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Items: 15


Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses.

Hockenberry AJ, Wilke CO.

Entropy (Basel). 2019 Oct;21(10). pii: 1000. doi: 10.3390/e21101000. Epub 2019 Oct 12.


Evolutionary couplings detect side-chain interactions.

Hockenberry AJ, Wilke CO.

PeerJ. 2019 Jul 8;7:e7280. doi: 10.7717/peerj.7280. eCollection 2019.


Assembly and functionality of the ribosome with tethered subunits.

Aleksashin NA, Leppik M, Hockenberry AJ, Klepacki D, Vázquez-Laslop N, Jewett MC, Remme J, Mankin AS.

Nat Commun. 2019 Feb 25;10(1):930. doi: 10.1038/s41467-019-08892-w.


Predicting bacterial growth conditions from mRNA and protein abundances.

Caglar MU, Hockenberry AJ, Wilke CO.

PLoS One. 2018 Nov 2;13(11):e0206634. doi: 10.1371/journal.pone.0206634. eCollection 2018.


Neisseria gonorrhoeae Exposed to Sublethal Levels of Hydrogen Peroxide Mounts a Complex Transcriptional Response.

Quillin SJ, Hockenberry AJ, Jewett MC, Seifert HS.

mSystems. 2018 Oct 2;3(5). pii: e00156-18. doi: 10.1128/mSystems.00156-18. eCollection 2018 Sep-Oct.


Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.

Hockenberry AJ, Jewett MC, Amaral LAN, Wilke CO.

Mol Biol Evol. 2018 Oct 1;35(10):2487-2498. doi: 10.1093/molbev/msy150.


A novel framework for evaluating the performance of codon usage bias metrics.

Liu SS, Hockenberry AJ, Jewett MC, Amaral LAN.

J R Soc Interface. 2018 Jan;15(138). pii: 20170667. doi: 10.1098/rsif.2017.0667.


Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands.

Hockenberry AJ, Stern AJ, Amaral LAN, Jewett MC.

Mol Biol Evol. 2018 Mar 1;35(3):582-592. doi: 10.1093/molbev/msx310.


Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency.

Hockenberry AJ, Pah AR, Jewett MC, Amaral LA.

Open Biol. 2017 Jan;7(1). pii: 160239. doi: 10.1098/rsob.160239.


NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.

Liu SS, Hockenberry AJ, Lancichinetti A, Jewett MC, Amaral LA.

PLoS Comput Biol. 2016 Nov 11;12(11):e1005184. doi: 10.1371/journal.pcbi.1005184. eCollection 2016 Nov.


Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent.

Yang C, Hockenberry AJ, Jewett MC, Amaral LAN.

G3 (Bethesda). 2016 Nov 8;6(11):3467-3474. doi: 10.1534/g3.116.032227.


Quantifying position-dependent codon usage bias.

Hockenberry AJ, Sirer MI, Amaral LA, Jewett MC.

Mol Biol Evol. 2014 Jul;31(7):1880-93. doi: 10.1093/molbev/msu126. Epub 2014 Apr 7.


Synthetic in vitro circuits.

Hockenberry AJ, Jewett MC.

Curr Opin Chem Biol. 2012 Aug;16(3-4):253-9. doi: 10.1016/j.cbpa.2012.05.179. Epub 2012 Jun 5. Review.


N-methyl-D-aspartate receptor mechanosensitivity is governed by C terminus of NR2B subunit.

Singh P, Doshi S, Spaethling JM, Hockenberry AJ, Patel TP, Geddes-Klein DM, Lynch DR, Meaney DF.

J Biol Chem. 2012 Feb 3;287(6):4348-59. doi: 10.1074/jbc.M111.253740. Epub 2011 Dec 16.


Computational investigation of the changing patterns of subtype specific NMDA receptor activation during physiological glutamatergic neurotransmission.

Singh P, Hockenberry AJ, Tiruvadi VR, Meaney DF.

PLoS Comput Biol. 2011 Jun;7(6):e1002106. doi: 10.1371/journal.pcbi.1002106. Epub 2011 Jun 30.

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