Nikki Gentle
@nikkigentle.bsky.social
Computational biologist. Studies how humans respond to RNA viruses.
Reposted by Nikki Gentle
A giant in molecular biology and virology has passed. RIP David Baltimore.
www.nytimes.com/2025/09/07/s...
www.nytimes.com/2025/09/07/s...
David Baltimore, Nobel-Winning Molecular Biologist, Dies at 87
www.nytimes.com
September 8, 2025 at 2:02 AM
A giant in molecular biology and virology has passed. RIP David Baltimore.
www.nytimes.com/2025/09/07/s...
www.nytimes.com/2025/09/07/s...
Reposted by Nikki Gentle
Hi everybody! I am super excited to share the work done during my PhD published in @nature today! We describe a new mechanism of self- vs. non-self RNA discrimination by showing how N-glycans shield glycoRNAs from stimulating endosomal RNA sensors www.nature.com/articles/s41...
RNA N-glycosylation enables immune evasion and homeostatic efferocytosis - Nature
N-glycans on glycoRNAs prevent innate immune sensing of endogenous small RNAs, and the natural mechanism they use demonstrates how glycoRNAs exist on the cell surface and in the endosomal network with...
www.nature.com
August 6, 2025 at 3:47 PM
Hi everybody! I am super excited to share the work done during my PhD published in @nature today! We describe a new mechanism of self- vs. non-self RNA discrimination by showing how N-glycans shield glycoRNAs from stimulating endosomal RNA sensors www.nature.com/articles/s41...
Reposted by Nikki Gentle
🚨 New preprint alert 🚨
We systematically benchmarked @nanoporetech.com 's modification-aware basecalling models released for RNA on sets of in vitro and in vivo sequences and made some curious observations 🧬🔍.
bit.ly/4lXqNul
Follow along for a little recap (1/12)
We systematically benchmarked @nanoporetech.com 's modification-aware basecalling models released for RNA on sets of in vitro and in vivo sequences and made some curious observations 🧬🔍.
bit.ly/4lXqNul
Follow along for a little recap (1/12)
Systematic benchmarking of basecalling models for RNA modification detection with highly multiplexed nanopore sequencing
Nanopore direct RNA sequencing (DRS) holds promise for advancing our understanding of the epitranscriptome by detecting RNA modifications in native RNA molecules. Recently, Oxford Nanopore Technologie...
bit.ly
July 14, 2025 at 4:00 PM
🚨 New preprint alert 🚨
We systematically benchmarked @nanoporetech.com 's modification-aware basecalling models released for RNA on sets of in vitro and in vivo sequences and made some curious observations 🧬🔍.
bit.ly/4lXqNul
Follow along for a little recap (1/12)
We systematically benchmarked @nanoporetech.com 's modification-aware basecalling models released for RNA on sets of in vitro and in vivo sequences and made some curious observations 🧬🔍.
bit.ly/4lXqNul
Follow along for a little recap (1/12)
Reposted by Nikki Gentle
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
www.biorxiv.org
May 9, 2025 at 10:49 AM
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Reposted by Nikki Gentle
#EpigeneticPower! Ivashkiv, Mishra &co show @natimmunol.bsky.social that anti-inflammatory IL-10 epigenetically silence IRF1 & IRF5 gene transcription by decreasing H3K27ac & chromatin accessibility, thus preventing sustained #interferons & IL6/TNF signaling! www.nature.com/articles/s41...
IL-10 targets IRF transcription factors to suppress IFN and inflammatory response genes by epigenetic mechanisms - Nature Immunology
Ivashkiv and colleagues show that IL-10 inhibits the expression and DNA binding of IRF1 and IRF5, two transcription factors that have an amplifying role in the induction of inflammatory NF-κB target g...
www.nature.com
April 22, 2025 at 4:14 PM
#EpigeneticPower! Ivashkiv, Mishra &co show @natimmunol.bsky.social that anti-inflammatory IL-10 epigenetically silence IRF1 & IRF5 gene transcription by decreasing H3K27ac & chromatin accessibility, thus preventing sustained #interferons & IL6/TNF signaling! www.nature.com/articles/s41...
Reposted by Nikki Gentle
Systemic inflammation impairs myelopoiesis and interferon type I responses in humans
www.nature.com/articles/s41...
@natimmunol.bsky.social
www.nature.com/articles/s41...
@natimmunol.bsky.social
April 18, 2025 at 4:34 PM
Systemic inflammation impairs myelopoiesis and interferon type I responses in humans
www.nature.com/articles/s41...
@natimmunol.bsky.social
www.nature.com/articles/s41...
@natimmunol.bsky.social
Reposted by Nikki Gentle
This statement from the NSF is insane.
Science is, in essence, designed to separate the true from the false.
Understanding how falsehoods spread is key to the scientific endeavor. It is not a violation of free speech to be proven wrong.
Science is, in essence, designed to separate the true from the false.
Understanding how falsehoods spread is key to the scientific endeavor. It is not a violation of free speech to be proven wrong.
April 18, 2025 at 8:51 PM
This statement from the NSF is insane.
Science is, in essence, designed to separate the true from the false.
Understanding how falsehoods spread is key to the scientific endeavor. It is not a violation of free speech to be proven wrong.
Science is, in essence, designed to separate the true from the false.
Understanding how falsehoods spread is key to the scientific endeavor. It is not a violation of free speech to be proven wrong.
Reposted by Nikki Gentle
"A GO term analysis? how is this helpful?"
March 28, 2025 at 2:18 PM
"A GO term analysis? how is this helpful?"
Reposted by Nikki Gentle
Apropos of nothing... a series of Pride and Prejudice memes.
March 25, 2025 at 8:41 PM
Apropos of nothing... a series of Pride and Prejudice memes.
Reposted by Nikki Gentle
Exclusive from me and Jon Cohen @science.org: NIH is terminating nearly 1000 grants in a series of batches. One, which conducts HIV and TB clinical trials in South Africa, was labelled as a "DEI" study that "harms the health of Americans." www.science.org/content/arti...
“Orchestrated assault”: New tsunami of NIH grant cuts hits South Africa hard
Agency moves to terminate nearly 1000 awards, including programs involving “DEI”
www.science.org
March 22, 2025 at 1:39 AM
Exclusive from me and Jon Cohen @science.org: NIH is terminating nearly 1000 grants in a series of batches. One, which conducts HIV and TB clinical trials in South Africa, was labelled as a "DEI" study that "harms the health of Americans." www.science.org/content/arti...
Reposted by Nikki Gentle
BREAKING Frightening cuts: In South Africa, #HIV and #TB cancellation letters for research grants funded by the US government started to roll in over the weekend.. bhekisisa.org/health-news-...
[BREAKING] Trump ends SA’s HIV and TB research grants - Bhekisisa
Cancellation letters, which end millions of rands of South African universities’ US-government funded HIV and TB research grants with immediate effect, started to roll in over the weekend. Fears are r...
bhekisisa.org
March 22, 2025 at 6:25 AM
BREAKING Frightening cuts: In South Africa, #HIV and #TB cancellation letters for research grants funded by the US government started to roll in over the weekend.. bhekisisa.org/health-news-...
Reposted by Nikki Gentle
South Africa and Trump — how we respond will come to define our country.
"It is worth reiterating: the only reason the issue is so consequential is because of the economic and military power of the US." www.dailymaverick.co.za/article/2025...
"It is worth reiterating: the only reason the issue is so consequential is because of the economic and military power of the US." www.dailymaverick.co.za/article/2025...
South Africa and Trump — how we respond will come to define our country
While the current dispute between South Africa and the Trump administration raises big questions about our foreign policy, we should not forget who we are as a nation. How our government responds to U...
www.dailymaverick.co.za
March 20, 2025 at 5:58 AM
South Africa and Trump — how we respond will come to define our country.
"It is worth reiterating: the only reason the issue is so consequential is because of the economic and military power of the US." www.dailymaverick.co.za/article/2025...
"It is worth reiterating: the only reason the issue is so consequential is because of the economic and military power of the US." www.dailymaverick.co.za/article/2025...
Reposted by Nikki Gentle
Toward single-molecule protein sequencing using nanopores - @unigroningen.bsky.social go.nature.com/3FL0g3k
March 18, 2025 at 1:39 PM
Toward single-molecule protein sequencing using nanopores - @unigroningen.bsky.social go.nature.com/3FL0g3k
Reposted by Nikki Gentle
Reposted by Nikki Gentle
Instead of using ChatGPT, why not just get a family member to lie to you while they set fire to a tree?
March 5, 2025 at 8:00 AM
Instead of using ChatGPT, why not just get a family member to lie to you while they set fire to a tree?
Reposted by Nikki Gentle
Here is what killing #USAID funding does--it kills #Basotho who are HIV positive. Pulling funding with no warning to a program that serves 350,000 HIV+ in #Lesotho and leaving them without access to life-saving meds.
Callous.
Uncaring.
Immoral.
www.dailymaverick.co.za/article/2025...
Callous.
Uncaring.
Immoral.
www.dailymaverick.co.za/article/2025...
Lesotho HIV programmes collapse after USAID decision
The US funding cuts have sparked fear of a surge in new infections as antiretroviral medicines become harder to get.
www.dailymaverick.co.za
March 5, 2025 at 3:06 PM
Here is what killing #USAID funding does--it kills #Basotho who are HIV positive. Pulling funding with no warning to a program that serves 350,000 HIV+ in #Lesotho and leaving them without access to life-saving meds.
Callous.
Uncaring.
Immoral.
www.dailymaverick.co.za/article/2025...
Callous.
Uncaring.
Immoral.
www.dailymaverick.co.za/article/2025...
Reposted by Nikki Gentle
Reposted by Nikki Gentle
South Africa faces its worst health crisis in 20 years. Worse than COVID, and one that will overshadow diabetes as a major killer, while pouring petrol on a dwindling TB fire. But it is preventable if our government steps up urgently.
Read groundup.org.za/article/sout... by Francois Venter
Read groundup.org.za/article/sout... by Francois Venter
Our HIV response will collapse without US funding - unless we act urgently
Reassurances that state clinics will pick up the lost services are empty
groundup.org.za
March 4, 2025 at 7:31 AM
South Africa faces its worst health crisis in 20 years. Worse than COVID, and one that will overshadow diabetes as a major killer, while pouring petrol on a dwindling TB fire. But it is preventable if our government steps up urgently.
Read groundup.org.za/article/sout... by Francois Venter
Read groundup.org.za/article/sout... by Francois Venter
Reposted by Nikki Gentle
The most extraordinary thing about James Harrison, who donated his rare plasma every 2 weeks for over 60 years and saved the lives of an estimated 2.4 million babies, is that he had to overcome a FEAR OF NEEDLES.
www.independent.co.uk/news/world/a...
www.independent.co.uk/news/world/a...
James Harrison, whose rare blood helped save millions of babies, dies at 88
By donating blood over 1,100 times, James Harrison helped develop Anti-D, a life-saving treatment for newborns at risk of Rhesus disease
www.independent.co.uk
March 4, 2025 at 7:28 AM
The most extraordinary thing about James Harrison, who donated his rare plasma every 2 weeks for over 60 years and saved the lives of an estimated 2.4 million babies, is that he had to overcome a FEAR OF NEEDLES.
www.independent.co.uk/news/world/a...
www.independent.co.uk/news/world/a...
Reposted by Nikki Gentle
www.news24.com/news24/south... A lot of people will die.
Trump orders immediate end to USAID funding for HIV organisations in SA | News24
Pepfar-funded HIV organisations in South Africa, who receive their funds through the United States Agency for International Development, woke up to letters that were sent overnight telling them their ...
www.news24.com
February 27, 2025 at 12:15 PM
www.news24.com/news24/south... A lot of people will die.
Reposted by Nikki Gentle
Reposted by Nikki Gentle
📣Excited to share my last postdoc paper with
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
February 27, 2025 at 2:21 AM
📣Excited to share my last postdoc paper with
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
Reposted by Nikki Gentle
Applicants of Black or mixed Black heritage can apply to my lab through the new Future Leaders in Biomedical Sciences programme. www.crick.ac.uk/careers-and-...
February 21, 2025 at 9:44 AM
Applicants of Black or mixed Black heritage can apply to my lab through the new Future Leaders in Biomedical Sciences programme. www.crick.ac.uk/careers-and-...
Reposted by Nikki Gentle
PREPRINT! Park et al. makes the case that we may be misunderstanding heterochromatin for past 30 years due to ChIP-Seq biases... 1/n
CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays https://www.biorxiv.org/content/10.1101/2025.02.03.636299v1
February 5, 2025 at 6:34 PM
PREPRINT! Park et al. makes the case that we may be misunderstanding heterochromatin for past 30 years due to ChIP-Seq biases... 1/n
Reposted by Nikki Gentle
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...
The distribution of highly deleterious variants across human ancestry groups
A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry...
www.biorxiv.org
February 2, 2025 at 7:00 PM
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...