Search

Your search keyword '"Smith-Erb M"' showing total 2 results
Start Over Author "Smith-Erb M" Publication Year Range Last 3 years
2 results on '"Smith-Erb M"'

1. Tissue and cellular spatiotemporal dynamics in colon aging.

Author

Daly AC, Cambuli F, Äijö T, Lötstedt B, Marjanovic N, Kuksenko O, Smith-Erb M, Fernandez S, Domovic D, Van Wittenberghe N, Drokhlyansky E, Griffin GK, Phatnani H, Bonneau R, Regev A, and Vickovic S

Abstract

Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology., Competing Interests: Competing interests A.R. is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and until August 31, 2020 was a SAB member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov and ThermoFisher Scientific. From August 1, 2020, A.R. is an employee of Genentech, and equity holder in Roche. S.V is an author on patents applied for by Spatial Transcriptomics AB (10X Genomics Inc). S.V. and A.R. are co-inventors on PCT/US2020/015481 relating to this work. The remaining authors declare no competing interests.

Published
2024
Full Text
View/download PDF

2. A weighted distance-based approach for deriving consensus tumor evolutionary trees.

Author

Guang Z, Smith-Erb M, and Oesper L

Subjects
Humans, Consensus, Biological Evolution, Programming, Linear, Algorithms, Triple Negative Breast Neoplasms
Abstract

Motivation: The acquisition of somatic mutations by a tumor can be modeled by a type of evolutionary tree. However, it is impossible to observe this tree directly. Instead, numerous algorithms have been developed to infer such a tree from different types of sequencing data. But such methods can produce conflicting trees for the same patient, making it desirable to have approaches that can combine several such tumor trees into a consensus or summary tree. We introduce The Weighted m-Tumor Tree Consensus Problem (W-m-TTCP) to find a consensus tree among multiple plausible tumor evolutionary histories, each assigned a confidence weight, given a specific distance measure between tumor trees. We present an algorithm called TuELiP that is based on integer linear programming which solves the W-m-TTCP, and unlike other existing consensus methods, allows the input trees to be weighted differently., Results: On simulated data we show that TuELiP outperforms two existing methods at correctly identifying the true underlying tree used to create the simulations. We also show that the incorporation of weights can lead to more accurate tree inference. On a Triple-Negative Breast Cancer dataset, we show that including confidence weights can have important impacts on the consensus tree identified., Availability: An implementation of TuELiP and simulated datasets are available at https://bitbucket.org/oesperlab/consensus-ilp/src/main/., (© The Author(s) 2023. Published by Oxford University Press.)

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results