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Noah Ollikainen · SciRah

Researcher profile · Semantic Scholar

Noah Ollikainen

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Noah Ollikainen — researcher profile on SciRah

h-index: 19
Works: 32
Citations: 5,161

Most-cited papers

Macromolecular modeling and design in Rosetta: recent methods and frameworks
Julia Koehler Leman, Brian D. Weitzner, S. Lewis, Jared Adolf-Bryfogle +104 more
2020Nature Methods822 citations Open access
Semantic Scholar
Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus
Sofia A. Quinodoz, Noah Ollikainen, B. Tabak, Ali Palla +16 more
2018Cell811 citations Open access
Semantic Scholar
Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans
D. David, Noah Ollikainen, J. Trinidad, Michael P. Cary +2 more
2010PLoS Biology643 citations Open access
Semantic Scholar
Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
Jesse M. Engreitz, Noah Ollikainen, M. Guttman
2016Nature reviews. Molecular cell biology559 citations
Semantic Scholar
SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses
Abhik K. Banerjee, M. Blanco, E. Bruce, D. Honson +18 more
2020Cell530 citations Open access
Semantic Scholar
Integrated spatial genomics reveals global architecture of single nuclei
Yodai Takei, Ji-Na Yun, Shi-Wei Zheng, Noah Ollikainen +9 more
2021Nature371 citations Open access
Semantic Scholar
RNA promotes the formation of spatial compartments in the nucleus
Sofia A. Quinodoz, Joanna W. Jachowicz, Prashant Bhat, Noah Ollikainen +9 more
2020bioRxiv342 citations Open access
Semantic Scholar
Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing
Chun-Kan Chen, M. Blanco, Constanza Jackson, E. Aznauryan +6 more
2016Science250 citations
Semantic Scholar
Computational design of a modular protein sense/response system
A. Glasgow, Yao-ming Huang, Daniel J. Mandell, M. Thompson +11 more
2019Science129 citations Open access
Semantic Scholar
Single-cell measurement of higher-order 3D genome organization with scSPRITE
Mary V. Arrastia, Joanna W. Jachowicz, Noah Ollikainen, M. Curtis +5 more
2021Nature Biotechnology119 citations Open access
Semantic Scholar
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.
Nitin Gupta, J. Benhamida, V. Bhargava, Daniel B. Goodman +11 more
2008Genome Research110 citations Open access
Semantic Scholar
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design
S. O. Conchúir, Kyle A. Barlow, Roland A. Pache, Noah Ollikainen +4 more
2015PLoS ONE82 citations Open access
Semantic Scholar
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
Noah Ollikainen, Re-Ne M. Jong, T. Kortemme
2015PLoS Comput. Biol.76 citations Open access
Semantic Scholar
Structural analysis of the evolution of steroid specificity in the mineralocorticoid and glucocorticoid receptors
M. Baker, Charlie Chandsawangbhuwana, Noah Ollikainen
2007BMC Evolutionary Biology51 citations Open access
Semantic Scholar
SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding
Sofia A. Quinodoz, Prashant Bhat, P. Chovanec, Joanna W. Jachowicz +4 more
2022Nature Protocols48 citations
Semantic Scholar
Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations”
Noah Ollikainen, Colin A. Smith, J. Fraser, T. Kortemme
2013Methods in Enzymology43 citations Open access
Semantic Scholar
Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation
Noah Ollikainen, T. Kortemme
2013PLoS Comput. Biol.36 citations Open access
Semantic Scholar
Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription
Isabel N. Goronzy, Sofia A. Quinodoz, Joanna W. Jachowicz, Noah Ollikainen +2 more
2022Cell Reports27 citations Open access
Semantic Scholar
Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition
C. Melero, Noah Ollikainen, I. Harwood, Joel Karpiak +1 more
2014Proceedings of the National Academy of Sciences of the United States of America21 citations Open access
Semantic Scholar
Evolution of the thyroid hormone, retinoic acid, ecdysone and liver X receptors.
Noah Ollikainen, Charlie Chandsawangbhuwana, M. Baker
2006Integrative and Comparative Biology19 citations Open access
Semantic Scholar
Systems-level effects of allosteric perturbations to a model molecular switch
Tina Perica, C. Mathy, Jie-Wei Xu, Gwendolyn M. Jang +9 more
2021Nature18 citations Open access
Semantic Scholar
A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells
Mary V. Arrastia, Joanna W. Jachowicz, Noah Ollikainen, M. Curtis +5 more
2020bioRxiv16 citations Open access
Semantic Scholar
Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus
Sofia A. Quinodoz, Noah Ollikainen, B. Tabak, Ali Palla +14 more
2017bioRxiv15 citations Open access
Semantic Scholar
Amino-acid site variability among natural and designed proteins
Eleisha L. Jackson, Noah Ollikainen, Arthur W. Covert, T. Kortemme +1 more
2013PeerJ15 citations Open access
Semantic Scholar
SAT-based protein design
Noah Ollikainen, E. Sentovich, Carlos Coelho, A. Kuehlmann +1 more
2009IEEE/ACM International Conference on Computer-Aided Design12 citations
Semantic Scholar
Baculovirus Phylogeny Based on Genome Rearrangements
Daniel B. Goodman, Noah Ollikainen, Chris Sholley
2007RECOMB Comparative Genomics Satellite Conference6 citations Open access
Semantic Scholar
Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence
Yodai Takei, Ji-Na Yun, Noah Ollikainen, Shi-Wei Zheng +8 more
2020bioRxiv2 citations Open access
Semantic Scholar
Flexible Backbone Methods for Predicting and Designing Peptide Specificity.
Noah Ollikainen
2017Methods in molecular biology2 citations
Semantic Scholar
Biophysical basis of cellular multi-specificity encoded in a model molecular switch
Tina Perica, C. Mathy, Jie-Wei Xu, Gwendolyn M. Jang +9 more
2020bioRxiv0 citations Open access
Semantic Scholar
covariation: Initial release associated with the publication
Noah Ollikainen, S. O'Connor
20150 citations
Semantic Scholar
Novel algorithms and benchmarks for computational protein design
Noah Ollikainen
20140 citations
Semantic Scholar
Structural analysis of HIV‐1 protease inhibition using physical models
Shannon Colton, Timothy Herman, K. Giles, B. Koo +3 more
20100 citations
Semantic Scholar

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