Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
Single-cell transcriptomics meets lineage tracing
L Kester, A Van Oudenaarden - Cell stem cell, 2018 - cell.com
Reconstructing lineage relationships between cells within a tissue or organism is a long-
standing aim in biology. Traditionally, lineage tracing has been achieved through the …
standing aim in biology. Traditionally, lineage tracing has been achieved through the …
Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling
Drug resistance in cancer is often linked to changes in tumor cell state or lineage, but the
molecular mechanisms driving this plasticity remain unclear. Using murine organoid and …
molecular mechanisms driving this plasticity remain unclear. Using murine organoid and …
[HTML][HTML] Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer
Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined
by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A,-N, and-P …
by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A,-N, and-P …
Deep generative modeling for single-cell transcriptomics
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they
suffer from technical noise and bias that must be modeled to account for the resulting …
suffer from technical noise and bias that must be modeled to account for the resulting …
Chromosomal instability drives metastasis through a cytosolic DNA response
Chromosomal instability is a hallmark of cancer that results from ongoing errors in
chromosome segregation during mitosis. Although chromosomal instability is a major driver …
chromosome segregation during mitosis. Although chromosomal instability is a major driver …
[HTML][HTML] Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer
The diverse malignant, stromal, and immune cells in tumors affect growth, metastasis, and
response to therapy. We profiled transcriptomes of∼ 6,000 single cells from 18 head and …
response to therapy. We profiled transcriptomes of∼ 6,000 single cells from 18 head and …
SAVER: gene expression recovery for single-cell RNA sequencing
In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts
present in each cell are sequenced. This leads to unreliable quantification of genes with low …
present in each cell are sequenced. This leads to unreliable quantification of genes with low …
Single-cell RNA-seq denoising using a deep count autoencoder
Single-cell RNA sequencing (scRNA-seq) has enabled researchers to study gene
expression at a cellular resolution. However, noise due to amplification and dropout may …
expression at a cellular resolution. However, noise due to amplification and dropout may …
An accurate and robust imputation method scImpute for single-cell RNA-seq data
The emerging single-cell RNA sequencing (scRNA-seq) technologies enable the
investigation of transcriptomic landscapes at the single-cell resolution. ScRNA-seq data …
investigation of transcriptomic landscapes at the single-cell resolution. ScRNA-seq data …