Searching journal content for articles similar to Foroozandeh Shahraki et al. 34 (3): 469.

Displaying results 1-10 of 684

For checked items

view abstracts
download to citation manager

Select this article
Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...University, Stanford, CA 94305, United States Abstract The fourth and final phase of the ENCODE consortium has newly profiled epigenetic activity in hundreds of human tissues. Chromatin state annotations created by segmentation and annotation (SAGA) methods, such as Segway, have emerged as the predominant...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...of genomic architectural stripes from Hi-C or Micro-C chromatin contact maps, that relies on robust image processing techniques and rigorous statistical tests for enrichment. Quagga outperforms other stripe detection methods in accuracy and is highly versatile, working with Hi-C, Micro-C, and other chromatin...
OPEN ACCESS ARTICLE
Select this article
Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...predict the directionality of change in chromatin accessibility between the reference and variant alleles across all SNVs. All models outperformed the state-of-the-art method ChromBPNet (Pampari et al. 2024) and the random baseline, where for each SNV, a value of 0 or 1 was randomly assigned according...
OPEN ACCESS ARTICLE
Select this article
Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS Qunlun Shen1,2, Shuqin Zhang1,3 and Shihua Zhang2,4,5 1School of Mathematical Sciences, Fudan University, Shanghai 200433, China; 2State Key Laboratory of Mathematical Sciences, Academy...
Select this article
Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
..., Barnett-Itzhaki Z, Jaitin D, Amann-Zalcenstein D, Lara-Astiaso D, Amit I. 2013. High-throughput chromatin immunoprecipitation for -wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc 8: 539–554. doi:10.1038/nprot.2013.023 ↵Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic...
Select this article
Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...mutant with respect to a fixed yet robust control, we computed a baseline of chromatin occupancy by merging every mutant's MNase-seq profile and subsampling to the same total mapped reads of an individual sample (see Methods). The chromatin profile of this baseline control is highly similar...
Select this article
Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
.... Finally, we determine cell-type-specific replication timing profiles, integrating our in vivo data sets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program, compared with somatic lineages, that aligns with chromatin state differences...
OPEN ACCESS ARTICLE
Select this article
Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...and inactive ERBS did (Fig. 1G).To assess the correlation between STARR-seq-based ERBS annotation and enhancer activity within the native chromatin context, we analyzed GRO-seq signal (GEO; GSE27463) (Hah et al. 2011) at ERBS following E2 stimulation, as enhancer transcription is a well-established readout...
Select this article
Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...responses. Anemia stress-dependent transcriptional regulation can be useful for developing clinical strategies to regenerate RBCs in chronic conditions. SNP regions annotated for associations to specific hematologic traits within anemia-sensitive chromatin accessible regions may represent new genetic...
Select this article
Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
..., chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Foroozandeh Shahraki et al. 34 (3): 469.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: