Absolutely love this perspective on AI in biopharma R&D by Daphne Koller, who knows a bit abt AI & biology & entrepreneurship: open.substack.com/pub/a16z/p/d... Deeply resonant & aligned w stuff @andreasbender.bsky.social @jackscannell.bsky.social & I (et al) have been talking (&writing...) abt

Drug Discovery Has No Magic Wands

On AI, human biology, and what it will actually take to discover transformative new medicines

open.substack.com

📢PUBLISHED @natgenet.nature.com 📰Pioneer transcription factors direct tissue-specific cohesin chromatin entry and three-dimensional genome organization. By Song Wang, Haiyang Guo and colleagues. ⬇️ www.nature.com/articles/s41...

Pioneer transcription factors direct tissue-specific cohesin chromatin entry and three-dimensional genome organization - Nature Genetics

Analyses in prostate cancer cell lines show that FOXA1 mediates tissue-specific recruitment of NIPBL to chromatin to orchestrate three-dimensional genome organization, acting in concert with ETS1 and ...

nature.com

Thank you @natgenet.nature.com for this nice Research Briefing www.nature.com/articles/s41... on our recent paper reporting live-cell measurements of Sox2 promoter bursting kinetics when varying its genomic distance from the SCR enhancer 👉 www.nature.com/articles/s41...

The genomic position of an enhancer modulates bursting dynamics of the cognate promoter - Nature Genetics

We show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...

nature.com

As my time in North Carolina winds down, I’ve been thinking a lot about community. Amidst all the chaos surrounding science lately, it’s been refreshing to be part of one that genuinely showed up for each other.

Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates

Anders Sejr Hansen@andersshansen.bsky.social · 2y ago

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

We know little about proteins required for long-range compartment 3D interactions, but this @kyleeagen.bsky.social lab preprint shows that NSD3 can make Mb-scale long-range compartment-like interactions: www.biorxiv.org/content/10.6...

Exciting news for the RNA research community! The Human RNome Project has been launched: a global effort to map all human RNAs and their chemical modifications. Proud to support it and contribute to the article in Genome Biology doi.org/10.1186/s130... #RNA #bioinformatics #RNAstructure #modomics

Unlocking the regulatory code of RNA: launching the Human RNome Project - Genome Biology

The human RNome, the complete set of RNA molecules in human cells, arises through complex processing and includes diverse molecular species. While research traditionally focuses on four canonical nucl...

genomebiology.biomedcentral.com

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project! If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further! rdcu.be/eLiT5

Characterization of induced cohesin loop extrusion trajectories in living cells

Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...

rdcu.be

It was an absolute pleasure to write a News&Views for @andersshansen.bsky.social lab's newest paper in NSMB. Here, the authors provide absolute quantification of chromatin loops genome-wide: www.nature.com/articles/s41...

Genome-wide absolute quantification of chromatin looping - Nature Structural & Molecular Biology

By calibrating Micro-C against live-imaging data in mouse embryonic stem cells, Jusuf et al. quantified 65,929 chromatin loops genome-wide, finding that most loops form pairwise interactions with an a...

nature.com

@dimitristypas.bsky.social · last mo.

In an associated News & Views, @fenaochs.bsky.social provides what I at least found an eloquent, insighftul and broad exemplification and contextualisation of what the study could mean for the field and what could follow. www.nature.com/articles/s41...

Wonderful, thought-provoking review by Sir Adrian Bird on cohesin loop extrusion as disrupter of chromatin organisation rather than generator. Great read! www.sciencedirect.com/science/arti...

Cohesin as an essential disruptor of chromosome organization

Cohesin is a multi-subunit molecular machine that is able to create lateral chromatin loops within a linear chromosome fiber. Despite intense study, a…

sciencedirect.com

UC Davis will no longer pay the difference so that GRFP recipients earn the same as other students. So mid-PhD students will lose nearly 25% of salary & new students will make less than their peers. Apply for the GRFP, it’s a wonderful help to your career. Just don’t come here if you get one.

"Federal officials offered the new details about the grant cancellations as part of an agreement with plaintiffs meant to spare the government an exhaustive, evidence-uncovering process known as discovery...That process could have required federal agencies to hand over more damaging records."

tony romm@tonyromm.bsky.social · 2w ago

NEW: In a stunning admission, the Trump administration admitted in court documents that it canceled billions in energy grants to states "based solely" on politics -- and whether that state was represented by Democrats and backed Harris in 2024. www.nytimes.com/2026/07/24/b...

4D Nucleome special issue of Science, featuring our paper "Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease–linked transcription factor", led by Zoe Grant in my lab and Zhuzhen Kuang in Katie Pollard's lab @gladstoneinst.bsky.social www.science.org/toc/science/...

Our latest is now out in @nataging.nature.com giving reason to celebrate! Led by talented Spiros Palikyras, it improves our preprint (posted 2 years ago!) dissecting the mechanism and functional consequences of CTCF clustering upon senescence commitment of human cells. www.nature.com/articles/s43...

Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program - Nature Aging

Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...

nature.com

"Corresponding authors who are men exhibit a small but significant advantage at Science, while authors based in China have a significant disadvantage. These associations are generally stronger in editorial review than in peer review" funded by 4 different NSF awards

Javi Ibarrondo@jibarrondo.bsky.social · 3w ago

Editorial and peer review dynamics at elite general science journals | Science Advances www.science.org/doi/10.1126/... 🧪

Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:

Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics

Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...

doi.org

Luca Giorgetti lab @FMI@lucagiorgetti.bsky.social · last yr.

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

my italian lessons start today, and I. AM. PUMPED.

Wow. “The three directorates are being required to pull back NSF proposals that have already passed peer review and have been recommended for funding. Some of the funds will be funnelled to another project, a brainchild of the White House OSTP.” www.nature.com/articles/d41...

NSF plans cuts to core science programmes to fund White House initiative

A proposed clawback of already distributed research funds comes as the US agency’s budget is already squeezed and it struggling to clear a backlog of grant applications.

nature.com

Interesting new R/Bioconductor workflow to call significant interactions. Will have to give this a try. f1000research.com/articles/13-...

F1000Research Article: A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops.

Read the latest article version by JP Flores, Eric Davis, Nicole Kramer, Michael I Love, Douglas H Phanstiel, at F1000Research.

f1000research.com

A new op-ed from @researchamerica.bsky.social grant recipient JP Flores explores why scientists must engage directly with communities, especially in an era where misinformation spreads fast.. Read more in Sci Politic sciencepolitics.org/2026/03/18/w...

We’re Training Scientists for a World That No Longer Exists - Science Politics

Science can help address pressing challenges, but only if we train scientists to communicate in the places people actually form beliefs.

sciencepolitics.org

Feed: "The Hechinger Report" By: JP Flores on Monday, February 16, 2026

OPINION: Pathways for future scientists are becoming scarce, threatening a strong and innovative workforce

If we want a scientific workforce capable of addressing the challenges we face, we must invest in scientists long before they become scientists. That means expanding research opportunities, supporting students early and building trust with communities.

hechingerreport.org

How do we think about science in this challenging era? JP Flores writes in Science Politics that science can help address pressing challenges, but only if we train scientists to communicate in the places people actually form beliefs. sciencepolitics.org/2026/03/18/w...

We’re Training Scientists for a World That No Longer Exists - Science Politics

Science can help address pressing challenges, but only if we train scientists to communicate in the places people actually form beliefs.

sciencepolitics.org

More than a quarter MILLION public comments. The administration still weakened protections for endangered species. I know everyone has their own lives, jobs, and problems to worry about, but a lot of people have been convinced that this is normal 😅 Photo from @emmascales.bsky.social

Robert Greenwald@robertgreenwald.bsky.social · 4w ago

Trump, Ending Decades of Protection, Opens Wild Habitats to Drilling and Mining www.nytimes.com/2026/07/10/c...

People really do love 1) talking for me, 2) never using the word “we”, & 3) adopting work others do and claiming it as their own lol

The People-First Chatbot Act is built on a careful foundation- the AI Bill of Rights-and brings real enforcement to protections that matter: safety, non-discrimination, privacy, transparency, and the right to a human alternative. I'm pleased to support it. foushee.house.gov/media/press-...

Reps. Foushee, Casar Introduce Legislation to Protect Children and Americans’ Privacy from AI Chatbot Harms and Require Chatbot Safety Assessments | U.S. Congresswoman Valerie Foushee

The Official U.S. Congressional website of Congresswoman Valerie Foushee

foushee.house.gov

(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:

Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning

Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...

rdcu.be

Happy to announce that I received tenure! This is all down to the brilliant team I get to work with every day and my collaborators and supportive colleagues. Now UCSF can’t get rid of me…

Congratulations to both Rishi Deshmukh and Sunny Eoh for funding of their NIH T32 proposals!!! So proud of them both and excited for all the cool science to come Two more corks on the line & a group photo with my 4yo's stuffed dog that she urged me to take with me today "to meet the lab"

Tagging the rest of our rockstar team here: @raungar.bsky.social @jpflores.rbind.io @alvinahere.bsky.social @tamigj.bsky.social @dianexue.bsky.social & (untaggable) Krystin Jones, Betzaida Maldonado, and Alyna Khan.

In what has been a labor of love & joyful collaboration, we are super excited to share our preprint on recommendations towards the ethical and accurate use of population descriptors generated from a survey by trainees, for trainees. www.biorxiv.org/content/10.6...

Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers

Despite the importance of population descriptors in human genomics research, many scientists struggle to translate evolving ethical guidelines into their computational workflows. To characterize this ...

biorxiv.org