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Protocol for predicting single- and multiple-dose-dependent gene expression using deep generative learning

利用深度生成学习预测单剂量和多剂量依赖性基因表达的方案

期刊:STAR Protocols

影响因子:1.3

doi:10.1016/j.xpro.2025.103932

Bowman, Derek E; Panda, Vishal; Marri, Daniel; Kana, Omar; Bhattacharya, Sudin

发表日期：2025

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Single-nucleus analysis of thoracic perivascular adipose tissue reveals critical changes in cell composition, communication, and gene regulatory networks induced by a high fat hypertensive diet

对胸腔血管周围脂肪组织进行单核分析，揭示了高脂高血压饮食诱导的细胞组成、通讯和基因调控网络的关键变化。

期刊:

影响因子:

doi:10.1101/2025.02.13.636878

Terrian, Leah; Thompson, Janice M; Bowman, Derek E; Panda, Vishal; Contreras, G Andres; Rockwell, Cheryl; Sather, Lisa; Fink, Gregory D; Lauver, D Adam; Nault, Rance; Watts, Stephanie W; Bhattacharya, Sudin

Integrins play a role in stress relaxation of perivascular adipose tissue.

整合素在血管周围脂肪组织的应力松弛中发挥作用

期刊:Pharmacological Research

影响因子:10.5

doi:10.1016/j.phrs.2024.107269

Watts Stephanie W, Thompson Janice M, Bhattacharya Sudin, Panda Vishal, Terrian Leah, Contreras Andres, Nault Rance

A cell atlas of thoracic aortic perivascular adipose tissue: a focus on mechanotransducers.

胸主动脉周围血管脂肪组织的细胞图谱：以机械转导器为重点

期刊:American Journal of Physiology-Heart and Circulatory Physiology

影响因子:4.1

doi:10.1152/ajpheart.00040.2024

Thompson Janice M, Watts Stephanie W, Terrian Leah, Contreras G Andres, Rockwell Cheryl, Rendon C Javier, Wabel Emma, Lockwood Lizbeth, Bhattacharya Sudin, Nault Rance

PVAT-conditioned media from Dahl S rats on high fat diet promotes inflammatory cytokine secretion by activated T cells prior to the development of hypertension

来自高脂饮食喂养的Dahl S大鼠的PVAT条件培养基可促进活化T细胞在发生高血压之前分泌炎症细胞因子。

期刊:PLoS One

影响因子:2.6

doi:10.1371/journal.pone.0302503

Jin, Yining; Liu, Sheng; Guzmán, Kimberly E; Kumar, Ramya K; Kaiser, Luca M; Garver, Hannah; Bernard, Jamie J; Bhattacharya, Sudin; Fink, Gregory D; Watts, Stephanie W; Rockwell, Cheryl E

Unique challenges and best practices for single cell transcriptomic analysis in toxicology

毒理学中单细胞转录组分析的独特挑战和最佳实践

期刊:

影响因子:

doi:10.1016/j.cotox.2024.100475

Filipovic, David; Kana, Omar; Marri, Daniel; Bhattacharya, Sudin

Generative modeling of single-cell gene expression for dose-dependent chemical perturbations

剂量依赖性化学扰动下单细胞基因表达的生成模型

期刊:Patterns

影响因子:7.4

doi:10.1016/j.patter.2023.100817

Kana, Omar; Nault, Rance; Filipovic, David; Marri, Daniel; Zacharewski, Tim; Bhattacharya, Sudin

Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants

可解释的全基因组芳烃受体-DNA结合预测模型揭示了组织特异性结合决定因素

期刊:Toxicological Sciences

影响因子:4.1

doi:10.1093/toxsci/kfad094

Filipovic, David; Qi, Wenjie; Kana, Omar; Marri, Daniel; LeCluyse, Edward L; Andersen, Melvin E; Cuddapah, Suresh; Bhattacharya, Sudin

信号转导

发表日期：2023

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Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box DNA motifs

预测哺乳动物组织特异性CLOCK-BMAL1与E-box DNA基序的结合

期刊:Scientific Reports

影响因子:3.9

doi:10.1038/s41598-023-34115-w

Marri, Daniel; Filipovic, David; Kana, Omar; Tischkau, Shelley; Bhattacharya, Sudin

Dynamical systems theory as an organizing principle for single-cell biology

动力系统理论作为单细胞生物学的组织原则

Protocol for predicting single- and multiple-dose-dependent gene expression using deep generative learning

利用深度生成学习预测单剂量和多剂量依赖性基因表达的方案

Single-nucleus analysis of thoracic perivascular adipose tissue reveals critical changes in cell composition, communication, and gene regulatory networks induced by a high fat hypertensive diet

对胸腔血管周围脂肪组织进行单核分析，揭示了高脂高血压饮食诱导的细胞组成、通讯和基因调控网络的关键变化。

Integrins play a role in stress relaxation of perivascular adipose tissue.

整合素在血管周围脂肪组织的应力松弛中发挥作用

A cell atlas of thoracic aortic perivascular adipose tissue: a focus on mechanotransducers.

胸主动脉周围血管脂肪组织的细胞图谱：以机械转导器为重点

PVAT-conditioned media from Dahl S rats on high fat diet promotes inflammatory cytokine secretion by activated T cells prior to the development of hypertension

来自高脂饮食喂养的Dahl S大鼠的PVAT条件培养基可促进活化T细胞在发生高血压之前分泌炎症细胞因子。

Unique challenges and best practices for single cell transcriptomic analysis in toxicology

毒理学中单细胞转录组分析的独特挑战和最佳实践

Generative modeling of single-cell gene expression for dose-dependent chemical perturbations

剂量依赖性化学扰动下单细胞基因表达的生成模型

Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants

可解释的全基因组芳烃受体-DNA结合预测模型揭示了组织特异性结合决定因素

Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box DNA motifs

预测哺乳动物组织特异性CLOCK-BMAL1与E-box DNA基序的结合