T. Schlick

Most-cited papers

Cohesin loss eliminates all loop domains
Suhas S. P. Rao, Su-Chen Huang, B. G. St Hilaire, Jesse M. Engreitz +18 more
2017Cell1,697 citations Open access
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Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions: a multiscale computational study
Rosana Collepardo-Guevara, G. Portella, M. Vendruscolo, D. Frenkel +2 more
2015Journal of the American Chemical Society158 citations Open access
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Uncovering the Polymerase-induced Cytotoxicty of an Oxidized Nucleotide
B. Freudenthal, W. A. Beard, L. Perera, D. D. Shock +3 more
2014Nature147 citations Open access
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Chromatin fiber polymorphism triggered by variations of DNA linker lengths
Rosana Collepardo-Guevara, T. Schlick
2014Proceedings of the National Academy of Sciences of the United States of America139 citations Open access
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Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes
S. Grigoryev, Gavin D. Bascom, Jenna M. Buckwalter, M. B. Schubert +2 more
2016Proceedings of the National Academy of Sciences of the United States of America117 citations Open access
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Scaling Molecular Dynamics Beyond 100,000 Processor Cores for Large-Scale Biophysical Simulations
Jaewoon Jung, W. Nishima, M. Daniels, Gavin D. Bascom +10 more
2019Journal of Computational Chemistry107 citations Open access
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Biomolecular modeling thrives in the age of technology
T. Schlick, Stephanie Portillo-Ledesma
2021Nature Computational Science97 citations Open access
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The Chromatin Fiber: Multiscale Problems and Approaches
Gungor Ozer, A. Luque, T. Schlick
2015Current Opinion in Structural Biology75 citations Open access
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Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field
T. Schlick, Stephanie Portillo-Ledesma, Christopher G. Myers, Lauren Beljak +12 more
2021Annual Review of Biophysics69 citations Open access
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Dynamic condensation of linker histone C-terminal domain regulates chromatin structure
A. Luque, Rosana Collepardo-Guevara, S. Grigoryev, T. Schlick
2014Nucleic Acids Research68 citations Open access
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Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation
P. A. Gómez-García, Stephanie Portillo-Ledesma, M. V. Neguembor, Martina Pesaresi +7 more
2021Cell Reports66 citations Open access
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To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element
T. Schlick, Qiyao Zhu, A. Dey, Swati Jain +2 more
2021bioRxiv64 citations Open access
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Graph-based sampling for approximating global helical topologies of RNA
Namhee Kim, Christian Laing, Shereef Elmetwaly, Se-Gun C. Jung +2 more
2014Proceedings of the National Academy of Sciences of the United States of America61 citations Open access
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Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub
Gavin D. Bascom, Christopher G. Myers, T. Schlick
2019Proceedings of the National Academy of Sciences of the United States of America59 citations Open access
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Opportunities and Challenges in RNA Structural Modeling and Design.
T. Schlick, A. Pyle
2017Biophysical Journal56 citations Open access
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Nucleosome clutches are regulated by chromatin internal parameters
Stephanie Portillo-Ledesma, Lucille H. Tsao, Meghna Wagley, M. Lakadamyali +2 more
2020Journal of Molecular Biology50 citations Open access
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Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element
T. Schlick, Qiyao Zhu, Swati Jain, Shuting Yan
2020bioRxiv49 citations Open access
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Linking Chromatin Fibers to Gene Folding by Hierarchical Looping.
Gavin D. Bascom, T. Schlick
2017Biophysical Journal43 citations Open access
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Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements
Gavin D. Bascom, K. Sanbonmatsu, T. Schlick
2016Journal of Physical Chemistry B42 citations Open access
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Sensitive effect of linker histone binding mode and subtype on chromatin condensation
O. Perišić, Stephanie Portillo-Ledesma, T. Schlick
2019Nucleic Acids Research41 citations Open access
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Adventures with RNA Graphs
T. Schlick
2017Methods41 citations Open access
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Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression
Shuting Yan, Qiyao Zhu, Swati Jain, T. Schlick
2022Nature Communications40 citations Open access
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Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry
A. Sridhar, Stephen E. Farr, G. Portella, T. Schlick +2 more
2020Proceedings of the National Academy of Sciences of the United States of America39 citations Open access
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Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells
Sarah G. Swygert, Dejun Lin, Stephanie Portillo-Ledesma, Po-Yen Lin +5 more
2021eLife36 citations Open access
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F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly
Swati Jain, T. Schlick
2017Journal of Molecular Biology34 citations Open access
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Genome Modeling: From chromatin fibers to genes
Stephanie Portillo-Ledesma, Zilong Li, T. Schlick
2022Current Opinion in Structural Biology33 citations Open access
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Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion
Gavin D. Bascom, Taejin Kim, T. Schlick
2017Journal of Physical Chemistry B33 citations Open access
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RAG-3D: a search tool for RNA 3D substructures
Maï Zahran, Cigdem Sevim Bayrak, Shereef Elmetwaly, T. Schlick
2015Nucleic Acids Research33 citations Open access
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Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.
A. Luque, Gungor Ozer, T. Schlick
2016Biophysical Journal32 citations Open access
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Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding.
Gavin D. Bascom, T. Schlick
2018Biophysical Journal30 citations Open access
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Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling
Stephanie Portillo-Ledesma, T. Schlick
2019Wiley Interdisciplinary Reviews. Computational Molecular Science25 citations Open access
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A pipeline for computational design of novel RNA-like topologies
Swati Jain, A. Laederach, S. B. Ramos, T. Schlick
2018Nucleic Acids Research25 citations Open access
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RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology
Namhee Kim, Zhe Zheng, Shereef Elmetwaly, T. Schlick
2014PLoS ONE25 citations Open access
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Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability
Shuting Yan, Qiyao Zhu, Jenna A. Hohl, Alex J. Dong +1 more
2023Proceedings of the National Academy of Sciences of the United States of America24 citations Open access
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Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach.
Namhee Kim, Maï Zahran, T. Schlick
2015Methods in Enzymology24 citations
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Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction
C. Bayrak, Namhee Kim, T. Schlick
2017Nucleic Acids Research22 citations Open access
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Graph Applications to RNA Structure and Function
Namhee Kim, Katherine N. Fuhr, T. Schlick
201322 citations
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Inverse Folding with RNA-As-Graphs Produces a Large Pool of Candidate Sequences with Target Topologies
Swati Jain, Yunwen Tao, T. Schlick
2019Journal of Structural Biology21 citations Open access
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Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment
O. Perišić, T. Schlick
2017Journal of Physical Chemistry B21 citations Open access
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Brownian Dynamics Simulations of Mesoscale Chromatin Fibers.
Zilong Li, Stephanie Portillo-Ledesma, T. Schlick
2022Biophysical Journal20 citations Open access
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Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs
Swati Jain, C. Bayrak, L. Petingi, T. Schlick
2018Genes20 citations Open access
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Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions
Lewis A Rolband, Damian Beasock, Yang Wang, Yao-Gen Shu +14 more
2022Computational and Structural Biotechnology Journal19 citations Open access
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An Extended Dual Graph Library and Partitioning Algorithm Applicable to Pseudoknotted RNA Structures
Swati Jain, Sera Saju, L. Petingi, T. Schlick
2019Methods18 citations Open access
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Challenges in RNA Structural Modeling and Design
A. Pyle, T. Schlick
2016Journal of Molecular Biology17 citations Open access
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Computational strategies to address chromatin structure problems
O. Perišić, T. Schlick
2016Physical Biology16 citations Open access
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Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach
Naoto Baba, Shereef Elmetwaly, Namhee Kim, T. Schlick
2015Journal of Molecular Biology16 citations Open access
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RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications
Qiyao Zhu, L. Petingi, T. Schlick
2022International Journal of Molecular Sciences13 citations Open access
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How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template.
Benedetta A. Sampoli Benítez, Zachary R. Barbati, K. Arora, J. Bogdanović +1 more
2013Biophysical Journal13 citations Open access
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Techniques and Challenges in Reconstructing 3D Genome Structures from 2D Chromosome Conformation Capture Data
Zilong Li, Stephanie Portillo-Ledesma, T. Schlick
2023Current Opinion in Cell Biology12 citations Open access
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A Fiedler Vector Scoring Approach for Novel RNA Motif Selection
Qiyao Zhu, T. Schlick
2021Journal of Physical Chemistry B12 citations Open access
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