Results 101 to 110 of about 64,018 (290)

Designing smart spatial omics experiments with S2-omics v1

A protocol describing the application of S2-omics on a colorectal cancer tissue section, designing 10x VisiumHD experiment. S2-omics is an end-to-end workflow that automatically selects regions of interest for spatial omics experiments using histology images.
Musu Yuan, Kaitian Jin, Hanying Yan, Amelia Schroeder, Chunyu Luo, Sicong Yao, Bernhard Domoulin, Jonathan Levinsohn, Tianhao Luo, Jean R. Clemenceau, Inyeop Jang, Minji Kim, Yunhe Liu, Minghua Deng, Emma E. Furth, Parker Wilson, Anupma Nayak, Idania Lubo, Luisa Maren Solis Soto, Linghua Wang, Jeong Hwan Park, Katalin Susztak, Tae Hyun Hwang, Mingyao Li   +23 more
openaire   +1 more source

Capture and Culture of Circulating Tumor Cells Using a Biodegradable 3D Scaffold for Patient‐Derived Xenograft Construction

Advanced Science, EarlyView.
A self‐supporting, biocompatible, and biodegradable 3D cellulose scaffold has been developed for efficient isolation and in situ expansion of circulating tumor cells (CTCs) from patient blood. Subsequently, the 3D cellulose scaffold with cultured CTCs is directly implanted into immunodeficient mice for constructing patient CTC‐derived xenograft (CDX ...
Yi‐Ke Wang, Ming Wang, Min Liu, Yi‐Jing Chen, Li‐Li Xu, Jin‐Ping Zhou, Fu‐Bing Wang, Shi‐Bo Cheng, Min Xie, Wei‐Hua Huang   +9 more
wiley   +1 more source

Pathway Tools version 23.0: Integrated Software for Pathway/Genome Informatics and Systems Biology

, 2019
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics operations.
Billington, Richard, Caspi, Ron, Karp, Peter D., Keseler, Ingrid M., Kothari, Anamika, Krummenacker, Markus, Midford, Peter E., Ong, Wai Kit, Paley, Suzanne M., Subhraveti, Pallavi   +9 more
core  

Designing smart spatial omics experiments with S2-omics v2

A protocol describing the application of S2-omics on a colorectal cancer tissue section, designing 10x VisiumHD experiment. S2-omics is an end-to-end workflow that automatically selects regions of interest for spatial omics experiments using histology images.
Musu Yuan, Kaitian Jin, Hanying Yan, Amelia Schroeder, Chunyu Luo, Sicong Yao, Bernhard Domoulin, Jonathan Levinsohn, Tianhao Luo, Jean R. Clemenceau, Inyeop Jang, Minji Kim, Yunhe Liu, Minghua Deng, Emma E. Furth, Parker Wilson, Anupma Nayak, Idania Lubo, Luisa Maren Solis Soto, Linghua Wang, Jeong Hwan Park, Katalin Susztak, Tae Hyun Hwang, Mingyao Li   +23 more
openaire   +1 more source

Integrated Single‐Cell and Spatial Transcriptomics Reveal Cell‐Type‐Specific Immune Regulatory Networks in Maize Responding to Southern Corn Rust

Advanced Science, EarlyView.
By integrating single‐nuclei and spatial transcriptomics, this study presents a stereoscopic landscape of maize leaf to Puccinia polysora infection. Epidermal and mesophyll cells initiate primary defenses via RLPs/RLKs and jasmonic acid signaling. Cell‐cell communication analyses further reveal the underlying the dynamics of the underlying immune ...
Qiongqiong Wang, Xinyan Sun, Yingchao Sun, Zeqiang Cheng, Zixiang Cheng, Shengbo Han, Ying Feng, Wenbo Yang, Huimin Li, Meichen Zhu, Xiaoling Wu, Jinghua Zhang, Jihua Tang, Honglian Li, Yanyong Cao, Canxing Duan, Yan Shi   +16 more
wiley   +1 more source

Metagenomics for Bacteriology [PDF]

, 2015
The study of bacteria, or bacteriology, has gone through transformative waves since its inception in the 1600s. It all started by the visualization of bacteria using light microscopy by Antonie van Leeuwenhoek, when he first described “animalcules ...
del Castillo, Erika, Izard, Jacques
core   +1 more source

Super‐Enhancer‐Driven SOX4/SMAD3 Mediate Membrane Remodeling by Regulating Phospholipid Metabolism to Accelerate Leukemia Progression

Advanced Science, EarlyView.
Chronic myeloid leukemia blast phase (CML‐BP) poses a severe therapeutic challenge. This study reveals that the super‐enhancer‐driven transcription factors SOX4 and SMAD3 form a cooperative axis critical for disease progression. They co‐activate the oncogenic kinase AXL and promote phospholipid remodeling via LPCAT1 to facilitate its signaling ...
Enzhe Lou, Peilong Lai, Guanjie Peng, Bo Lu, Lizhen Jiang, Xinyue Li, Jinghong Chen, Ladi Mo, Qiong Mao, Haichuan Zhang, Jinxin Fang, Yi Meng, Aochu Liu, Yingyin Gao, Andong Huang, Wenhui Lin, Shiwen Hu, Zerong Guan, Xiaolan Ye, Zhenguo Liu, Liling Jiang, Yueyuan Zheng, Xianping Shi   +22 more
wiley   +1 more source

Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases

Genome Medicine
Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same ...
Paul Kiessling, Christoph Kuppe
doaj   +1 more source

Complete spatially resolved gene expression is not necessary for identifying spatial domains

Cell Genomics
Summary: Spatially resolved transcriptomics (SRT) technologies have revolutionized the study of tissue organization. We introduce a graph convolutional network with an attention and positive emphasis mechanism, termed BINARY, relying exclusively on ...
Senlin Lin, Yan Cui, Fangyuan Zhao, Zhidong Yang, Jiangning Song, Jianhua Yao, Yu Zhao, Bin-Zhi Qian, Yi Zhao, Zhiyuan Yuan   +9 more
doaj   +1 more source

Convergence in Agriculture: Evidence from the European Regions [PDF]

Although there have been numerous studies on regional convergence, agriculture has received far less attention. In this study, the intention is to augment the existing literature by testing for convergence in agricultural productivity among the EU-26 ...
Alexiadis, Stilianos
core   +1 more source