Frontiers in Bioinformatics | Single Cell Bioinformatics section | New and Recent Articles https://www.frontiersin.org/journals/bioinformatics/sections/single-cell-bioinformatics RSS Feed for Single Cell Bioinformatics section in the Frontiers in Bioinformatics journal | New and Recent Articles en-us Frontiers Feed Generator,version:1 2026-05-13T06:16:02.95+00:00 60 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1767362 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1767362 <![CDATA[Machine learning approaches for biomarker discovery using single-cell RNA sequencing]]> 2026-04-02T00:00:00Z Review Gabriel DewaC. Mee Ling MunierSara BallouzRaymond Louie https://www.frontiersin.org/articles/10.3389/fbinf.2026.1672671 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1672671 <![CDATA[Integrating trajectory inference and self-explainable predictive models to explore cell state transitions in breast cancer at single-cell resolution]]> 2026-03-04T00:00:00Z Original Research Vanessa VerrinaMarianna TaliaEugenio CesarioSantina CapalboDomenica ScordamagliaRosamaria LappanoAnna Maria MigliettaMarcello MaggioliniSabrina Giordano https://www.frontiersin.org/articles/10.3389/fbinf.2025.1715821 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1715821 <![CDATA[Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges]]> 2026-01-27T00:00:00Z Review Boris Tchatchoua NgassamHuilin NiuSunny PangValeryia ShydlouskayaTallulah S. Andrews https://www.frontiersin.org/articles/10.3389/fbinf.2025.1697212 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1697212 <![CDATA[High-dimensional co-expression network analysis reveals persistent TRH gene expression throughout axolotl telencephalon regeneration]]> 2026-01-12T00:00:00Z Original Research Iveth Gómez-MoralesAdriana P. Mendizabal-RuizJ. Alejandro MoralesTeresa Romero-Gutiérrez https://www.frontiersin.org/articles/10.3389/fbinf.2025.1740715 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1740715 <![CDATA[Integrative transcriptomic analysis reveals microglial metabolic-inflammatory crosstalk of HK2–HSPA5–TNF axis after intracerebral hemorrhage]]> 2026-01-12T00:00:00Z Original Research Yi ZhangYongqian LiuWei MengXiaobo YuXiaojun Xu https://www.frontiersin.org/articles/10.3389/fbinf.2025.1713975 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1713975 <![CDATA[SpaLLM: a general framework for spatial domain identification with large language models]]> 2026-01-12T00:00:00Z Original Research Zeyu ZouZiheng Duan https://www.frontiersin.org/articles/10.3389/fbinf.2025.1684227 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1684227 <![CDATA[Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data]]> 2025-12-11T00:00:00Z Technology and Code Yuya SatoToru AsahiKosuke Kataoka https://www.frontiersin.org/articles/10.3389/fbinf.2025.1636240 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1636240 <![CDATA[Comprehensive analysis of multi-omics vaccine response data using MOFA and Stabl algorithms]]> 2025-11-13T00:00:00Z Original Research Aanya GuptaKoji AbeHolden T. Maecker https://www.frontiersin.org/articles/10.3389/fbinf.2025.1630161 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1630161 <![CDATA[Quantitative measures to assess the quality of cellular indexing of transcriptomes and epitopes by sequencing data]]> 2025-09-18T00:00:00Z Methods Jie SunRobert MorrisonSoyeon KimKairuo YanHyun Jung Park https://www.frontiersin.org/articles/10.3389/fbinf.2025.1641491 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1641491 <![CDATA[TCRscape: a single-cell multi-omic TCR profiling toolkit]]> 2025-09-05T00:00:00Z Technology and Code Roman Perik-ZavodskiiOlga Perik-ZavodskaiaMarina VolynetsSaleh AlrhmounSergey Sennikov https://www.frontiersin.org/articles/10.3389/fbinf.2025.1626153 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1626153 <![CDATA[Analysis of histone modifications in key cellular subpopulations in the context of azoospermia using spermatogenic single-cell RNA-seq data]]> 2025-07-18T00:00:00Z Original Research Qiu WangHong YangFang LiSong GeLing JiXiaofeng Li https://www.frontiersin.org/articles/10.3389/fbinf.2025.1562410 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1562410 <![CDATA[Optimization of clustering parameters for single-cell RNA analysis using intrinsic goodness metrics]]> 2025-06-11T00:00:00Z Original Research Nicolina SciaraffaAntonino GaglianoLuigi AugugliaroClaudia Coronnello https://www.frontiersin.org/articles/10.3389/fbinf.2025.1554010 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1554010 <![CDATA[Primer on machine learning applications in brain immunology]]> 2025-04-17T00:00:00Z Mini Review Niklas BinderAshkan KhavaranRoman Sankowski https://www.frontiersin.org/articles/10.3389/fbinf.2025.1519468 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1519468 <![CDATA[Seurat function argument values in scRNA-seq data analysis: potential pitfalls and refinements for biological interpretation]]> 2025-02-12T00:00:00Z Technology and Code Mikhail ArbatskyEkaterina VasilyevaVeronika SysoevaEkaterina SeminaValeri SavelievKseniya Rubina https://www.frontiersin.org/articles/10.3389/fbinf.2024.1499514 https://www.frontiersin.org/articles/10.3389/fbinf.2024.1499514 <![CDATA[Editorial: Women in bioinformatics]]> 2024-10-08T00:00:00Z Editorial Irma Martínez-FloresConstanza Cárdenas CarvajalViviana Monje-Galvan https://www.frontiersin.org/articles/10.3389/fbinf.2024.1417428 https://www.frontiersin.org/articles/10.3389/fbinf.2024.1417428 <![CDATA[A systematic overview of single-cell transcriptomics databases, their use cases, and limitations]]> 2024-07-08T00:00:00Z Mini Review Mahnoor N. GondalSaad Ur Rehman ShahArul M. ChinnaiyanMarcin Cieslik https://www.frontiersin.org/articles/10.3389/fbinf.2024.1347276 https://www.frontiersin.org/articles/10.3389/fbinf.2024.1347276 <![CDATA[Predicting cell population-specific gene expression from genomic sequence]]> 2024-03-04T00:00:00Z Original Research Lieke MichielsenMarcel J. T. ReindersAhmed Mahfouz https://www.frontiersin.org/articles/10.3389/fbinf.2024.1340339 https://www.frontiersin.org/articles/10.3389/fbinf.2024.1340339 <![CDATA[Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network]]> 2024-03-04T00:00:00Z Original Research Marin TruchiCaroline LacouxCyprien GilleJulien FassyVirginie MagnoneRafael Lopes GoncalvesCédric Girard-RiboulleauIris Manosalva-PenaMarine Gautier-IsolaKevin LebrigandPascal BarbrySalvatore SpicugliaGeorges VassauxRoger RezzonicoMichel BarlaudBernard Mari https://www.frontiersin.org/articles/10.3389/fbinf.2023.1211819 https://www.frontiersin.org/articles/10.3389/fbinf.2023.1211819 <![CDATA[Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets]]> 2023-08-10T00:00:00Z Methods Wanxin LiJules MironeAshok PrasadNina MiolaneCarine LegrandKhanh Dao Duc https://www.frontiersin.org/articles/10.3389/fbinf.2023.1120290 https://www.frontiersin.org/articles/10.3389/fbinf.2023.1120290 <![CDATA[Gene representation in scRNA-seq is correlated with common motifs at the 3′ end of transcripts]]> 2023-05-15T00:00:00Z Original Research Xinling LiGreg GibsonPeng Qiu