ParaMask: a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data Bastiaan TjengMale ArimondAndrea Fulgione Methodology Open access 24 October 2025 Article: 368
Unlocking the regulatory code of RNA: launching the Human RNome Project The International Human RNome Project Consortium Comment Open access 24 October 2025 Article: 367
Identification of microprotein-coding intronic polyadenylation isoforms and function in genotoxic anticancer drug response Alexandre DevauxIris TanakaMartin Dutertre Research Open access 23 October 2025 Article: 366
ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets Jonas NiemannYuejiao HuangHannes Schroeder Database Open access 23 October 2025 Article: 365
Author Correction: CpG island turnover events predict evolutionary changes in enhancer activity Acadia A. KocherEmily V. DutrowJames P. Noonan Author Correction Open access 22 October 2025 Article: 363
Propensity for proto-gene emergence in bacteria Md. Hassan uz‑ZamanHoward Ochman Research Open access 22 October 2025 Article: 362
iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis Nosheen HussainRyan MerritJose Gutierrez-Marcos Methodology Open access 22 October 2025 Article: 361
Efficient glycosylase-mediated base editing with minimal off-target effects in mammalian embryos Yinghui WeiXi CaoXiaolong Wang Brief Report Open access 21 October 2025 Article: 360
Cell Decoder: decoding cell identity with multi-scale explainable deep learning Jun ZhuZeyang ZhangCheng Chang Methodology Open access 20 October 2025 Article: 359
Insights, opportunities, and challenges provided by large cell atlases Martin HembergFederico MariniIvana Jelic Review Open access 20 October 2025 Article: 358
Publisher Correction: The genomic footprints of migration: how ancient DNA reveals our history of mobility Matthew P. WilliamsChristian D. Huber Publisher Correction Open access 20 October 2025 Article: 357
SPAmix: a scalable, accurate, and universal analysis framework for large-scale genetic association studies in admixed populations Yuzhuo MaHe XuWenjian Bi Research Open access 16 October 2025 Article: 356
Reference genome bias in light of species-specific chromosomal reorganization and translocations Marius F. MaurstadSiv Nam Khang HoffSissel Jentoft Research Open access 15 October 2025 Article: 355
sCCIgen: a high-fidelity spatially resolved transcriptomics data simulator for cell–cell interaction studies Xiaoyu SongJoselyn C. Chavez-FuentesGuo-Cheng Yuan Methodology Open access 15 October 2025 Article: 354
iPro-MP: a BERT-based model to predict multiple prokaryotic promoters Wei SuYuhe YangHao Lin Research Open access 13 October 2025 Article: 353
Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development Xiaosa XuHuiqiong LinJorge Dubcovsky Research Open access 13 October 2025 Article: 352
A novel gene expression stability metric to unveil homeostasis and regulation Mengjie Chen Method Open access 10 October 2025 Article: 351
GIMIC: smoothed graph-image representation of microbiome samples induce an optimal distance Oshrit ShtosselYoram Louzoun Methodology Open access 09 October 2025 Article: 350
Evaluating the potential and limitations of nanopore adaptive sampling for targeted transcriptome sequencing Nicole DeBruyneFeng WangLan Lin Methodology Open access 09 October 2025 Article: 349
Author Correction: MOADE: a multimodal autoencoder for dissociating bulk multi-omics data Jiao SunAyesha A. MalikQian Li Author Correction Open access 09 October 2025 Article: 348
A molecular census to elucidate the demixing mechanism of membraneless organelles Cheryn AliFernando MuzzopappaFabian Erdel Research Open access 09 October 2025 Article: 347
Engineered virus-like particle-assembled Vegfa-targeting Cas9 ribonucleoprotein treatment alleviates neovascularization in wet age-related macular degeneration Jun WuHyewon JangJeong Hun Kim Research Open access 09 October 2025 Article: 346
Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats Jingyi XuXiaodong ChenShengru Wu Research Open access 09 October 2025 Article: 345
Pan-S-locus analysis reveals insights into the origin and evolution of self-incompatibility in the orange subfamily Jianbing HuZezhen DuLijun Chai Research Open access 07 October 2025 Article: 344
A ternary-code DNA methylome atlas of mouse tissues Sol Moe LeeDavid C. GoldbergWanding Zhou Research Open access 07 October 2025 Article: 343
High-precision cell-type mapping and annotation of single-cell spatial transcriptomics with STAMapper Qunlun ShenKangning DongShihua Zhang Methodology Open access 07 October 2025 Article: 342
Structural and evolutionary features of red algal UV sex chromosomes Agnieszka P. LipinskaGuillaume CossardSusana M. Coelho Research Open access 07 October 2025 Article: 341
Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution Luzhang JiQihang ZouChenfei Wang Methodology Open access 06 October 2025 Article: 340
SpatPPI: a geometric deep learning model for predicting protein–protein interactions involving intrinsically disordered regions Zeyu XuYanhao ZhuJuntao Liu Methodology Open access 06 October 2025 Article: 339
Silent mutations in coding regions of Hepatitis C virus affect patterns of HCV RNA structures and attenuate viral replication and pathogenesis Roba DabourShaked BergmanTamir Tuller Research Open access 06 October 2025 Article: 338
A nucleoporin-associated signaling cascade controls plant immunity via histone modification Leiwen PanShun PengShui Wang Research Open access 06 October 2025 Article: 337
Potential synthetic associations created by epistasis Hai-Jun LiuJingxian FuMagnus Nordborg Brief Report Open access 06 October 2025 Article: 336
xCell 2.0: robust algorithm for cell type proportion estimation predicts response to immune checkpoint blockade Almog AngelLoai NaomDvir Aran Research Open access 03 October 2025 Article: 335
Biology-driven insights into the power of single-cell foundation models Jialu WuQing YeTingjun Hou Research Open access 03 October 2025 Article: 334
Unico: a unified model for cell-type resolution genomics from heterogeneous omics data Zeyuan Johnson ChenElior RahmaniEran Halperin Method Open access 03 October 2025 Article: 333
Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE Zihan DongWei JiangHongyu Zhao Methodology Open access 03 October 2025 Article: 332
GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density Mitchell ConeryJames A. PippinStruan F. A. Grant Research Open access 03 October 2025 Article: 331
Phase-separating fusion proteins drive cancer by upsetting transcription regulation Nazanin FarahiTamas LazarRita Pancsa Research Open access 02 October 2025 Article: 330
WUSCHEL-dependent chromatin regulation in maize inflorescence development at single-cell resolution Sohyun BangXuan ZhangRobert J. Schmitz Research Open access 02 October 2025 Article: 329
BLEND: probabilistic cellular deconvolution with individualized single-cell reference integration Penghui HuangManqi CaiJiebiao Wang Methodology Open access 02 October 2025 Article: 328
Phylogenomics provides comprehensive insights into the evolutionary relationships among cultivated buckwheat species Yaliang ShiBo LiMeiliang Zhou Research Open access 01 October 2025 Article: 327
The rise of historical epigenomics and temporal analysis of gene regulation Clare E. HolleleyErin E. Hahn Brief Report Open access 01 October 2025 Article: 326
MOADE: a multimodal autoencoder for dissociating bulk multi-omics data Jiao SunAyesha A. MalikQian Li Methodology Open access 30 September 2025 Article: 325
G-quadruplex structural motifs modulate protein–RNA interactions within the transcriptome Uditi BhattCameron W. EvansNicole M. Smith Research Open access 30 September 2025 Article: 324
\(\Phi\)-Space: continuous phenotyping of single-cell multi-omics data Jiadong MaoYidi DengKim-Anh Lê Cao Methodology Open access 30 September 2025 Article: 323
SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies Wenjie PengLiubin ZhangMiaoxin Li Methodology Open access 30 September 2025 Article: 322
DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning Zhigang MaJiazi ZhangZefu Lu Methodology Open access 29 September 2025 Article: 321
Characterization of the transposable element landscape shaping the Ectocarpus genome Erica DinataleRory J. CraigSusana M. Coelho Research Open access 29 September 2025 Article: 320
The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow Ziming ZhongMark BaileyRichard Mott Research Open access 29 September 2025 Article: 319
Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis Kejing DongYicheng GaoQi Liu Research Open access 29 September 2025 Article: 318
