Peter L. Wang

Reference-free discovery with barcoded single-cell sequencing

Roozbeh Dehghannasiri, Marek Kokot, Alexander L. Starr, Jamie Maziarz et autres

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FunctionaL Assigning Sequence Homing (FLASH) maps phenotype to sequence with deep and machine learning

Daniel J. Cotter, Marie‐Claire Harrison, Arjun Rustagi, Peter L. Wang et autres

Genome-wide association studies (GWAS) map genetic variation to a reference genome and correlate variants to phenotypes. Yet, GWAS and similar procedures have limitations, including an inability to predict phenotype on variants never seen during the discovery phase and difficulty integrating structural variants. …

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sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing

Roozbeh Dehghannasiri, Marek Kokot, Alexander L. Starr, Jamie Maziarz et autres

Abstract Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by other mechanisms that diversify the transcriptome such as splicing and V(D)J …

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Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment

Carina Shiau, Jingyi Cao, Dennis Gong, Mark Gregory et autres

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Abstract 4901: High-resolution spatial transcriptomics identifies candidate genes facilitating perineural invasion

Deniz G. Olgun, Peter L. Wang, Ryan Zhao, Dennis Gong et autres

Abstract Perineural invasion (PNI), or the invasion of cancer to the space surrounding nerves, is associated with poor prognosis, but the underlying molecular factors that drive its initiation and progression are poorly understood. To explore this systematically, we applied a 6000-plex spatial …

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Ultra-efficient, unified discovery from microbial sequencing with SPLASH and precise statistical assembly

George Henderson, Adam Gudys, Tavor Z. Baharav, Punit Sundaramurthy et autres

Abstract Bacteria comprise > 12% of Earth’s biomass and profoundly impact human and planetary health. 1 Many key biological functions of microbes, and functions differentiating strains, are conferred or modified by genome plasticity including mobilization of genetic elements, phage integration, and CRISPR …

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SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery

Kaitlin Chaung, Tavor Z. Baharav, George Henderson, Ivan N. Zheludev et autres

Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific …

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DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery

Jordi Abante, Peter L. Wang, Julia Salzman

Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in …

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SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

Kaitlin Chaung, Tavor Z. Baharav, George Henderson, Ivan N. Zheludev et autres

The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/497555. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The …

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Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

Carina Shiau, Jingyi Cao, Mark Gregory, Dennis Gong et autres

ABSTRACT In combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect the remodeling of multicellular neighborhoods and cell–cell interactions in human pancreatic cancer associated with specific malignant subtypes and neoadjuvant …

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PDAC-SMI transcript locations

Carina Shiau, Jingyi Cao, Dennis Gong, Mark Gregory et autres

This record contains the spatial locations of transcripts in the PDAC-SMI data.

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PDAC-SMI transcript locations

Carina Shiau, Jingyi Cao, Dennis Gong, Mark Gregory et autres

This record contains the spatial locations of transcripts in the PDAC-SMI data.

us, jp (code pays fourni par la source)