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Dylan Sosa

@dylansosa.bsky.social
197 followers 406 following 5 posts

molecular evolution postdoc @Harvard

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Reposted by Dylan Sosa
Dr Hannah M. Rowland @hannahmrowland.bsky.social · 01/10/2026
Hope your day was better than Darwin’s, on this day 165 years ago
I am very poorly today & very stupid & hate everybody &everything.

Charles Darwin
Letter to Charles Lyell
1st October 1861
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でんか @k-hermit.com · 26/09/2026
全方向つるすべ
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Mike McQuaid @mikemcquaid.com · 13/09/2026
Today, I’m proud to announce Homebrew 7.0.0. The most significant changes since 6.0.0 are faster installations, stronger sandboxing, native macOS app, vulnerability checks, advisory database, end of macOS 10.15 support and Intel Macs to Tier 3.
brew.sh
7.0.0
Today, I’m proud to announce Homebrew 7.0.0. The most significant changes since 6.0.0 are faster installations and upgrades, stronger sandboxing, a native macOS app, built-in vulnerability checks and an advisory database, the end of macOS 10.15 support and Intel Macs moving to Tier 3.
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Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 11/09/2026
MBE Senior Editor Rasmus Nielsen and SMBE Past President Ziheng Yang have been awarded the 2026 Balzan Prize for Molecular Evolution: Decoding Patterns of Genomic Change. www.balzan.org/en/updates/t...
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Joint Genome Institute @jgi.doe.gov · 09/09/2026
Perspective: Pangenomes are Only as Powerful as their Annotation Method Are researchers wasting resources following false trails — due to variations in interpretative methods? 🖥️🧬 🌱 @tomasbruna.bsky.social Full story below⬇️
jgi.doe.gov
Perspective: Pangenomes are Only as Powerful as their Annotation Method | Joint Genome Institute
Researchers may be wasting resources following false trails due to variations in interpretative methods.
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Chris Millard @chrismillard83.bsky.social · 09/09/2026
this is perhaps the most useful thing that LLMs and GenAI have done: to provoke people into articulating (over again) that even the 'hardest' of 'hard sciences' are human endeavours, with human meaning, and concerned with human understanding of the significance of the world we all inhabit
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Heather Physioc / HP Conservation @heatherphysioc.bsky.social · 05/09/2026
Wildlife conservation, hunting, and fishing are perfectly compatible with proper land management, agency funding and a supported workforce. Instead, the USFWS has lost 36% of its workforce under the second Trump administration. ourpubliclandsandwaters.substack.com/p/us-fish-an...
ourpubliclandsandwaters.substack.com
U.S. Fish and Wildlife Service Has Lost 36% of Its Workforce Under the Second Trump Administration
Meanwhile, even with fewer staff, the agency just completed the largest expansion of hunting and fishing access in its entire history
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Nozomu Yachie @nzmyachie.bsky.social · 04/09/2026
Maybe it’s time to say goodbye to UMAP and other low-dimensional embeddings (at least in many single-cell analyses). We developed MILK to encode single-cell populations into tree representations at unprecedented scales. www.biorxiv.org/content/10.6... Here’s what MILK is: 🧵
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Simon W Davis @woodforbrains.bsky.social · 03/09/2026
Ho-LEE fuck democrats-appropriations.house.gov/news/press-r...
democrats-appropriations.house.gov
Defense Officials Attempt to Raid NIH Funds to Cover Department of Defense Activities
House Appropriations Committee Ranking Member Rosa DeLauro (D-CT-03) has learned that officials at the Department of Defense (DoD) are working to divert billions of dollars from the National Institute...
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Di Jiang @dijiang319.bsky.social · 01/09/2026
Last week @science.org De novo design of RNA pseudoknots with deep learning | Science www.science.org/doi/10.1126/...
science.org
De novo design of RNA pseudoknots with deep learning
RNA design has been hindered by the limited accuracy of three-dimensional (3D) structure prediction. In this study, we show that intricate RNA structures can be generated with current deep learning to...
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Janet Song @janetsong.bsky.social · 28/08/2026
Excited to see this out! Work led by Riley Mangan, in collaboration with my lab, identifies linCREs as a new set of genomic elements that may play functional roles in human evolution.
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Carl Zimmer @carlzimmer.com · 26/08/2026
Nature honors Dolly Parton's scientific legacy. www.nature.com/articles/d41...
nature.com
Dolly Parton dies aged 80 – researchers celebrate her contributions to science
The country singer was an advocate for vaccines, public health, literacy and marginalized communities.
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Jeffrey Mervis @policyhound.bsky.social · 19/08/2026
NSF is touting a dozen new solicitations announced this week as evidence that basic research still rules. But that's not what's really going on. www.science.org/content/arti...
science.org
Is NSF’s new call for research proposals good news? Scientists and staffers have doubts
The long-delayed 12 solicitations only cover some disciplines—and promise to give them much less money
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Junhong Choi @choijunhong.bsky.social · 11/08/2026
Excited to share the first preprint from our lab! We combined a DNA Typewriter lineage recorder with clone-resolved founder profiling to find what makes metastatic potential heritable in lung cancer xenografts. 1/13 www.biorxiv.org/content/10.6...
biorxiv.org
Time-resolved lineage recording reveals a pre-existing, heritable cell state underlying metastatic potential
Metastasis causes most cancer deaths, yet no recurrent mutation specifically drives it, raising the possibility that metastatic potential is a non-genetic yet heritable cell state. Classic experiments...
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Rob Patro @robp.bsky.social · 10/08/2026
All open source: piscem-rs, rapidgzip-core & thread-broker (standalone crate; bring your own producer/consumer). Now also in salmon 2.5.0 & coming to the alevin-fry ecosystem to turbocharge workflows. Maybe rapidgzip & thread-broker can help you too! Props to paraseq for making consumers easy! 8/8
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Science Magazine @science.org · 08/08/2026
The U.S. Senate has approved a temporary spending bill that blocks the White House Office of Management and Budget from implementing proposed changes in the rules affecting trillions of dollars of federal spending. scim.ag/4gjAh2O
scim.ag
Senate votes to block rule giving White House more control over research
Language is part of bill to fund government until mid-December
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(1/n) Excited to share close collab w @bloodgenes.bsky.social led by Varshini & Chun-jie et al How to induce expression of key genes while silencing much of the genome during Erythropoiesis? A: Matchmaker CREs load cohesin near key genes to promote looping & exp: www.biorxiv.org/content/10.6...
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Evgeny Kvon @evgenykvon.bsky.social · 05/08/2026
A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...
biorxiv.org
Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions
Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...
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Nature Portfolio @natureportfolio.nature.com · 05/08/2026
A paper in Nature presents the highest resolution observations of the Sun’s visible surface reported to date. The time-sequenced images provide a more complex picture of the Sun’s surface layer than previously seen, giving new insights into the magnetically active regions within this layer. 🔭🧪
go.nature.com
Ubiquitous Kelvin–Helmholtz instabilities driving plasma mixing on the Sun - Nature
High-spatial-resolution observations of the solar photosphere reveal a far more complex and dynamic solar scene than previously observed and show that ubiquitous Kelvin–Helmholtz instabilities drive plasma mixing on the Sun.
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Franck Polleux @franckp.bsky.social · 05/08/2026
I am exciting to highlight our new study published today in @cp-neuron.bsky.social. This work represents over 6 years of effort by an incredibly talented postdoc, Carlos Diaz-Salazar, in collaboration with @krzischlab.bsky.social, @bhadurilab.bsky.social at UCLA and Mercedes Paredes lab at UCSF 👇 🧵
cell.com
Human-specific SRGAP2 paralogs synchronize neotenic microglial maturation and synaptic development
Using a combination of microglia-specific conditional mouse knockout and knockin approaches and xenotransplantation of human iPSC-derived microglia, Diaz-Salazar et al. demonstrate that the human-spec...
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Alison Meynert @ameynert.bsky.social · 05/08/2026
DivRef is a resource for including common human variants and haplotypes in CRISPR off-target searches. I rebuilt the generation workflow to make its inputs, assumptions and population choices easier to inspect and change. blog.fulcrumgenomics.com/p/a-crispr-o...
blog.fulcrumgenomics.com
A CRISPR off-target search is only as good as the sequences it searches
Rebuilding DivRef so CRISPR off-target searches can account for human variation
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Joanna Masel @joannamasel.bsky.social · 04/08/2026
We derive a working hypothesis for how the genetic code evolved, by assuming LUCA-depleted amino acids came early, using codons we infer via the 2-1-3 rule. We validate with independent data and a control ordering ecoevorxiv.org/repository/v... @seekingluca.bsky.social @hanonmcshea.bsky.social 1/13
ecoevorxiv.org
The series of genetic codes that preceded our own
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026
Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below
nature.com
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
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Yulin Zhang @yulinzhang.bsky.social · 30/07/2026
Good news! Our paper (with @aabiddanda.github.io @sarahaj34.bsky.social @codushlaine.bsky.social and Priya Moorjani) is now officially online! www.science.org/doi/10.1126/...
science.org
Recovering signatures of archaic hominin introgression using ancestral recombination graphs
Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unad...
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Nature @nature.com · 28/07/2026
Nature research paper: Subnuclear genome compartmentalization controls bivalent chromatin activity go.nature.com/4vRsVZd
go.nature.com
Subnuclear genome compartmentalization controls bivalent chromatin activity - Nature
Knowledge of the spatial location of a gene is necessary to understand its epigenomic regulation.
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Harvard_MCB @harvardmcb.bsky.social · 27/07/2026
MCB Junior Fellow Wins Two Prestigious Evolutionary Science Awards— First Dual Honor in 25 Years 🧪 🧬 #AcademicSky #higherEd www.mcb.harvard.edu/department/n... @wendyssae.bsky.social @nbellono.bsky.social @naoshigeuchida.bsky.social @harvard.edu @sse-evolution.bsky.social @eseb.bsky.social
mcb.harvard.edu
MCB Junior Fellow Wins Two Prestigious Evolutionary Science Awards— First Dual Honor in 25 Years - Harvard University - Department of Molecular & Cellular Biology
Wendy Valencia-Montoya, a Junior Fellow in the Harvard Society of Fellows affiliated with the lab of MCB Professor Nick Bellono, has been awarded two of the most coveted […]
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Joanna Masel @joannamasel.bsky.social · 27/07/2026
Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social
academic.oup.com
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models
Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig
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Jenna Norton @jenna-m-norton.bsky.social · 22/07/2026
Remember when NIH Director Jay Bhattacharya said there were no banned words and NIH Program Officers were making them up? Here’s the proof he lied: apnews.com/article/cali... I know, Jay Bhattacharya lying is not news. But it’s still really validating to have the admission.
apnews.com
White House admits it used keywords to kill billions worth of California research grants
Federal agencies that terminated more than a thousand research grants at the University of California last year admitted that they used keywords related to diversity, gender, vaccine hesitancy and COV...
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WIRED @wired.com · 17/07/2026
Yesterday, WIRED learned that Madison Square Garden was suing us for our accurate reporting. We stand by our work. That’s why we’re removing the paywall from two of the MSG stories they don’t want you to read, making them free for everyone.
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Kang Wu @wukang.bsky.social · 11/07/2026
Annotate gel image using #tidyplots See the code at: tidyplots-book.pages.dev/more-custom-... #stats #dataviz #phd
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ChimeraX @chimerax.ucsf.edu · 10/07/2026
A new ChimeraX tool MorphometricsX from Ben Barad's lab colors cell membranes in electron tomography according to thickness, curvature and other properties. Available from ChimeraX menu Tools / More Tools....
ChimeraX user interface for MorphometricsX
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Nicholas Bellono @nbellono.bsky.social · 10/07/2026
Octopuses have unique ribosomes that make proteins more accurately - an adaptation that emerged alongside their expanded nervous systems. @sarareardon.bsky.social in @science.org: www.science.org/content/arti...
science.org
A molecular quirk unique to octopuses makes them better at building proteins
Certain shallow-water species carry a mutation that reduces translation errors and prevents toxic protein buildup
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Science Magazine @science.org · 09/07/2026
Springer Nature has reversed the more than decade-old retraction of two papers by legendary physicist and Nobel laureate Max Planck, saying the initial action was based on human error. scim.ag/3TouJuS
scim.ag
Springer Nature restores Max Planck’s mysteriously retracted papers
Publisher denies a bot was to blame for withdrawing famed physicist’s work
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Elena Rivas @rivaselenarivas.bsky.social · 28/03/2026
www.nature.com/articles/s42...
nature.com
What does it take to learn the rules of RNA base pairing? A lot less than you may think - Communications Biology
Deep-learning models typically require large parameter spaces and extensive training data. Here the authors demonstrate that learning the fundamental biological rules of RNA base pairing can be achiev...
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SeYeon Chung @seyeonchung.bsky.social · 28/06/2026
So grateful for the new Kathy Matthews Endowment for the Bloomington Drosophila Stock Center. A wonderful tribute by Kathy's husband, Lawrence Washington, that will help preserve Kathy's legacy and support the fly community for years to come. biology.indiana.edu/news-events/...
biology.indiana.edu
Major gift to establish endowment for IU Drosophila Stock Center
IU Biology news: The IU Stock Center maintains thousands of documented, living genetic strains of Drosophila melanogaster, a small fruit fly that has served as one of science’s most powerful tools for...
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Neil Shubin @neilshubin.bsky.social · 25/06/2026
My editorial in this week’s Science @aaas.org www.science.org/doi/10.1126/... 🧪
science.org
The enduring pursuit of science in America
Imagine an American organization that convenes scientific experts not to advance any ideology or interest but to provide the nation with a clear understanding of complex problems. Imagine this body wo...
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Denis Wirtz @deniswirtz.bsky.social · 22/06/2026
3D reconstruction reveals highly conserved vascular network architecture despite phylogenetic diversity spanning >300M years of evolution. Moer here: www.biorxiv.org/content/10.6...
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Simons Foundation @simonsfoundation.org · 21/06/2026
Happy #WorldMusicDay! Renowned saxophonist Marcus Garrick Miller invites audiences to see #math in a different light through the joy of music. Read more about our #InfiniteSums math ambassador: bit.ly/4vcmtfA
bit.ly
Math Ambassadors: Marcus Garrick Miller
Miller, a saxophonist, discusses how he bridges math and music and his upcoming performance at the Brooklyn Public Library’s Night in the Library: The Philosophy of Mathematics.
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raw9371 @raw937.bsky.social · 19/06/2026
Most high-performance bioinformatics software written 10 years from now will be in Rust. 🦀 Today we released rustyomestats — our first Rust crate ⚡ Genome size 🧬 GC content 📊 N50/L50/U50 🔬 Codon density 🚀 FASTA parsing GitHub: lnkd.in/dDw2KNuX Rust is the way. #RustLang #Bioinformatics
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Admirable Women @admirablewomen.bsky.social · 16/06/2026
Cytogeneticist Dr. Barbara McClintock won the 1983 #Nobel Prize in Physiology or Medicine for her study of corn chromosomes--revolutionizing the field of cytogenetics. She is the only woman to be awarded an unshared Nobel Prize in this category. She was born #OTD in 1902. #WomenInSTEM
A black-and-white photograph from 1947 of American cytogeneticist Dr. Barbara McClintock (1902–1992), who would later win the 1983 Nobel Prize in Physiology or Medicine for discovering genetic transposition. She is seated in her laboratory at Cold Spring Harbor, deeply absorbed in her scientific work. Looking downward with a focused, serious expression, she wears delicate wire-rimmed glasses and a light-colored, buttoned lab coat over a collared shirt pinned with a round brooch. Her short, dark hair is parted to the side. Her right hand holds a fine tool over a petri dish, while her left hand rests carefully on the edge of another dish next to a glass specimen vial. On the table stands a large, black vintage compound microscope with multiple metal objectives. The composition centers on her meticulous hands and face, with a softly blurred background of lab shelves and window light, creating an intense, studious mood of historical scientific discovery.
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Peter Andolfatto @pandolfatto.bsky.social · 16/06/2026
1/n Check out our new paper, spearheaded by @fborne.bsky.social, just out in PLoS Genetics doi.org/10.1371/jour....
doi.org
Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein
Author summary Proteins fold into three-dimensional structures that are essential for their function. Because these structures depend on interactions among amino acids, the fitness effect of a mutatio...
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Nicholas Bellono @nbellono.bsky.social · 16/06/2026
How did animal senses evolve? Max Coyle et al. used choanoflagellates to uncover TRPW, ancient ion channels predating animal somatosensory receptors. TRPW links microbial prey ecology to evolution of receptor structure, sensory organelles, & multicellular processing. www.biorxiv.org/content/10.6...
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 15/06/2026
People. @ksamuk.bsky.social and others have made this argument before. There’s good software to do this right. Here’s the argument again: Invariant sites matter! They’re not in your standard vcf and many programs pretend they are anyway. academic.oup.com/gbe/article/...
academic.oup.com
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi
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John Hawks @johnhawks.net · 12/06/2026
It is a very challenging position that @neilshubin.bsky.social walks into as leader of @nasonline.org with partisan division over many areas of scientific work. Illuminating interview with @carlzimmer.com as he takes office. www.nytimes.com/2026/06/12/s...
nytimes.com
Neil Shubin on Trusted Science in a ‘Deeply Partisan Age’
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Cara Brook @caraebrook.bsky.social · 12/06/2026
The Brook lab is searching for a Postdoctoral Scholar, broadly in the field of 'Bat Infectious Diseases.' See here for details and a link to apply: brooklab.org/join/postdoc. Application review begins on June 25 and will be rolling thereafter!
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Science Magazine @science.org · 11/06/2026
New research in Science reveals that the Venus flytrap's snap is triggered by a rapid softening of the epidermal cell walls, uncovering the physical mechanism behind this remarkable movement. Learn more in this week's issue: scim.ag/4fXQ9sn
A Venus flytrap (Dionaea muscipula) leaf closes around a trapped fly. Photo: Alex Hyde/NPL/Minden Pictures
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Aurora Ruiz-Herrera @aruizherrera.bsky.social · 10/06/2026
🚨 New paper in Nature 🚨 Thrilled to be part of this fascinating collaborative study! 👉 SIRT7 regulates dosage compensation and safeguards the female X chromosome rdcu.be/fnEZQ A great example of how chromatin regulation continues to reveal unexpected layers of genome control!
rdcu.be
SIRT7 regulates dosage compensation and safeguards the female X chromosome
Nature - SIRT7 safeguards X-chromosome integrity and dosage balance with autosomes.
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Gregg Gonsalves @gregggonsalves.bsky.social · 03/06/2026
Holden Thorp is an institutionalist. He's been a university chancellor, provost, now EiC of Science. When institutionalists pull the fire alarm, we listen, because the call to action he issued this week exposes the dire nature of the threat we are facing. 1/ www.science.org/doi/10.1126/...
science.org
Another red alert for American science
Although research has bipartisan support in the US Congress, and trust in science is above 75% across the country, the Trump administration seems as determined as ever to mortally wound the nation’s s...
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Kristian G. Andersen @kgandersen.bsky.social · 02/06/2026
On OMB's proposal to make all grants political: "Speak up! Now’s the time! Standing by the side of the room, glancing around nervously and hoping that somebody else does something will lead us to disaster. These are not normal times, so stop acting as if they are." www.science.org/content/blog...
science.org
Action! Action Now.
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