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Author Details

Noah Ollikainen
California Institute of Technology
2006
22
16
Nevan J Krogan (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
34426703Single-cell measurement of higher-order 3D genome organization with scSPRITE.Nat Biotechnol2022
36450242Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription.Cell Rep2022
35013617SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding.Nat Protoc2022
34646016Systems-level effects of allosteric perturbations to a model molecular switch.Nature2021
33505024Integrated spatial genomics reveals global architecture of single nuclei.Nature2021
32483333Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nat Methods2020
33080218SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses.Cell2020
31754004Computational design of a modular protein sense-response system.Science2019
29887377Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.Cell2018
28236238Flexible Backbone Methods for Predicting and Designing Peptide Specificity.Methods Mol Biol2017
27492478Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.Science2016
27780979Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression.Nat Rev Mol Cell Biol2016
26397464Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.PLoS Comput Biol2015
26335248A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.PLoS One2015
25313039Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.Proc Natl Acad Sci U S A2014
23422426Flexible backbone sampling methods to model and design protein alternative conformations.Methods Enzymol2013
24255821Amino-acid site variability among natural and designed proteins.PeerJ2013
24244128Computational protein design quantifies structural constraints on amino acid covariation.PLoS Comput Biol2013
20711477Widespread protein aggregation as an inherent part of aging in C. elegans.PLoS Biol2010
18426904Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.Genome Res2008
17306029Structural analysis of the evolution of steroid specificity in the mineralocorticoid and glucocorticoid receptors.BMC Evol Biol2007
21672787Evolution of the thyroid hormone, retinoic acid, ecdysone and liver X receptors.Integr Comp Biol2006
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Collaborators

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University of California san francisco
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University of California san francisco
Co-authored papers 2
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Co-authored papers 1
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Co-authored papers 1
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Jesse M Engreitz
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Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
Co-authored papers 1
David G Lambright
University of Massachusetts Medical School
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Jeliazko R Jeliazkov
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Rocco Moretti
Co-authored papers 1
Michael S Pacella
Co-authored papers 1
Michael C Thompson
University of California
Co-authored papers 1
Daisuke Kuroda
The University of Tokyo
Co-authored papers 1
Elizabeth Soehalim
Co-authored papers 1
Release 1.2