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Items: 14

1.

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.

Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M.

Cell. 2018 Jul 26;174(3):744-757.e24. doi: 10.1016/j.cell.2018.05.024. Epub 2018 Jun 7.

PMID:
29887377
2.

Flexible Backbone Methods for Predicting and Designing Peptide Specificity.

Ollikainen N.

Methods Mol Biol. 2017;1561:173-187. doi: 10.1007/978-1-4939-6798-8_10.

PMID:
28236238
3.

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression.

Engreitz JM, Ollikainen N, Guttman M.

Nat Rev Mol Cell Biol. 2016 Dec;17(12):756-770. doi: 10.1038/nrm.2016.126. Epub 2016 Oct 26. Review.

PMID:
27780979
4.

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.

Chen CK, Blanco M, Jackson C, Aznauryan E, Ollikainen N, Surka C, Chow A, Cerase A, McDonel P, Guttman M.

Science. 2016 Oct 28;354(6311):468-472. Epub 2016 Aug 4.

PMID:
27492478
5.

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

Ollikainen N, de Jong RM, Kortemme T.

PLoS Comput Biol. 2015 Sep 23;11(9):e1004335. doi: 10.1371/journal.pcbi.1004335. eCollection 2015.

6.

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

Ó Conchúir S, Barlow KA, Pache RA, Ollikainen N, Kundert K, O'Meara MJ, Smith CA, Kortemme T.

PLoS One. 2015 Sep 3;10(9):e0130433. doi: 10.1371/journal.pone.0130433. eCollection 2015.

7.

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.

Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15426-31. doi: 10.1073/pnas.1410624111. Epub 2014 Oct 13.

8.

Amino-acid site variability among natural and designed proteins.

Jackson EL, Ollikainen N, Covert AW 3rd, Kortemme T, Wilke CO.

PeerJ. 2013 Nov 12;1:e211. doi: 10.7717/peerj.211. eCollection 2013.

9.

Computational protein design quantifies structural constraints on amino acid covariation.

Ollikainen N, Kortemme T.

PLoS Comput Biol. 2013;9(11):e1003313. doi: 10.1371/journal.pcbi.1003313. Epub 2013 Nov 14.

10.

Flexible backbone sampling methods to model and design protein alternative conformations.

Ollikainen N, Smith CA, Fraser JS, Kortemme T.

Methods Enzymol. 2013;523:61-85. doi: 10.1016/B978-0-12-394292-0.00004-7.

11.

Widespread protein aggregation as an inherent part of aging in C. elegans.

David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, Kenyon C.

PLoS Biol. 2010 Aug 10;8(8):e1000450. doi: 10.1371/journal.pbio.1000450.

12.

Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.

Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA.

Genome Res. 2008 Jul;18(7):1133-42. doi: 10.1101/gr.074344.107. Epub 2008 Apr 21.

13.
14.

Evolution of the thyroid hormone, retinoic acid, ecdysone and liver X receptors.

Ollikainen N, Chandsawangbhuwana C, Baker ME.

Integr Comp Biol. 2006 Dec;46(6):815-26. doi: 10.1093/icb/icl035. Epub 2006 Aug 30.

PMID:
21672787

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