Searching journal content for articles similar to Drew et al. 21 (11): 1981.

Displaying results 1-10 of 26

For checked items

view abstracts
download to citation manager

Select this article
Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...of proteins at proteomic scales. AlphaFold2 can provide reliable in silico modeled structures roughly as good as experimentally determined structures. Combining experimental structures in PDB and computationally modeled structures by AlphaFold2 should allow us to analyze protein structures on a large scale...
Select this article
Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
.... Overall, ∼90% of the affected partners are expressed in at least 80% of the corresponding carriers, giving a moderate but significant higher rate than that of unaffected partners (Methods) (Supplemental Fig. 8A). Although expression data are limited in coverage across multiple sequencing projects, we...
Select this article
Method: Proteome-wide discovery of mislocated proteins in cancer
- KiYoung Lee,
- Kyunghee Byun,
- Wonpyo Hong,
- Han-Yu Chuang,
- Chan-Gi Pack,
- Enkhjargal Bayarsaikhan,
- Sun Ha Paek,
- Hyosil Kim,
- Hye Young Shin,
- Trey Ideker,
- and Bonghee Lee
Genome Res. August 2013 23: 1283-1294; Published in Advance May 14, 2013, doi:10.1101/gr.155499.113
...for conditions of interest are projected onto protein–protein interaction networks. As proof-of-principle, we use this approach to develop a proteomewide map of protein locations during the progression of glioma. From the conditional locations, we identify over 150 proteins that likely mislocate in glioma...
Select this article
LETTER: Bacillus subtilis During Feast and Famine: Visualization of the Overall Regulation of Protein Synthesis During Glucose Starvation by Proteome Analysis
- Jörg Bernhardt,
- Jimena Weibezahn,
- Christian Scharf,
- and Michael Hecker
Genome Res. February 1, 2003 13: 224-237; doi:10.1101/gr.905003
...of the growth curve facilitates visualization of the developmental processes at the proteomics scale. During glucose starvation a substantial reprogramming of the protein synthesis pattern was found, with 150 proteins synthesized de novo and cessation of the synthesis of almost 400 proteins. Proteins induced...
Select this article
Methods: Gene prediction and verification in a compact genome with numerous small introns
- Aaron E. Tenney,
- Randall H. Brown,
- Charles Vaske,
- Jennifer K. Lodge,
- Tamara L. Doering,
- and Michael R. Brent
Genome Res. November 2004 14: 2330-2335; Published in Advance October 12, 2004, doi:10.1101/gr.2816704
...a prediction-driven PCR approach with a modest EST sequencing effort, it would be possible to produce annotation based on native cDNA sequence for most of the genes in Cryptococcus neoformans or any other single-celled eukaryote. The RT–PCR approach is related to a number of so-called “ORFEOME” projects...
Select this article
Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...properties, including sequential similarity (CpG density) and sequential distance, to genomic structure by projecting the structure-related eigenvectors on these sequence properties. Reflected by the projection of E1 (Fig. 3F), the dominant factor in structure determination changes from sequential similarity...
Select this article
Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...of variations across a population, whereas we highlight conservation across species in the context of AS. To the best of our knowledge, we are the first to do it. Effectively, we consider a pan-transcriptome across multiple species. As a consequence, we do not need to rely on a central species and project...
Select this article
Method: Identifying gene function and module connections by the integration of multispecies expression compendia
- Hao Li,
- Daria Rukina,
- Fabrice P.A. David,
- Terytty Yang Li,
- Chang-Myung Oh,
- Arwen W. Gao,
- Elena Katsyuba,
- Maroun Bou Sleiman,
- Andrea Komljenovic,
- Qingyao Huang,
- Robert W. Williams,
- Marc Robinson-Rechavi,
- Kristina Schoonjans,
- Stephan Morgenthaler,
- and Johan Auwerx
Genome Res. December 2019 29: 2034-2045; Published in Advance November 21, 2019, doi:10.1101/gr.251983.119
...research projects—an effort that is still far from being complete (Edwards et al. 2011; Pandey et al. 2014; Dolgin 2017; Stoeger et al. 2018). Traditionally, gene function has been elucidated through experimental approaches, including the evaluation of the phenotypic consequences of gain- or loss...
OPEN ACCESS ARTICLE
Select this article
Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...tissues, organs, and developmental processes by expanding the complexity of the transcriptome and thus of the proteome (Mudge et al. 2011; Ragle et al. 2015; Angiolini et al. 2019). Aberrant splicing has been frequently linked to various diseases, including cancer (Zhang et al. 2019), aging (Adusumalli et...
Select this article
Method: Models of human core transcriptional regulatory circuitries
- Violaine Saint-André,
- Alexander J. Federation,
- Charles Y. Lin,
- Brian J. Abraham,
- Jessica Reddy,
- Tong Ihn Lee,
- James E. Bradner,
- and Richard A. Young
Genome Res. March 2016 26: 385-396; Published in Advance February 3, 2016, doi:10.1101/gr.197590.115
..., leading someday to circuitry-directed therapeutic interventions. Methods ChIP-seq data H3K27ac ChIP-seq data were either downloaded fromGEO (accession numbers in Supplemental Table S1) or generously shared by the NIH Roadmap Epi project (Bernstein et al. 2010). ChIP-seq data for H3K27ac (Kwiatkowski et al...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Drew et al. 21 (11): 1981.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: