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Method: Robust chromatin state annotation
- Mehdi Foroozandeh Shahraki,
- Marjan Farahbod,
- and Maxwell W. Libbrecht
Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
...process may be imperfect; for example, in our running example, base state 6_Enha(B) overlaps with verification state 10_Prom_fla(V), and the mismatch in chromatin state category likely results from an error in the interpreter, not the annotations themselves.Pairwise overlap does not fully capture...
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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
...integrative summary of such data sets. Here, we present the ENCODE4 Catalog of Segway Annotations, a set of sample-specific -wide chromatin state annotations of 234 human biosamples inferred from 1,794 genomics experiments. This catalog identifies genomic elements, accurately captures cell type...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...in a final panel size of 22,314 regions for Panel 1 and 48,507 regions for Panel 2. The software then designed KAPA Target Enrichment Probes covering the inputted regions. These probes are 120 bp in length and, following hybridization with genomic DNA, can be captured through a bead-based capture method...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...for their ability to integrate high-dimensional features have recently been applied to the field of liquid biopsy. In this review, we highlight various AI and ML approaches in cfDNA-based diagnostics. We first introduce the biology of cell-free DNA and basic concepts of ML and AI technologies. We then discuss...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...-resolved assemblies. This graph is modeled as a DAG, in which each node is labeled with a DNA sequence, and edges represent the adjacency of these sequences along known haplotypes. Any path through this graph can represent an existing haplotype or a recombinant mosaic of segments from multiple haplotypes.In the Li...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...conjugation, canonical DNA repair proteins have distinctive activity in the MAC and MIC during 267 meiosis (Loidl 2021). Taken together with the established chromatin state-dependent repair 268 pathways, these observations strongly suggest the presence of unique, nucleus-specific repair 269 9 mechanisms...
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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...implicated in the regulation of diverse biological processes, including spermatogenesis, heat shock response, ultraviolet-induced DNA damage response and maternal mRNA clearance. Despite the recognized significance of m6A in mRNA regulation, limited studies have focused on the targeted and efficient...
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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
...analog bromodeoxyuridine (BrdU) to label replicating DNA. Next, GSC-like or CySC-like nuclei were extracted and sorted via flow cytometry into four S-phase fractions corresponding to early, early-mid, late-mid, and late S phase, based on their DNA content (Fig. 4A; Supplemental Fig. S5A–C). Brd...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...of sequencing platforms are used for -wide cfDNA sequencing, including Illumina sequencing, Oxford Nanopore Technologies (nanopore) sequencing, and PacBio sequencing (Cristiano et al. 2019; Choy et al. 2022; Lau et al. 2023), with Illumina sequencing being the predominant platform owing to its low-cost per base...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...is a growing trend and an effective supplement to laboratory methods (Wang et al. 2024a).In recent years, considerable progress has been made in predicting DNA methylation sites. Researchers have developed a series of effective DNA methylation site predictors based on traditional ML and recent deep learning...
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