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Getting to the bottom of lncRNA mechanism: structure–function relationships

Mammalian genome, 2022-06, Vol.33 (2), p.343-353

Sanbonmatsu, Karissa

2022

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Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR

Current opinion in structural biology, 2019-04, Vol.55 (C), p.104-113

Sanbonmatsu, Karissa Y

2019

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Towards structural classification of long non-coding RNAs

Biochimica et biophysica acta, 2016-01, Vol.1859 (1), p.41-45

Sanbonmatsu, Karissa Y.

2016

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Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

Nucleic acids research, 2012-06, Vol.40 (11), p.5034-5051

2012

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Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps

Journal of chemical information and modeling, 2020-05, Vol.60 (5), p.2436-2442

2020

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A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

Molecular cell, 2016-10, Vol.64 (1), p.37-50

2016

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Computational studies of molecular machines: the ribosome

Current opinion in structural biology, 2012-04, Vol.22 (2), p.168-174

Sanbonmatsu, Karissa Y

2012

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Tackling structures of long noncoding RNAs

International Journal of Molecular Sciences, 2013-12, Vol.14 (12), p.23672-23684

2013

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Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

Journal of molecular biology, 2013-10, Vol.425 (19), p.3731-3746

2013

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Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model

Bioscience reports, 2017-12, Vol.37 (6)

2017

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Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information

BMC bioinformatics, 2023-11, Vol.24 (1), p.1-441, Article 441

2023

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Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

Cell, 2014-07, Vol.158 (1), p.121-131

2014

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Connecting the kinetics and energy landscape of tRNA translocation on the ribosome

PLoS computational biology, 2013-03, Vol.9 (3), p.e1003003-e1003003

2013

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Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations

Journal of computational chemistry, 2019-08, Vol.40 (21), p.1919-1930

2019

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Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

Nature communications, 2020-01, Vol.11 (1), p.148-148, Article 148

2020

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Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding

Nature communications, 2023-09, Vol.14 (1), p.5582-15, Article 5582

2023

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Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts

Journal of molecular biology, 2022-09, Vol.434 (18), p.167788-167788, Article 167788

2022

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COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

Cell reports (Cambridge), 2016-09, Vol.16 (12), p.3087-3096

2016

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Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

Proceedings of the National Academy of Sciences - PNAS, 2021-10, Vol.118 (42), p.1

2021

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Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements

The journal of physical chemistry. B, 2016-08, Vol.120 (33), p.8642-8653

2016

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Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES

Molecular cell, 2015-02, Vol.57 (3), p.422-432

2015

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Chemical probing profiling of 2’-deoxyguanosine sensing RNA reveals magnesium ion-dependent conformational switching

Biophysical journal, 2023-02, Vol.122 (3), p.444a-444a

2023

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Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

PLoS computational biology, 2020-11, Vol.16 (11), p.e1008293-e1008293

2020

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Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

RNA (Cambridge), 2024-08, Vol.30 (8), p.992-1010

2024

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Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection

Journal of molecular biology, 2020-04, Vol.432 (9), p.3064-3077

2020

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Getting to the bottom of lncRNA mechanism: structure–function relationships

Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR

Towards structural classification of long non-coding RNAs

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

Computational studies of molecular machines: the ribosome

Tackling structures of long noncoding RNAs

Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model

Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

Connecting the kinetics and energy landscape of tRNA translocation on the ribosome

Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding

Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements

Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES

Chemical probing profiling of 2’-deoxyguanosine sensing RNA reveals magnesium ion-dependent conformational switching

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection

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