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Items: 1 to 50 of 159

1.

Unearthing fungal chemodiversity and prospects for drug discovery.

Greco C, Keller NP, Rokas A.

Curr Opin Microbiol. 2019 May 6;51:22-29. doi: 10.1016/j.mib.2019.03.002. [Epub ahead of print] Review.

PMID:
31071615
2.

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 Apr 3;128:60-73. doi: 10.1016/j.fgb.2019.04.002. [Epub ahead of print]

PMID:
30953838
3.

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.

4.

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.

5.

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
6.

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.

7.

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.

8.

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.

9.

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.

PMID:
30415838
10.

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.

11.

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.

12.

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.

13.

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
14.

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
15.

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.

16.

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
17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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
33.

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.

34.

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.

35.

Contentious relationships in phylogenomic studies can be driven by a handful of genes.

Shen XX, Hittinger CT, Rokas A.

Nat Ecol Evol. 2017 Apr 10;1(5):126. doi: 10.1038/s41559-017-0126.

36.

Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans.

Zhao L, Zhou X, Rokas A, Cone RD.

Sci Rep. 2017 Jul 18;7(1):5684. doi: 10.1038/s41598-017-05962-1.

37.

MybA, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus.

Valsecchi I, Sarikaya-Bayram Ö, Wong Sak Hoi J, Muszkieta L, Gibbons J, Prevost MC, Mallet A, Krijnse-Locker J, Ibrahim-Granet O, Mouyna I, Carr P, Bromley M, Aimanianda V, Yu JH, Rokas A, Braus GH, Saveanu C, Bayram Ö, Latgé JP.

Mol Microbiol. 2017 Sep;105(6):880-900. doi: 10.1111/mmi.13744. Epub 2017 Jul 21.

38.

WetA bridges cellular and chemical development in Aspergillus flavus.

Wu MY, Mead ME, Kim SC, Rokas A, Yu JH.

PLoS One. 2017 Jun 28;12(6):e0179571. doi: 10.1371/journal.pone.0179571. eCollection 2017.

39.

The gene family that cheats Mendel.

Shropshire JD, Rokas A.

Elife. 2017 Jun 20;6. pii: e28567. doi: 10.7554/eLife.28567. Erratum in: Elife. 2017 Aug 22;6:.

40.

Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues.

Fidler AL, Darris CE, Chetyrkin SV, Pedchenko VK, Boudko SP, Brown KL, Gray Jerome W, Hudson JK, Rokas A, Hudson BG.

Elife. 2017 Apr 18;6. pii: e24176. doi: 10.7554/eLife.24176.

41.

A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants.

Wisecaver JH, Borowsky AT, Tzin V, Jander G, Kliebenstein DJ, Rokas A.

Plant Cell. 2017 May;29(5):944-959. doi: 10.1105/tpc.17.00009. Epub 2017 Apr 13.

42.

Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains.

Steenwyk J, Rokas A.

G3 (Bethesda). 2017 May 5;7(5):1475-1485. doi: 10.1534/g3.117.040105.

43.

Mammalian pregnancy.

Abbot P, Rokas A.

Curr Biol. 2017 Feb 20;27(4):R127-R128. doi: 10.1016/j.cub.2016.10.046.

44.

CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes.

Ortiz JF, Rokas A.

Mol Biol Evol. 2017 Jan;34(1):215-229. doi: 10.1093/molbev/msw227. Epub 2016 Oct 20.

PMID:
28007975
45.

Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus.

Lind AL, Smith TD, Saterlee T, Calvo AM, Rokas A.

G3 (Bethesda). 2016 Dec 7;6(12):4023-4033. doi: 10.1534/g3.116.033084.

46.

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.

Shen XX, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A.

G3 (Bethesda). 2016 Dec 7;6(12):3927-3939. doi: 10.1534/g3.116.034744.

47.

In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies.

Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A.

G3 (Bethesda). 2016 Nov 8;6(11):3655-3662. doi: 10.1534/g3.116.034249.

48.

Comparative genomics of biotechnologically important yeasts.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.

49.

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference.

Shen XX, Salichos L, Rokas A.

Genome Biol Evol. 2016 Sep 2;8(8):2565-80. doi: 10.1093/gbe/evw179.

50.

Comprehensive RNA profiling of villous trophoblast and decidua basalis in pregnancies complicated by preterm birth following intra-amniotic infection.

Ackerman WE 4th, Buhimschi IA, Eidem HR, Rinker DC, Rokas A, Rood K, Zhao G, Summerfield TL, Landon MB, Buhimschi CS.

Placenta. 2016 Aug;44:23-33. doi: 10.1016/j.placenta.2016.05.010. Epub 2016 May 30.

PMID:
27452435

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