Frontiers in Bioinformatics | Single Cell Bioinformatics

Methods

Accepted on 29 Jul 2025

Quantitative measures to assess the quality of Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data

in Single Cell Bioinformatics

Jie Sun
Robert Morrison
Soyeon Kim
Kairuo Yan
Hyun Jung Park

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630161

184 views

Original Research

Published on 18 Jul 2025

Analysis of histone modifications in key cellular subpopulations in the context of azoospermia using spermatogenic single-cell RNA-seq data

in Single Cell Bioinformatics

Qiu Wang
Hong Yang
Fang Li
Song Ge
Ling Ji
Xiaofeng Li

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1626153

901 views

Original Research

Published on 11 Jun 2025

Optimization of clustering parameters for single-cell RNA analysis using intrinsic goodness metrics

in Single Cell Bioinformatics

Nicolina Sciaraffa
Antonino Gagliano
Luigi Augugliaro
Claudia Coronnello

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562410

1,247 views

Mini Review

Published on 17 Apr 2025

Primer on machine learning applications in brain immunology

in Single Cell Bioinformatics

Niklas Binder
Ashkan Khavaran
Roman Sankowski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1554010

2,125 views

Technology and Code

Published on 12 Feb 2025

Seurat function argument values in scRNA-seq data analysis: potential pitfalls and refinements for biological interpretation

in Single Cell Bioinformatics

Mikhail Arbatsky
Ekaterina Vasilyeva
Veronika Sysoeva
Ekaterina Semina
Valeri Saveliev
Kseniya Rubina

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1519468

2,275 views
1 citation

Editorial

Published on 08 Oct 2024

Editorial: Women in bioinformatics

in Single Cell Bioinformatics

Irma Martínez-Flores
Constanza Cárdenas Carvajal
Viviana Monje-Galvan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1499514

1,320 views

Mini Review

Published on 08 Jul 2024

A systematic overview of single-cell transcriptomics databases, their use cases, and limitations

in Single Cell Bioinformatics

Mahnoor N. Gondal
Saad Ur Rehman Shah
Arul M. Chinnaiyan
Marcin Cieslik

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1417428

7,725 views
6 citations

Original Research

Published on 04 Mar 2024

Predicting cell population-specific gene expression from genomic sequence

in Single Cell Bioinformatics

Lieke Michielsen
Marcel J. T. Reinders
Ahmed Mahfouz

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1347276

3,906 views
2 citations

Original Research

Published on 04 Mar 2024

Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network

in Single Cell Bioinformatics

Marin Truchi
Caroline Lacoux
Cyprien Gille
Julien Fassy
Virginie Magnone
Rafael Lopes Goncalves
Cédric Girard-Riboulleau
Iris Manosalva-Pena
Marine Gautier-Isola
Kevin Lebrigand

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1340339

2,787 views
1 citation

Methods

Published on 10 Aug 2023

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets

in Single Cell Bioinformatics

Wanxin Li
Jules Mirone
Ashok Prasad
Nina Miolane
Carine Legrand
Khanh Dao Duc

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1211819

2,035 views

Original Research

Published on 15 May 2023

Gene representation in scRNA-seq is correlated with common motifs at the 3′ end of transcripts

in Single Cell Bioinformatics

Xinling Li
Greg Gibson
Peng Qiu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1120290

4,131 views
1 citation

Original Research

Published on 12 Apr 2023

Gene length is a pivotal feature to explain disparities in transcript capture between single transcriptome techniques

in Single Cell Bioinformatics

Ricardo R. Pavan
Fabiola Diniz
Samir El-Dahr
Giovane G. Tortelote

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1144266

3,412 views
1 citation