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Research: A 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 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...strand and tested whether the editing may be associated with cis-NAT transcription. Complementarily, we focused on regions exhibiting expression of both strands and testedwhether they undergo editing. To detect highly edited regions, we employed the hyperediting approach (Methods) (Porath et al. 2014...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
.... The average genomic size of mitotic loops is smaller in chicken (200–300 kb) compared to human (400–600 kb) and especially mouse (1–1.5 Mb). Interestingly, we find that this difference is correlated with the genomic length of q-arms in these species, a finding we confirm by microscopy measurements...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...and materials managed by SFARI. The close integration enables SFARIBase to automatically manage GPF's user accounts and permissions, reflecting the status of researchers’ requests and approvals for genotypic and phenotypic data sets, ensuring consistency and a seamless experience for researchers interacting...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...quickly. It is hard to imagine how this might happen, but it is known that smRNAs that are loaded onto AGO have biases (Mi et al. 2008), and thus some may be more stable with longer half-lives. Another possibility is that these structures correlate with degradation through other, non-DCL pathways. Some...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic s Tomáš Brůna1,4,5, Alexandre Lomsadze2,4 and Mark Borodovsky1,2,3 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; 2Wallace H. Coulter Department of Biomedical...
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Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
...-occurrence of BTKC481S and additional CLL driver mutations, as well as BTK-mutant subclonal phenotypes.ResultsLong-read sequencing with MAS-seq expands transcript and variant coverageWe generated long-read scRNA-seq data for the pretreatment and relapse samples from six CLL patients who developed BTKC481S mutations...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...used functional inferences based on human gene expression profiles or in vitro screening, the comprehensive and deep phenotyping offered by HPO provides a more systematic perspective on the functional roles of human disease genes. We found a moderate but statistically significant inverse correlation...
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Method: Variations in antibody repertoires correlate with vaccine responses
- Yana Safonova,
- Sung Bong Shin,
- Luke Kramer,
- James Reecy,
- Corey T. Watson,
- Timothy P.L. Smith,
- and Pavel A. Pevzner
Genome Res. April 2022 32: 791-804; Published in Advance March 31, 2022, doi:10.1101/gr.276027.121
...IGenotype. We further analyzed IGenotypes across all 204 animals for finding their correlations with various phenotypes. The IGenotypes of 204 animals across 52 GSVs form a 52 × 204 IGenotype matrix, an analog of a genotype matrix that describes both genomic SNPs and SHMs (Fig. 4A).View larger version...
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Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...with HEK3 and VEGFA spacers was highly correlated between the sgRNA and pegRNA data sets (R2 > 0.8), whereas the EMX1 spacer correction is somewhat weaker (R2 of 0.6), likely owing to the lower numbers of sites detected overall in the EMX1 data set (Supplemental Fig. S8E–G). These data support the notion...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...in the enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypes relative to the primary tumor. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from peripheral blood. Most CTC...

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