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Article
Scanorama: integrating large and diverse single-cell transcriptomic datasets
Merging diverse single-cell RNA sequencing (scRNA-seq) data from numerous experiments, laboratories and technologies can uncover important biological insights. Nonetheless, integrating scRNA-seq data encounter...
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Chapter and Conference Paper
Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets
Finding related individuals in genomic datasets is a necessary step in many genetic analysis workflows and has broader societal value as a tool for retrieving lost relatives. However, detecting such relationsh...
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Article
Open AccessSCA: recovering single-cell heterogeneity through information-based dimensionality reduction
Dimensionality reduction summarizes the complex transcriptomic landscape of single-cell datasets for downstream analyses. Current approaches favor large cellular populations defined by many genes, at the expen...
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Article
The scverse project provides a computational ecosystem for single-cell omics data analysis
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Article
Navigating bottlenecks and trade-offs in genomic data analysis
Genome sequencing and analysis allow researchers to decode the functional information hidden in DNA sequences as well as to study cell to cell variation within a cell population. Traditionally, the primary bot...
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Article
Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN
Single-particle cryogenic electron microscopy (cryo-EM) has emerged as a powerful technique to visualize the structural landscape sampled by a protein complex. However, algorithmic and computational bottleneck...
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Article
Open AccessSequre: a high-performance framework for secure multiparty computation enables biomedical data sharing
Secure multiparty computation (MPC) is a cryptographic tool that allows computation on top of sensitive biomedical data without revealing private information to the involved entities. Here, we introduce Sequre...
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Article
Open AccessGenome-wide map** of somatic mutation rates uncovers drivers of cancer
Identification of cancer driver mutations that confer a proliferative advantage is central to understanding cancer; however, searches have often been limited to protein-coding sequences and specific non-coding...
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Article
Developmental dynamics of RNA translation in the human brain
The precise regulation of gene expression is fundamental to neurodevelopment, plasticity and cognitive function. Although several studies have profiled transcription in the develo** human brain, there is a g...
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Article
Open AccessIdentification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
Cynomolgus macaque (Macaca fascicularis) is an attractive animal model for the study of human disease and is extensively used in biomedical research. Cynomolgus macaques share behavioral, physiological, and genom...
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Article
Open AccessConformational landscape of the yeast SAGA complex as revealed by cryo-EM
Spt-Ada-Gcn5-Acetyltransferase (SAGA) is a conserved multi-subunit complex that activates RNA polymerase II-mediated transcription by acetylating and deubiquitinating nucleosomal histones and by recruiting TAT...
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Protocol
Enriching and Characterizing T Cell Repertoires from 3′ Barcoded Single-Cell Whole Transcriptome Amplification Products
play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor ( ) sequences that encode T cell is critical for elucidating the antigenic determinants of imm...
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Article
Open AccessAuthor Correction: Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
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Article
Open AccessTruly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
Using real-world evidence in biomedical research, an indispensable complement to clinical trials, requires access to large quantities of patient data that are typically held separately by multiple healthcare i...
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Article
A Python-based programming language for high-performance computational genomics
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Article
Assessing single-cell transcriptomic variability through density-preserving data visualization
Nonlinear data visualization methods, such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP), summarize the complex transcriptomic landscape of single...
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Article
Open AccessSchema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities
A complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease status, or gene expression. Technological advances in single-cell profil...
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Article
Large mosaic copy number variations confer autism risk
Although germline de novo copy number variants (CNVs) are known causes of autism spectrum disorder (ASD), the contribution of mosaic (early-developmental) copy number variants (mCNVs) has not been explored. In...
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Article
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many imaged protein complexes exhibit conformational and composit...
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Article
Structures of radial spokes and associated complexes important for ciliary motility
In motile cilia, a mechanoregulatory network is responsible for converting the action of thousands of dynein motors bound to doublet microtubules into a single propulsive waveform. Here, we use two complementa...
