Jess Whittle

We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...

03.04.2025 14:30 — 👍 75    🔁 38    💬 1    📌 5

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...

Delighted to have our Perturb-multiome paper, led by #JorgeMartinRufino and @hemagene.bsky.social from our lab, published today in @science.org. Please check out this powerful approach to decipher gene regulatory networks enriched for genetic variation: www.science.org/doi/10.1126/...

03.04.2025 23:57 — 👍 118    🔁 29    💬 2    📌 1

CellPie: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization Abstract. Spatially resolved transcriptomics has enabled the study of expression of genes within tissues while retaining their spatial identity. Most spati

Check out our new paper "CellPie" in @narjournal.bsky.social for integrating high-d spatial transcriptomics data and histology through a scalable jointNMF implementation. 🧬

academic.oup.com/nar/article/...

@mrattray.bsky.social @miqbal13.bsky.social @will-morgans.bsky.social

02.04.2025 09:02 — 👍 5    🔁 4    💬 0    📌 0

A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells Residing at the top of the hematopoietic hierarchy, long-term hematopoietic stem cells (HSCs) are capable of self-renewal and sustained blood cell regeneration. Over the past decades, single-cell and ...

New pre-print from Thomas Höfer, Daniel Hübschmann, @haas_lab and myself, with first authors @Esther_RCorrea @FloGrunschlager and Tamar Nizharadze doi.org/10.1101/2025... @DKFZ @NCT_HD @ChariteBerlin @hi_stem_lab BIH & MDC

05.02.2025 10:55 — 👍 52    🔁 22    💬 1    📌 6

1/x Online now: Our work on platelet aging and inflammation in @bloodjournal.bsky.social led by superstar PhD student Afra Anjum: ashpublications.org/blood/articl...

23.01.2025 10:38 — 👍 31    🔁 9    💬 2    📌 1

Enjoying the Lake District in its winter coat ❄️

11.01.2025 22:05 — 👍 0    🔁 0    💬 0    📌 0

Stem cell-like states confer poor outcomes in blood cancer—but what mechanisms drive this and how can they be therapeutically targeted? In our new preprint, we show how a single TF represses one enhancer to maintain a subset of high-risk leukemias: 🧵👇
www.biorxiv.org/content/10.1...

02.01.2025 14:47 — 👍 21    🔁 8    💬 1    📌 2

1/ 🎄 What’s the best gift under the tree for a computational biologist? 🎁 A new experimental assay that refines our view of gene regulation: ACCESS-ATAC! This creative idea from Richard Sherwood was developed collaboratively between his lab and mine. #Genomics
www.biorxiv.org/content/10.1...

23.12.2024 15:18 — 👍 105    🔁 31    💬 2    📌 2

1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.1101/2024.12.11.627935v1

12.12.2024 14:48 — 👍 112    🔁 47    💬 3    📌 4

Lentiviral Gene Therapy with CD34+ Hematopoietic Cells for Hemophilia A | NEJM Severe hemophilia A is managed with factor VIII replacement or hemostatic products that stop or prevent bleeding. Data on gene therapy with hematopoietic stem-cell (HSC)–based expression of factor ...

Gene therapy showing some nice preliminary results in a small cohort of patients with severe Haemophilia A. Very impressive findings!

www.nejm.org/doi/full/10....

12.12.2024 11:16 — 👍 1    🔁 0    💬 0    📌 0

The dynamics of hematopoiesis over the human lifespan - Nature Methods This Resource presents an atlas classifying the age-related changes in human hematopoietic stem and progenitor cells from gestation through aging.

Just in time for #ASH24, our latest paper is out. We performed scRNA-seq on HSPCs over human development, maturation, and postnatal aging. We looked at dynamics of HSPC subsets, lineage biases, HSC level priming, and identified a developmentally restricted human HSC.
www.nature.com/articles/s41...

05.12.2024 12:52 — 👍 55    🔁 14    💬 2    📌 2