Host and microbiome multi-omics integration: applications and methodologies
The study of the microbial community—the microbiome—associated with a human host is a
maturing research field. It is increasingly clear that the composition of the human’s …
maturing research field. It is increasingly clear that the composition of the human’s …
[HTML][HTML] CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data
P Lin, M Troup, JWK Ho - Genome biology, 2017 - Springer
Most existing dimensionality reduction and clustering packages for single-cell RNA-seq (scRNA-seq)
data deal with dropouts by heavy modeling and computational machinery. Here, …
data deal with dropouts by heavy modeling and computational machinery. Here, …
Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury
…, M Xaymardan, V Janbandhu, K Wystub-Lis, JWK Ho… - Elife, 2019 - elifesciences.org
10.7554/eLife.43882.001 Besides cardiomyocytes (CM), the heart contains numerous
interstitial cell types which play key roles in heart repair, regeneration and disease, including …
interstitial cell types which play key roles in heart repair, regeneration and disease, including …
[HTML][HTML] Comparative analysis of metazoan chromatin organization
Genome function is dynamically regulated in part by chromatin, which consists of the histones,
non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis …
non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis …
Testing and validating machine learning classifiers by metamorphic testing
Machine learning algorithms have provided core functionality to many application domains
– such as bioinformatics, computational linguistics, etc. However, it is difficult to detect faults …
– such as bioinformatics, computational linguistics, etc. However, it is difficult to detect faults …
[HTML][HTML] Scalability and validation of big data bioinformatics software
This review examines two important aspects that are central to modern big data bioinformatics
analysis – software scalability and validity. We argue that not only are the issues of …
analysis – software scalability and validity. We argue that not only are the issues of …
[HTML][HTML] NAD deficiency, congenital malformations, and niacin supplementation
Background Congenital malformations can be manifested as combinations of phenotypes
that co-occur more often than expected by chance. In many such cases, it has proved difficult …
that co-occur more often than expected by chance. In many such cases, it has proved difficult …
Intercalated discs: multiple proteins perform multiple functions in non-failing and failing human hearts
The intercalated disc (ICD) occupies a central position in the transmission of force, electrical
continuity and chemical communication between cardiomyocytes. Changes in its structure …
continuity and chemical communication between cardiomyocytes. Changes in its structure …
[HTML][HTML] ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis
Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip)
or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein…
or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein…
[HTML][HTML] An innovative approach for testing bioinformatics programs using metamorphic testing
Background Recent advances in experimental and computational technologies have fueled
the development of many sophisticated bioinformatics programs. The correctness of such …
the development of many sophisticated bioinformatics programs. The correctness of such …