407 papers
The authors developed the ChIP-FRiP pipeline to systematically analyze 140 cohesin ChIP-seq datasets, revealing that antibody background and technical variability significantly distort binding patterns, and subsequently proposed a spike-in-based correction strategy integrated with biophysical simulations to enable accurate comparative analysis of cohesin positioning.
This study evaluates and improves differential gene expression inference in human metatranscriptomes by demonstrating that current methods fail on real data despite simulated benchmarks, then validating a robust approach using mock communities and gnotobiotic mice while introducing a genome-level filtering strategy to overcome confounding factors like low prevalence.
This study demonstrates that elevated postnatal maternal licking and grooming can mitigate the negative neurodevelopmental impacts of prenatal bisphenol exposure in rats by normalizing *Esrrg* gene expression and altering DNA methylation patterns in the hypothalamus, suggesting that postnatal tactile stimulation may serve as an effective intervention against endocrine-disrupting chemical risks.
This study demonstrates that neural networks trained on human and mouse ENCODE data can effectively infer chromatin regulation annotations across diverse species, including cattle, pigs, chickens, and fish, by leveraging FAANG experimental data for validation and showing particular accuracy even for non-conserved sequences.
This study reveals that superabundant microRNAs, specifically miR-1275 and miR-6724, are transcribed from human rDNA spacer promoters flanked by CTCF, processed and exported rapidly independent of canonical pathways, and function as circulating cancer biomarkers with potential general regulatory roles.
This study presents a high-quality, chromosome-level reference genome assembly for the Western Spadefoot (*Spea hammondii*), a vernal pool specialist amphibian facing habitat loss and potential federal listing, to enable critical population genomic assessments for its conservation.
This manuscript has been withdrawn because the *Catonephele numilia* specimen was misidentified as *Catonephele acontius*, rendering the reported *C. numilia* genome data invalid while the *C. acontius* data remains unaffected.
This study presents a haplotype-resolved, chromosome-level genome assembly of an aneuploid *Phalaenopsis* cultivar that elucidates the specific genetic mechanisms, including enhancer polymorphisms and homoeologous gene variations, underlying the orchid's diverse lip morphology, venation, and color patterns, thereby establishing a framework for marker-assisted breeding.
This study demonstrates that while silica-column-based DNA extraction (NucleoSpin Microbial) yields the highest genomic completeness and analytical depth for Oxford Nanopore sequencing, paramagnetic bead-based protocols offer a viable, portable alternative for frontline antimicrobial resistance surveillance, highlighting a critical trade-off between field deployability and high-resolution genomic characterization.
By combining a complete, gap-free genome assembly of strain F1C1 with a pangenomic analysis of the *Ralstonia solanacearum* species complex, this study reveals that accessory genome functional architecture is systematically organized into 651 recurrent integration spots enriched for adaptive functions, providing a new framework for understanding pathogen evolution and improving disease management.
This study elucidates the dynamic interplay between chromatin accessibility and transcriptome remodeling in the pregnant mouse myometrium, revealing that the temporal transition from late gestation to labor is driven by stage-specific binding of JUND and progesterone receptor isoforms (PRA and PRB) that regulate gene expression and chromatin states.
This study demonstrates that extracting ancient DNA from seed embryos rather than leaves offers a superior, non-destructive alternative for whole-genome sequencing of historical plant specimens, particularly in tropical species where embryos yield higher endogenous DNA content and better preservation due to protective husks.
This study utilizes comparative pan-genomics of clinical *Fusarium solani* species complex members to reveal extensive genomic variation, including polyphyletic human pathogenicity, diverse accessory chromosomes, dynamic non-coding RNA networks, and horizontally transferred Starship elements, providing critical insights into the evolutionary mechanisms driving multi-kingdom virulence.
PolyGenie is an open-source, reproducible Nextflow pipeline that standardizes the execution and interactive visualization of polygenic risk score-based phenome-wide association studies (PheWAS) across diverse population cohorts.
This study presents the high-quality, near-chromosome-scale genome assembly of the beneficial agricultural fungus *Trichoderma gamsii* strain T035, providing a crucial resource to elucidate its biocontrol mechanisms and advance sustainable plant protection strategies.
This study presents the first complete, telomere-to-telomere genome assembly of the malaria-blocking microsporidian symbiont *Microsporidia* sp. MB from *Anopheles coluzzii* in Burkina Faso, revealing its 9.16 Mb tetraploid genome structure, unique telomeric motifs, and reduced infection machinery to facilitate future malaria control research.
ChIANet is a multimodal deep learning framework that accurately predicts protein-mediated 3D chromatin architectures from binding profiles alone, revealing that genome folding is dynamically shaped by functional context and regulatory targets across diverse cellular and cancer states.
This study introduces rDNAmine, a novel bioinformatic toolkit and chromosome-specific DNA extraction method for analyzing long repetitive genomic sequences without global alignment, validated through the discovery of distinct structural polymorphisms in the rDNA arrays of *Saccharomyces cerevisiae* and *Candida albicans*.
This study provides a genome-wide characterization of dual-coding regions (DCRs) in humans, revealing that over 1,200 genes utilize alternative reading frames to produce conserved, often disordered peptide variants that likely fine-tune gene regulation and functional diversity through mechanisms such as protein truncation and nonsense-mediated decay.
This study utilizes high-resolution Micro-C mapping across a breast cancer progression model to reveal that genome reorganization involves early large-scale compartmental shifts and later fine-scale structural changes in topologically associated domains and loops, which functionally drive gene expression alterations through rewired enhancer-promoter interactions.