Results 51 to 60 of about 426,916 (271)

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data. [PDF]

PLoS ONE, 2017
An increasing number of single cell transcriptome and epigenome technologies, including single cell ATAC-seq (scATAC-seq), have been recently developed as powerful tools to analyze the features of many individual cells simultaneously.
Chengchen Zhao, Sheng'en Hu, Xiao Huo, Yong Zhang   +3 more
doaj   +1 more source

Stochastic variation in the FOXM1 transcription program mediates replication stress tolerance

Molecular Oncology, EarlyView.
Cellular heterogeneity is a major cause of drug resistance in cancer. Segeren et al. used single‐cell transcriptomics to investigate gene expression events that correlate with sensitivity to the DNA‐damaging drugs gemcitabine and prexasertib. They show that dampened expression of transcription factor FOXM1 and its target genes protected cells against ...
Hendrika A. Segeren, Kathryn A. Wierenga, Frank M. Riemers, Elsbeth A. van Liere, Bart Westendorp   +4 more
wiley   +1 more source

High-Frequency Promoter Firing Links THO Complex Function to Heavy Chromatin Formation

Cell Reports, 2013
The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic.
John Mouaikel, Sébastien Z. Causse, Mathieu Rougemaille, Yves Daubenton-Carafa, Corinne Blugeon, Sophie Lemoine, Frédéric Devaux, Xavier Darzacq, Domenico Libri   +8 more
doaj   +1 more source

Calculating Kolmogorov Complexity from the Transcriptome Data [PDF]

arXiv, 2017
Information entropy is used to summarize transcriptome data, but ignoring zero count data contained them. Ignoring zero count data causes loss of information and sometimes it was difficult to distinguish between multiple transcriptomes. Here, we estimate Kolmogorov complexity of transcriptome treating zero count data and distinguish similar ...
arxiv  

Bayesian Flexible Modelling of Spatially Resolved Transcriptomic Data [PDF]

arXiv, 2023
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the measurement of gene expressions at the single cell level along with the spatial locations of these cells in the tissue.
arxiv  

Targeting PRAME directly or via EZH2 inhibition overcomes retinoid resistance and represents a novel therapy for keratinocyte carcinoma

Molecular Oncology, EarlyView.
The study evaluated the function and therapeutic implications of PRAME in basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). The findings demonstrate that PRAME impairs keratinocyte differentiation pathways. Furthermore, PRAME impairs anticancer response to retinoid compounds in BCC and SCC cells.
Brandon Ramchatesingh, Amelia Martinez Villarreal, Philippe Lefrançois, Jennifer Gantchev, Sriraam Sivachandran, Samy Abou Setah, Ivan V. Litvinov   +6 more
wiley   +1 more source

Gene Expression Profile Related to the Progression of Preneoplastic Nodules toward Hepatocellular Carcinoma in Rats

Neoplasia: An International Journal for Oncology Research, 2006
In this study, we investigated the time course gene expression profile of preneoplastic nodules and hepatocellular carcinomas (HCC) to define the genes implicated in cancer progression in a resistant hepatocyte model. Tissues that included early nodules (
Julio Isael Pérez-Carréon, Cristina López-García, Samia Fattel-Fazenda, Evelia Arce-Popoca, Leticia Alemán-Lazarini, Sergio Hernández-García, Véronique Le Berre, Sergueï Sokol, Jean Marie Francois, Saúl Villa-Treviño   +9 more
doaj   +1 more source

Assessment of the impact of using a reference transcriptome in mapping short RNA-Seq reads. [PDF]

PLoS ONE, 2014
RNA-Seq has become increasingly popular in transcriptome profiling. The major challenge in RNA-Seq data analysis is the accurate mapping of junction reads to their genomic origins.
Shanrong Zhao
doaj   +1 more source

Classification of acute myeloid leukemia based on multi‐omics and prognosis prediction value

Molecular Oncology, EarlyView.
The Unsupervised AML Multi‐Omics Classification System (UAMOCS) integrates genomic, methylation, and transcriptomic data to categorize AML patients into three subtypes (UAMOCS1‐3). This classification reveals clinical relevance, highlighting immune and chromosomal characteristics, prognosis, and therapeutic vulnerabilities.
Yang Song, Zhe Wang, Guangji Zhang, Jiangxue Hou, Kaiqi Liu, Shuning Wei, Yan Li, Chunlin Zhou, Dong Lin, Min Wang, Hui Wei, Jianxiang Wang, Tao Cheng, Yingchang Mi   +13 more
wiley   +1 more source

TOMM20 as a driver of cancer aggressiveness via oxidative phosphorylation, maintenance of a reduced state, and resistance to apoptosis

Molecular Oncology, EarlyView.
TOMM20 increases cancer aggressiveness by maintaining a reduced state with increased NADH and NADPH levels, oxidative phosphorylation (OXPHOS), and apoptosis resistance while reducing reactive oxygen species (ROS) levels. Conversely, CRISPR‐Cas9 knockdown of TOMM20 alters these cancer‐aggressive traits.
Ranakul Islam, Megan E. Roche, Zhao Lin, Diana Whitaker‐Menezes, Victor Diaz‐Barros, Eurico Serrano, Maria Paula Martinez Cantarin, Nancy J. Philp, Atrayee Basu Mallick, Ubaldo Martinez‐Outschoorn   +9 more
wiley   +1 more source