Searching journal content for articles similar to Navin et al. 31 (10): ix.

Displaying results 1-10 of 67

For checked items

view abstracts
download to citation manager

Select this article
Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...following the chromium single-cell multiome ATAC and gene expression reagent kits V1 user guide (10x Genomics). Nuclei were counted (Cellometer K2 counter); transposition was performed in 10 µL for 60 min at 37°C targeting up to 10,000 nuclei, before loading of the Chromium chip J (PN-2000264) for GEM...
Select this article
Perspective: Tagmentation-based single-cell genomics
- Andrew C. Adey
Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
...is that, in laying out the diversity of molecular techniques at each stage of these assay platforms, new ideas may arise for others to pursue that will further advance the field of single-cell genomics.A rich history of scientific achievements precedes the use of Tn5 transposase for sequencing...
Select this article
Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...(Kang et al. 2016; Lee et al. 2020; Thompson et al. 2020; Wang et al. 2020a), which may obscure the nuanced contributions of cell-type-specific regulatory elements and molecular networks activated during regeneration. The recent advancement of single-cell genomic technology has empowered the dissection...
OPEN ACCESS ARTICLE
Select this article
Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...; Rodriguez-Fraticelli et al. 2018). Additionally, in the “TracerSeq” study (Wagner et al. 2018), it was employed in the reconstruction of single-cell lineage histories in zebrafish, leveraging gene expression landscapes. Recently, episomes were used for cell transfection and genomic integration...
OPEN ACCESS ARTICLE
Select this article
Method: Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries
- Matthew Wiens,
- Hossein Farahani,
- R. Wilder Scott,
- T. Michael Underhill,
- and Ali Bashashati
Genome Res. August 2024 34: 1196-1210; Published in Advance August 15, 2024, doi:10.1101/gr.277066.122
...studies apply these two approaches to the Chromium (10x Genomics) scRNA-seq and scATAC-seq methodologies. However, Chromium-based libraries may offer additional challenges to variant calling compared with existing single-cell methodologies, raising questions regarding the validity of variants obtained...
Select this article
Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...Katharine M. Jenike1, Lucía Campos-Domínguez2, Marilou Boddé3, José Cerca4,6, Christina N. Hodson5, Michael C. Schatz1 and Kamil S. Jaron3 1Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA; 2Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus...
OPEN ACCESS ARTICLE
Select this article
Method: A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data
- Norah Alghamdi,
- Wennan Chang,
- Pengtao Dang,
- Xiaoyu Lu,
- Changlin Wan,
- Silpa Gampala,
- Zhi Huang,
- Jiashi Wang,
- Qin Ma,
- Yong Zang,
- Melissa Fishel,
- Sha Cao,
- and Chi Zhang
Genome Res. October 2021 31: 1867-1884; Published in Advance July 22, 2021, doi:10.1101/gr.271205.120
...heterogeneity and metabolic interplay between cells are known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single-cell metabolomics technology, we are yet to establish systematic understanding of the intra-tissue metabolic heterogeneity...
OPEN ACCESS ARTICLE
Select this article
Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
- Salem Malikic,
- Farid Rashidi Mehrabadi,
- Simone Ciccolella,
- Md. Khaledur Rahman,
- Camir Ricketts,
- Ehsan Haghshenas,
- Daniel Seidman,
- Faraz Hach,
- Iman Hajirasouliha,
- and S. Cenk Sahinalp
Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
...also indicate that the addition of VAF constraints, derived even from a single bulk sample, can improve tree reconstruction accuracy. Note that the RF distance is not a good measure for comparing tumor phylogenies derived from single-cell genomic sequencing, which suffer from high sequencing noise...
OPEN ACCESS ARTICLE
Select this article
Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...et al. 2013a). Thesemethodologies allow for epitope-based detection of proteins and interacting partners for which high quality or specific antibodies are not available, as well as tracking of cellular proteins in real time on a single-cell basis. In addition, conditional alleles are useful...
OPEN ACCESS ARTICLE
Select this article
Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...mechanisms 25 linking aging and PD pathology remain unclear. Leveraging advancements in single-cell 26 genomics, this study utilizes single-nucleus multiome sequencing to capture transcriptomic and 27 epigenetic profiles from 40,125 cells across the lifespan of the mouse substantia nigra. Our 28 analysis...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Navin et al. 31 (10): ix.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: