Protein sequencing, one molecule at a time
BM Floyd, EM Marcotte - Annual review of biophysics, 2022 - annualreviews.org
Despite tremendous gains over the past decade, methods for characterizing proteins have
generally lagged behind those for nucleic acids, which are characterized by extremely high …
generally lagged behind those for nucleic acids, which are characterized by extremely high …
Microfluidic single-cell transcriptomics: moving towards multimodal and spatiotemporal omics
Cells are the basic units of life with vast heterogeneity. Single-cell transcriptomics unveils
cell-to-cell gene expression variabilities, discovers novel cell types, and uncovers the critical …
cell-to-cell gene expression variabilities, discovers novel cell types, and uncovers the critical …
Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data
Identification of cell populations often relies on manual annotation of cell clusters using
established marker genes. However, the selection of marker genes is a time-consuming …
established marker genes. However, the selection of marker genes is a time-consuming …
MUON: multimodal omics analysis framework
D Bredikhin, I Kats, O Stegle - Genome biology, 2022 - Springer
Advances in multi-omics have led to an explosion of multimodal datasets to address
questions from basic biology to translation. While these data provide novel opportunities for …
questions from basic biology to translation. While these data provide novel opportunities for …
Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development
A Sur, Y Wang, P Capar, G Margolin, MK Prochaska… - Developmental Cell, 2023 - cell.com
During development, animals generate distinct cell populations with specific identities,
functions, and morphologies. We mapped transcriptionally distinct populations across …
functions, and morphologies. We mapped transcriptionally distinct populations across …
Variant to function mapping at single-cell resolution through network propagation
Genome-wide association studies in combination with single-cell genomic atlases can
provide insights into the mechanisms of disease-causal genetic variation. However …
provide insights into the mechanisms of disease-causal genetic variation. However …
The tidyomics ecosystem: Enhancing omic data analyses
WJ Hutchison, TJ Keyes, Tidyomics Consortium… - Nature …, 2024 - nature.com
The growth of omic data presents evolving challenges in data manipulation, analysis and
integration. Addressing these challenges, Bioconductor provides an extensive community …
integration. Addressing these challenges, Bioconductor provides an extensive community …
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
Rigorous record-keeping and quality control are required to ensure the quality,
reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light …
reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light …
Single-cell RNA-sequencing of mammalian brain development: insights and future directions
E Vinsland, S Linnarsson - Development, 2022 - journals.biologists.com
Understanding human brain development is of fundamental interest but is also very
challenging. Single-cell RNA-sequencing studies in mammals have revealed that brain …
challenging. Single-cell RNA-sequencing studies in mammals have revealed that brain …
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
A Rigano, S Ehmsen, SU Öztürk, J Ryan, A Balashov… - Nature …, 2021 - nature.com
For quality, interpretation, reproducibility and sharing value, microscopy images should be
accompanied by detailed descriptions of the conditions that were used to produce them …
accompanied by detailed descriptions of the conditions that were used to produce them …