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Items: 24

1.

Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes.

Pham JY, Ogbunugafor CB, Nguyen Ba AN, Hartl DL.

Microbiologyopen. 2020 Feb;9(2):e968. doi: 10.1002/mbo3.968. Epub 2019 Nov 28.

2.

High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast.

Nguyen Ba AN, Cvijović I, Rojas Echenique JI, Lawrence KR, Rego-Costa A, Liu X, Levy SF, Desai MM.

Nature. 2019 Nov;575(7783):494-499. doi: 10.1038/s41586-019-1749-3. Epub 2019 Nov 13.

PMID:
31723263
3.

Efficient production of large-size optical Schrödinger cat states.

Mikheev EV, Pugin AS, Kuts DA, Podoshvedov SA, An NB.

Sci Rep. 2019 Oct 4;9(1):14301. doi: 10.1038/s41598-019-50703-1.

4.

Proteome-wide signatures of function in highly diverged intrinsically disordered regions.

Zarin T, Strome B, Nguyen Ba AN, Alberti S, Forman-Kay JD, Moses AM.

Elife. 2019 Jul 2;8. pii: e46883. doi: 10.7554/eLife.46883.

5.

Evolthon: A community endeavor to evolve lab evolution.

Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Aharon Hefetz N, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y.

PLoS Biol. 2019 Mar 29;17(3):e3000182. doi: 10.1371/journal.pbio.3000182. eCollection 2019 Mar.

6.

Modular epistasis and the compensatory evolution of gene deletion mutants.

Rojas Echenique JI, Kryazhimskiy S, Nguyen Ba AN, Desai MM.

PLoS Genet. 2019 Feb 15;15(2):e1007958. doi: 10.1371/journal.pgen.1007958. eCollection 2019 Feb.

7.

Experimental Studies of Evolutionary Dynamics in Microbes.

Cvijović I, Nguyen Ba AN, Desai MM.

Trends Genet. 2018 Sep;34(9):693-703. doi: 10.1016/j.tig.2018.06.004. Epub 2018 Jul 17. Review.

8.

Entanglement of photons in their dual wave-particle nature.

Rab AS, Polino E, Man ZX, Ba An N, Xia YJ, Spagnolo N, Lo Franco R, Sciarrino F.

Nat Commun. 2017 Oct 13;8(1):915. doi: 10.1038/s41467-017-01058-6.

9.

Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments.

Nguyen Ba AN, Strome B, Osman S, Legere EA, Zarin T, Moses AM.

PLoS Genet. 2017 Apr 14;13(4):e1006735. doi: 10.1371/journal.pgen.1006735. eCollection 2017 Apr.

10.

Simultaneous observation of particle and wave behaviors of entangled photons.

Man ZX, Xia YJ, An NB.

Sci Rep. 2017 Feb 13;7:42539. doi: 10.1038/srep42539.

11.

Selection maintains signaling function of a highly diverged intrinsically disordered region.

Zarin T, Tsai CN, Nguyen Ba AN, Moses AM.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1450-E1459. doi: 10.1073/pnas.1614787114. Epub 2017 Feb 6.

12.

Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library.

Youn JY, Friesen H, Nguyen Ba AN, Liang W, Messier V, Cox MJ, Moses AM, Andrews B.

G3 (Bethesda). 2017 Mar 10;7(3):911-921. doi: 10.1534/g3.116.038471.

13.

Controlling heat flows among three reservoirs asymmetrically coupled to two two-level systems.

Man ZX, An NB, Xia YJ.

Phys Rev E. 2016 Oct;94(4-1):042135. Epub 2016 Oct 26.

PMID:
27841562
14.

Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions.

Khan T, Douglas GM, Patel P, Nguyen Ba AN, Moses AM.

Genome Biol Evol. 2015 Jun 4;7(6):1815-26. doi: 10.1093/gbe/evv105.

15.

The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism.

Gógl G, Schneider KD, Yeh BJ, Alam N, Nguyen Ba AN, Moses AM, Hetényi C, Reményi A, Weiss EL.

PLoS Biol. 2015 May 12;13(5):e1002146. doi: 10.1371/journal.pbio.1002146. eCollection 2015 May.

16.

Non-Markovian dynamics of a two-level system in the presence of hierarchical environments.

Man ZX, An NB, Xia YJ.

Opt Express. 2015 Mar 9;23(5):5763-76. doi: 10.1364/OE.23.005763.

PMID:
25836806
17.

Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.

Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003977. doi: 10.1371/journal.pcbi.1003977. eCollection 2014 Dec.

18.

A high-definition view of functional genetic variation from natural yeast genomes.

Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.

Mol Biol Evol. 2014 Apr;31(4):872-88. doi: 10.1093/molbev/msu037. Epub 2014 Jan 14.

19.

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome.

Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, Nieduszynski CA.

BMC Genomics. 2013 Jan 31;14:69. doi: 10.1186/1471-2164-14-69.

20.

Proteome-wide discovery of evolutionary conserved sequences in disordered regions.

Nguyen Ba AN, Yeh BJ, van Dyk D, Davidson AR, Andrews BJ, Weiss EL, Moses AM.

Sci Signal. 2012 Mar 13;5(215):rs1. doi: 10.1126/scisignal.2002515.

21.

Predicting kinase substrates using conservation of local motif density.

Lai AC, Nguyen Ba AN, Moses AM.

Bioinformatics. 2012 Apr 1;28(7):962-9. doi: 10.1093/bioinformatics/bts060. Epub 2012 Feb 1.

PMID:
22302575
22.

A quantitative literature-curated gold standard for kinase-substrate pairs.

Sharifpoor S, Nguyen Ba AN, Youn JY, van Dyk D, Friesen H, Douglas AC, Kurat CF, Chong YT, Founk K, Moses AM, Andrews BJ.

Genome Biol. 2011;12(4):R39. doi: 10.1186/gb-2011-12-4-r39. Epub 2011 Apr 14. Erratum in: Genome Biol. 2012;13(5):417. Young, Ji-Young [corrected to Youn, Ji-Young].

23.

Evolution of characterized phosphorylation sites in budding yeast.

Nguyen Ba AN, Moses AM.

Mol Biol Evol. 2010 Sep;27(9):2027-37. doi: 10.1093/molbev/msq090. Epub 2010 Apr 5.

PMID:
20368267
24.

NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.

Nguyen Ba AN, Pogoutse A, Provart N, Moses AM.

BMC Bioinformatics. 2009 Jun 29;10:202. doi: 10.1186/1471-2105-10-202.

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