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Items: 1 to 50 of 175

1.

Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese.

Bodinaku I, Shaffer J, Connors AB, Steenwyk JL, Biango-Daniels MN, Kastman EK, Rokas A, Robbat A, Wolfe BE.

MBio. 2019 Oct 15;10(5). pii: e02445-19. doi: 10.1128/mBio.02445-19.

2.

Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536.

Mead ME, Raja HA, Steenwyk JL, Knowles SL, Oberlies NH, Rokas A.

Microbiol Resour Announc. 2019 Sep 19;8(38). pii: e00890-19. doi: 10.1128/MRA.00890-19.

3.

Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence.

Zhou X, Lutteropp S, Czech L, Stamatakis A, von Looz M, Rokas A.

Syst Biol. 2019 Aug 29. pii: syz058. doi: 10.1093/sysbio/syz058. [Epub ahead of print]

PMID:
31504977
4.

The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins.

Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A.

Genome Biol Evol. 2019 Sep 1;11(9):2574-2592. doi: 10.1093/gbe/evz183.

5.

Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity.

Baltrus DA, Cuomo CA, Dennehy JJ, Dunning Hotopp JC, Maresca JA, Newton ILG, Rasko DA, Rokas A, Roux S, Stajich JE.

Microbiol Resour Announc. 2019 Sep 5;8(36). pii: e00954-19. doi: 10.1128/MRA.00954-19.

6.

Treehouse: a user-friendly application to obtain subtrees from large phylogenies.

Steenwyk JL, Rokas A.

BMC Res Notes. 2019 Aug 27;12(1):541. doi: 10.1186/s13104-019-4577-5.

7.

The Aspergillus fumigatus Mismatch Repair MSH2 Homolog Is Important for Virulence and Azole Resistance.

Dos Reis TF, Silva LP, de Castro PA, do Carmo RA, Marini MM, da Silveira JF, Ferreira BH, Rodrigues F, Lind AL, Rokas A, Goldman GH.

mSphere. 2019 Aug 7;4(4). pii: e00416-19. doi: 10.1128/mSphere.00416-19.

8.

Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation.

Moon JM, Capra JA, Abbot P, Rokas A.

Bioessays. 2019 Sep;41(9):e1900072. doi: 10.1002/bies.201900072. Epub 2019 Aug 2. Review.

PMID:
31373044
9.

Variation and selection on codon usage bias across an entire subphylum.

LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A.

PLoS Genet. 2019 Jul 31;15(7):e1008304. doi: 10.1371/journal.pgen.1008304. eCollection 2019 Jul.

10.

Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution.

Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH.

Curr Biol. 2019 Aug 5;29(15):2555-2562.e8. doi: 10.1016/j.cub.2019.06.056. Epub 2019 Jul 25.

11.

Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata.

Wang M, Fu H, Shen XX, Ruan R, Rokas A, Li H.

Mol Plant Pathol. 2019 Oct;20(10):1425-1438. doi: 10.1111/mpp.12848. Epub 2019 Jul 11.

12.

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium.

Steenwyk JL, Shen XX, Lind AL, Goldman GH, Rokas A.

MBio. 2019 Jul 9;10(4). pii: e00925-19. doi: 10.1128/mBio.00925-19.

13.

Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication.

Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A.

Evol Med Public Health. 2019 May 17;2019(1):93-103. doi: 10.1093/emph/eoz015. eCollection 2019.

14.

Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues.

Moon JM, Capra JA, Abbot P, Rokas A.

G3 (Bethesda). 2019 Aug 8;9(8):2761-2774. doi: 10.1534/g3.119.400186.

15.

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts.

Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT, Rokas A.

PLoS Biol. 2019 May 21;17(5):e3000255. doi: 10.1371/journal.pbio.3000255. eCollection 2019 May.

16.

Nutritional Heterogeneity Among Aspergillus fumigatus Strains Has Consequences for Virulence in a Strain- and Host-Dependent Manner.

Ries LNA, Steenwyk JL, de Castro PA, de Lima PBA, Almeida F, de Assis LJ, Manfiolli AO, Takahashi-Nakaguchi A, Kusuya Y, Hagiwara D, Takahashi H, Wang X, Obar JJ, Rokas A, Goldman GH.

Front Microbiol. 2019 Apr 24;10:854. doi: 10.3389/fmicb.2019.00854. eCollection 2019.

17.

Unearthing fungal chemodiversity and prospects for drug discovery.

Greco C, Keller NP, Rokas A.

Curr Opin Microbiol. 2019 Oct;51:22-29. doi: 10.1016/j.mib.2019.03.002. Epub 2019 May 6. Review.

PMID:
31071615
18.

Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism.

Gao S, Gold SE, Wisecaver JH, Zhang Y, Guo L, Ma LJ, Rokas A, Glenn AE.

Fungal Genet Biol. 2019 Jul;128:60-73. doi: 10.1016/j.fgb.2019.04.002. Epub 2019 Apr 3.

PMID:
30953838
19.

Mapping the Fungal Battlefield: Using in situ Chemistry and Deletion Mutants to Monitor Interspecific Chemical Interactions Between Fungi.

Knowles SL, Raja HA, Wright AJ, Lee AML, Caesar LK, Cech NB, Mead ME, Steenwyk JL, Ries LNA, Goldman GH, Rokas A, Oberlies NH.

Front Microbiol. 2019 Feb 19;10:285. doi: 10.3389/fmicb.2019.00285. eCollection 2019.

20.

Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data.

Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A.

Int J Mol Sci. 2019 Mar 1;20(5). pii: E1072. doi: 10.3390/ijms20051072.

21.

Eukaryotic Acquisition of a Bacterial Operon.

Kominek J, Doering DT, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT.

Cell. 2019 Mar 7;176(6):1356-1366.e10. doi: 10.1016/j.cell.2019.01.034. Epub 2019 Feb 21.

PMID:
30799038
22.

Characterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatus.

Mead ME, Knowles SL, Raja HA, Beattie SR, Kowalski CH, Steenwyk JL, Silva LP, Chiaratto J, Ries LNA, Goldman GH, Cramer RA, Oberlies NH, Rokas A.

mSphere. 2019 Feb 20;4(1). pii: e00018-19. doi: 10.1128/mSphere.00018-19.

23.

Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research.

Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, Muglia LJ, Ober C, England SK, Macones G, Driscoll D, Parry S, Shaw GM, Stevenson DK, Simpson JL, Thomson E, Butte AJ; March of Dimes Prematurity Research Centers.

Sci Data. 2018 Dec 18;5(1):3. doi: 10.1038/s41597-018-0004-3.

24.

integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth.

Eidem HR, Steenwyk JL, Wisecaver JH, Capra JA, Abbot P, Rokas A.

BMC Med Genomics. 2018 Nov 19;11(1):107. doi: 10.1186/s12920-018-0426-y.

25.

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.

Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A.

Cell. 2018 Nov 29;175(6):1533-1545.e20. doi: 10.1016/j.cell.2018.10.023. Epub 2018 Nov 8.

26.

Enabling precision medicine in neonatology, an integrated repository for preterm birth research.

Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, England SK, Parry S, Shaw GM, Simpson JL, Thomson E, Butte AJ; March of Dimes Prematurity Research Centers.

Sci Data. 2018 Nov 6;5:180219. doi: 10.1038/sdata.2018.219. Erratum in: Sci Data. 2018 Dec 18;5(1):3.

27.

Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans.

Segal ES, Gritsenko V, Levitan A, Yadav B, Dror N, Steenwyk JL, Silberberg Y, Mielich K, Rokas A, Gow NAR, Kunze R, Sharan R, Berman J.

MBio. 2018 Oct 30;9(5). pii: e02048-18. doi: 10.1128/mBio.02048-18.

28.

Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts.

Krause DJ, Kominek J, Opulente DA, Shen XX, Zhou X, Langdon QK, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT.

Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):11030-11035. doi: 10.1073/pnas.1806268115. Epub 2018 Oct 8.

29.

Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases.

Shi R, Shen XX, Rokas A, Eichman BF.

Bioessays. 2018 Nov;40(11):e1800133. doi: 10.1002/bies.201800133. Epub 2018 Sep 28. Review.

PMID:
30264543
30.

The power of discussion: Support for women at the fungal Gordon Research Conference.

Riquelme M, Aime MC, Branco S, Brand A, Brown A, Glass NL, Kahmann R, Momany M, Rokas A, Trail F.

Fungal Genet Biol. 2018 Dec;121:65-67. doi: 10.1016/j.fgb.2018.09.007. Epub 2018 Sep 24. No abstract available.

PMID:
30261275
31.

Correction: Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth.

Huusko JM, Karjalainen MK, Graham BE, Zhang G, Farrow EG, Miller NA, Jacobsson B, Eidem HR, Murray JC, Bedell B, Breheny P, Brown NW, Bødker FL, Litterman NK, Jiang PP, Russell L, Hinds DA, Hu Y; 23andMe Research Team, Rokas A, Teramo K, Christensen K, Williams SM, Rämet M, Kingsmore SF, Ryckman KK, Hallman M, Muglia LJ.

PLoS Genet. 2018 Sep 13;14(9):e1007673. doi: 10.1371/journal.pgen.1007673. eCollection 2018 Sep.

32.

The birth, evolution and death of metabolic gene clusters in fungi.

Rokas A, Wisecaver JH, Lind AL.

Nat Rev Microbiol. 2018 Dec;16(12):731-744. doi: 10.1038/s41579-018-0075-3. Review.

PMID:
30194403
33.

Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi.

Wu MY, Mead ME, Lee MK, Ostrem Loss EM, Kim SC, Rokas A, Yu JH.

MBio. 2018 Aug 21;9(4). pii: e01130-18. doi: 10.1128/mBio.01130-18.

34.

Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth.

Huusko JM, Karjalainen MK, Graham BE, Zhang G, Farrow EG, Miller NA, Jacobsson B, Eidem HR, Murray JC, Bedell B, Breheny P, Brown NW, Bødker FL, Litterman NK, Jiang PP, Russell L, Hinds DA, Hu Y; 23andMe Research Team, Rokas A, Teramo K, Christensen K, Williams SM, Rämet M, Kingsmore SF, Ryckman KK, Hallman M, Muglia LJ.

PLoS Genet. 2018 Jul 12;14(7):e1007394. doi: 10.1371/journal.pgen.1007394. eCollection 2018 Jul. Erratum in: PLoS Genet. 2018 Sep 13;14(9):e1007673.

35.

Fungal Isocyanide Synthases and Xanthocillin Biosynthesis in Aspergillus fumigatus.

Lim FY, Won TH, Raffa N, Baccile JA, Wisecaver J, Rokas A, Schroeder FC, Keller NP.

MBio. 2018 May 29;9(3). pii: e00785-18. doi: 10.1128/mBio.00785-18.

36.

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.

Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH.

Nat Commun. 2018 May 14;9(1):1887. doi: 10.1038/s41467-018-04374-7.

37.

Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage.

Gonçalves C, Wisecaver JH, Kominek J, Oom MS, Leandro MJ, Shen XX, Opulente DA, Zhou X, Peris D, Kurtzman CP, Hittinger CT, Rokas A, Gonçalves P.

Elife. 2018 Apr 12;7. pii: e33034. doi: 10.7554/eLife.33034.

38.

The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.

Fidler AL, Boudko SP, Rokas A, Hudson BG.

J Cell Sci. 2018 Apr 9;131(7). pii: jcs203950. doi: 10.1242/jcs.203950. Review.

39.

An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human Pathogen Aspergillus fumigatus.

Lind AL, Lim FY, Soukup AA, Keller NP, Rokas A.

mSphere. 2018 Mar 14;3(2). pii: e00050-18. doi: 10.1128/mSphere.00050-18. eCollection 2018 Mar-Apr.

40.

Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation.

Steenwyk JL, Rokas A.

Front Microbiol. 2018 Feb 22;9:288. doi: 10.3389/fmicb.2018.00288. eCollection 2018. Review.

41.

Factors driving metabolic diversity in the budding yeast subphylum.

Opulente DA, Rollinson EJ, Bernick-Roehr C, Hulfachor AB, Rokas A, Kurtzman CP, Hittinger CT.

BMC Biol. 2018 Mar 2;16(1):26. doi: 10.1186/s12915-018-0498-3.

42.

Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology.

Moon JM, Aronoff DM, Capra JA, Abbot P, Rokas A.

G3 (Bethesda). 2018 Mar 28;8(4):1315-1325. doi: 10.1534/g3.118.200035.

43.

Inverted formin 2 regulates intracellular trafficking, placentation, and pregnancy outcome.

Lamm KYB, Johnson ML, Baker Phillips J, Muntifering MB, James JM, Jones HN, Redline RW, Rokas A, Muglia LJ.

Elife. 2018 Jan 8;7. pii: e31150. doi: 10.7554/eLife.31150.

44.

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets.

Zhou X, Shen XX, Hittinger CT, Rokas A.

Mol Biol Evol. 2018 Feb 1;35(2):486-503. doi: 10.1093/molbev/msx302.

45.

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species.

Lind AL, Wisecaver JH, Lameiras C, Wiemann P, Palmer JM, Keller NP, Rodrigues F, Goldman GH, Rokas A.

PLoS Biol. 2017 Nov 17;15(11):e2003583. doi: 10.1371/journal.pbio.2003583. eCollection 2017 Nov.

46.

Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC.

Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF.

EMBO J. 2018 Jan 4;37(1):63-74. doi: 10.15252/embj.201797833. Epub 2017 Oct 20.

47.

Embracing Uncertainty in Reconstructing Early Animal Evolution.

King N, Rokas A.

Curr Biol. 2017 Oct 9;27(19):R1081-R1088. doi: 10.1016/j.cub.2017.08.054. Review.

48.

The transformative potential of an integrative approach to pregnancy.

Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A.

Placenta. 2017 Sep;57:204-215. doi: 10.1016/j.placenta.2017.07.010. Epub 2017 Jul 15. Review.

PMID:
28864013
49.

Correction: Heredity: The gene family that cheats Mendel.

Shropshire JD, Rokas A.

Elife. 2017 Aug 22;6. pii: e31295. doi: 10.7554/eLife.31295. No abstract available.

50.

Chlamydomonas reinhardtii LFO1 Is an IsdG Family Heme Oxygenase.

Lojek LJ, Farrand AJ, Wisecaver JH, Blaby-Haas CE, Michel BW, Merchant SS, Rokas A, Skaar EP.

mSphere. 2017 Aug 16;2(4). pii: e00176-17. doi: 10.1128/mSphere.00176-17. eCollection 2017 Jul-Aug.

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