Searching journal content for articles similar to Di Donato et al. 26 (5): 681.

Displaying results 1-10 of 83

For checked items

view abstracts
download to citation manager

Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
OPEN ACCESS ARTICLE
Select this article
Method: Modeling and predicting cancer clonal evolution with reinforcement learning
- Stefan Ivanovic and
- Mohammed El-Kebir
Genome Res. July 2023 33: 1078-1088; Published in Advance June 21, 2023, doi:10.1101/gr.277672.123
...to the 77 patients with reported clonal prevalences. Again, for training efficiency reasons for our particular RL implementation (Supplemental Material A.1.4), we removed patients with more than 10 mutated genes. We arrived at n = 75 patients with m = 22 total mutated genes. One reason we chose to analyze...
Select this article
Method: Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9
- Daniel Agudelo,
- Sophie Carter,
- Minja Velimirovic,
- Alexis Duringer,
- Jean-François Rivest,
- Sébastien Levesque,
- Jeremy Loehr,
- Mathilde Mouchiroud,
- Denis Cyr,
- Paula J. Waters,
- Mathieu Laplante,
- Sylvain Moineau,
- Adeline Goulet,
- and Yannick Doyon
Genome Res. January 2020 30: 107-117; Published in Advance January 3, 2020, doi:10.1101/gr.255414.119
...Versatile and robust editing with Streptococcus thermophilus CRISPR1-Cas9 Daniel Agudelo1, Sophie Carter1, Minja Velimirovic1, Alexis Duringer1, Jean-François Rivest1, Sébastien Levesque1, Jeremy Loehr1, Mathilde Mouchiroud2, Denis Cyr3, Paula J. Waters3, Mathieu Laplante2,4, Sylvain Moineau5...
Select this article
Research: A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
...) The number of genes expressed ≥2 RPM varies only slightly across tissues. (E) Correlation analysis identifies the Tip as the most distinctive cell type (red), followed by the vasculature (blue). Overall expression in the two clonal layers is highly correlated (brown). Expression profiles of leaf primordia...
OPEN ACCESS ARTICLE
Select this article
Method: Single-cell mutational profiling and clonal phylogeny in cancer
- Nicola E. Potter,
- Luca Ermini,
- Elli Papaemmanuil,
- Giovanni Cazzaniga,
- Gowri Vijayaraghavan,
- Ian Titley,
- Anthony Ford,
- Peter Campbell,
- Lyndal Kearney,
- and Mel Greaves
Genome Res. December 2013 23: 2115-2125; Published in Advance September 20, 2013, doi:10.1101/gr.159913.113
...Sanger Sequencing. This case was expected to have a simple but informative clonal architecture involving a P2RY8-CRLF2 fusion gene, loss of CDKN2A, and an IL7R mutation involving the deletion of 8 base pairs and the insertion of 10 nonconsensus base pairs in exon 6. The subclonal genetic architecture...
Select this article
Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...techniques. Here, we present devider, an algorithm for haplotyping small sequences, such as viruses or genes, from long-read sequencing. devider uses a positional de Bruijn graph with sequence-to-graph alignment on an alphabet of informative alleles to provide a fast assembly-inspired approach compatible...
Select this article
Research: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- Juan L. Mateo,
- Debbie L.C. van den Berg,
- Maximilian Haeussler,
- Daniela Drechsel,
- Zachary B. Gaber,
- Diogo S. Castro,
- Paul Robson,
- Q. Richard Lu,
- Gregory E. Crawford,
- Paul Flicek,
- Laurence Ettwiller,
- Joachim Wittbrodt,
- François Guillemot,
- and Ben Martynoga
Genome Res. January 2015 25: 41-56; Published in Advance October 7, 2014, doi:10.1101/gr.173435.114
...@gmail.com, juan.mateo@cos.uni-heidelberg.deAbstractThe gene regulatory network (GRN) that supports neural stem cell (NS cell) self-renewal has so far been poorly characterized. Knowledge of the central transcription factors (TFs), the noncoding gene regulatory regions that they bind to, and the genes whose...
Select this article
Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
OPEN ACCESS ARTICLE
Select this article
Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
.... While single-cell DNA sequencing, such as Mission Bio Tapestri, provides insight into clonality upon drug resistance (Thompson et al. 2022), it lacks transcriptome profiling per cell. In contrast, scRaCH-seq offers short-read whole transcriptomic data and mutation status if the mRNA of the targeted gene...
OPEN ACCESS ARTICLE
Select this article
Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
..., STMSC captures intra- and interstage heterogeneity in cancer development, offering novel insights into the complexity of pathological tissue structures.Spatial transcriptomics (ST) technologies have revolutionized biotechnology by enabling precise localization of gene expression within tissues, offering...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Di Donato et al. 26 (5): 681.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: