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Items: 29

1.

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.

VanBuren R, Wai CM, Colle M, Wang J, Sullivan S, Bushakra JM, Liachko I, Vining KJ, Dossett M, Finn CE, Jibran R, Chagné D, Childs K, Edger PP, Mockler TC, Bassil NV.

Gigascience. 2018 Aug 1;7(8). doi: 10.1093/gigascience/giy094.

2.

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.

Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, Liachko I, Snelling TJ, Dewhurst RJ, Walker AW, Roehe R, Watson M.

Nat Commun. 2018 Feb 28;9(1):870. doi: 10.1038/s41467-018-03317-6.

3.

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data.

Jibran R, Dzierzon H, Bassil N, Bushakra JM, Edger PP, Sullivan S, Finn CE, Dossett M, Vining KJ, VanBuren R, Mockler TC, Liachko I, Davies KM, Foster TM, Chagné D.

Hortic Res. 2018 Feb 7;5:8. doi: 10.1038/s41438-017-0013-y. eCollection 2018.

4.

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.

Smukowski Heil C, Burton JN, Liachko I, Friedrich A, Hanson NA, Morris CL, Schacherer J, Shendure J, Thomas JH, Dunham MJ.

Yeast. 2018 Jan;35(1):71-84. doi: 10.1002/yea.3280. Epub 2017 Oct 19.

PMID:
28892574
5.

Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly.

Peichel CL, Sullivan ST, Liachko I, White MA.

J Hered. 2017 Sep 1;108(6):693-700. doi: 10.1093/jhered/esx058.

6.

The dynamic three-dimensional organization of the diploid yeast genome.

Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ.

Elife. 2017 May 24;6. pii: e23623. doi: 10.7554/eLife.23623.

7.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP.

Nat Genet. 2017 Apr;49(4):643-650. doi: 10.1038/ng.3802. Epub 2017 Mar 6.

8.

Differential paralog divergence modulates genome evolution across yeast species.

Sanchez MR, Miller AW, Liachko I, Sunshine AB, Lynch B, Huang M, Alcantara E, DeSevo CG, Pai DA, Tucker CM, Hoang ML, Dunham MJ.

PLoS Genet. 2017 Feb 14;13(2):e1006585. doi: 10.1371/journal.pgen.1006585. eCollection 2017 Feb.

9.

Evolution of protein phosphorylation across 18 fungal species.

Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J.

Science. 2016 Oct 14;354(6309):229-232.

PMID:
27738172
10.

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome.

Burrack LS, Hutton HF, Matter KJ, Clancey SA, Liachko I, Plemmons AE, Saha A, Power EA, Turman B, Thevandavakkam MA, Ay F, Dunham MJ, Berman J.

PLoS Genet. 2016 Sep 23;12(9):e1006317. doi: 10.1371/journal.pgen.1006317. eCollection 2016 Sep.

11.

Characterization of a panARS-based episomal vector in the methylotrophic yeast Pichia pastoris for recombinant protein production and synthetic biology applications.

Camattari A, Goh A, Yip LY, Tan AH, Ng SW, Tran A, Liu G, Liachko I, Dunham MJ, Rancati G.

Microb Cell Fact. 2016 Aug 11;15(1):139. doi: 10.1186/s12934-016-0540-5.

12.

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation.

Hoggard T, Liachko I, Burt C, Meikle T, Jiang K, Craciun G, Dunham MJ, Fox CA.

G3 (Bethesda). 2016 Apr 7;6(4):993-1012. doi: 10.1534/g3.116.027904.

13.

The fitness consequences of aneuploidy are driven by condition-dependent gene effects.

Sunshine AB, Payen C, Ong GT, Liachko I, Tan KM, Dunham MJ.

PLoS Biol. 2015 May 26;13(5):e1002155. doi: 10.1371/journal.pbio.1002155. eCollection 2015 May.

14.

Accurate identification of centromere locations in yeast genomes using Hi-C.

Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS.

Nucleic Acids Res. 2015 Jun 23;43(11):5331-9. doi: 10.1093/nar/gkv424. Epub 2015 May 4.

15.

An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis.

Million-Weaver S, Samadpour AN, Moreno-Habel DA, Nugent P, Brittnacher MJ, Weiss E, Hayden HS, Miller SI, Liachko I, Merrikh H.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1096-105. doi: 10.1073/pnas.1416651112. Epub 2015 Feb 23.

16.

Origin replication complex binding, nucleosome depletion patterns, and a primary sequence motif can predict origins of replication in a genome with epigenetic centromeres.

Tsai HJ, Baller JA, Liachko I, Koren A, Burrack LS, Hickman MA, Thevandavakkam MA, Rusche LN, Berman J.

MBio. 2014 Sep 2;5(5):e01703-14. doi: 10.1128/mBio.01703-14.

17.

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps.

Burton JN, Liachko I, Dunham MJ, Shendure J.

G3 (Bethesda). 2014 May 22;4(7):1339-46. doi: 10.1534/g3.114.011825.

18.

GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

Liachko I, Youngblood RA, Tsui K, Bubb KL, Queitsch C, Raghuraman MK, Nislow C, Brewer BJ, Dunham MJ.

PLoS Genet. 2014 Mar 6;10(3):e1004169. doi: 10.1371/journal.pgen.1004169. eCollection 2014 Mar.

19.

An autonomously replicating sequence for use in a wide range of budding yeasts.

Liachko I, Dunham MJ.

FEMS Yeast Res. 2014 Mar;14(2):364-7. doi: 10.1111/1567-1364.12123. Epub 2013 Dec 2.

20.

High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast.

Liachko I, Youngblood RA, Keich U, Dunham MJ.

Genome Res. 2013 Apr;23(4):698-704. doi: 10.1101/gr.144659.112. Epub 2012 Dec 12.

21.

Novel features of ARS selection in budding yeast Lachancea kluyveri.

Liachko I, Tanaka E, Cox K, Chung SC, Yang L, Seher A, Hallas L, Cha E, Kang G, Pace H, Barrow J, Inada M, Tye BK, Keich U.

BMC Genomics. 2011 Dec 28;12:633. doi: 10.1186/1471-2164-12-633.

22.

A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.

Liachko I, Bhaskar A, Lee C, Chung SC, Tye BK, Keich U.

PLoS Genet. 2010 May 13;6(5):e1000946. doi: 10.1371/journal.pgen.1000946.

23.

Alternative mechanisms for coordinating polymerase alpha and MCM helicase.

Lee C, Liachko I, Bouten R, Kelman Z, Tye BK.

Mol Cell Biol. 2010 Jan;30(2):423-35. doi: 10.1128/MCB.01240-09. Epub 2009 Nov 16.

24.

Novel DNA binding properties of the Mcm10 protein from Saccharomyces cerevisiae.

Eisenberg S, Korza G, Carson J, Liachko I, Tye BK.

J Biol Chem. 2009 Sep 11;284(37):25412-20. doi: 10.1074/jbc.M109.033175. Epub 2009 Jul 15.

25.

Functional screen of human MCM2-7 variant alleles for disease-causing potential.

Steere NA, Yamaguchi S, Andrews CA, Liachko I, Nakamura T, Shima N.

Mutat Res. 2009 Jun 18;666(1-2):74-8. doi: 10.1016/j.mrfmmm.2009.03.006. Epub 2009 Mar 27.

PMID:
19481678
26.

Mcm10 mediates the interaction between DNA replication and silencing machineries.

Liachko I, Tye BK.

Genetics. 2009 Feb;181(2):379-91. doi: 10.1534/genetics.108.099101. Epub 2008 Dec 8.

27.

Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast.

Keich U, Gao H, Garretson JS, Bhaskar A, Liachko I, Donato J, Tye BK.

BMC Bioinformatics. 2008 Sep 12;9:372. doi: 10.1186/1471-2105-9-372.

28.

A viable allele of Mcm4 causes chromosome instability and mammary adenocarcinomas in mice.

Shima N, Alcaraz A, Liachko I, Buske TR, Andrews CA, Munroe RJ, Hartford SA, Tye BK, Schimenti JC.

Nat Genet. 2007 Jan;39(1):93-8. Epub 2006 Dec 3.

PMID:
17143284
29.

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