scRNA‐seq data analysis method to improve analysis performance

J Lu, Y Sheng, W Qian, M Pan, X Zhao… - IET …, 2023 - Wiley Online Library
With the development of single‐cell RNA sequencing technology (scRNA‐seq), we have the
ability to study biological questions at the level of the individual cell transcriptome …

K-nearest-neighbors induced topological PCA for single cell RNA-sequence data analysis

S Cottrell, Y Hozumi, GW Wei - Computers in biology and medicine, 2024 - Elsevier
Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells,
which has given us insights into cell–cell communication, cell differentiation, and differential …

[HTML][HTML] Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations

Z Chen, J Goldwasser, P Tuckman, J Liu… - Nature …, 2022 - nature.com
In the era of single-cell sequencing, there is a growing need to extract insights from data with
clustering methods. Here, we introduce Forest Fire Clustering, an efficient and interpretable …

[HTML][HTML] The transcriptional portraits of the neural crest at the individual cell level

AG Erickson, P Kameneva, I Adameyko - Seminars in cell & developmental …, 2023 - Elsevier
Since the discovery of this cell population by His in 1850, the neural crest has been under
intense study for its important role during vertebrate development. Much has been learned …

[HTML][HTML] popsicleR: AR package for pre-processing and quality control analysis of single cell RNA-seq data

F Grandi, J Caroli, O Romano, M Marchionni… - Journal of Molecular …, 2022 - Elsevier
The advent of single-cell sequencing is providing unprecedented opportunities to
disentangle tissue complexity and investigate cell identities and functions. However, the …

Simpler and faster development of tumor phylogeny pipelines

S Ali, S Ciccolella, L Lucarella, GD Vedova… - Journal of …, 2021 - liebertpub.com
In the recent years, there has been an increasing amount of single-cell sequencing studies,
producing a considerable number of new data sets. This has particularly affected the field of …

[HTML][HTML] Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends

M Sehgal, S Ramu, JM Vaz, YR Ganapathy… - Translational …, 2024 - Elsevier
Colorectal cancer (CRC) is highly heterogeneous with variable survival outcomes and
therapeutic vulnerabilities. A commonly used classification system in CRC is the Consensus …

Multiomic spatial mapping of myocardial infarction and implications for personalized therapy

D Schumacher, R Kramann - Arteriosclerosis, Thrombosis, and …, 2023 - Am Heart Assoc
Ischemic heart disease including myocardial infarction is still the leading cause of death
worldwide. Although the survival early after myocardial infarction has been significantly …

[HTML][HTML] Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data

Q Jiang, S Zhang, L Wan - PLoS Computational Biology, 2022 - journals.plos.org
Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However,
dynamic inference of an evolving cell population from time series scRNA-seq data is …

[HTML][HTML] Bioinformatics for wet-lab scientists: practical application in sequencing analysis

V Laub, K Devraj, L Elias, D Schulte - BMC genomics, 2023 - Springer
Background Genomics data is available to the scientific community after publication of
research projects and can be investigated for a multitude of research questions. However, in …