Evan Biederstedt
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View article: scTab: Scaling cross-tissue single-cell annotation models
scTab: Scaling cross-tissue single-cell annotation models Open
Identifying cellular identities is a key use case in single-cell transcriptomics. While machine learning has been leveraged to automate cell annotation predictions for some time, there has been little progress in scaling neural networks to…
View article: Gene panel selection for targeted spatial transcriptomics
Gene panel selection for targeted spatial transcriptomics Open
View article: Scaling cross-tissue single-cell annotation models
Scaling cross-tissue single-cell annotation models Open
Identifying cellular identities (both novel and well-studied) is one of the key use cases in single-cell transcriptomics. While supervised machine learning has been leveraged to automate cell annotation predictions for some time, there has…
View article: Gene panel selection for targeted spatial transcriptomics
Gene panel selection for targeted spatial transcriptomics Open
Targeted spatial transcriptomics hold particular promise in analysis of complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes…
View article: Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes
Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes Open
View article: Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals
Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals Open
Summary Tissue- and organism-level biological processes often involve coordinated action of multiple distinct cell types. Current computational methods for the analysis of single-cell RNA-sequencing (scRNA-seq) data, however, are not desig…
View article: Haplotype-enhanced inference of somatic copy number profiles from single-cell transcriptomes
Haplotype-enhanced inference of somatic copy number profiles from single-cell transcriptomes Open
Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. However, their relationship and relative contribution to tumor evolution and therapy resistance are not well-understood. Single-ce…
View article: An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates Open
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related rese…
View article: A strategy for building and using a human reference pangenome
A strategy for building and using a human reference pangenome Open
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and sta…
View article: An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates Open
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related rese…
View article: NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index Open
Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack…
View article: Phase and context shape the function of composite oncogenic mutations
Phase and context shape the function of composite oncogenic mutations Open
View article: A strategy for building and using a human reference pangenome
A strategy for building and using a human reference pangenome Open
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and sta…
View article: Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia
Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia Open
View article: The Human Pangenome
The Human Pangenome Open
View article: NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
NovoGraph: Human genome graph construction from multiple long-read de novo assemblies Open
Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the im…
View article: NovoGraph: Genome graph construction from multiple long-read de novo assemblies
NovoGraph: Genome graph construction from multiple long-read de novo assemblies Open
Genome graphs are emerging as an important novel approach to the analysis of high-throughput sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved…