Results 21 to 30 of about 2,352,277 (290)

Counterfactual inference for single-cell gene expression analysis [PDF]

, 2021
AbstractFinding a causal gene is a fundamental problem in genomic medicine. We present a causal inference framework that prioritizes disease genes by adjusting confounders without prior knowledge of control variables. We demonstrate that our method substantially improves statistical power in simulations and real-world data analysis of 70k brain cells ...
Yongjin Park, Manolis Kellis
openaire   +1 more source

SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization [PDF]

PeerJ, 2021
Single-cell RNA-sequencing is a rapidly evolving technology that enables us to understand biological processes at unprecedented resolution. Single-cell expression analysis requires a complex data processing pipeline, and the pipeline is divided into two ...
Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda   +3 more
doaj   +2 more sources

Integrated microfluidic bioprocessor for single-cell gene expression analysis [PDF]

Proceedings of the National Academy of Sciences, 2008
An integrated microdevice is developed for the analysis of gene expression in single cells. The system captures a single cell, transcribes and amplifies the mRNA, and quantitatively analyzes the products of interest. The key components of the microdevice include integrated nanoliter metering pumps, a 200-nL RT-PCR reactor with a single-cell capture pad,
Nicholas M, Toriello, Erik S, Douglas, Numrin, Thaitrong, Sonny C, Hsiao, Matthew B, Francis, Carolyn R, Bertozzi, Richard A, Mathies   +6 more
openaire   +2 more sources

A convenient, optimized pipeline for isolation, fluorescence microscopy and molecular analysis of live single cells [PDF]

, 2014
BACKGROUND: Heterogeneity within cell populations is relevant to the onset and progression of disease, as well as development and maintenance of homeostasis.
Colleen P Ziegler, Deirdre R Meldrum, Honor L Glenn, Jordan R Yaron, Thai H Tran   +4 more
core   +8 more sources

SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data.

PLoS Computational Biology, 2021
The single-cell RNA sequencing (scRNA-seq) technologies obtain gene expression at single-cell resolution and provide a tool for exploring cell heterogeneity and cell types.
Jing Qi, Yang Zhou, Zicen Zhao, Shuilin Jin   +3 more
doaj   +1 more source

SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data

BMC Bioinformatics, 2020
Background With the rapid development of single-cell genomics, technologies for parallel sequencing of the transcriptome and genome in each single cell is being explored in several labs and is becoming available. This brings us the opportunity to uncover
Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang
doaj   +1 more source

A microfluidic processor for gene expression profiling of single human embryonic stem cells [PDF]

, 2008
The gene expression of human embryonic stem cells (hESC) is a critical aspect for understanding the normal and pathological development of human cells and tissues.
Chen, Yan, Marcus, Joshua S., Quake, Stephen R., Scherer, Axel, Taylor, Clive R., Weiner, Leslie P., Zhong, Jiang F.   +6 more
core   +1 more source

Imaging cell lineage with a synthetic digital recording system [PDF]

, 2020
Cell lineage plays a pivotal role in cell fate determination. Chow et al. demonstrate the use of an integrase-based synthetic barcode system called intMEMOIR, which uses the serine integrase Bxb1 to perform irreversible nucleotide edits.
Budde, Mark W., Cabrera, Maria, Cai, Long, Cho, Soomin, Chow, Ke-Huan K., Elowitz, Michael B., Frieda, Kirsten L., Granados, Alejandro A., Huang, Ting-hao, Koulena, Noushin, Lois, Carlos, Yoon, Shinae   +11 more
core   +1 more source

Gene Expression Analysis by Multiplex Single-Cell RT-PCR [PDF]

, 2019
Brain circuit assemblies comprise different cellular subpopulations that exhibit morphological, electrophysiological, and molecular diversity. Here we describe a protocol which, combined with whole-cell patch-clamp recording and morphological reconstruction, allows the transcriptomic analysis of the recorded cell.
Tricoire, Ludovic, Cauli, Bruno, Lambolez, Bertrand   +2 more
openaire   +3 more sources

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation [PDF]

Annual Review of Genetics, 2016
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional ...
Maria, Vera, Jeetayu, Biswas, Adrien, Senecal, Robert H, Singer, Hye Yoon, Park   +4 more
openaire   +2 more sources