steven hoffman

Before AGBT Kicks Off, Ultima Unveils the UG 200 genengnews.com/topics/omics/b…

To do this, we used genome-scale CRISPR activation (CRISPRa) to turn on every gene and measure precise editing. One surprising finding: Many genes that are never or very lowly expressed (in human K562 cells) can enhance precise repair.

Inspired by @JswLab, we generated a mini Genome-wide Perturb-seq, using just two 10x lanes (!). Far too much data for one tweet (or one Figure), but it works beautifully. The ability to assess the molecular function of every gene in an afternoon is mind-boggling

I miss open seating on @SouthwestAir

In case you’re late to my favorite Olympic performance enhancing scandal, here are the details of penis inflate-gate.

Big news! We are teaming up with @NVIDIAHealth to accelerate virtual cell model development to unlock news insights about human biology czi.co/48SctA6 #NVIDIAGTC

Introducing Tahoe-x1 (Tx1) by @tahoe_ai. A 3-billion-parameter, single-cell foundation model that learns unified representations of genes, cells, and drugs, achieving state-of-the-art performance across cancer-relevant cell biology benchmarks, open-sourced on @huggingface. 🧵

Today @AnthropicAI released PubMed integration for Claude. No hallucinations. Just real science, real data. As a beta tester, this has been a game changer—like having a supercharged research assistant. Here are 6 prompts that will transform how you search the literature. A 🧵

We’re launching our Claude for Life Sciences initiative today, including new bioinformatics Skills, and new MCPs from @benchling, @BioRender, PubMed, @WileyGlobal, @Sagebio, @10xGenomics and more: anthropic.com/news/claude-fo…

Welcome to #ASHG25! We’re kicking off five incredible days of learning, connecting, and inspiring. We’re so glad you’re here, let’s make this unforgettable! 📲Download our mobile app: pheedloop.com/ASHG25/ #ASHG

CRISPR came from yogurt bacteria. GLP-1s came from Gila monster venom. Taq polymerase came from hot spring bacteria. As much as we like to think that progress in biotech is driven by human design, our biggest breakthroughs over the years have all originated from nature.

In case you missed yesterday’s announcement, registration for The Festival of Genomics & Biodata is now open! You don’t want to miss out on the UK’s largest life sciences event, so make sure you get your ticket now. More info here: hubs.la/Q03MJnJr0 #FOG2026

"Only ~0.02%-3.1% of [a cell's] genome" is being transcribed at any given moment. Other interesting takeaways from this new paper: > If you pool together a bunch of cells of the SAME type (like primary immune cells from a mouse's spleen), and you measure the transcription for each of them, you'll find that ~67% of the genome is active collectively. But at a SINGLE cell level, only like 0.04% of the genome is active. There is huge heterogeneity between cells, even of the same type. This heterogeneity disappears when we do bulk RNA-seq and measure cells together. > About 31% of a cell's transcription comes from known protein-coding genes. The rest of transcription happens in regions that don't make proteins. In other words, more "non-coding" DNA is transcribed than "coding" DNA. > There is a surprising disconnect between RNA production & decay at the single-cell level. If you look at thousands of cells together, the rate of RNA production (how fast genes are transcribed) usually matches the rate of RNA decay (how fast old transcripts are degraded). This makes sense, because cells presumably would want to keep a fairly steady balance of RNA levels. But when scFLUENT-seq was used to look at individual cells, this "rule" broke down! For a given mRNA, some cells were making a lot of new copies even if old copies weren’t being degraded much, while other cells had the opposite. So transcription and decay don't seem to be tightly matched within a single cell at a given time after all. The balance between production + decay is only true in bulk.

We’ve announced plans to open a new site in Houston, the second of 4 new locations coming to the U.S. The $6.5 billion facility will bring an expected 4,615 jobs and help boost domestic medicine manufacturing.

want to up-level your bioinformatics skills? End-to-end tutorial on RNAseq analysis 👇 Chatomics! new blog post: Do not repeat yourself: List column to do RNAseq differential expression analysis divingintogeneticsandgenomics.com/post/list-colu…

Best practices for @UltimaGenomics Analysis: link.ultimagenomics.com/199ff0

My resignation letter from CDC. Dear Dr. Houry, I am writing to formally resign from my position as Director of the National Center for Immunization and Respiratory Diseases at the Centers for Disease Control and Prevention (CDC), effective August 28, 2025, close of business.   I am happy to stay on for two weeks to provide transition, if requested. This decision has not come easily, as I deeply value the work that the CDC does in safeguarding public health and am proud of my contributions to that critical mission. However, after much contemplation and reflection on recent developments and perspectives brought to light by Secretary Robert F. Kennedy Jr., I find that the views he and his staff have shared challenge my ability to continue in my current role at the agency and in the service of the health of the American people. Enough is enough. While I hold immense respect for the institution and my colleagues, I believe that it is imperative to align my professional responsibilities to my system of ethics and my understanding of the science of infectious disease, immunology, and my promise to serve the American people.  This step is necessary to ensure that I can contribute effectively in a capacity that allows me to remain true to my principles. I am unable to serve in an environment that treats CDC as a tool to generate policies and materials that do not reflect scientific reality and are designed to hurt rather than to improve the public’s health.  The recent change in the adult and children’s immunization schedule threaten the lives of the youngest Americans and pregnant people.   The data analyses that supported this decision have never been shared with CDC despite my respectful requests to HHS and other leadership.  This lack of meaningful engagement was further compounded by a “frequently asked questions” document written to support the Secretary’s directive that was circulated by HHS without input from CDC subject matter experts and that cited studies that did not support the conclusions that were attributed to these authors.  Having worked in local and national public health for years, I have never experienced such radical non-transparency, nor have I seen such unskilled manipulation of data to achieve a political end rather than the good of the American people. It is untenable to serve in an organization that is not afforded the opportunity to discuss decisions of scientific and public health importance released under the moniker of CDC.  The lack of communication by HHS and other CDC political leadership that culminates in social media posts announcing major policy changes without prior notice demonstrate a disregard of normal communication channels and common sense.  Having to retrofit analyses and policy actions to match inadequately thought-out announcements in poorly scripted videos or page long X posts should not be how organizations responsible for the health of people should function.  Some examples include the announcement of the change in the COVID-19 recommendations for children and pregnant people, the firing of scientists from ACIP by X post and an op-ed rather than direct communication with these valuable experts, the announcement of new ACIP members by X before onboarding and vetting have completed, and the release of term of reference for an ACIP workgroup that ignored all feedback from career staff at CDC. The recent term of reference for the COVID vaccine work group created by this ACIP puts people of dubious intent and more dubious scientific rigor in charge of recommending vaccine policy to a director hamstrung and sidelined by an authoritarian leader.   Their desire to please a political base will result in death and disability of vulnerable children and adults.  Their base should be the people they serve not a political voting bloc. I have always been first to challenge scientific and public health dogma in my career and was excited by the opportunity to do so again.  I was optimistic that there would be an opportunity to brief the Secretary about key topics such as measles, avian influenza, and the highly coordinated approach to the respiratory virus season.  Such briefings would allow exchange of ideas and a shared path to support the vision of “Making America Healthy Again.”  We are seven months into the new administration, and no CDC subject matter expert from my Center has ever briefed the Secretary.  I am not sure who the Secretary is listening to, but it is quite certainly not to us.  Unvetted and conflicted outside organizations seem to be the sources HHS use over the gold standard science of CDC and other reputable sources.  At a hearing, Secretary Kennedy said that Americans should not take medical advice from him.  To the contrary, an appropriately briefed and inquisitive Secretary should be a source of health information for the people he serves. As it stands now, I must agree with him, that he should not be considered a source of accurate information. The intentional eroding of trust in low-risk vaccines favoring natural infection and unproven remedies will bring us to a pre-vaccine era where only the strong will survive and many if not all will suffer.  I believe in nutrition and exercise.  I believe in making our food supply healthier, and I also believe in using vaccines to prevent death and disability.  Eugenics plays prominently in the rhetoric being generated and is derivative of a legacy that good medicine and science should continue to shun. The recent shooting at CDC is not why I am resigning.  My grandfather, who I am named after, stood up to fascist forces in Greece and lost his life doing so.  I am resigning to make him and his legacy proud.   I am resigning because of the cowardice of a leader that cannot admit that HIS and his minions’ words over decades created an environment where violence like this can occur.  I reject his and his colleagues’ thoughts and prayers, and advise they direct those to people that they have not actively harmed. For decades, I have been a trusted voice for the LGBTQ community when it comes to critical health topics.  I must also cite the recklessness of the administration in their efforts to erase transgender populations, cease critical domestic and international HIV programming, and terminate key research to support equity as part of my decision. Public health is not merely about the health of the individual, but it is about the health of the community, the nation, the world. The nation’s health security is at risk and is in the hands of people focusing on ideological self-interest. I want to express my heartfelt gratitude for the opportunities for growth, learning, and collaboration that I have been afforded during my time at the CDC. It has been a privilege to work alongside such dedicated professionals who are committed to improving the health and well-being of communities across the nation even when under attack from within both physically and psychologically. Thank you once again for the support and guidance I have received from you and previous CDC leadership throughout my tenure. I wish the CDC continued success in its vital mission and that HHS reverse its dangerous course to dismantle public health as a practice and as an institution.  If they continue the current path, they risk our personal well-being and the security of the United States. Sincerely, Demetre C. Daskalakis MD MPH (he/his/him)

We put a blog post together to tell you about all that went behind the scenes for @arcinstitute's Virtual Cell Challenge: (1) the modality used for genetic perturbations, (2) choice of single cell RNA seq chemistry, (3) which cell line to use for the challenge, (4) which genes to perturb, (5) the quality considerations for the resulting dataset, and (6) how we defined performance metrics for perturbation predictions.

Most people know that ALS is a deadly disease. But most don't know that an ALS diagnosis is often missed at early disease stages due to lack of specific biomarkers. Now, a plasma proteomic signature of 33 proteins (based on Olink Explore) achieved discrimination of >95%!

Mackinac Island in Northern Michigan, where cars are banned and Amazon delivers by horse.