9 papers · ranked by Valyu relevance
Hyunwook Koh
In high-dimensional omics studies, researchers often conduct kernel association testing to power-fully detect the relationship of the genetic or microbial composition with human health or disease. Especially, in human microbiome studies, its dimension reduction analysis follows to visually represent complex microbiome…
Parisa Shahnazari, Kaveh Kavousi, Hamid Reza Khorram Khorshid, Bahram Goliaei + 1 more
Integrating multiple omics modalities is a crucial strategy in cancer research, particularly in metabolomics, enabling early detection and detailed exploration of cancer biomarker signatures. This study evaluates five strategies for integrating metabolomics data from liquid chromatography-mass spectrometry, gas…
Sairu Shi, Shu Kong, Qingwei Zhang, Ji Zhang
Microbial dysregulation may lead to the occurrence of diseases, and using microbe and drug data to infer the microbe-drug association has attracted extensive attention. There have been many studies to build association prediction models, but most of them are through biological experiments, which are time-consuming and…
Abdullah Karaaslanli, Satabdi Saha, Selin Aviyente, Tapabrata Maiti
Characterizing the underlying topology of gene regulatory networks is one of the fundamental problems of systems biology. Ongoing developments in high throughput sequencing technologies has made it possible to capture the expression of thousands of genes at the single cell resolution. However, inherent cellular…
Rajintha Gunawardena, Ptolemaios G. Sarrigiannis, Daniel J. Blackburn, Fei He
For the characterisation and diagnosis of neurological disorders, dynamical, causal and crossfrequency coupling analysis using the EEG has gained considerable attention. Due to high computational costs in implementing some of these methods, the selection of important EEG channels is crucial. The channel selection…
Hyunwook Koh
There are numerous potential confounders, including genetic, environmental, technical, and demographic factors. These factors may be known or unknown, measured or unmeasured; hence, it is extremely challenging to capture them in downstream data analysis. However, randomized block design is an efficient design technique…
Samantha Petti, Carlos Martí-Gómez, Justin B. Kinney, Juannan Zhou + 1 more
Mappings from biological sequences (DNA, RNA, protein) to quantitative measures of sequence functionality play an important role in contemporary biology. We are interested in the related tasks of (i) inferring predictive sequence-to-function maps and (ii) decomposing sequence-function maps to elucidate the…
Anirban Chakraborty, Chloe Mattila, Debashis Ghosh, Brian Neelon + 1 more
High-throughput bulk and single-cell omics technologies enable comprehensive molecular profiling, yet identifying compact, biologically interpretable marker sets that distinguish cell types, conditions, or disease states remains challenging. Standard pipelines rely on univariate differential expression tests, which…
Wei Zhang, Hanchen Huang, Lily Wang, Brian D. Lehmann + 1 more
High-throughput technologies now produce a wide array of omics data, from genomic and transcriptomic profiles to epigenomic and proteomic measurements. Integrating these diverse data types can yield deeper insights into the biological mechanisms driving complex traits and diseases. Yet, extracting key shared biomarkers…