Ian Driver
@biodriver.bsky.social
Head of Bioinformatics at Gordian Biotechnology. Open science proponent. Runner. 🧬🖥️🏃🏻
Reposted by Ian Driver
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
Reposted by Ian Driver
Tahoe-x1: Scaling Perturbation-Trained Single-CellFoundation Models to 3 Billion Parameters https://www.biorxiv.org/content/10.1101/2025.10.23.683759v1
October 24, 2025 at 12:04 AM
Tahoe-x1: Scaling Perturbation-Trained Single-CellFoundation Models to 3 Billion Parameters https://www.biorxiv.org/content/10.1101/2025.10.23.683759v1
Reposted by Ian Driver
Perturbation-aware representation learning for in vivo genetic screens https://www.biorxiv.org/content/10.1101/2025.10.15.682661v1
October 16, 2025 at 12:47 AM
Perturbation-aware representation learning for in vivo genetic screens https://www.biorxiv.org/content/10.1101/2025.10.15.682661v1
Reposted by Ian Driver
FUSED: CROSS-DOMAIN INTEGRATION OF FOUNDATION MODELS FOR CANCER DRUG RESPONSE PREDICTION https://www.biorxiv.org/content/10.1101/2025.09.30.679434v1
October 2, 2025 at 12:47 AM
FUSED: CROSS-DOMAIN INTEGRATION OF FOUNDATION MODELS FOR CANCER DRUG RESPONSE PREDICTION https://www.biorxiv.org/content/10.1101/2025.09.30.679434v1
Reposted by Ian Driver
Announcing our latest publication, just out today
@NatureComms, advancing our understanding of interstitial lung disease. Congrats to co-senior authors Drs. Jeremy Katzen and Kostas Alysandratos and their teams @Penn @CReM_Boston. Check it out here: www.nature.com/articles/s41...
@NatureComms, advancing our understanding of interstitial lung disease. Congrats to co-senior authors Drs. Jeremy Katzen and Kostas Alysandratos and their teams @Penn @CReM_Boston. Check it out here: www.nature.com/articles/s41...
Aberrant intermediate alveolar epithelial cells promote pathogenic activation of lung fibroblasts in preclinical fibrosis models - Nature Communications
The direct contribution of aberrant epithelial cells to lung fibrosis is largely unknown. The authors use murine and human systems to identify how these cells activate fibroblasts, and how reciprocal signals cause them to enter a profibrotic state.
www.nature.com
September 30, 2025 at 10:14 PM
Announcing our latest publication, just out today
@NatureComms, advancing our understanding of interstitial lung disease. Congrats to co-senior authors Drs. Jeremy Katzen and Kostas Alysandratos and their teams @Penn @CReM_Boston. Check it out here: www.nature.com/articles/s41...
@NatureComms, advancing our understanding of interstitial lung disease. Congrats to co-senior authors Drs. Jeremy Katzen and Kostas Alysandratos and their teams @Penn @CReM_Boston. Check it out here: www.nature.com/articles/s41...
Reposted by Ian Driver
Domain-Invariant Feature Learning for Patient-Level Phenotype Prediction from Single-Cell Data https://www.biorxiv.org/content/10.1101/2025.09.22.677881v1
September 25, 2025 at 8:47 AM
Domain-Invariant Feature Learning for Patient-Level Phenotype Prediction from Single-Cell Data https://www.biorxiv.org/content/10.1101/2025.09.22.677881v1
Reposted by Ian Driver
Single Cell Foundation Models Evaluation (scFME) for In-Silico Perturbation https://www.biorxiv.org/content/10.1101/2025.09.22.677811v1
September 24, 2025 at 7:47 PM
Single Cell Foundation Models Evaluation (scFME) for In-Silico Perturbation https://www.biorxiv.org/content/10.1101/2025.09.22.677811v1
Reposted by Ian Driver
Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
September 22, 2025 at 10:54 AM
Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
Reposted by Ian Driver
@biorxivpreprint.bsky.social Bispecific Targeting of CHI3L1 and PD-1/PD-L1 Axis as a Novel Therapeutic Strategy for Idiopathic Pulmonary Fibrosis
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 22, 2025 at 4:23 PM
@biorxivpreprint.bsky.social Bispecific Targeting of CHI3L1 and PD-1/PD-L1 Axis as a Novel Therapeutic Strategy for Idiopathic Pulmonary Fibrosis
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ian Driver
Inflammation-inducible IL-1-targeted therapy using an rAAV vector as a long-lasting, pathophysiologic treatment for chronic inflammatory diseases @moltherapy.bsky.social @umasschan.bsky.social
www.cell.com/molecular-th...
www.cell.com/molecular-th...
September 20, 2025 at 4:45 PM
Inflammation-inducible IL-1-targeted therapy using an rAAV vector as a long-lasting, pathophysiologic treatment for chronic inflammatory diseases @moltherapy.bsky.social @umasschan.bsky.social
www.cell.com/molecular-th...
www.cell.com/molecular-th...
Reposted by Ian Driver
Metabolomic, Lipidomic, and Enterohormone Changes in the Progression from MASLD to MASH https://www.biorxiv.org/content/10.1101/2025.09.16.676598v1
September 19, 2025 at 3:30 AM
Metabolomic, Lipidomic, and Enterohormone Changes in the Progression from MASLD to MASH https://www.biorxiv.org/content/10.1101/2025.09.16.676598v1
Reposted by Ian Driver
Nutrient-Sensing Nuclear Receptor PPARα Controls Liver Proteostasis https://www.biorxiv.org/content/10.1101/2025.09.01.673563v1
September 5, 2025 at 11:02 PM
Nutrient-Sensing Nuclear Receptor PPARα Controls Liver Proteostasis https://www.biorxiv.org/content/10.1101/2025.09.01.673563v1
Reposted by Ian Driver
PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 4, 2025 at 5:09 AM
PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ian Driver
scAgeClock: a single-cell transcriptome based human aging clock model using gated multi-head attention neural networks https://www.biorxiv.org/content/10.1101/2025.08.29.673183v1
September 3, 2025 at 12:47 PM
scAgeClock: a single-cell transcriptome based human aging clock model using gated multi-head attention neural networks https://www.biorxiv.org/content/10.1101/2025.08.29.673183v1
Reposted by Ian Driver
Single-cell atlas of human liver and blood immune cells across fatty liver disease stages reveals distinct signatures linked to liver dysfunction and fibrogenesis @natimmunol.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 29, 2025 at 9:25 PM
Single-cell atlas of human liver and blood immune cells across fatty liver disease stages reveals distinct signatures linked to liver dysfunction and fibrogenesis @natimmunol.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ian Driver
Targeting acid ceramidase enhances collagen degradation by hepatic stellate cells via PKCα and MMP-1, uncovering a pathway to reverse liver fibrosis
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
August 28, 2025 at 2:12 AM
Targeting acid ceramidase enhances collagen degradation by hepatic stellate cells via PKCα and MMP-1, uncovering a pathway to reverse liver fibrosis
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Ian Driver
Reposted by Ian Driver
SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.08.04.668429v1
https://www.biorxiv.org/content/10.1101/2025.08.04.668429v1
August 6, 2025 at 7:01 AM
SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.08.04.668429v1
https://www.biorxiv.org/content/10.1101/2025.08.04.668429v1
Reposted by Ian Driver
Higher eQTL power reveals signals that boost GWAS colocalization https://www.biorxiv.org/content/10.1101/2025.08.05.668745v1
August 6, 2025 at 6:32 AM
Higher eQTL power reveals signals that boost GWAS colocalization https://www.biorxiv.org/content/10.1101/2025.08.05.668745v1
Reposted by Ian Driver
Delighted to share our latest review in Nature Reviews Neuroscience!
We examine the growing evidence that vascular dysfunction plays a key role in cognitive decline in ageing and dementia, and argue that preserving/restoring CBF should be central to future therapies.
www.nature.com/articles/s41...
We examine the growing evidence that vascular dysfunction plays a key role in cognitive decline in ageing and dementia, and argue that preserving/restoring CBF should be central to future therapies.
www.nature.com/articles/s41...
The vascular contribution to cognitive decline in ageing and dementia - Nature Reviews Neuroscience
Growing evidence suggests that reduced cerebral blood flow contributes to cognitive decline in ageing and dementia. Attwell and colleagues discuss the underlying mechanisms and functional consequences...
www.nature.com
August 5, 2025 at 10:26 AM
Delighted to share our latest review in Nature Reviews Neuroscience!
We examine the growing evidence that vascular dysfunction plays a key role in cognitive decline in ageing and dementia, and argue that preserving/restoring CBF should be central to future therapies.
www.nature.com/articles/s41...
We examine the growing evidence that vascular dysfunction plays a key role in cognitive decline in ageing and dementia, and argue that preserving/restoring CBF should be central to future therapies.
www.nature.com/articles/s41...
Reposted by Ian Driver
scMomer: A modality-aware pretraining framework for single-cell multi-omics modeling under missing modality conditions https://www.biorxiv.org/content/10.1101/2025.08.04.668374v1
August 5, 2025 at 4:48 PM
scMomer: A modality-aware pretraining framework for single-cell multi-omics modeling under missing modality conditions https://www.biorxiv.org/content/10.1101/2025.08.04.668374v1
Reposted by Ian Driver
GeneAgent is a language agent using large language models and self-verification to improve gene set function annotation.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
GeneAgent: self-verification language agent for gene-set analysis using domain databases - Nature Methods
GeneAgent is a language agent using large language models and self-verification to improve gene-set function annotation.
www.nature.com
July 29, 2025 at 4:36 PM
GeneAgent is a language agent using large language models and self-verification to improve gene set function annotation.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ian Driver
Optimizing murine sample sizes for RNA-seq studies revealed from large-scale comparative analysis - www.biorxiv.org/content/10.1...
Optimizing murine sample sizes for RNA-seq studies revealed from large-scale comparative analysis
Determining the appropriate sample size (N) for comparative biological experiments is critical for obtaining reliable results. In order to determine the N, the usual approach is to perform a power cal...
www.biorxiv.org
July 26, 2025 at 11:41 PM
Optimizing murine sample sizes for RNA-seq studies revealed from large-scale comparative analysis - www.biorxiv.org/content/10.1...
I planted milkweed and Monarch butterflies actually showed up. A small win.
July 16, 2025 at 2:10 PM
I planted milkweed and Monarch butterflies actually showed up. A small win.
Reposted by Ian Driver
GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model https://www.biorxiv.org/content/10.1101/2025.07.03.663009v1
July 9, 2025 at 7:46 PM
GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model https://www.biorxiv.org/content/10.1101/2025.07.03.663009v1