| Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus SA Quinodoz, N Ollikainen, B Tabak, A Palla, JM Schmidt, E Detmar, ... Cell 174 (3), 744-757. e24, 2018 | 757 | 2018 |
| Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans DC David, N Ollikainen, JC Trinidad, MP Cary, AL Burlingame, C Kenyon PLoS biology 8 (8), e1000450, 2010 | 700 | 2010 |
| Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression JM Engreitz, N Ollikainen, M Guttman Nature reviews Molecular cell biology 17 (12), 756-770, 2016 | 600 | 2016 |
| Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020 | 597 | 2020 |
| SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses AK Banerjee, MR Blanco, EA Bruce, DD Honson, LM Chen, A Chow, ... Cell 183 (5), 1325-1339. e21, 2020 | 536 | 2020 |
| Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing CK Chen, M Blanco, C Jackson, E Aznauryan, N Ollikainen, C Surka, ... Science 354 (6311), 468-472, 2016 | 295 | 2016 |
| Integrated spatial genomics reveals global architecture of single nuclei Y Takei, J Yun, S Zheng, N Ollikainen, N Pierson, J White, S Shah, ... Nature 590 (7845), 344-350, 2021 | 265 | 2021 |
| RNA promotes the formation of spatial compartments in the nucleus SA Quinodoz, JW Jachowicz, P Bhat, N Ollikainen, AK Banerjee, ... Cell 184 (23), 5775-5790. e30, 2021 | 242 | 2021 |
| Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes N Gupta, J Benhamida, V Bhargava, D Goodman, E Kain, I Kerman, ... Genome research 18 (7), 1133-1142, 2008 | 130 | 2008 |
| Computational design of a modular protein sense-response system AA Glasgow, YM Huang, DJ Mandell, M Thompson, R Ritterson, ... Science 366 (6468), 1024-1028, 2019 | 104 | 2019 |
| Coupling protein side-chain and backbone flexibility improves the re-design of protein-ligand specificity N Ollikainen, RM de Jong, T Kortemme PLoS computational biology 11 (9), e1004335, 2015 | 88 | 2015 |
| A web resource for standardized benchmark datasets, metrics, and Rosetta protocols for macromolecular modeling and design S ó Conchúir, KA Barlow, RA Pache, N Ollikainen, K Kundert, MJ O'Meara, ... PLOS one 10 (9), e0130433, 2015 | 85 | 2015 |
| Single-cell measurement of higher-order 3D genome organization with scSPRITE MV Arrastia, JW Jachowicz, N Ollikainen, MS Curtis, C Lai, SA Quinodoz, ... Nature biotechnology 40 (1), 64-73, 2022 | 71 | 2022 |
| Structural analysis of the evolution of steroid specificity in the mineralocorticoid and glucocorticoid receptors ME Baker, C Chandsawangbhuwana, N Ollikainen BMC evolutionary biology 7, 1-10, 2007 | 61 | 2007 |
| Flexible backbone sampling methods to model and design protein alternative conformations N Ollikainen, CA Smith, JS Fraser, T Kortemme Methods in enzymology 523, 61-85, 2013 | 48 | 2013 |
| Computational protein design quantifies structural constraints on amino acid covariation N Ollikainen, T Kortemme PLoS computational biology 9 (11), e1003313, 2013 | 44 | 2013 |
| SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding SA Quinodoz, P Bhat, P Chovanec, JW Jachowicz, N Ollikainen, E Detmar, ... Nature protocols 17 (1), 36-75, 2022 | 34 | 2022 |
| Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition C Melero, N Ollikainen, I Harwood, J Karpiak, T Kortemme Proceedings of the National Academy of Sciences 111 (43), 15426-15431, 2014 | 28 | 2014 |
| Amino-acid site variability among natural and designed proteins EL Jackson, N Ollikainen, AW Covert III, T Kortemme, CO Wilke PeerJ 1, e211, 2013 | 25 | 2013 |
| Evolution of the thyroid hormone, retinoic acid, ecdysone and liver X receptors N Ollikainen, C Chandsawangbhuwana, ME Baker Integrative and Comparative Biology 46 (6), 815-826, 2006 | 19 | 2006 |
