Searching journal content for articles similar to Lawlor et al. 27 (2): 208.

Displaying results 1-10 of 19

For checked items

view abstracts
download to citation manager

Select this article
Method: Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation
- Yang Zhou,
- Qiongyu Sheng,
- Jing Qi,
- Jiao Hua,
- Bo Yang,
- Lei Wan,
- and Shuilin Jin
Genome Res. May 2023 33: 750-762; Published in Advance June 12, 2023, doi:10.1101/gr.277522.122
...Yang Zhou, Qiongyu Sheng, Jing Qi, Jiao Hua, Bo Yang, Lei Wan and Shuilin Jin School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001 Corresponding author: jinsl@hit.edu.cnAbstractFor most biological and medical applications of single-cell transcriptomics...
Select this article
Method: Likelihood-based deconvolution of bulk gene expression data using single-cell references
- Dan D. Erdmann-Pham,
- Jonathan Fischer,
- Justin Hong,
- and Yun S. Song
Genome Res. October 2021 31: 1794-1806; Published in Advance July 22, 2021, doi:10.1101/gr.272344.120
...of bulk gene expression profiles is complicated by distinct cell type mixtures in each sample that obscure whether observed differences are actually caused by changes in the expression levels themselves or are simply a result of differing cell type compositions. Single-cell technology has made it possible...
Select this article
Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...-wide transcriptomes of thousands of cells in a single scRNA-seq experiment (Aldridge and Teichmann 2020). Recent years have brought on continued development of single-cell technologies. The cost of single-cell experiments continues to cheapen. Technologies that enable the measurement of new information...
OPEN ACCESS ARTICLE
Select this article
Method: A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics
- Justin Lakkis,
- David Wang,
- Yuanchao Zhang,
- Gang Hu,
- Kui Wang,
- Huize Pan,
- Lyle Ungar,
- Muredach P. Reilly,
- Xiangjie Li,
- and Mingyao Li
Genome Res. October 2021 31: 1753-1766; Published in Advance May 25, 2021, doi:10.1101/gr.271874.120
...with each fit. The numbers of clusters selected were 5, 9, 11, 14, and 18, respectively. As shown in Supplemental Figure S24A, even when the number of clusters is increased from 5 to 18, the cells were still separated mainly by their gold standard cell type labels. Closer examination of the UMAPs revealed...
OPEN ACCESS ARTICLE
Select this article
Method: Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
- Yu-Jui Ho,
- Naishitha Anaparthy,
- David Molik,
- Grinu Mathew,
- Toby Aicher,
- Ami Patel,
- James Hicks,
- and Molly Gale Hammell
Genome Res. September 2018 28: 1353-1363; Published in Advance July 30, 2018, doi:10.1101/gr.234062.117
...over millions of cells that may vary widely, single-cell RNA-seq (scRNA-seq) can be used to investigate the subtle but crucial differences in transcriptomic landscape that differentiate cellular state. Populations of cells that possess very similar gross cellular phenotypes might have remarkably...
Select this article
Method: End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
- Alan Derr,
- Chaoxing Yang,
- Rapolas Zilionis,
- Alexey Sergushichev,
- David M. Blodgett,
- Sambra Redick,
- Rita Bortell,
- Jeremy Luban,
- David M. Harlan,
- Sebastian Kadener,
- Dale L. Greiner,
- Allon Klein,
- Maxim N. Artyomov,
- and Manuel Garber
Genome Res. October 2016 26: 1397-1410; Published in Advance July 28, 2016, doi:10.1101/gr.207902.116
...(mBMDCs) stimulated with LPS, and compared these data to our previously generated full-length RNA-seq data (Garber et al. 2012). We also applied ESAT to single-cell RNA-seq from approximately 1000 rat pancreatic islet cells using a new droplet barcoding method for single-cell transcriptomics (Klein...
OPEN ACCESS ARTICLE
Select this article
Resource: Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
- Alexandra C. Nica,
- Halit Ongen,
- Jean-Claude Irminger,
- Domenico Bosco,
- Thierry Berney,
- Stylianos E. Antonarakis,
- Philippe A. Halban,
- and Emmanouil T. Dermitzakis
Genome Res. September 2013 23: 1554-1562; Published in Advance May 28, 2013, doi:10.1101/gr.150706.112
..., important biological insights into cell-type–specific expression signatures are revealed when comparing detailed RNA profiles of purified beta cells with those of whole islets or ‘‘nonbeta’’ cells. We find substantial evidence for differential expression between beta cells and islets, with more than 5000...
Select this article
Resource: Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
- Ozren Bogdanović,
- Ana Fernandez-Miñán,
- Juan J. Tena,
- Elisa de la Calle-Mustienes,
- Carmen Hidalgo,
- Ila van Kruysbergen,
- Simon J. van Heeringen,
- Gert Jan C. Veenstra,
- and José Luis Gómez-Skarmeta
Genome Res. October 2012 22: 2043-2053; Published in Advance May 16, 2012, doi:10.1101/gr.134833.111
...transcriptome age index mirrors ontogenetic divergence patterns. Nature 468: 815–818. Ernst J, Kheradpour P,Mikkelsen TS, ShoreshN,Ward LD, EpsteinCB, Zhang X, Wang L, Issner R, Coyne M, et al. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43–49. Gaulton KJ, Nammo...
Select this article
Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...clustering of samples by cell type, genotype, and age. A single linkage method was used for the hierarchical clustering of columns. (C) Principal component analysis (PCA) based on whole-transcriptome expression data highlights clear separation between different MN subtypes, with genotype and age also...
OPEN ACCESS ARTICLE
Select this article
Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Lawlor et al. 27 (2): 208.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: