field
"the African academic is spending
their precious time contributing to your success. How are you contributing to theirs?"
"the African academic is spending
their precious time contributing to your success. How are you contributing to theirs?"
Reposted by Emma Doughty
As more Global North countries swing towards the far right & openly become anti-immigrant, global health is even more a field for those with visa privilege
www.forbes.com/sites/madhuk...
www.forbes.com/sites/madhuk...
Passport And Visa Privileges In Global Health
The field of global health is extraordinarily unequal, with privileged people and institutions in the global North dominating all aspects of global health. One form of privilege, the passports and vis...
www.forbes.com
February 25, 2025 at 1:23 PM
As more Global North countries swing towards the far right & openly become anti-immigrant, global health is even more a field for those with visa privilege
www.forbes.com/sites/madhuk...
www.forbes.com/sites/madhuk...
Trump's actions seem to be having a knock-on effect all over the place
www.theguardian.com/politics/202...
www.theguardian.com/politics/202...
Starmer slashes aid to fund major increase in defence spending
Announcement prompts concerns that PM is pandering to US president and warnings over consequences of aid cuts
www.theguardian.com
February 26, 2025 at 9:53 AM
Trump's actions seem to be having a knock-on effect all over the place
www.theguardian.com/politics/202...
www.theguardian.com/politics/202...
Reposted by Emma Doughty
Another is to support getting journals into local, high quality networks like @scielo.org. Resources like Redalyc (Mexico), TCC Africa, etc. We shouldn't force non-English communities to index in "our" indices. #r2rconf
February 25, 2025 at 10:22 AM
Another is to support getting journals into local, high quality networks like @scielo.org. Resources like Redalyc (Mexico), TCC Africa, etc. We shouldn't force non-English communities to index in "our" indices. #r2rconf
Reposted by Emma Doughty
Landmark paper claxon!
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
February 18, 2025 at 9:27 AM
Landmark paper claxon!
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
I've worked on cholera and its fascinating (two chromosome) genome, but beyond the data are very real human stories and public health need. This article gets at it well. www.theguardian.com/global-devel...
Dirty water and endless wars: why cholera outbreaks are on the rise again
The number of cases globally has surged since 2021, as war and the climate crisis pile pressure on vaccine supplies
www.theguardian.com
February 14, 2025 at 11:31 AM
I've worked on cholera and its fascinating (two chromosome) genome, but beyond the data are very real human stories and public health need. This article gets at it well. www.theguardian.com/global-devel...
Take away: Bacterial vaccines could reduce use of antibiotics, not only to treat bacterial infections, but all diseases.
Decreasing the likelihood that an unknown disease has bacterial cause means prescribers are less likely to use antibiotics across all disease.
www.thelancet.com/journals/lan...
Decreasing the likelihood that an unknown disease has bacterial cause means prescribers are less likely to use antibiotics across all disease.
www.thelancet.com/journals/lan...
Eliminate prescribers' uncertainty to catalyse the impact of vaccines on antibiotic use
The Article by Elizabeth T Rogawski McQuade and colleagues1 estimated the potential
effects of Shigella, enterotoxigenic Escherichia coli, Campylobacter, norovirus, adenovirus,
and rotavirus vaccines ...
www.thelancet.com
February 12, 2025 at 9:35 AM
Take away: Bacterial vaccines could reduce use of antibiotics, not only to treat bacterial infections, but all diseases.
Decreasing the likelihood that an unknown disease has bacterial cause means prescribers are less likely to use antibiotics across all disease.
www.thelancet.com/journals/lan...
Decreasing the likelihood that an unknown disease has bacterial cause means prescribers are less likely to use antibiotics across all disease.
www.thelancet.com/journals/lan...
We're not being replaced by AI yet!
AI can be immensely useful, but its "knowledge" is only as good as the algorithms and underlying data, and even asking chatbots to undertake processes is subject to weird error. A useful tool, like many others, rather than a replacement for us
AI can be immensely useful, but its "knowledge" is only as good as the algorithms and underlying data, and even asking chatbots to undertake processes is subject to weird error. A useful tool, like many others, rather than a replacement for us
Language models are great for tasks where you can handle a small % chance of nonsense (rough prototyping, idea critiques etc)
But people are realising many tasks are not like that…
But people are realising many tasks are not like that…
If flagship AI messes up cheese facts, maybe we shouldn't let it take over the running of the US Treasury quite yet eh.
BBC News - Google remakes Super Bowl ad after AI cheese gaffe
www.bbc.com/news/article...
BBC News - Google remakes Super Bowl ad after AI cheese gaffe
www.bbc.com/news/article...
February 10, 2025 at 5:17 PM
We're not being replaced by AI yet!
AI can be immensely useful, but its "knowledge" is only as good as the algorithms and underlying data, and even asking chatbots to undertake processes is subject to weird error. A useful tool, like many others, rather than a replacement for us
AI can be immensely useful, but its "knowledge" is only as good as the algorithms and underlying data, and even asking chatbots to undertake processes is subject to weird error. A useful tool, like many others, rather than a replacement for us
Reposted by Emma Doughty
I can't even begin to explain how bad this for science and for America
www.nytimes.com/2025/02/09/s...
www.nytimes.com/2025/02/09/s...
February 10, 2025 at 1:01 AM
I can't even begin to explain how bad this for science and for America
www.nytimes.com/2025/02/09/s...
www.nytimes.com/2025/02/09/s...
Reposted by Emma Doughty
What a great start to #HIVTestingWeek!
BHIVA is delighted to see Sir Keir Starmer continue his commitment to getting the UK to zero new #HIV transmissions by taking an HIV test.
This makes him the first PM ever to do so publicly, which we hope will encourage others to do the same.
#HIVSky #IDSky
BHIVA is delighted to see Sir Keir Starmer continue his commitment to getting the UK to zero new #HIV transmissions by taking an HIV test.
This makes him the first PM ever to do so publicly, which we hope will encourage others to do the same.
#HIVSky #IDSky
Sir Keir calls on others to follow lead after becoming first PM to take HIV test
Metro was invited to Downing Street for the historic moment.
metro.co.uk
February 10, 2025 at 8:42 AM
What a great start to #HIVTestingWeek!
BHIVA is delighted to see Sir Keir Starmer continue his commitment to getting the UK to zero new #HIV transmissions by taking an HIV test.
This makes him the first PM ever to do so publicly, which we hope will encourage others to do the same.
#HIVSky #IDSky
BHIVA is delighted to see Sir Keir Starmer continue his commitment to getting the UK to zero new #HIV transmissions by taking an HIV test.
This makes him the first PM ever to do so publicly, which we hope will encourage others to do the same.
#HIVSky #IDSky
Reposted by Emma Doughty
#USA: "We urge the US government to immediately resume funding of critical humanitarian and health aid, either through rescinding relevant orders freezing funding or expanding the current narrow humanitarian waiver to cover all necessary health and humanitarian programs." - @avrilbenoit.bsky.social
February 8, 2025 at 4:20 AM
#USA: "We urge the US government to immediately resume funding of critical humanitarian and health aid, either through rescinding relevant orders freezing funding or expanding the current narrow humanitarian waiver to cover all necessary health and humanitarian programs." - @avrilbenoit.bsky.social
Reposted by Emma Doughty
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Antimicrobial resistance: a concise update
Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately
5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted
and cohesive...
www.thelancet.com
February 5, 2025 at 10:02 AM
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Feeling very late to the party! Glad to see lots of scientists from Twitter in this friendlier environment! ❤️
February 5, 2025 at 12:58 PM
Feeling very late to the party! Glad to see lots of scientists from Twitter in this friendlier environment! ❤️