Tamar Schlick

发表

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

Yang Song, Lei Hua, Namhee Kim, 2016, PloS one.

Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms.

Tamar Schlick, T. Schlick, 2003, Biophysical journal.

Biomolecular Modeling and Simulation: The Productive Trajectory of a Field

Tamar Schlick, Rosana Collepardo-Guevara, 2011 .

Innovations in biomolecular modeling and simulation: Volumes 1 and 2

Tamar Schlick, T. Schlick, 2012 .

Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations

Tamar Schlick, T. Schlick, 1999, Computational Molecular Dynamics.

The Template Pattern

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

Remark on Algorithm 702—the updated truncated Newton minimization package

Tamar Schlick, Dexuan Xie, T. Schlick, 1999, TOMS.

Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization

Tamar Schlick, Dexuan Xie, T. Schlick, 2000 .

Searching for 2D RNA geometries in bacterial genomes

Tamar Schlick, Uri Laserson, Hin Hark Gan, 2004, SCG '04.

Computational strategies to address chromatin structure problems

Tamar Schlick, Ognjen Perišić, T. Schlick, 2016, Physical biology.

Computational approaches to 3D modeling of RNA

Christian Laing, Tamar Schlick, T. Schlick, 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications

Tamar Schlick, Dexuan Xie, T. Schlick, 1999, SIAM J. Optim..

Numerical Experience with Limited-Memory Quasi-Newton and Truncated Newton Methods

François-Xavier Le Dimet, Tamar Schlick, Ionel Michael Navon, 1993, SIAM J. Optim..

RAGPOOLS: RNA-As-Graph-Pools - a web server for assisting the design of structured RNA pools for in vitro selection

Namhee Kim, Tamar Schlick, Hin Hark Gan, 2007, Bioinform..

A new pair of algorithms for potential energy minimization and molecular dynamics simulations

Tamar Schlick, Michael L. Overton, Charles S. Peskin, 1989 .

Tamar Schlick, T. Schlick, 2010, Molecular Modeling and Simulation: An Interdisciplinary Guide.

New Algorithms for Macromolecular Simulation

Tamar Schlick, Benedict Leimkuhler, Robert D. Skeel, 2006 .

Object-Oriented Analysis and Design

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

ANERGY TO SYNERGY-THE ENERGY FUELING THE RXCOVEA FRAMEWORK.

Tamar Schlick, Alfredo Ferro, Bud Mishra, 2020, International journal for multiscale computational engineering.

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

Christian Laing, Tamar Schlick, Nam Hee Kim, 2013 .

New Algorithms for Macromolecular Simulation (Lecture Notes in Computational Science and Engineering)

Tamar Schlick, Benedict Leimkuhler, Ron Elber, 2006 .

Design Patterns and Threads

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.

Tamar Schlick, Louis Petingi, Swati Jain, 2019, Methods.

Algorithmic Challenges in Computational Molecular Biophysics

Laxmikant V. Kale, Tamar Schlick, Robert D. Skeel, 1999 .

Inverse Folding with RNA-As-Graphs Produces a Large Pool of Candidate Sequences with Target Topologies.

Tamar Schlick, Swati Jain, Yunwen Tao, 2019, Journal of structural biology.

Faculty Opinions recommendation of An algorithmic game-theory approach for coarse-grain prediction of RNA 3D structure.

Tamar Schlick, 2013 .

RAG: RNA-As-Graphs web resource

Namhee Kim, Tamar Schlick, Uri Laserson, 2004, BMC Bioinformatics.

TNPACK—a truncated Newton minimization package for large-scale problems: II. Implementation examples

Tamar Schlick, Aaron L. Fogelson, T. Schlick, 1992, TOMS.

Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules

Tamar Schlick, T. Schlick, 2009, F1000 biology reports.

Graphical User Interfaces Using Swing

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

A truncated Newton minimizer adapted for CHARMM and biomolecular applications

Tamar Schlick, Bernard R. Brooks, Philippe Derreumaux, 1994, J. Comput. Chem..

Search strategies, minimization algorithms, and molecular dynamics simulations for exploring conformational spaces of nuclear acids

Tamar Schlick, Michael L. Overton, Charles S. Peskin, 1990 .

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms

Tamar Schlick, Xiaoliang Qian, Danny Barash, 2003, J. Comput. Chem..

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

Namhee Kim, Tamar Schlick, Shereef Elmetwaly, 2011, BMC Bioinformatics.

Patterns at Work: Multiple Graphs

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

A Primer on Scientific Programming with Python Fifth Edition

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2020 .

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

Tamar Schlick, Giulio Quarta, Ken Sin, 2012, PLoS Comput. Biol..

Opportunities and Challenges in RNA Structural Modeling and Design.

Tamar Schlick, Anna Marie Pyle, T. Schlick, 2017, Biophysical journal.

Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots

Tamar Schlick, Louis Petingi, 2019, AlCoB.

New Approaches to Potential Energy Minimization and Molecular Dynamics Algorithms

Tamar Schlick, T. Schlick, 1991, Comput. Chem..

Molecular Dynamics: Further Topics

Tamar Schlick, T. Schlick, 2010 .

Remark on Algorithm 566

Tamar Schlick, Victoria Z. Averbukh, Samuel Figueroa, 1994, TOMS.

Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure

Tamar Schlick, T. Schlick, Tamar Schlick, 2009, F1000 biology reports.

Identification of novel RNA design candidates by clustering the extended RNA-as-graphs library.

Tamar Schlick, Swati Jain, Qiyao Zhu, 2020, Biochimica et biophysica acta. General subjects.

Faculty Opinions recommendation of Multiple conformational selection and induced fit events take place in allosteric propagation.

Tamar Schlick, 2014 .

Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach.

Tamar Schlick, Louis Petingi, T. Schlick, 2017, IAENG international journal of computer science.

Computational challenges in simulating large DNA over long times

Jing Huang, Tamar Schlick, Xiaoliang Qian, 2000, Comput. Sci. Eng..

LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit‐integration and normal mode techniques

Tamar Schlick, Guihua Zhang, T. Schlick, 1993, J. Comput. Chem..

An adaptive multigrid technique for evaluating long-range forces in biomolecular simulations

Tamar Schlick, Leonid Y. Zaslavsky, T. Schlick, 1998, Appl. Math. Comput..

A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications

Tamar Schlick, Robert D. Skeel, Guihua Zhang, 1997, SIAM J. Sci. Comput..

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm

Qing Zhang, Tamar Schlick, Daniel A. Beard, 2003, J. Comput. Chem..

Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach.

Namhee Kim, Tamar Schlick, Mai Zahran, 2015, Methods in enzymology.

Time-Trimming Tricks for Dynamic Ways & Means Simulations: Splitting Force Updates to Reduce Computational Work

Tamar Schlick, T. Schlick, 2001 .

TNPACK—A truncated Newton minimization package for large-scale problems: I. Algorithm and usage

Tamar Schlick, Aaron L. Fogelson, T. Schlick, 1992, TOMS.

Navigating the Database

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

Reinterpreting Joseph Wright's An Experiment on a Bird in the Air Pump in the 21st Century Genomics Revolution

Tamar Schlick, T. Schlick, 2004 .

A Java Client for MDSplus

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

A More Lenient Stopping Rule for Line Search Algorithms

Tamar Schlick, Dexuan Xie, T. Schlick, 2002, Optim. Methods Softw..

Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps

Moshe Israeli, Ron Kimmel, Tamar Schlick, 2003, Journal of Mathematical Imaging and Vision.

An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization

Tamar Schlick, Alexander Tropsha, Dexuan Xie, 2000, J. Chem. Inf. Comput. Sci..

Network Theory Tools for RNA Modeling.

Namhee Kim, Tamar Schlick, Louis Petingi, 2013, WSEAS transactions on mathematics.

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

Tamar Schlick, Yunlang Li, T. Schlick, 2013, PLoS Comput. Biol..

Modified Cholesky Factorizations for Sparse Preconditioners

Tamar Schlick, T. Schlick, 1993, SIAM J. Sci. Comput..

Design Patterns for e-Science

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

Interactive Graphics Using Mouse Events

Timothy J. Barth, David E. Keyes, Tamar Schlick, 2007 .

Eight Suggestions for Future Leaders of Science and Technology

Tamar Schlick, 2020 .

Graph Applications to RNA Structure and Function

Tamar Schlick, Namhee Kim, Katherine Niccole Fuhr, 2013 .

Computational Genomics Using Graph Theory

Tamar Schlick, 2005 .

RAG-Web: RNA structure prediction/design using RNA-As-Graphs

Tamar Schlick, Shereef Elmetwaly, Swati Jain, 2020, Bioinform..

A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID)

Tamar Schlick, Xiaoliang Qian, Daniel Strahs, 2001, J. Comput. Chem..

Final Report of the M(sup 3) Workshop at NYU, October 12-14, 2000

Tamar Schlick, Gan Hin Hark, 2002 .

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

Tamar Schlick, Swati Jain, T. Schlick, 2017, Journal of molecular biology.

Algorithm 702: TNPACK–a truncated Newton minimization package for large-scale problems: I. Algorithm and usage

Tamar Schlick, Aaron L. Fogelson, 1992, TOMS.

Adventures with RNA graphs.

Tamar Schlick, T. Schlick, 2018, Methods.

HESFCN - A Fortran package of Hessian Subroutines for Testing Nonlinear Optimization Software

Tamar Schlick, Samuel Figueroa, V. Averbukh, 1992 .

Special Section On Multiscale Modeling In Biology

Tamar Schlick, Ken A. Dill, K. Dill, 2006, Multiscale Model. Simul..

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

Tamar Schlick, Yuji Sugita, Jaewoon Jung, 2019, J. Comput. Chem..

Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs

Tamar Schlick, Louis Petingi, Swati Jain, 2018, Genes.

Monte Carlo Techniques

Tamar Schlick, T. Schlick, 2010 .

Implementation of the Schnabel & Eskow modified Cholesky factorization in the context of large-scale nonlinear optimization

Tamar Schlick, 1990 .

Molecular Modeling and Simulation: An Interdisciplinary Guide

Tamar Schlick, T. Schlick, 2010 .

Uncovering the Polymerase-induced Cytotoxicty of an Oxidized Nucleotide

Taejin Kim, Tamar Schlick, Lalith E. Perera, 2014, Nature.

Faculty Opinions recommendation of Computational approaches toward the design of pools for the in vitro selection of complex aptamers.

Tamar Schlick, 2011 .

Lecture Notes in Computational Science and Engineering

Dirk Pflüger, Tamar Schlick, Michael Griebel, 2010 .

From butterflies to bits: A sweeping vision for the code of life

Tamar Schlick, 2021 .

Macroscopic modeling and simulations of supercoiled DNA with bound proteins

Tamar Schlick, T. Schlick, Jing Huang, 2002 .

Analysis of protein sequence/structure similarity relationships.

Tamar Schlick, Samuela Pasquali, Hin Hark Gan, 2002, Biophysical journal.

A recipe for evaluating and differentiating cos ϕ expressions

Tamar Schlick, 1989 .

Multivariate Minimization in Computational Chemistry

Tamar Schlick, T. Schlick, 2010 .

Forced unraveling of chromatin fibers with nonuniform linker DNA lengths

Tamar Schlick, Gungor Ozer, Rosana Collepardo-Guevara, 2015, Journal of physics. Condensed matter : an Institute of Physics journal.

Toward Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber * Experimental Foundations Nucleosome Array Folding in Vitro: the 30-nm Fiber

Tamar Schlick, T. Schlick, S. Grigoryev, 2022 .

Mesoscale simulations of two nucleosome-repeat length oligonucleosomes.

Tamar Schlick, T. Schlick, Ognjen Perisić, 2009, Physical chemistry chemical physics : PCCP.

Molecular modeling: An interdisciplinary guide

Tamar Schlick, T. Schlick, 2010 .

Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion.

Tamar Schlick, T. Schlick, Jing Huang, 2003, Biophysical journal.

Computational generation and screening of RNA motifs in large nucleotide sequence pools

Namhee Kim, Tamar Schlick, Hin Hark Gan, 2010, Nucleic acids research.

Trefoil Knotting Revealed by Molecular Dynamics Simulations of Supercoiled DNA

Tamar Schlick, Wilma K. Olson, T. Schlick, 1992, Science.

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

Tamar Schlick, Rosana Collepardo-Guevara, T. Schlick, 2012, Nucleic acids research.

A Combined Wormlike-Chain and Bead Model for Dynamic Simulations of Long Linear DNA

Tamar Schlick, Alexander Vologodskii, T. Schlick, 1997 .

Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach

Tamar Schlick, Uri Laserson, Hin Hark Gan, 2006 .

The 2013 Nobel Prize in Chemistry Celebrates Computations in Chemistry and Biology

Tamar Schlick, T. Schlick, 2013 .

Can classical equations simulate quantum‐mechanical behavior? a molecular dynamics investigation of a diatomic molecule with a morse potential

Tamar Schlick, Charles S. Peskin, T. Schlick, 1989 .

Analysis of riboswitch structure and function by an energy landscape framework.

Namhee Kim, Tamar Schlick, Joseph A. Izzo, 2009, Journal of molecular biology.

Mathematical and Biological Scientists Assess the State-of-the-Art in RNA Science at an IMA Workshop RNA in Biology, Bioengineering and Biotechnology

Tamar Schlick, T. Schlick, 2010 .

Modeling studies of chromatin fiber structure as a function of DNA linker length.

Tamar Schlick, Ognjen Perišić, Rosana Collepardo-Guevara, 2010, Journal of molecular biology.

Linking Chromatin Fibers to Gene Folding by Hierarchical Looping.

Tamar Schlick, Gavin Bascom, T. Schlick, 2017, Biophysical journal.

Geometry Optimization: 2

Tamar Schlick, T. Schlick, 2002 .

Innovations in Biomolecular Modeling and Simulations

Tamar Schlick, T. Schlick, 2012 .

Computational Methods for Macromolecules: Challenges and Applications

Tamar Schlick, Hin Hark Gan, T. Schlick, 2002 .

Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs

Tamar Schlick, Uri Laserson, Hin Hark Gan, 2005, Nucleic acids research.

Application of Fourier analysis to computer simulation of supercoiled DNA conformation

Guohua Liu, Tamar Schlick, Wilma K. Olson, 1995 .

Long timestep dynamics of peptides by the dynamics driver approach

Tamar Schlick, Philippe Derreumaux, T. Schlick, 1995, Proteins.

Chromatin fiber polymorphism triggered by variations of DNA linker lengths

Tamar Schlick, Rosana Collepardo-Guevara, T. Schlick, 2014, Proceedings of the National Academy of Sciences.

Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm

Tamar Schlick, Karunesh Arora, T. Schlick, 2003 .

Computational methods for macromolecules: Challenges and applications - Proceedings of the 3rd international workshop on algorithms for macromolecular modelling, New York, October 12-14, 2000

Tamar Schlick, Hin Hark Gan, T. Schlick, 2002 .

A powerful truncated Newton method for potential energy minimization

Tamar Schlick, Michael L. Overton, M. Overton, 2018 .

From Macroscopic to Mesoscopic Models of Chromatin Folding

Tamar Schlick, T. Schlick, 2009 .

Pursuing Laplace's vision on modern computers

Tamar Schlick, T. Schlick, 1996 .

Structural motifs in ribosomal RNAs: Implications for RNA design and genomics

Tamar Schlick, Nahum Shiffeldrim, Julie Zorn, 2004, Biopolymers.

Translational and vibrational energy dependence of the cross section for H + C2H4 .fwdarw. C2H5*

Tamar Schlick, William L. Hase, T. Schlick, 1981 .

Unbiased rotational moves for rigid-body dynamics.

Tamar Schlick, Daniel A Beard, T. Schlick, 2003, Biophysical journal.

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.

Tamar Schlick, Michele Vendruscolo, Modesto Orozco, 2015, Journal of the American Chemical Society.

The effect of linker histone's nucleosome binding affinity on chromatin unfolding mechanisms.

Tamar Schlick, Rosana Collepardo-Guevara, T. Schlick, 2011, Biophysical journal.

A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.

Tamar Schlick, Gaurav Arya, T. Schlick, 2009, The journal of physical chemistry. A.

Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs

Tamar Schlick, Samuela Pasquali, Hin Hark Gan, 2005, Nucleic acids research.

Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass

Tamar Schlick, Karunesh Arora, T. Schlick, 2006, Protein science : a publication of the Protein Society.

Inertial stochastic dynamics. I. Long-time-step methods for Langevin dynamics

Tamar Schlick, Daniel A. Beard, T. Schlick, 2000 .

Partitioning RNAs into pseudonotted and pseudoknot-free regions modeled as Dual Graphs

Tamar Schlick, Louis Petingi, 2016 .

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

Tamar Schlick, Rosana Collepardo-Guevara, Antoni Luque, 2014, Nucleic acids research.

The chromatin fiber: multiscale problems and approaches.

Tamar Schlick, Gungor Ozer, Antoni Luque, 2015, Current opinion in structural biology.

Inertial stochastic dynamics. II. Influence of inertia on slow kinetic processes of supercoiled DNA

Tamar Schlick, Daniel A. Beard, T. Schlick, 2000 .

Challenges in RNA Structural Modeling and Design.

Tamar Schlick, Anna Marie Pyle, 2016, Journal of molecular biology.

A modular strategy for generating starting conformations and data structures of polynucleotide helices for potential energy calculations

Tamar Schlick, T. Schlick, 1988 .

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Tamar Schlick, Gaurav Arya, T. Schlick, 2009, Proceedings of the National Academy of Sciences.

Flexible histone tails in a new mesoscopic oligonucleosome model.

Tamar Schlick, Gaurav Arya, T. Schlick, 2006, Biophysical journal.

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo.

Tamar Schlick, Gaurav Arya, T. Schlick, 2007, The Journal of chemical physics.

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

Tamar Schlick, Gavin Bascom, T. Schlick, 2016, Proceedings of the National Academy of Sciences.

Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model

Tamar Schlick, T. Schlick, G. Ramachandran, 1996 .

Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model

Tamar Schlick, Gaurav Arya, T. Schlick, 2006, Proceedings of the National Academy of Sciences.