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Michele Di Pierro · SciRah

Researcher profile · Semantic Scholar

Michele Di Pierro

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Michele Di Pierro — researcher profile on SciRah

h-index: 15
Works: 45
Citations: 1,563

Most-cited papers

Transferable model for chromosome architecture
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, P. Wolynes +1 more
2016Proceedings of the National Academy of Sciences of the United States of America331 citations Open access
Semantic Scholar
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
G. Nir, Irene Farabella, Cynthia Pérez Estrada, Carl G. Ebeling +25 more
2018bioRxiv251 citations Open access
Semantic Scholar
3D genomics across the tree of life identifies condensin II as a determinant of architecture type
Claire Hoencamp, Olga Dudchenko, Ahmed M. O. Elbatsh, Sumitabha Brahmachari +60 more
2021Science206 citations Open access
Semantic Scholar
A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for all Long Range Forces
Michele Di Pierro, R. Elber, B. Leimkuhler
2015Journal of Chemical Theory and Computation168 citations Open access
Semantic Scholar
Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes
Michele Di Pierro, D. Potoyan, P. Wolynes, J. Onuchic
2018Proceedings of the National Academy of Sciences of the United States of America148 citations Open access
Semantic Scholar
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization
Hannah L. Harris, Hui-Ya Gu, M. Olshansky, Ailun Wang +26 more
2023Nature Communications143 citations Open access
Semantic Scholar
Exploring chromosomal structural heterogeneity across multiple cell lines
Ryan R. Cheng, Vinícius G. Contessoto, Erez Lieberman Aiden, P. Wolynes +2 more
2020bioRxiv48 citations Open access
Semantic Scholar
Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion
Sumitabha Brahmachari, Vinícius G. Contessoto, Michele Di Pierro, J. Onuchic
2022bioRxiv41 citations Open access
Semantic Scholar
The interplay of chromatin phase separation and lamina interactions in nuclear organization
Rabia Laghmach, Michele Di Pierro, D. Potoyan
2021bioRxiv32 citations Open access
Semantic Scholar
Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes
Rabia Laghmach, Michele Di Pierro, D. Potoyan
2019bioRxiv31 citations Open access
Semantic Scholar
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome
Vinícius G. Contessoto, Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas +5 more
2019bioRxiv30 citations Open access
Semantic Scholar
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues
Vinícius G. Contessoto, Olga Dudchenko, Erez Lieberman Aiden, P. Wolynes +2 more
2022bioRxiv23 citations Open access
Semantic Scholar
Optimizing Potentials for a Liquid Mixture: A New Force Field for a tert-Butanol and Water Solution
Michele Di Pierro, M. Mugnai, R. Elber
2014Journal of Physical Chemistry B22 citations Open access
Semantic Scholar
Deciphering the structure of the condensin protein complex
D. Krepel, Ryan R. Cheng, Michele Di Pierro, J. Onuchic
2018Proceedings of the National Academy of Sciences of the United States of America18 citations Open access
Semantic Scholar
A Liquid State Perspective on Dynamics of Chromatin Compartments
Rabia Laghmach, Michele Di Pierro, D. Potoyan
2022Frontiers in Molecular Biosciences17 citations Open access
Semantic Scholar
Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes
Benjamin S. Ruben, Sumitabha Brahmachari, Vinícius G. Contessoto, Ryan R. Cheng +3 more
2022bioRxiv12 citations Open access
Semantic Scholar
Inner workings of gene folding
Michele Di Pierro
2019Proceedings of the National Academy of Sciences of the United States of America10 citations Open access
Semantic Scholar
Energy landscape analysis of the development of the chromosome structure across the cell cycle
Vinícius G. Contessoto, A. B. Oliveira, Sumitabha Brahmachari, P. Wolynes +2 more
2025Proceedings of the National Academy of Sciences of the United States of America7 citations Open access
Semantic Scholar
Four-Dimensional Mesoscale Liquid Model of Nucleus Resolves Chromatin’s Radial Organization
Rabia Laghmach, Michele Di Pierro, D. Potoyan
2024PRX life6 citations Open access
Semantic Scholar
An associative memory Hamiltonian model for DNA and nucleosomes
Wei-Qi Lu, J. Onuchic, Michele Di Pierro
2022bioRxiv4 citations Open access
Semantic Scholar
Fast simulation of polymer chains.
C. Hartmann, C. Schütte, G. Kalibaeva, Michele Di Pierro +1 more
2009Journal of Chemical Physics4 citations
Semantic Scholar
Learning Genomic Energy Landscapes from Experiments
Michele Di Pierro, Ryan R. Cheng, Bin Zhang, J. Onuchic +1 more
2019Modeling the 3D Conformation of Genomes3 citations
Semantic Scholar
Quantifying the influence of genetic context on duplicated mammalian genes
Alexander S. Moffett, Andrea Falc'on-Cort'es, Michele Di Pierro
2025bioRxiv2 citations Open access
Semantic Scholar
Mesoscale liquid model of chromatin recapitulates large-scale organization of eukaryotic cell nuclei
Rabia Laghmach, Michele Di Pierro, D. Potoyan
20192 citations
Semantic Scholar
The Energy Landscape of Human Chromosomes
Michele Di Pierro
20172 citations Open access
Semantic Scholar
Book of Abstracts. The 1st Next Generation Conversations: Albany at Ruston 2024 (The 21st Albany Conversation)
Thomas C. Bishop, Kelly M. Thayer, R. Young, Wilma K. Olson +45 more
2024Journal of Biomolecular Structure and Dynamics1 citations
Semantic Scholar
Landscapes of genomic architecture across evolution
Michele Di Pierro
2022Biophysical Journal1 citations Open access
Semantic Scholar
Quantifying the Influence of Genetic Context on Duplicated Mammalian Genes
Alexander S. Moffett, Andrea Falc'on-Cort'es, Michele Di Pierro
2026Molecular biology and evolution0 citations Open access
Semantic Scholar
3D genome architecture regulates the traffic of transcription factors throughout human chromosomes
Amit Das, Ryan R. Cheng, D. Potoyan, Michele Di Pierro
2026bioRxiv0 citations
Semantic Scholar
Random, fragile, or correlated: Mechanisms of synteny decay in mammals.
Alexander S. Moffett, Michele Di Pierro
2026Proceedings of the National Academy of Sciences of the United States of America0 citations Open access
Semantic Scholar
Random, fragile, or correlated: Mechanisms of synteny decay in mammals
Alexander S. Moffett, Michele Di Pierro
2025bioRxiv0 citations
Semantic Scholar
Understanding the physical processes behind DNA-DNA proximity ligation assays
Bernardo J. Zubillaga Herrera, Amit Das, Linden Burack, Ailun Wang +1 more
2025bioRxiv0 citations Open access
Semantic Scholar
BPS2025 - The role of motors and phase separation in genome folding
Michele Di Pierro
2025Biophysical Journal0 citations Open access
Semantic Scholar
Understanding the physical processes behind DNA-DNA proximity ligation assays
Bernardo J. Zubillaga Herrera, Amit Das, Linden Burack, Ailun Wang +1 more
2025Research Square0 citations
Semantic Scholar
Landscapes of genomic architecture across evolution
Michele Di Pierro
2024Biophysical Journal0 citations Open access
Semantic Scholar
Illuminating the link between nuclear geometry and chromatin structures through 4D nucleus modeling
Rabia Laghmach, Michele Di Pierro, D. Potoyan
2024Biophysical Journal0 citations Open access
Semantic Scholar
Abstract 1527 Informing models of in-silico DNA digestion
Linden Burack, Bernardo Herrera, Michele Di Pierro
2024Journal of Biological Chemistry0 citations Open access
Semantic Scholar
3D genome architecture regulates the traffic of transcription factors throughout human chromosomes.
Amit Das, Ryan R. Cheng, D. Potoyan, Michele Di Pierro
2023Biophysical Journal0 citations Open access
Semantic Scholar
4D Mesoscale liquid model of nucleus resolves chromatin’s radial organization
Rabia Laghmach, Michele Di Pierro, D. Potoyan
2023bioRxiv0 citations Open access
Semantic Scholar
Understanding the three-dimentional structures of chromatins at nucleosome resolution.
Ailun Wang, Michele Di Pierro
2023Biophysical Journal0 citations Open access
Semantic Scholar
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.
Vinícius G. Contessoto, Olga Dudchenko, Erez Lieberman Aiden, P. Wolynes +2 more
2023Biophysical Journal0 citations Open access
Semantic Scholar
Kilobase-Level Nuclear Compartments Separate Active Regulatory Elements From Adjacent Regions
Hui-Ya Gu, Hannah L. Harris, M. Olshansky, Ailun Wang +26 more
2022Social Science Research Network0 citations
Semantic Scholar
Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility
Ryan R. Cheng, Esteban Dodero-Rojas, Michele Di Pierro, J. Onuchic
2021bioRxiv0 citations Open access
Semantic Scholar
The Three-Dimensional Architecture of the Human Genome: It's Nuclear Physics!
Michele Di Pierro
2019Biophysical Journal0 citations Open access
Semantic Scholar
De Novo Chromosome Structure Prediction
Michele Di Pierro, Ryan R. Cheng, Erez Lieberman Aiden, P. Wolynes +1 more
20170 citations
Semantic Scholar
Optimization of force fields for molecular dynamics
Michele Di Pierro
20140 citations
Semantic Scholar

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Vinícius G. Contessoto×8
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