Todd M. Lowe

About

Todd M. Lowe is a faculty member at the Baskin School of Engineering at UC Santa Cruz. The school emphasizes socially responsible innovation across various engineering disciplines, including health engineering, climate and sustainability, machine learning, artificial intelligence, games, and human computer interaction. The university fosters a collaborative environment where faculty and students work together to create technology with a positive societal impact, leveraging top-tier research resources and interdisciplinary approaches. While the page highlights the school's research areas, community engagement, and institutional achievements, it does not provide specific details about Todd M. Lowe's individual research focus, background, or key contributions.

Research topics

• Biology
• Genetics
• Computational biology
• Evolutionary biology
• Biochemistry

Selected publications

• tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

  Nucleic Acids Research · 2021-07-27 · 1935 citations

  articleOpen accessSenior author

  tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and functional prediction of tRNAs has become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype- and clade-specific models, greatly improving tRNAscan-SE's ability to identify and classify both ty…

  PublisherDOI

• RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

  Nucleic Acids Research · 2020-10-06 · 412 citations

  articleOpen access

  RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable…

  PublisherOA PDFDOI

• The UCSC SARS-CoV-2 Genome Browser

  Nature Genetics · 2020-09-09 · 100 citations

  articleOpen access

  The UCSC SARS-CoV-2 Genome Browser ( https://genome.ucsc.edu/covid19.html ) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT–PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.

  PublisherOA PDFDOI

• R2DT: a comprehensive platform for visualizing RNA secondary structure

  Nucleic Acids Research · 2025-02-08 · 21 citations

  articleOpen access

  RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-…

  PublisherDOI

• A hypoxia-responsive tRNA-derived small RNA confers renal protection through RNA autophagy

  Science · 2025-07-17 · 17 citations

  articleOpen access

  Transfer RNA-derived small RNAs (tsRNAs or tDRs) perform a range of cellular functions. Here, we showed that tRNA-Asp-GTC-3'tDR, a hypoxia-induced tDR derived from the 3' end of tRNA-Asp-GTC, activated autophagic flux in kidney cells and its silencing blocked autophagic flux. Functional gain-/loss-of-function studies in murine kidney disease models demonstrated a substantial renoprotective function of tRNA-Asp-GTC-3'tDR. Mechanistically, tRNA-Asp-GTC-3'tDR assembled stable G-quadruplex structure…

  PublisherOA PDFDOI

Recent grants

• High-Throughput Small RNA Sequencing in Archaea

  NSF · $809k · 2008–2012

• Community Center for Archaeal and Extremophile Genome Research

  NSF · $810k · 2007–2012

• A Unified Atlas of Dynamic tRNA Function

  NIH · $4.6M · 2012–2024

Frequent coauthors

• Patricia P. Chan

  37 shared

• Patrick P. Dennis

  31 shared

• Leroy Hood

  Institute for Systems Biology

  25 shared

• Young Ah Goo

  James S. McDonnell Foundation

  24 shared

• Stephen R. Lasky

  24 shared

• Gregory G. Mahairas

  24 shared

• Vésteinn Thórsson

  24 shared

• Min Pan

  Guangzhou Medical University

  24 shared

Education

• Ph.D., Genetics

  Washington University in St. Louis

  1999

Awards & honors

• Richard E. Green, Lifetime Achievement Award (2025)
• Mike Beck, Innovator of the Year (2025)
• NeuroSWARM3, developed by the Yanik Lab led by Ahmet A. Yani…
• Bud Colligan, Community Changemaker (2025)
• XR Experience Jury Award at SXSW (2026)

Similar researchers at University of California, Santa Cruz

• Carol Greiderh-100
• John Tamkunh-55
• William Sullivanh-55