Explanipedia

MutagenesisForge: A Framework for Modeling Codon-Level Mutational Biases and Calculating dN/dS Open

Cooper Koers, Rob Bierman, Huixin Xu, Joshua M. Akey · 2025

The ratio of nonsynonymous (d N ) to synonymous (d S ) substitutions in protein-coding genes is a fundamental metric in molecular evolution to test hypotheses about the relative contributions of genetic drift and natural selection in shapi…

Author response: Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells Open

Roozbeh Dehghannasiri, George Henderson, Rob Bierman, Tavor Z. Baharav, Kaitlin Chaung , et al. · 2025

Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells Open

Roozbeh Dehghannasiri, George Henderson, Rob Bierman, Tavor Z. Baharav, Kaitlin Chaung , et al. · 2025

Myriad mechanisms diversify the sequence content of eukaryotic transcripts at both the DNA and RNA levels, leading to profound functional consequences. Examples of this diversity include RNA splicing and V(D)J recombination. Currently, the…

Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells Open

Roozbeh Dehghannasiri, George Henderson, Rob Bierman, Tavor Z. Baharav, Kaitlin Chaung , et al. · 2025

Myriad mechanisms diversify the sequence content of eukaryotic transcripts at both the DNA and RNA levels, leading to profound functional consequences. Examples of this diversity include RNA splicing and V(D)J recombination. Currently, the…

Landscape of human protein-coding somatic mutations across tissues and individuals Open

Huixin Xu, Rob Bierman, Dayna T. Akey, Cooper Koers, Troy J. Comi , et al. · 2025

Although somatic mutations are fundamentally important to human biology, disease, and aging, many outstanding questions remain about their rates, spectrum, and determinants in apparently healthy tissues. Here, we performed high-coverage ex…

Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation Open

Rob Bierman, Jui M. Dave, Daniel M. Greif, Julia Salzman · 2024

Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Furthermore, these studies link localization to RNA isoform expression, …

Author response: Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation Open

Rob Bierman, Jui M. Dave, Daniel M. Greif, Julia Salzman · 2024

Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung Open

Ting-Hsuan Wu, Kyle J. Travaglini, Arjun Rustagi, Duo Xu, Yue Zhang , et al. · 2024

Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and …

Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation Open

Rob Bierman, Jui M. Dave, Daniel M. Greif, Julia Salzman · 2023

Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Further, these studies link localization to RNA isoform expression, espe…

Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation Open

Rob Bierman, Jui M. Dave, Daniel M. Greif, Julia Salzman · 2023

Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Furthermore, these studies link localization to RNA isoform expression, …

Author response: Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation Open

Rob Bierman, Jui M. Dave, Daniel M. Greif, Julia Salzman · 2023

Unsupervised Reference-Free Inference Reveals Unrecognized Regulated Transcriptomic Complexity in Human Single Cells Open

Roozbeh Dehghannasiri, George Henderson, Rob Bierman, Kaitlin Chaung, Tavor Z. Baharav , et al. · 2023

Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells Open

Roozbeh Dehghannasiri, George Henderson, Rob Bierman, Tavor Z. Baharav, Kaitlin Chaung , et al. · 2022

Myriad mechanisms diversify the sequence content of eukaryotic transcripts at both the DNA and RNA levels, leading to profound functional consequences. Examples of this diversity include RNA splicing and V(D)J recombination. Currently, the…

Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation Open

Rob Bierman, Jui M. Dave, Daniel M. Greif, Julia Salzman · 2022

Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Further, these studies link localization to RNA isoform expression, espe…

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs Open

John E. Gorzynski, Hannah N. De Jong, David Amar, Craig D. Hughes, Alexander G. Ioannidis , et al. · 2020

During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We h…

Statistical algorithms improve accuracy of gene fusion detection Open

Gillian L. Hsieh, Rob Bierman, Linda Szabo, Alex Gia Lee, Donald E. Freeman , et al. · 2017

Gene fusions are known to play critical roles in tumor pathogenesis. Yet, sensitive and specific algorithms to detect gene fusions in cancer do not currently exist. In this paper, we present a new statistical algorithm, MACHETE (Mismatched…

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