Publications by authors named "Noah Ollikainen"

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Origin and novel transport pathways of bacterial hopanoids.
Evan C Lawrence, Huiqiao Pan, Noah Ollikainen, Brittany J Belin

bioRxiv· July 2025

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Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus.
Fei Ma, Noah Ollikainen, Hansen Du, Fatima Zohra Braikia, Nina Cui

Nat Commun· March 2025

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TCF1 dosage determines cell fate during T cell development.
Anjali Verma, Bridget Aylward, Fei Ma, Cheryl A Sherman, Laura Chopp, Noah Ollikainen

Sci Adv· November 2024

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Three-dimensional chromatin reorganization regulates B cell development during ageing.
Fei Ma, Yaqiang Cao, Hansen Du, Fatima Zohra Braikia, Le Zong, Noah Ollikainen

Nat Cell Biol· June 2024

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Unraveling the Tcrb interactome.
Noah Ollikainen, Ranjan Sen

J Exp Med· February 2024

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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, Prashant Bhat

Cell Rep· November 2022

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Single-cell measurement of higher-order 3D genome organization with scSPRITE.
Mary V Arrastia, Joanna W Jachowicz, Noah Ollikainen, Matthew S Curtis, Charlotte Lai

Nat Biotechnol· January 2022

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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, Peter Chovanec, Joanna W Jachowicz, Noah Ollikainen

Nat Protoc· January 2022

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Systems-level effects of allosteric perturbations to a model molecular switch.
Tina Perica, Christopher J P Mathy, Jiewei Xu, Gwendolyn Μ Jang, Yang Zhang, Noah Ollikainen

Nature· November 2021

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RNA promotes the formation of spatial compartments in the nucleus.
Sofia A Quinodoz, Joanna W Jachowicz, Prashant Bhat, Noah Ollikainen, Abhik K Banerjee

Cell· November 2021

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Integrated spatial genomics reveals global architecture of single nuclei.
Yodai Takei, Jina Yun, Shiwei Zheng, Noah Ollikainen, Nico Pierson

Nature· February 2021

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SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses.
Abhik K Banerjee, Mario R Blanco, Emily A Bruce, Drew D Honson, Linlin M Chen, Noah Ollikainen

Cell· November 2020

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Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Julia Koehler Leman, Brian D Weitzner, Steven M Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Noah Ollikainen

Nat Methods· July 2020

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Computational design of a modular protein sense-response system.
Anum A Glasgow, Yao-Ming Huang, Daniel J Mandell, Michael Thompson, Ryan Ritterson, Noah Ollikainen

Science· November 2019

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Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.
Sofia A Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt

Cell· July 2018

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Flexible Backbone Methods for Predicting and Designing Peptide Specificity.
Noah Ollikainen

Methods Mol Biol· February 2018

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Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression.
Jesse M Engreitz, Noah Ollikainen, Mitchell Guttman

Nat Rev Mol Cell Biol· December 2016

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Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.
Chun-Kan Chen, Mario Blanco, Constanza Jackson, Erik Aznauryan, Noah Ollikainen

Science· October 2016

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A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.
Shane Ó Conchúir, Kyle A Barlow, Roland A Pache, Noah Ollikainen, Kale Kundert

PLoS One· May 2016

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Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.
Noah Ollikainen, René M de Jong, Tanja Kortemme

PLoS Comput Biol· March 2016

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Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.
Cristina Melero, Noah Ollikainen, Ian Harwood, Joel Karpiak, Tanja Kortemme

Proc Natl Acad Sci U S A· October 2014

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Computational protein design quantifies structural constraints on amino acid covariation.
Noah Ollikainen, Tanja Kortemme

PLoS Comput Biol· July 2014

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Amino-acid site variability among natural and designed proteins.
Eleisha L Jackson, Noah Ollikainen, Arthur W Covert, Tanja Kortemme, Claus O Wilke

PeerJ· November 2013

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Flexible backbone sampling methods to model and design protein alternative conformations.
Noah Ollikainen, Colin A Smith, James S Fraser, Tanja Kortemme

Methods Enzymol· August 2013

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Widespread protein aggregation as an inherent part of aging in C. elegans.
Della C David, Noah Ollikainen, Jonathan C Trinidad, Michael P Cary, Alma L Burlingame

PLoS Biol· August 2010

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