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RNAprofiling 2.0: Enhanced Cluster Analysis of Structural Ensembles.
Publication Type: Academic Journal
Source(s): Journal of molecular biology [J Mol Biol] 2023 Jul 15; Vol. 435 (14), pp. 168047. Date of Electronic Publication: 2023 Mar 17.
Abstract: Understanding the base pairing of an RNA sequence provides insight into its molecular structure. By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes them into pr...
The complete sequence of a human Y chromosome.
Publication Type: Academic Journal
Source(s): Nature [Nature] 2023 Sep; Vol. 621 (7978), pp. 344-354. Date of Electronic Publication: 2023 Aug 23.
Abstract: The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications 1-3 . As a result, more than half of the Y chromosome is mi...
Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review.
Publication Type: Academic Journal
Source(s): Analytica chimica acta [Anal Chim Acta] 2023 Aug 08; Vol. 1268, pp. 341330. Date of Electronic Publication: 2023 May 08.
Abstract: Peptide sequencing is of great significance to fundamental and applied research in the fields such as chemical, biological, medicinal and pharmaceutical sciences. With the rapid development of mass spectrometry and sequencing algorithms, de-novo peptid...
DNA Sequencing in Adults With Acute Myeloid Leukemia to Detect Residual Disease Prior to Hematopoietic Cell Transplant-Reply.
Publication Type: Report
Source(s): JAMA [JAMA] 2023 Jul 11; Vol. 330 (2), pp. 190-191.
A novel f-divergence based generative adversarial imputation method for scRNA-seq data analysis.
Publication Type: Academic Journal
Source(s): PloS one [PLoS One] 2023 Nov 10; Vol. 18 (11), pp. e0292792. Date of Electronic Publication: 2023 Nov 10 (Print Publication: 2023).
Abstract: Comprehensive analysis of single-cell RNA sequencing (scRNA-seq) data can enhance our understanding of cellular diversity and aid in the development of personalized therapies for individuals. The abundance of missing values, known as dropouts, makes th...
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.
Publication Type: Academic Journal
Source(s): Genome biology [Genome Biol] 2023 Oct 19; Vol. 24 (1), pp. 236. Date of Electronic Publication: 2023 Oct 19.
Abstract: Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimension...
A cell abundance analysis based on efficient PAM clustering for a better understanding of the dynamics of endometrial remodelling.
Publication Type: Academic Journal
Source(s): BMC bioinformatics [BMC Bioinformatics] 2023 Nov 22; Vol. 24 (1), pp. 440. Date of Electronic Publication: 2023 Nov 22.
Abstract: Background: Single-cell RNA sequencing (scRNA-seq) is a powerful tool for investigating cell abundance changes during tissue regeneration and remodeling processes. Differential cell abundance supports the initial clustering of all cells; then, the numb...
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
Publication Type: Academic Journal
Source(s): F1000Research [F1000Res] 2023 Nov 10; Vol. 12, pp. 684. Date of Electronic Publication: 2023 Nov 10 (Print Publication: 2023).
Abstract: Background: Single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed in recent years. The droplet-based single cell platforms enable the profiling of gene expression in tens of thousands of cells per sample. The goal of a typical scRN...
A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples.
Publication Type: Academic Journal
Source(s): Nature communications [Nat Commun] 2023 Nov 10; Vol. 14 (1), pp. 7286. Date of Electronic Publication: 2023 Nov 10.
Abstract: Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories o...