Research output

Research output per year 1981 2006 2010 2021 2023

• 208 Article
• 25 Chapter
• 17 Review article
• 11 Chapter (peer-reviewed)
• 39 More
  • 10 Editorial
  • 7 Other report
  • 6 Comment/debate
  • 4 Book
  • 4 Conference contribution
  • 3 Foreword/postscript
  • 1 Paper
  • 1 Conference article
  • 1 Letter
  • 1 Short survey
  • 1 Special issue

Research output per year

Research output per year

Search results

• 2017

  Partitioning and classification of RNA secondary structures into pseudonotted and pseudoknot-free regions using a graph-theoretical approach

  Petingi, L. & Schlick, T., 2017, In: IAENG International Journal of Computer Science. 44, 2, p. 241-246 6 p.

  Research output: Contribution to journal › Article › peer-review

  • RNA 100%

• RNA Structural Variability and Functional Versatility Challenge RNA Structural Modeling and Design

  Schlick, T. & Pyle, A., Jul 25 2017, In: Biophysical journal. 113, 2, p. E1-E2

  Research output: Contribution to journal › Editorial › peer-review

  Open Access

• Unraveling Genome Biophysics

  Schlick, T. & Loew, L., Feb 7 2017, In: Biophysical journal. 112, 3, p. E1-E2

  Research output: Contribution to journal › Editorial › peer-review

  Open Access

• Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction

  Bayrak, C. S., Kim, N. & Schlick, T., May 19 2017, In: Nucleic acids research. 45, 9, p. 5414-5422 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA 100%
  • Nucleotide Motifs 31%
  • Conserved Sequence 29%
  • Base Pairing 24%
  • Datasets 19%
• 2016

  Challenges in RNA Structural Modeling and Design

  Pyle, A. M. & Schlick, T., Feb 27 2016, In: Journal of Molecular Biology. 428, 5, p. 733-735 3 p.

  Research output: Contribution to journal › Editorial › peer-review

• CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

  Hua, L., Song, Y., Kim, N., Laing, C., Wang, J. T. L. & Schlick, T., Jan 1 2016, In: PloS one. 11, 1, e0147097.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA 100%
  • Software 13%

• Computational strategies to address chromatin structure problems

  Perišić, O. & Schlick, T., Jun 24 2016, In: Physical Biology. 13, 3, 035006.

  Research output: Contribution to journal › Article › peer-review

  • Chromatin 100%
  • Polymers 18%
  • DNA 17%
  • Chromosomes 16%
  • Gene Expression 12%

• Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin

  Luque, A., Ozer, G. & Schlick, T., Jun 7 2016, In: Biophysical journal. 110, 11, p. 2309-2319 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Nucleosomes 100%
  • Chromatin 75%
  • DNA 47%
  • Macromolecular Substances 13%
  • Amoeba 12%

• Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

  Grigoryev, S. A., Bascom, G., Buckwalter, J. M., Schubert, M. B., Woodcock, C. L. & Schlick, T., Feb 2 2016, In: Proceedings of the National Academy of Sciences of the United States of America. 113, 5, p. 1238-1243 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Nucleosomes 100%
  • Metaphase 94%
  • Chromatin 75%
  • Chromosomes 67%
  • Interphase 28%

• Insertion of oxidized nucleotide triggers rapid DNA polymerase opening

  Kim, T., Freudenthal, B. D., Beard, W. A., Wilson, S. H. & Schlick, T., May 19 2016, In: Nucleic acids research. 44, 9, p. 4409-4424 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • DNA-Directed DNA Polymerase 100%
  • Nucleotides 71%
  • Crystallography 64%
  • Hydrogen Bonding 53%
  • Guanine 52%

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

  Bascom, G. D., Sanbonmatsu, K. Y. & Schlick, T., Aug 25 2016, In: Journal of Physical Chemistry B. 120, 33, p. 8642-8653 12 p.

  Research output: Contribution to journal › Article › peer-review

  • chromatin 100%
  • genes 90%
  • Genes 73%
  • Fibers 52%
  • Fiber 49%

• Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach

  Baba, N., Elmetwaly, S., Kim, N. & Schlick, T., Feb 27 2016, In: Journal of Molecular Biology. 428, 5, p. 811-821 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cluster Analysis 100%
  • RNA 77%
  • Nucleotide Motifs 36%
  • Cataloging 21%
  • Nucleotides 11%
• 2015

  Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions: A multiscale computational study

  Collepardo-Guevara, R., Portella, G., Vendruscolo, M., Frenkel, D., Schlick, T. & Orozco, M., Aug 19 2015, In: Journal of the American Chemical Society. 137, 32, p. 10205-10215 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Acetylation 100%
  • Gene expression regulation 55%
  • Chromatin 51%
  • Epigenomics 51%
  • Nuclear magnetic resonance 34%

• Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: A hierarchical graph sampling approach

  Kim, N., Zahran, M. & Schlick, T., 2015, Methods in Enzymology. Academic Press Inc., p. 115-135 21 p. (Methods in Enzymology; vol. 553).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • Riboswitch 100%
  • RNA Structure 87%
  • Tertiary Structure 68%
  • Sampling 53%
  • RNA 45%

• Forced unraveling of chromatin fibers with nonuniform linker DNA lengths

  Ozer, G., Collepardo-Guevara, R. & Schlick, T., Feb 18 2015, In: Journal of Physics Condensed Matter. 27, 6, 064113.

  Research output: Contribution to journal › Article › peer-review

  • chromatin 100%
  • DNA 79%
  • deoxyribonucleic acid 70%
  • Chromatin 68%
  • Fibers 52%

• RAG-3D: A search tool for RNA 3D substructures

  Zahran, M., Sevim Bayrak, C., Elmetwaly, S. & Schlick, T., Oct 30 2015, In: Nucleic acids research. 43, 19, p. 9474-9488 15 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA 100%
  • Databases 13%
  • Datasets 8%

• The chromatin fiber: Multiscale problems and approaches

  Ozer, G., Luque, A. & Schlick, T., 2015, In: Current Opinion in Structural Biology. 31, p. 124-139 16 p.

  Research output: Contribution to journal › Review article › peer-review

  • Chromatin 94%
  • Chromatin Assembly and Disassembly 62%
  • Post Translational Protein Processing 54%
  • DNA 29%

• Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide

  Freudenthal, B. D., Beard, W. A., Perera, L., Shock, D. D., Kim, T., Schlick, T. & Wilson, S. H., Jan 29 2015, In: Nature. 517, 7536, p. 635-639 5 p.

  Research output: Contribution to journal › Article › peer-review

  • 8-oxodeoxyguanosine triphosphate 100%
  • Nucleotides 43%
  • Adenine 18%
  • Base Pairing 15%
  • Mutagenesis 15%
• 2014

  Chromatin fiber polymorphism triggered by variations of DNA linker lengths

  Collepardo-Guevara, R. & Schlick, T., Jun 3 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 22, p. 8061-8066 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Chromatin 100%
  • Nucleosomes 88%
  • DNA 63%
  • Interphase 21%
  • Cell Cycle 14%

• Dynamic condensation of linker histone C-terminal domain regulates chromatin structure

  Luque, A., Collepardo-Guevara, R., Grigoryev, S. & Schlick, T., Jul 8 2014, In: Nucleic acids research. 42, 12, p. 7553-7560 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Chromatin 94%
  • Nucleosomes 78%
  • DNA 29%
  • Epigenomics 11%
  • Ions 11%

• Graph-based sampling for approximating global helical topologies of RNA

  Kim, N., Laing, C., Elmetwaly, S., Jung, S., Curuksu, J. & Schlick, T., Mar 18 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 11, p. 4079-4084 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA 100%
  • Data Mining 43%
  • Nucleotides 14%

• Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations

  Jung, S. & Schlick, T., Jan 21 2014, In: Biophysical journal. 106, 2, p. 447-458 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Internal Ribosome Entry Sites 100%
  • Foot-and-Mouth Disease Virus 95%
  • RNA 48%
  • RNA Folding 13%
  • Nucleotide Motifs 11%

• Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways

  Li, Y., Freudenthal, B. D., Beard, W. A., Wilson, S. H. & Schlick, T., Mar 5 2014, In: Journal of the American Chemical Society. 136, 9, p. 3630-3639 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Metal ions 100%
  • DNA-Directed DNA Polymerase 78%
  • DNA 72%
  • Ions 63%
  • Metals 60%

• RNA graph partitioning for the discovery of RNA modularity: A novel application of graph partition algorithm to biology

  Kim, N., Zheng, Z., Elmetwaly, S. & Schlick, T., Sep 4 2014, In: PloS one. 9, 9, e106074.

  Research output: Contribution to journal › Article › peer-review

  • RNA Structure 100%
  • graphs 81%
  • Partition 73%
  • Biological Sciences 53%
  • RNA 51%
• 2013

  Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site

  Jung, S. & Schlick, T., Feb 2013, In: Nucleic acids research. 41, 3, p. 1483-1495 13 p.

  Research output: Contribution to journal › Article › peer-review

  • Internal Ribosome Entry Sites 100%
  • Foot-and-Mouth Disease Virus 95%
  • RNA 48%
  • Molecular Dynamics Simulation 15%
  • Viral Proteins 14%

• "Gate-keeper" Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides

  Li, Y. & Schlick, T., May 2013, In: PLoS computational biology. 9, 5, e1003074.

  Research output: Contribution to journal › Article › peer-review

  • deoxyguanosine triphosphate 100%
  • Nucleotides 80%
  • DNA-Directed DNA Polymerase 72%
  • DNA-directed DNA polymerase 69%
  • Rearrangement 69%

• Graph applications to RNA structure and function

  Kim, N., Fuhr, K. N. & Schlick, T., Jan 1 2013, Biophysics of RNA Folding. Springer New York, p. 23-51 29 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • RNA Structure 100%
  • RNA 51%
  • Secondary Structure 21%
  • Biological Science Disciplines 10%
  • Untranslated RNA 9%

• Graph-based sampling approach for approximating global helical topologies of RNA

  Kim, N., Laing, C., Elmetwaly, S., Jung, S., Curuksu, J. & Schlick, T., 2013, In: PLoS One. 8, 8, e71947.

  Research output: Contribution to journal › Article › peer-review

• How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template

  Sampoli Benítez, B., Barbati, Z. R., Arora, K., Bogdanovic, J. & Schlick, T., Dec 3 2013, In: Biophysical journal. 105, 11, p. 2559-2568 10 p.

  Research output: Contribution to journal › Article › peer-review

  • DNA polymerase X 100%
  • Catalytic Domain 47%
  • Kinetics 28%
  • Nucleotides 21%
  • African Swine Fever Virus 20%

• Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments

  Collepardo-Guevara, R. & Schlick, T., Apr 2013, In: Biochemical Society Transactions. 41, 2, p. 494-500 7 p.

  Research output: Contribution to journal › Review article › peer-review

  • Computer Simulation 100%
  • Chromatin 93%
  • Force 71%
  • Fiber 67%
  • Single Molecule Imaging 48%

• Network theory tools for RNA modeling

  Kim, N., Petingi, L. & Schlick, T., Sep 2013, In: WSEAS Transactions on Mathematics. 12, 9, p. 941-955 15 p.

  Research output: Contribution to journal › Article › peer-review

  • Network Theory 100%
  • Network theory (graphs) 86%
  • RNA 84%
  • Graph 66%
  • Modeling 45%

• Predicting Helical Topologies in RNA Junctions as Tree Graphs

  Laing, C., Jung, S., Kim, N., Elmetwaly, S., Zahran, M. & Schlick, T., Aug 26 2013, In: PloS one. 8, 8, e71947.

  Research output: Contribution to journal › Article › peer-review

  • RNA 100%
  • RNA Folding 27%
  • Intuition 25%
  • Data Mining 21%
  • Biological Phenomena 17%

• The 2013 Nobel prize in chemistry celebrates computations in chemistry and biology

  Schlick, T., 2013, SIAM News, 46, 10, p. 1-4.

  Research output: Contribution to specialist publication › Article
• 2012

  A new toolkit for modeling RNA from a pseudo-torsional space: Commentary on "discrete RNA libraries from pseudo-torsional space" by Humphris-Narayanan and Pyle (J. Mol. Biol. March 2012)

  Kim, N. & Schlick, T., Aug 3 2012, In: Journal of Molecular Biology. 421, 1, p. 1-5 5 p.

  Research output: Contribution to journal › Comment/debate › peer-review

• Chapter 4: Intrinsic motions of DNA polymerases underlie their remarkable specificity and selectivity and suggest a hybrid substrate binding mechanism

  Foley, M. C., Arora, K. & Schlick, T., 2012, Innovations in Biomolecular Modeling and Simulations. Schlick, T. (ed.). p. 81-110 30 p. (RSC Biomolecular Sciences).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

• Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes

  Collepardo-Guevara, R. & Schlick, T., Oct 2012, In: Nucleic acids research. 40, 18, p. 8803-8817 15 p.

  Research output: Contribution to journal › Article › peer-review

  • Ions 88%
  • DNA 59%
  • Genes 42%
  • Chromatin 26%
  • Elastic Modulus 17%

• Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function

  Quarta, G., Sin, K. & Schlick, T., Feb 2012, In: PLoS computational biology. 8, 2, e1002368.

  Research output: Contribution to journal › Article › peer-review

  • Energy Landscape 100%
  • Riboswitch 98%
  • Ligands 85%
  • Gene expression 70%
  • Rearrangement 69%

• Innovations in biomolecular modeling and simulation: Volumes 1 and 2

  Schlick, T. (ed.), 2012, Royal Society of Chemistry.

  Research output: Book/Report › Book

• Perspective: Pre-chemistry conformational changes in DNA polymerase mechanisms

  Schlick, T., Arora, K., Beard, W. A. & Wilson, S. H., Dec 2012, In: Theoretical Chemistry Accounts. 131, 12, p. 1-8 8 p., 1287.

  Research output: Contribution to journal › Article › peer-review

  • deoxyribonucleic acid 100%
  • chemistry 94%
  • Chemistry 64%
  • catalysis 42%
  • synthesis 39%

• Predicting coaxial helical stacking in RNA junctions

  Laing, C., Wen, D., Wang, J. T. L. & Schlick, T., Jan 2012, In: Nucleic acids research. 40, 2, p. 487-498 12 p.

  Research output: Contribution to journal › Article › peer-review

  • RNA 100%
  • Decision Trees 44%
  • Data Mining 43%
  • Forests 42%

• Preface: Modelers to the rescue

  Schlick, T., 2012, Innovations in Biomolecular Modeling and Simulations. Schlick, T. (ed.). p. v-ix (RSC Biomolecular Sciences).

  Research output: Chapter in Book/Report/Conference proceeding › Foreword/postscript

• Toward convergence of experimental studies and theoretical modeling of the chromatin fiber

  Schlick, T., Hayes, J. & Grigoryev, S., Feb 17 2012, In: Journal of Biological Chemistry. 287, 8, p. 5183-5191 9 p.

  Research output: Contribution to journal › Short survey › peer-review

  • Chromatin Assembly and Disassembly 100%
  • Chromatin 75%
  • Theoretical Models 69%
  • Fiber 54%
  • Nucleosomes 20%

• Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzymes pathway

  Li, Y., Gridley, C. L., Jaeger, J., Sweasy, J. B. & Schlick, T., Jun 20 2012, In: Journal of the American Chemical Society. 134, 24, p. 9999-10010 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Coulomb interactions 100%
  • Static Electricity 74%
  • Enzymes 72%
  • DNA-Directed DNA Polymerase 70%
  • DNA 65%
• 2011

  Biomolecular modeling and simulation: A field coming of age

  Schlick, T., Collepardo-Guevara, R., Halvorsen, L. A., Jung, S. & Xiao, X., May 2011, In: Quarterly Reviews of Biophysics. 44, 2, p. 191-228 38 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Folding 100%
  • History 31%
  • Kinetics 30%
  • RNA 29%
  • Technology 27%

• Biomolecular modeling and simulation: The productive trajectory of a field

  Schlick, T. & Collepardo-Guevara, R., Jul 2011, SIAM News, 44, p. 1, 8.

  Research output: Contribution to specialist publication › Article

• Computational approaches to RNA structure prediction, analysis, and design

  Laing, C. & Schlick, T., Jun 2011, In: Current Opinion in Structural Biology. 21, 3, p. 306-318 13 p.

  Research output: Contribution to journal › Review article › peer-review

  • RNA 100%
  • RNA Folding 44%
  • Nucleotide Motifs 37%
  • Protein Folding 33%
  • Biological Phenomena 27%

• Cyber science and engineering: Report of the High Performance Task Force on grand challenges in cyber science and engineering

  National Science Foundation, Mar 2011, National Science Foundation. (http://www.nsf.gov/od/oci/taskforces/)

  Research output: Book/Report › Other report

• DNA polymerases structure, function, and modeling

  Schlick, T., Jan 1 2011, Molecular Machines. World Scientific Publishing Co., p. 49-66 18 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

• RAG: An update to the RNA-As-Graphs resource

  Izzo, J. A., Kim, N., Elmetwaly, S. & Schlick, T., May 31 2011, In: BMC bioinformatics. 12, 219.

  Research output: Contribution to journal › Article › peer-review

  • RNA 100%
  • Update 80%
  • Resources 77%
  • Secondary Structure 73%
  • RNA Structure 55%

• The effect of linker histones nucleosome binding affinity on chromatin unfolding mechanisms

  Collepardo-Guevara, R. & Schlick, T., Oct 5 2011, In: Biophysical journal. 101, 7, p. 1670-1680 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Nucleosomes 100%
  • Chromatin 75%
  • DNA 23%
  • DNA Replication 10%
  • Transcriptional Activation 9%