Time-of-day immunochemotherapy in nonsmall cell lung cancer: a randomized phase 3 trial - Nature Medicine In this randomized phase 3 trial, patients with treatment-naive stage III–IV nonsmall cell lung cancer who received sintilimab or pembrolizumab in combination with chemotherapy early in the day (befor...

Stunning how much time-of-day for immunochemotherapy in lung cancer seems to matter, where treatment earlier in the day improves outcomes. Interesting study published this week www.nature.com/articles/s41...

Post Doc PD DD PCCD At Johnson & Johnson, we believe health is everything. Our strength in healthcare innovation empowers us to build a world where complex diseases are prevented, treated, and cured, where treatments...

We're looking for a post-doc to support target discovery in lymphoma using single-cell and spatial 'omics modalities.

You will be embedded in our Discovery Statistics organization, and supported by myself and colleagues. Feel free to reach out for any additional information.

tinyurl.com/36uyca7f

After two weeks, I'm finally done!

In this post, I explain different approaches for solving linear regression in R: directly, using QR, singular value and Cholesky decompositions, and do some benchmarking for comparison with in-built approaches.

thomvolker.github.io/blog/2506_re...

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...

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...

Transcriptome-wide characterization of genetic perturbations Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these screens are often noisy due to cost and technical ...

New preprint from Ajay Nadig @nadigajay.bsky.social in Luke O'Connor's lab, with "a suite of statistical tools for formally modeling distributions of DE effects from RNA-seq experiments, including Perturb-seq"

www.biorxiv.org/content/10.1...

Colossal Bioscience did not revive dire wolves, despite a sensationalist Time Magazine cover story.

Making genetically modified animals that are cosplaying as extinct species is not de-extinction.

A screenshot of the release notes for radEmu v2. Text available at https://github.com/statdivlab/radEmu/releases

We've just released radEmu v2.0.0 🥳🦤😻

`remotes::install_github("statdivlab/radEmu")`

A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!

Release notes: github.com/statdivlab/r...

A single neuron (white) shown with 5,600 of the axons (blue) that connect to it. The synapses that make these connections are shown in green. The cell body (central core) of the neuron is about 14 micrometers across.

In Science, researchers detail a nanoscale-resolution reconstruction of a millimeter-scale fragment of human cerebral cortex, giving an unprecedented view into the structural organization of brain tissue at the supracellular, cellular, and subcellular levels. scim.ag/3FvpAKy #BrainAwarenessWeek

Univariate-Guided Sparse Regression In this paper, we introduce ``UniLasso'' -- a novel statistical method for sparse regression. This two-stage approach preserves the signs of the univariate coefficients and leverages their magnitude. ...

I am happy to announce our new paper "Univariate-guided sparse regression". It's a new lasso that leverages the signs and magnitude of univariate coefficients .
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...

This is long overdue, but over the winter break we were finally able to write up our sgdGMF paper:
arxiv.org/abs/2412.20509

We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/

www.encodeproject.org/single-cell/...

Causal inference on human behaviour - Nature Human Behaviour In this Review, Drew Bailey et al. present an accessible, non-technical overview of key challenges for causal inference in studies of human behaviour as well as methodological solutions to these chall...

A few papers I think worth reading. Mostly open access.

Causal inference is hard:

www.nature.com/articles/s41...

Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data? Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the re...

Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)

Luckily for you, @aaronkwc.bsky.social has!

Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?

Check it out 👇
www.biorxiv.org/content/10.1...

🧪🧬💻