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Generalized Born Implicit Solvent Models for Biomolecules

Annual review of biophysics, 2019-05, Vol.48, p.275

2019

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The nucleosome: from structure to function through physics

Current opinion in structural biology, 2019-06, Vol.56, p.119-130

2019

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Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Biophysical journal, 2015-03, Vol.108 (5), p.1153-1164

2015

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Protonation and pK changes in protein–ligand binding

Quarterly reviews of biophysics, 2013-05, Vol.46 (2), p.181-209

2013

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Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

Epigenetics & chromatin, 2018-03, Vol.11 (1), p.11-11, Article 11

2018

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Partially Assembled Nucleosome Structures at Atomic Detail

Biophysical journal, 2017-02, Vol.112 (3), p.460-472

2017

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Linear relationship between peak and season-long abundances in insects

PloS one, 2018-02, Vol.13 (2), p.e0193110-e0193110

2018

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The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies

Epigenetics & chromatin, 2024-05, Vol.17 (1), p.13-13, Article 13

2024

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The Role of Correlation and Solvation in Ion Interactions with B-DNA

Biophysical journal, 2016-01, Vol.110 (2), p.315-326

2016

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Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

Epigenetics & chromatin, 2023-05, Vol.16 (1), p.21-21

2023

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How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch

Insects (Basel, Switzerland), 2021-10, Vol.12 (10), p.932

2021

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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

Nucleic acids research, 2012-07, Vol.40 (Web Server issue), p.W537

2012

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Point charges optimally placed to represent the multipole expansion of charge distributions

PloS one, 2013-07, Vol.8 (7), p.e67715-e67715

2013

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Charge State of the Globular Histone Core Controls Stability of the Nucleosome

Biophysical journal, 2010-09, Vol.99 (5), p.1577-1585

2010

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Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement

Epigenetics & chromatin, 2018-01, Vol.11 (1), p.3-3, Article 3

2018

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Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach

PloS one, 2014-03, Vol.9 (3), p.e91943-e91943

2014

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Correction to “Fast Polarizable Water Model for Atomistic Simulations”

Journal of chemical theory and computation, 2023-01, Vol.19 (1), p.377-377

2023

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Bounds on Absolute Gypsy Moth (Lymantria dispar dispar) (Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps

Insects (Basel, Switzerland), 2020-10, Vol.11 (10), p.673

2020

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Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure

Journal of molecular biology, 2021-03, Vol.433 (6), p.166683-166683, Article 166683

2021

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Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes

Cells (Basel, Switzerland), 2020-02, Vol.9 (2), p.339

2020

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Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei

Biophysical journal, 2023-02, Vol.122 (3), p.69a-69a

2023

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Spermine Condenses DNA, but Not RNA Duplexes

Biophysical journal, 2017-01, Vol.112 (1), p.22-30

2017

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Why double-stranded RNA resists condensation

Nucleic acids research, 2014-09, Vol.42 (16), p.10823

2014

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Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

Biophysical journal, 2010-03, Vol.98 (5), p.872-880

2010

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The Curious Case of Strongly Bent DNA

Biophysical journal, 2020-02, Vol.118 (3), p.377a-377a

Onufriev, Alexey V.

2020

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Generalized Born Implicit Solvent Models for Biomolecules

The nucleosome: from structure to function through physics

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Protonation and pK changes in protein–ligand binding

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

Partially Assembled Nucleosome Structures at Atomic Detail

Linear relationship between peak and season-long abundances in insects

The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies

The Role of Correlation and Solvation in Ion Interactions with B-DNA

Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

Point charges optimally placed to represent the multipole expansion of charge distributions

Charge State of the Globular Histone Core Controls Stability of the Nucleosome

Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement

Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach

Correction to “Fast Polarizable Water Model for Atomistic Simulations”

Bounds on Absolute Gypsy Moth (Lymantria dispar dispar) (Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps

Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure

Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes

Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei

Spermine Condenses DNA, but Not RNA Duplexes

Why double-stranded RNA resists condensation

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

The Curious Case of Strongly Bent DNA

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