Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Network medicine in the age of biomedical big data

AR Sonawane, ST Weiss, K Glass, A Sharma - Frontiers in Genetics, 2019 - frontiersin.org
Network medicine is an emerging area of research dealing with molecular and genetic
interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale …

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

E Madissoon, A Wilbrey-Clark, RJ Miragaia… - Genome biology, 2020 - Springer
Abstract Background The Human Cell Atlas is a large international collaborative effort to
map all cell types of the human body. Single-cell RNA sequencing can generate high-quality …

[HTML][HTML] The Human Cell Atlas bone marrow single-cell interactive web portal

SB Hay, K Ferchen, K Chetal, HL Grimes… - Experimental …, 2018 - Elsevier
Highlights•Interactive resource for bone marrow donor variation between cell
populations.•Deep evaluation of Human Cell Atlas (HCA) data spanning eight donors and …

Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease

MM Uddin, NQH Nguyen, B Yu, JA Brody… - Nature …, 2022 - nature.com
Age-related changes to the genome-wide DNA methylation (DNAm) pattern observed in
blood are well-documented. Clonal hematopoiesis of indeterminate potential (CHIP) …

Single-cell (multi) omics technologies

L Chappell, AJC Russell, T Voet - Annual review of genomics …, 2018 - annualreviews.org
Single-cell multiomics technologies typically measure multiple types of molecule from the
same individual cell, enabling more profound biological insight than can be inferred by …

Dynamic enhancer landscapes in human craniofacial development

SS Rajderkar, K Paraiso, ML Amaral, M Kosicki… - Nature …, 2024 - nature.com
The genetic basis of human facial variation and craniofacial birth defects remains poorly
understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal …

Data integration challenges for machine learning in precision medicine

M Martínez-García, E Hernández-Lemus - Frontiers in medicine, 2022 - frontiersin.org
A main goal of Precision Medicine is that of incorporating and integrating the vast corpora on
different databases about the molecular and environmental origins of disease, into analytic …

Omics-based approaches to guide the design of biomaterials

AL Kersey, TU Nguyen, B Nayak, I Singh, AK Gaharwar - Materials Today, 2023 - Elsevier
Recent developments in biomedical engineering have focused on designing smart and bio-
responsive materials. However, a critical step in designing this next generation of …

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data

N Johansen, G Quon - Genome biology, 2019 - Springer
Abstract scRNA-seq dataset integration occurs in different contexts, such as the identification
of cell type-specific differences in gene expression across conditions or species, or batch …