Searching journal content for articles similar to Khrameeva et al. 30 (5): 776.

Displaying results 1-10 of 5525

For checked items

view abstracts
download to citation manager

Select this article
Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
- Quanyou Cai,
- Lihui Lin,
- Xin Liu,
- and Jiekai Chen
Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
...:Simulation-based evaluation of spatial reconstruction accuracyTo benchmark Polyomino against deconvolution-based spatial mapping methods, we constructed a simulation framework based on the STARMAP data set, which provides single-cell-resolution spatial transcriptomic data from the mouse brain. Spatial locations and gene...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...isoform reads and Illumina short reads available for three HGSOC patient samples sequenced at single-cell resolution. Here, tumor samples were derived from omental metastases, and for patient-1 and patient-3, matched normal omentum samples were available and similarly processed and analyzed for comparison...
OPEN ACCESS ARTICLE
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
..., which is characterized by several waves of gene upregulation and downregulation. We identified and in vivo validated cell-type-specific and position-specific regeneration-responsive enhancers and constructed regulatory networks by cell type and stage. Our single-cell resolution transcriptomic...
OPEN ACCESS ARTICLE
Select this article
Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
..., bacteria and yeast (Oelen et al. 2022), and influenza A (Randolph et al. 2021). Although different immune stimuli have been studied at single-cell resolution, the response to glucocorticoids has not been previously examined.Here, we used scRNA-seq to study the dynamics of the transcriptional response...
OPEN ACCESS ARTICLE
Select this article
Resource: The Drosophila brain on cocaine at single-cell resolution
- Brandon M. Baker,
- Sneha S. Mokashi,
- Vijay Shankar,
- Jeffrey S. Hatfield,
- Rachel C. Hannah,
- Trudy F.C. Mackay,
- and Robert R.H. Anholt
Genome Res. October 2021 31: 1927-1937; Published in Advance May 25, 2021, doi:10.1101/gr.268037.120
...Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE152495. R code that was used to perform Seurat-based analyses with TopKLists is included in Supplemental Code and is available at GitHub (https://github.com/vshanka23/The-Drosophila-Brain-on-Cocaine-at-Single-Cell-Resolution...
OPEN ACCESS ARTICLE
Select this article
Resource: The accessible chromatin landscape of the murine hippocampus at single-cell resolution
- John R. Sinnamon,
- Kristof A. Torkenczy,
- Michael W. Linhoff,
- Sarah A. Vitak,
- Ryan M. Mulqueen,
- Hannah A. Pliner,
- Cole Trapnell,
- Frank J. Steemers,
- Gail Mandel,
- and Andrew C. Adey
Genome Res. May 2019 29: 857-869; Published in Advance April 1, 2019, doi:10.1101/gr.243725.118
.... Corresponding authors: adey@ohsu.edu, sinnamon@ohsu.eduAbstractHere we present a comprehensive map of the accessible chromatin landscape of the mouse hippocampus at single-cell resolution. Substantial advances of this work include the optimization of a single-cell combinatorial indexing assay for transposase...
Select this article
Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
..., catalyzed by the adenosine deaminase acting on RNA (ADAR) enzymes, is a posttranscriptional process that modifies RNA sequences and diversifies the transcriptome. ADARs bind to double-stranded RNA (dsRNA) and their specificity and efficiency are affected by the structural properties of these substructures...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
- Ryan O'Hara,
- Enzo Tedone,
- Andrew Ludlow,
- Ejun Huang,
- Beatrice Arosio,
- Daniela Mari,
- and Jerry W. Shay
Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
OPEN ACCESS ARTICLE
Select this article
Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...by their significant overlap (∼48%) with expression quantitative trait loci (eQTL) (Wang et al. 2018; Walker et al. 2019) and transcriptome-wide association study findings from fetal human brain (Gandal et al. 2018; Walker et al. 2019). Of the resulting panel of ∼72,000 targets, 65,000 were new as compared to Panel 1...
Select this article
Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Khrameeva et al. 30 (5): 776.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: