Jiadong Lin

Atlas-scale single-cell analysis beyond in-memory paradigm with scAtlasPy

Xu Han, Yangzhan Ye, Senpeng Zhang, Runzhi Xie et autres

Abstract Single-cell atlases are rapidly outgrowing the memory capacity of standard workstations, challenging the in-memory paradigm underlying mainstream computational ecosystems. Here, scAtlasPy decouples scale of atlas from memory capacity by leveraging the disk-resident computing. It enables full-resolution analysis of a 100-million-cell atlas …

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Atlas-scale single-cell analysis beyond in-memory paradigm with scAtlasPy

Xu Han, Yangzhan Ye, Senpeng Zhang, Runzhi Xie et autres

A scalable Python platform for atlas-scale single-cell omics analysis beyond in-memory limits.scAtlasPy is a Python platform for analyzing cell atlases that are too large to fit in memory. It extends familiar single-cell analysis workflows to atlas-scale datasets, supporting preprocessing, dimensionality reduction, clustering, …

A high-resolution human pangenome structural variant resource for improved disease association

Jiadong Lin, Jonas A. Gustafson, Julie Wertz, Yang Sui et autres

Long-read sequencing (LRS) and diploid genome assembly have enabled nearly complete structural variant (SV) discovery. Using 293 nearly complete genomes, we characterize the full spectrum of genetic variation and show that while 99% of the variants between any two genomes are single …

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Human acrocentric chromosome short-arm de novo mutation and recombination

Jiadong Lin, Francesco Kumara Mastrorosa, Michelle D. Noyes, DongAhn Yoo et autres

Highly repetitive short arms of human acrocentric chromosomes have remained largely inaccessible to studies of meiotic recombination and de novo mutation. Integrating long-read and complementary sequencing approaches, we created 156 phased short arms and assessed 107 transmissions from 23 samples in a …

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Complex structural variation, phylogeny, and disease associations of the mucin pangenome

Elizabeth G. Plender, Timofey Prodanov, Jiadong Lin, Isaac Wong et autres

Mucins are large glycoproteins that provide hydration and barrier function to epithelial tissues. Although genetically heterogeneous, all mucins harbor a large exon composed of variable number tandem repeats (VNTRs). Short-read sequencing has limited our understanding of mucin VNTR diversity and makes disease …

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needLR: long-read structural variant annotation with population-scale frequency estimation

Jonas A. Gustafson, Jiadong Lin, Evan E. Eichler, Danny E. Miller

SUMMARY: We present needLR, a structural variant (SV) annotation tool that can be used for filtering and prioritization of candidate pathogenic SVs from long-read sequencing data using population allele frequencies, annotations for genomic context, and gene-phenotype associations. When using population data from …

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Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants

Ningxin Dang, Peng Jia, Jiadong Lin, Yutong Xie et autres

Single nucleotide variant calling protocols routinely discard calls in the regions immediately flanking structural variants (often 50 bp either side) because it is technically challenging to call them accurately. Although there are undoubtedly true variants of interest in these regions, many remain …

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Highly accurate ab initio gene annotation with ANNEVO

Pengyu Zhang, Tun Xu, Songbo Wang, Xiaofei Yang et autres

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Physics-Aware Semantic Graph Classifier for Remote Sensing Images

Lingling Li, Jiadong Lin, Licheng Jiao, Fang Liu et autres

Remote sensing scenes face the challenges of high inter class similarity and high intra class diversity in classification. Methods based on deep learning have advanced the field by learning discriminative features, but these methods have two key limitations: 1) the scope of …

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A Triple-Crosslinking Strategy within a Bis-Donor Architecture: Breaking the Trade-off between Electro-Optic Activity and Thermal Stability

Jiadong Lin, Yanzhe Gan, Xingtao Wang, Lin Li et autres

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Human acrocentric chromosome short arm de novo mutation and recombination

Jiadong Lin, Francesco Kumara Mastrorosa, Michelle D. Noyes, DongAhn Yoo et autres

ABSTRACT The extraordinary repetitive content of human acrocentric short arms has prevented detailed investigations into recombination and de novo mutation. Integrating multiple sequencing technologies, we created 156 phased short arms and assessed 107 intergenerational transmissions from 23 samples in a four-generation pedigree. …

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Structural and transduction patterns of human-specific polymorphic SVA insertions

Ashley E. Kirby, Mark G. Loftus, Emily Golba, Haley Abel et autres

BACKGROUND: SINE variable number tandem repeat Alu elements (SVAs) are a unique group of hominid-specific composite retrotransposons with highly variable internal structure. They represent the youngest TE family in humans and contribute to genetic diversity, evolution, and disease. Recent findings indicate that …

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