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D-Index & Metrics

Engineering and Technology

D-Index
30
Citations
13697
World Ranking
9739
National Ranking
2774

Overview

Niles A. Pierce is a researcher affiliated with the California Institute of Technology in the United States. Their work primarily focuses on biochemistry, genetics, and molecular biology, contributing to a total of 37 publications in this field. The research spans several subfields including molecular biology, infectious diseases, biomedical engineering, genetics, and physiology.

The scientist's research addresses advanced biosensing and bioanalysis techniques, molecular biology techniques and applications, RNA and protein synthesis mechanisms, single-cell and spatial transcriptomics, DNA and nucleic acid chemistry, SARS-CoV-2 detection and testing, as well as biosensors and analytical detection. These topics reflect a broad range of interests centered on molecular processes and analytical methods at the cellular level.

Niles A. Pierce has contributed to multiple publication venues, with frequent work appearing in:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Methods in molecular biology
  • Development
  • ACS Synthetic Biology
  • ACS Chemical Biology

Their recent papers include:

  • "Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization," 2021, Development
  • "A Unified Dynamic Programming Framework for the Analysis of Interacting Nucleic Acid Strands: Enhanced Models, Scalability, and Speed," 2020, ACS Synthetic Biology
  • "High-Performance Allosteric Conditional Guide RNAs for Mammalian Cell-Selective Regulation of CRISPR/Cas," 2021, ACS Synthetic Biology
  • "Multiplexed Quantitative In Situ Hybridization with Subcellular or Single-Molecule Resolution Within Whole-Mount Vertebrate Embryos: qHCR and dHCR Imaging (v3.0)," 2020, Methods in molecular biology
  • "Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization," 2021, bioRxiv (Cold Spring Harbor Laboratory)

Frequent co-authors collaborating with Niles A. Pierce include:

  • Samuel J. Schulte
  • Maayan Schwarzkopf
  • Harry M. T. Choi
  • Mark E. Fornace
  • Mike C. Liu

Best Publications

  • NUPACK: Analysis and design of nucleic acid systems

    Joseph N. Zadeh;Conrad D. Steenberg;Justin S. Bois;Brian R. Wolfe

  • Programming biomolecular self-assembly pathways

    Peng Yin;Harry M. T. Choi;Colby R. Calvert;Niles A. Pierce

  • An Introduction to the Adjoint Approach to Design

    Michael B. Giles;Niles A. Pierce

  • Optimum aerodynamic design using the Navier-Stokes equations

    A. Jameson;Luigi Martinelli;N. A. Pierce

  • Programmable in situ amplification for multiplexed imaging of mRNA expression

    Harry M T Choi;Joann Y Chang;Le A Trinh;Jennifer E Padilla

  • Optimum aerodynamic design using the navier-stokes equations

    A. Jameson;N. A. Pierce;L. Martinelli

  • A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots

    Robert M. Dirks;Niles A. Pierce

  • Thermodynamic Analysis of Interacting Nucleic Acid Strands

    Robert M. Dirks;Justin S. Bois;Joseph M. Schaeffer;Erik Winfree

  • Algorithm Developments for Discrete Adjoint Methods

    Michael B. Giles;Mihai C. Duta;Jens-Dominik Müller;Niles A. Pierce

  • Adjoint Recovery of Superconvergent Functionals from PDE Approximations

    Niles A. Pierce;Michael B. Giles

  • An autonomous polymerization motor powered by DNA hybridization.

    Suvir Venkataraman;Robert M. Dirks;Paul W. K. Rothemund;Erik Winfree

  • Adjoint equations in CFD: duality, boundary conditions and solution behaviour

    M. B. Giles;N. A. Pierce

  • Protein Design is NP-hard

    Niles A. Pierce;Erik Winfree

  • Paradigms for computational nucleic acid design

    Robert M. Dirks;Milo M Lin;Erik Winfree;Niles A. Pierce

  • Nucleic acid sequence design via efficient ensemble defect optimization.

    Joseph N. Zadeh;Brian R. Wolfe;Niles A. Pierce

  • Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.

    Sheel Shah;Sheel Shah;Eric Lubeck;Maayan Schwarzkopf;Ting Fang He

  • An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.

    Robert M. Dirks;Niles A. Pierce

  • Conformational splitting: a more powerful criterion for dead-end elimination

    Niles A. Pierce;Jan A. Spriet;Johan Desmet;Stephen L. Mayo

  • Analytic adjoint solutions for the quasi-one-dimensional Euler equations

    Michael B. Giles;Niles A. Pierce

  • Adjoint and defect error bounding and correction for functional estimates

    Niles A. Pierce;Michael B. Giles

  • Exact rotamer optimization for protein design

    D. Benjamin Gordon;Geoffrey K. Hom;Stephen L. Mayo;Niles A. Pierce

  • Preconditioned Multigrid Methods for Compressible Flow Calculations on Stretched Meshes

    Niles A. Pierce;Michael B. Giles

  • Improved- lift and drag estimates using adjoint Euler equations

    Michael B. Giles;Niles A. Pierce

  • Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering

    Brian R. Wolfe;Nicholas J. Porubsky;Joseph N. Zadeh;Robert M. Dirks

Frequent Co-Authors

Michael B. Giles
Michael B. Giles University of Oxford
Erik Winfree
Erik Winfree California Institute of Technology
Scott E. Fraser
Scott E. Fraser University of Southern California
Antony Jameson
Antony Jameson Texas A&M University
Stephen L. Mayo
Stephen L. Mayo California Institute of Technology
Juan J. Alonso
Juan J. Alonso Stanford University
Brian M. Stoltz
Brian M. Stoltz California Institute of Technology
Zhen-Gang Wang
Zhen-Gang Wang California Institute of Technology
Barbara J. Wold
Barbara J. Wold California Institute of Technology
Paul W. Sternberg
Paul W. Sternberg California Institute of Technology

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