Noah Ollikainen
Noah Ollikainen
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Cited by
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
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
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
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
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
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
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
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
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
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
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, ...
PLOS one 10 (9), e0130433, 2015
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
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
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
Computational protein design quantifies structural constraints on amino acid covariation
N Ollikainen, T Kortemme
PLoS computational biology 9 (11), e1003313, 2013
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
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
Amino-acid site variability among natural and designed proteins
EL Jackson, N Ollikainen, AW Covert III, T Kortemme, CO Wilke
PeerJ 1, e211, 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
SAT-based protein design
N Ollikainen, E Sentovich, C Coelho, A Kuehlmann, T Kortemme
2009 IEEE/ACM International Conference on Computer-Aided Design-Digest of …, 2009
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Articles 1–20