Searching journal content for articles similar to Goren et al. 18 (2): 214.

Displaying results 1-10 of 119

For checked items

view abstracts
download to citation manager

Select this article
Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi, Xinjiang 830054, China ↵6 These authors contributed equally to this work. Corresponding authors: cmx2009920734@gmail.com, fuliangcaonjfu@163.comAbstractAlternative splicing (AS) regulates gene expression and increases...
Select this article
Research: Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites in C. elegans
- James Matthew Ragle,
- Sol Katzman,
- Taylor F. Akers,
- Sergio Barberan-Soler,
- and Alan M. Zahler
Genome Res. July 2015 25: 982-994; Published in Advance April 28, 2015, doi:10.1101/gr.186783.114
..., those separated by ≤18 nucleotides, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis -elements that define the adjacent sites. Identification of the intron's 3′ end depends upon sequence elements that define the branchpoint, polypyrimidine tract...
Select this article
Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...—such as the IG heavy chain, light chains, and T cell receptor (TR) loci—encode the genes responsible for antibodies/B cell receptors as well as TRs. However, these contain many gene copies, are highly repetitive, and are host to a variety of structural variants (Watson and Breden 2012; Watson et al. 2013, 2017...
OPEN ACCESS ARTICLE
Select this article
Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...of heterochromatin in polytenic tissues systematically lowers sequencing coverage of these regions in adult flies. This phenomenon differs from the “missing exons” we are investigating here and does not cause assembly problems.A detailed investigation of the missing exonsOur results show that certain regions...
Select this article
LETTER: Evolution of alternative splicing after gene duplication
- Zhixi Su,
- Jianmin Wang,
- Jun Yu,
- Xiaoqiu Huang,
- and Xun Gu
Genome Res. February 2006 16: 182-189; Published in Advance December 19, 2005, doi:10.1101/gr.4197006
...against premature protein truncation is reduced by alternative splicing and diploidy. Trends Genet. 20 : 472 -475. ↵ Xing, Y., Resch, A., and Lee, C. 2004 . The multiassembly problem: Reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res. 14 : 426 -441. ↵ Yu, W.P., Brenner, S...
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
...beads. To focus on individual candidate genes predicted to be bound by the protein of interest, precipitated DNA can be analyzed using qPCR with primers designed specifically against the regulatory sequences of the GOIs. Alternatively, in ChIP-seq following precipitation, cross-links are reversed...
OPEN ACCESS ARTICLE
Select this article
Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA ↵3 These authors contributed equally to this work. Corresponding author: jsanfor2@ucsc.eduAbstractAlternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms, leading to transcripts with distinct...
OPEN ACCESS ARTICLE
Select this article
Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...aggregation faces a more complicated problem, as peptides, especially modified versions, may exhibit different behaviors and functional roles than their nonmodified counterparts. Further, the data quality between both fields differs a lot. Bulk RNA-seq typically provides sufficiently high read counts, whereas...
Select this article
Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...al. 2021).However, owing to its inherently noisy nature, some repetitive parts of the were still recalcitrant to assembly approaches (Nurk et al. 2020; Rhie et al. 2021). Whereas sophisticated application of long-read data to assembly problems has unarguably led to several examples of advancing...
OPEN ACCESS ARTICLE
Select this article
Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...compute kinship coefficients instead of MHE. For comparison, we implemented an alternative MPC solution based on prior work on GWAS (Cho et al. 2018). We found that the MPC approach is consistently eight times slower than SF-Relate for varying data set sizes, resulting in an estimated runtime of ∼5 days...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Goren et al. 18 (2): 214.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: