Jess Whittle
@jesswhittle.bsky.social
PhD Student @ UoM/CRUK MI (Georges Lacaud’s Lab)
Interested in gene regulation in haematopoiesis and AML.
Interested in gene regulation in haematopoiesis and AML.
Reposted by 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...
April 3, 2025 at 2:30 PM
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...
Reposted by Jess Whittle
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/...
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...
www.science.org
April 3, 2025 at 11:57 PM
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/...
Reposted by Jess Whittle
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
academic.oup.com/nar/article/...
@mrattray.bsky.social @miqbal13.bsky.social @will-morgans.bsky.social
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
academic.oup.com
April 2, 2025 at 9:02 AM
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
academic.oup.com/nar/article/...
@mrattray.bsky.social @miqbal13.bsky.social @will-morgans.bsky.social
Reposted by Jess Whittle
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
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 ...
doi.org
February 5, 2025 at 10:55 AM
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
Reposted by Jess Whittle
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...
January 23, 2025 at 10:39 AM
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...
Enjoying the Lake District in its winter coat ❄️
January 11, 2025 at 10:05 PM
Enjoying the Lake District in its winter coat ❄️
Reposted by Jess Whittle
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...
www.biorxiv.org/content/10.1...
January 2, 2025 at 2:47 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Jess Whittle
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...
www.biorxiv.org/content/10.1...
December 23, 2024 at 3:18 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Jess Whittle
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
biorxiv.org/content/10.1101/2024.12.11.627935v1
December 12, 2024 at 2:48 PM
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
biorxiv.org/content/10.1101/2024.12.11.627935v1
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....
www.nejm.org/doi/full/10....
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 ...
www.nejm.org
December 12, 2024 at 11:16 AM
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....
www.nejm.org/doi/full/10....
Reposted by Jess Whittle
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...
www.nature.com/articles/s41...
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.
www.nature.com
December 5, 2024 at 12:52 PM
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...
www.nature.com/articles/s41...