ArticleNature methods2015
Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.
- Assessing the relationship between toxicity and economic cost of oncological target agents: A systematic review of clinical trials.PloS one · 2017Pooled it
- Objective clustering protocol for single-molecule data: A lifetime vs. intensity study.Biophysical reports · 2026Article
- Structural Characterization of Protein-Nucleic Acid Complexes: An Overview of the Recent Innovation in the Analytic Methods.International journal of molecular sciences · 2025Review
- Foundation model for efficient biological discovery in single-molecule time traces.Nature methods · 2025Article
- Single bacterial resolvases first exploit, then constrain intrinsic dynamics of the Holliday junction to direct recombination.Nucleic acids research · 2021Article
- Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning.Nature communications · 2020Article
- Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy.Molecules (Basel, Switzerland) · 2020Review
- Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure.Nucleic acids research · 2020Article
- SHAPE Probing Reveals Human rRNAs Are Largely Unfolded in Solution.Biochemistry · 2019Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
- Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity.Biophysical journal · 2019Article
- Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope.Cold Spring Harbor perspectives in biology · 2019Review
- An automated Bayesian pipeline for rapid analysis of single-molecule binding data.Nature communications · 2019Article
- Structural dynamics of the N-terminal domain and the Switch loop of Prp8 during spliceosome assembly and activation.Nucleic acids research · 2018Review
- Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World.Chemical reviews · 2018Review
- Methodologies for studying the spliceosome's RNA dynamics with single-molecule FRET.Methods (San Diego, Calif.) · 2017Review
- RNA splicing process analysis for identifying antisense oligonucleotide inhibitors with padlock probe-based isothermal amplification.Chemical science · 2017Article
- ICON: An Adaptation of Infinite HMMs for Time Traces with Drift.Biophysical journal · 2017Article
- An Introduction to Infinite HMMs for Single-Molecule Data Analysis.Biophysical journal · 2017Review
- Single-Molecule Analysis beyond Dwell Times: Demonstration and Assessment in and out of Equilibrium.Biophysical journal · 2016Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
We report Single Molecule Cluster Analysis (SiMCAn), which utilizes hierarchical clustering of hidden Markov modeling-fitted single-molecule fluorescence resonance energy transfer (smFRET) trajectories to dissect the complex conformational dynamics of biomolecular machines. We used this method to study the conformational dynamics of a precursor mRNA during the splicing cycle as carried out by the spliceosome. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify the signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified an open conformation adopted late in splicing by a 3' splice-site mutant, invoking a mechanism for substrate proofreading. SiMCAn enables rapid interpretation of complex single-molecule behaviors and should prove useful for the comprehensive analysis of a plethora of dynamic cellular machines.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.