The energetics and physiological impact of cohesin extrusion L Vian, A Pękowska, SSP Rao, KR Kieffer-Kwon, S Jung, L Baranello, ... Cell 173 (5), 1165-1178. e20, 2018 | 533 | 2018 |
Transferable model for chromosome architecture M Di Pierro, B Zhang, EL Aiden, PG Wolynes, JN Onuchic Proceedings of the National Academy of Sciences 113 (43), 12168-12173, 2016 | 304 | 2016 |
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling G Nir, I Farabella, C Pérez Estrada, CG Ebeling, BJ Beliveau, HM Sasaki, ... PLoS genetics 14 (12), e1007872, 2018 | 238 | 2018 |
De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture M Di Pierro, RR Cheng, E Lieberman Aiden, PG Wolynes, JN Onuchic Proceedings of the National Academy of Sciences 114 (46), 12126-12131, 2017 | 217 | 2017 |
3D genomics across the tree of life reveals condensin II as a determinant of architecture type C Hoencamp, O Dudchenko, AMO Elbatsh, S Brahmachari, ... Science 372 (6545), 984-989, 2021 | 166 | 2021 |
A stochastic algorithm for the isobaric–isothermal ensemble with Ewald summations for all long range forces M Di Pierro, R Elber, B Leimkuhler Journal of chemical theory and computation 11 (12), 5624-5637, 2015 | 148 | 2015 |
Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes M Di Pierro, DA Potoyan, PG Wolynes, JN Onuchic Proceedings of the National Academy of Sciences 115 (30), 7753-7758, 2018 | 140 | 2018 |
Exploring chromosomal structural heterogeneity across multiple cell lines RR Cheng, VG Contessoto, E Lieberman Aiden, PG Wolynes, M Di Pierro, ... Elife 9, e60312, 2020 | 45 | 2020 |
Automated optimization of potential parameters M Di Pierro, R Elber Journal of chemical theory and computation 9 (8), 3311-3320, 2013 | 42 | 2013 |
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization HL Harris, H Gu, M Olshansky, A Wang, I Farabella, Y Eliaz, A Kalluchi, ... Nature communications 14 (1), 3303, 2023 | 35 | 2023 |
The interplay of chromatin phase separation and lamina interactions in nuclear organization R Laghmach, M Di Pierro, DA Potoyan Biophysical Journal 120 (22), 5005-5017, 2021 | 32 | 2021 |
Optimizing Potentials for a Liquid Mixture: A New Force Field for a tert-Butanol and Water Solution M Di Pierro, ML Mugnai, R Elber The Journal of Physical Chemistry B 119 (3), 836-849, 2015 | 27 | 2015 |
Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes R Laghmach, M Di Pierro, DA Potoyan Biophysical Journal 118 (9), 2130-2140, 2020 | 26 | 2020 |
Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion S Brahmachari, VG Contessoto, M Di Pierro, JN Onuchic Nucleic Acids Research 50 (8), 4258-4271, 2022 | 25 | 2022 |
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome VG Contessoto, RR Cheng, A Hajitaheri, E Dodero-Rojas, MF Mello, ... Nucleic Acids Research 49 (D1), D172-D182, 2021 | 24 | 2021 |
Deciphering the structure of the condensin protein complex D Krepel, RR Cheng, M Di Pierro, JN Onuchic Proceedings of the National Academy of Sciences 115 (47), 11911-11916, 2018 | 18 | 2018 |
A liquid state perspective on dynamics of chromatin compartments R Laghmach, M Di Pierro, D Potoyan Frontiers in Molecular Biosciences 8, 781981, 2022 | 13 | 2022 |
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues VG Contessoto, O Dudchenko, E Aiden, PG Wolynes, JN Onuchic, ... Nature Communications 14 (326), https://doi.org/10.1038/s41467-023-35909, 2023 | 11 | 2023 |
Inner workings of gene folding M Di Pierro Proceedings of the National Academy of Sciences 116 (11), 4774-4775, 2019 | 10 | 2019 |
Fast simulation of polymer chains C Hartmann, C Schütte, G Kalibaeva, M Di Pierro, G Ciccotti The Journal of chemical physics 130 (14), 2009 | 5 | 2009 |