Bakhtiari, M.* ; Bonn, S.* ; Theis, F.J. ; Zolotareva, O.* & Baumbach, J.* FedscGen: Privacy-preserving federated batch effect correction of single-cell RNA sequencing data. Genome Biol. 26:216 (2025)
Francioli, D.* et al. Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale. Genome Biol. 26:148 (2025)
Kang, S.* et al. DelSIEVE: Cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data. Genome Biol. 26:255 (2025)
Maddhesiya, P. et al. Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner. Genome Biol. 26:100 (2025)
Bradfeld, J.P.* et al. Author Correction: Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes. Genome Biol. 25:129 (2024)
Bradfield, J.P.* et al. Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes. Genome Biol. 25:22 (2024)
Curion, F. et al. hadge: A comprehensive pipeline for donor deconvolution in single-cell studies. Genome Biol. 25:109 (2024)
Curion, F. et al. Panpipes: A pipeline for multiomic single-cell and spatial transcriptomic data analysis. Genome Biol. 25:181 (2024)
Hains, A.E.* et al. Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy. Genome Biol. 25:319 (2024)
Karollus, A.* et al. Species-aware DNA language models capture regulatory elements and their evolution. Genome Biol. 25:83 (2024)
Lange, M. et al. Mapping lineage-traced cells across time points with moslin. Genome Biol. 25:277 (2024)
Critical Assessment of Genome Interpretation Consortium (Müller, N.S.) & Critical Assessment of Genome Interpretation Consortium (Eraslan, G.) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol. 25:46 (2024)
Oksza-Orzechowski, K.* et al. CaClust: Linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants. Genome Biol. 25:286 (2024)
Sarfraz, I.* et al. MAMS: Matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data. Genome Biol. 25:205 (2024)
Wang, W. ; Wang, Y.* ; Lyu, R.* & Grün, D.* Scalable identification of lineage-specific gene regulatory networks from metacells with NetID. Genome Biol. 25:275 (2024)
Yu, Y.* et al. Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration. Genome Biol. 25:13 (2024)
Horlacher, M. et al. Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning. Genome Biol. 24:180 (2023)
Karollus, A.* ; Mauermeier, T.* & Gagneur, J. Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers. Genome Biol. 24, 56:56 (2023)
Li, S.* et al. Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data. Genome Biol. 24:80 (2023)
Sánchez Quant, E.S. ; Richter, M. ; Colomé-Tatché, M. & Martinez Jimenez, C.P. Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge. Genome Biol. 24:234 (2023)
Galle, E.* et al. H3K18 lactylation marks tissue-specific active enhancers. Genome Biol. 23:207 (2022)
Janjic, A.* et al. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol. 23:88 (2022)
Kanoni, S.* et al. Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis. Genome Biol. 23:268 (2022)
Azodi, C.B* ; Zappia, L. ; Oshlack, A.* & McCarthy, D.J.* splatPop: Simulating population scale single-cell RNA sequencing data. Genome Biol. 22:341 (2021)
Buchka, S.* ; Hapfelmeier, A.* ; Gardner, P.P.* ; Wilson, R. & Boulesteix, A.L.* On the optimistic performance evaluation of newly introduced bioinformatic methods. Genome Biol. 22:152 (2021)
Cheng, J.* ; Çelik, M.H.* ; Kundaje, A.* & Gagneur, J. Publisher Correction: MTSplice predicts effects of genetic variants on tissue-specific splicing. Genome Biol. 22:107 (2021)
Cheng, J.* ; Çelik, M.H.* ; Kundaje, A.* & Gagneur, J. MTSplice predicts effects of genetic variants on tissue-specific splicing. Genome Biol. 22:94 (2021)
Fischer, D.S. et al. Sfaira accelerates data and model reuse in single cell genomics. Genome Biol. 22:248 (2021)
McCartney, D.L.* et al. Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging. Genome Biol. 22:194 (2021)
Witte, F.* et al. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol. 22:191 (2021)
Zappia, L. & Theis, F.J. Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape. Genome Biol. 22:301 (2021)
Hofmeister, B.T.* et al. A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol. 21:259 (2020)
Hoser, S.M.* et al. Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing. Genome Biol. 21:299 (2020)
Lähnemann, D.* et al. Eleven grand challenges in single-cell data science. Genome Biol. 21:31 (2020)
Lloyd, K.C.K.* et al. The deep genome project. Genome Biol. 21:18 (2020)
Shahryary, Y.* et al. AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biol. 21:33023650 (2020)
Ashuach, T.* et al. MPRAnalyze: Statistical framework for massively parallel reporter assays. Genome Biol. 20:183 (2019)
Hanna, C.W.* et al. Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues. Genome Biol. 20:225 (2019)
Monat, C.* et al. TRITEX: Chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol. 20:284 (2019)
Uzbas, F. et al. BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis. Genome Biol. 20:155 (2019)
Wolf, F.A. et al. PAGA: Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20:59 (2019)
Keeble-Gagnère, G.* et al. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biol. 19:112 (2018)
Prins, B.P.* et al. Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6. Genome Biol. 19:87 (2018)
Thind, A.K.* et al. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biol. 19:104 (2018)
Wicker, T.* et al. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol. 19:103 (2018)
Wolf, F.A. ; Angerer, P. & Theis, F.J. SCANPY: Large-scale single-cell gene expression data analysis. Genome Biol. 19:15 (2018)
Zannas, A.S.* et al. Correction: Lifetime stress accelerates epigenetic aging in an urban, African American cohort: Relevance of glucocorticoid signaling [Genome Biol., 16, 1, (2015) (266)] DOI: 10.1186/s13059-015-0828-5. Genome Biol. 19:61 (2018)
Buettner, F. ; Pratanwanich, N.* ; McCarthy, D.J.* ; Marioni, J.C.* & Stegle, O.* f-scLVM: Scalable and versatile factor analysis for single-cell RNA-seq. Genome Biol. 18:212 (2017)
Farnham, A.* et al. Early career researchers want Open Science. Genome Biol. 18:221 (2017)
Heinig, M. et al. Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy. Genome Biol. 18:170 (2017)
Jansen, I.E.* et al. Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing. Genome Biol. 18:22 (2017)
Bakker, B.* et al. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biol. 17:115 (2016)
Izzo, A.* & Schneider, R. H1 gets the genome in shape. Genome Biol. 17:8 (2016)
Ligthart, S.* et al. DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases. Genome Biol. 17:255 (2016)
Unterseer, S. et al. A comprehensive study of the genomic differentiation between temperate Dent and Flint maize. Genome Biol. 17:137 (2016)
van den Bos, H.* et al. Erratum to: Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons [Genome Biol, (2016), 17, 116]. Genome Biol. 17:143 (2016)
van den Bos, H.* et al. Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons. Genome Biol. 17:116 (2016)
Tsang, J.C.H.* et al. Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. Genome Biol. 16:178 (2015)
Zannas, A.S.* et al. Lifetime stress accelerates epigenetic aging in an urban, African American cohort: Relevance of glucocorticoid signaling. Genome Biol. 16:266 (2015)
Muñoz-Amatriaín, M.* et al. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 14:R58 (2013)
Philippe, R.* et al. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol. 14:R64 (2013)
Simon,  M.M.* et al. A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. Genome Biol. 14:R82 (2013)
Lechner, M. et al. CIDeR: Multifactorial interaction networks in human diseases. Genome Biol. 13:R62 (2012)
Ruepp, A. et al. PhenomiR: A knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 11:R6 (2010)
Eck, S.H. et al. Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol. 10:R82 (2009)
Kastenmüller, G. ; Schenk, M.E. ; Gasteiger, J.* & Mewes, H.-W. Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol. 10:R28 (2009)
Loewenstein, Y.* et al. Protein function annotation by homology-based inference. Genome Biol. 10:207 (2009)
Webb, K.J. et al. Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biol. 10:R81 (2009)
Antonov, A.V. ; Dietmann, S. & Mewes, H.-W. KEGG spider: Interpretation of genomics data in the context of the global gene metabolic network. Genome Biol. 9:R179 (2008)
Schmidt, T. & Frishman, D. Assignment of isochores for all completely sequenced vertebrate genomes using a consensus. Genome Biol. 9:R104 (2008)
Caldwell, R.B. et al. Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. Genome Biol. 6, 6-6.9 (2004)
Schrick, K.* ; Nguyen, D.* ; Karlowski, W.M. & Mayer, K.F.X. START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors. Genome Biol. 5, R41-R41-16 (2004)
Kosarev, P. ; Mayer, K.F.X. & Hardtke, C.S.* Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome. Genome Biol. 3 (2002)
Landgrebe, J.* ; Wurst, W. & Welzl, G. Permutation-validated principal components analysis of microarray data. Genome Biol. 3, 3-11 (2002)