Tobias Sargeant

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Žiga Avsec, Natasha S. Latysheva, Jun Cheng, Guido Novati et autres

Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Existing methods trade off between input sequence length and prediction resolution, thereby limiting their modality scope and performance. We present AlphaGenome, which …

us, gb (code pays fourni par la source)

Predictions for AlphaMissense

Jun Cheng, Guido Novati, Joshua Pan, Clare Bycroft et autres

This repository provide AlphaMissense predictions. Please see the README for more details. For questions about AlphaMissense or the prediction Database please email alphamissense@google.com.

gb (code pays fourni par la source)

Accurate proteome-wide missense variant effect prediction with AlphaMissense

Jun Cheng, Guido Novati, Joshua Pan, Clare Bycroft et autres

The vast majority of missense variants observed in the human genome are of unknown clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on human and primate variant population frequency databases to predict missense variant pathogenicity. By combining structural context and …

gb (code pays fourni par la source)

Predictions for AlphaMissense

Jun Cheng, Guido Novati, Joshua Pan, Clare Bycroft et autres

This repository provide AlphaMissense predictions. Please see the README for more details. For questions about AlphaMissense or the prediction Database please email alphamissense@google.com.

gb (code pays fourni par la source)

Source code for AlphaMissense

Jun Cheng, Guido Novati, Joshua Pan, Clare Bycroft et autres

This package provides the AlphaMissense model implementation. This implementation is provided for reproducibility of the AlphaMissense 2023 publication.

gb (code pays fourni par la source)

In vivo clonal tracking reveals evidence of haemangioblast and haematomesoblast contribution to yolk sac haematopoiesis

Christine Biben, Tom Weber, Kathryn S. Potts, Jarny Choi et autres

During embryogenesis, haematopoietic and endothelial lineages emerge closely in time and space. It is thought that the first blood and endothelium derive from a common clonal ancestor, the haemangioblast. However, investigation of candidate haemangioblasts in vitro revealed the capacity for mesenchymal differentiation, …

au (code pays fourni par la source)

3104 – CLONAL MULTI-OMICS METHODS SIS-SEQ AND SIS-SKEW REVEAL BCOR AS A NEGATIVE REGULATOR OF EMERGENCY DENDRITIC CELL DEVELOPMENT

Shalin H. Naik, Luyi Tian, Sara Tomei, Jaring Schreuder et autres

SuperFreq: Integrated mutation detection and clonal tracking in cancer

Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski

Analysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves.Monitoring the expansion and contraction of distinct clones helps to reveal the mutations that initiate the disease and those that drive progression.Existing approaches for clonal tracking …

au (code pays fourni par la source)

MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets

Sébastien Lemieux, Tobias Sargeant, David Laperrière, Houssam Ismail et autres

Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Spanning Trees Inferred Clustering …

ca, au (code pays fourni par la source)

IgLibQC: quality control pipeline for the construction of antibody libraries

Monther Alhamdoosh, Chao‐Guang Chen, Milica Ng, Georgina Sansome et autres

During the past two decades, a large number of antibody libraries have been constructed to meet the needs of drug discovery and diagnostic processes. The advent of next-generation sequencing (NGS) technology has enabled scientists to rigorously assess library size, quality, diversity and …

au (code pays fourni par la source)

Haemopedia: An Expression Atlas of Murine Hematopoietic Cells

Carolyn A. de Graaf, Jarny Choi, Tracey M. Baldwin, Jessica E. Bolden et autres

Hematopoiesis is a multistage process involving the differentiation of stem and progenitor cells into distinct mature cell lineages. Here we present Haemopedia, an atlas of murine gene-expression data containing 54 hematopoietic cell types, covering all the mature lineages in hematopoiesis. We include …

au, cn (code pays fourni par la source)

Mouse prenatal platelet-forming lineages share a core transcriptional program but divergent dependence on MPL

Kathryn S. Potts, Tobias Sargeant, Caleb A. Dawson, Emma C. Josefsson et autres

The thrombopoietic environment of the neonate is established during prenatal life; therefore, a comprehensive understanding of platelet-forming cell development during embryogenesis is critical to understanding the etiology of early-onset thrombocytopenia. The recent discovery that the first platelet-forming cells of the conceptus are …

au (code pays fourni par la source)