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Items: 38

1.

Transcriptomic analysis of the oleaginous yeast Lipomyces starkeyi during lipid accumulation on enzymatically treated corn stover hydrolysate.

Pomraning KR, Collett JR, Kim J, Panisko EA, Culley DE, Dai Z, Deng S, Hofstad BA, Butcher MG, Magnuson JK.

Biotechnol Biofuels. 2019 Jun 26;12:162. doi: 10.1186/s13068-019-1510-z. eCollection 2019.

2.

Conversion of depolymerized sugars and aromatics from engineered feedstocks by two oleaginous red yeasts.

Rodriguez A, Ersig N, Geiselman GM, Seibel K, Simmons BA, Magnuson JK, Eudes A, Gladden JM.

Bioresour Technol. 2019 Aug;286:121365. doi: 10.1016/j.biortech.2019.121365. Epub 2019 Apr 22.

PMID:
31030073
3.

Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides.

Otoupal PB, Ito M, Arkin AP, Magnuson JK, Gladden JM, Skerker JM.

mSphere. 2019 Mar 20;4(2). pii: e00099-19. doi: 10.1128/mSphere.00099-19.

4.

A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable.

Leynaud-Kieffer LMC, Curran SC, Kim I, Magnuson JK, Gladden JM, Baker SE, Simmons BA.

PLoS One. 2019 Jan 17;14(1):e0210243. doi: 10.1371/journal.pone.0210243. eCollection 2019.

5.

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica.

Pomraning KR, Bredeweg EL, Kerkhoven EJ, Barry K, Haridas S, Hundley H, LaButti K, Lipzen A, Yan M, Magnuson JK, Simmons BA, Grigoriev IV, Nielsen J, Baker SE.

mSphere. 2018 Dec 5;3(6). pii: e00541-18. doi: 10.1128/mSphere.00541-18.

6.

Correction to: Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger.

Reilly MC, Amaike Campen S, Simmons BA, Baker SE, Gladden JM, Magnuson JK.

Methods Mol Biol. 2018;1796:E1. doi: 10.1007/978-1-4939-7877-9_22.

PMID:
30374680
7.

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.

Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR.

Nat Genet. 2018 Dec;50(12):1688-1695. doi: 10.1038/s41588-018-0246-1. Epub 2018 Oct 22.

PMID:
30349117
8.

Deletion of the KU70 homologue facilitates gene targeting in Lipomyces starkeyi strain NRRL Y-11558.

Dai Z, Pomraning KR, Deng S, Hofstad BA, Panisko EA, Rodriguez D, Butcher MG, Culley DE, Magnuson JK.

Curr Genet. 2019 Feb;65(1):269-282. doi: 10.1007/s00294-018-0875-z. Epub 2018 Aug 18.

PMID:
30121731
9.

Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger.

Reilly MC, Amaike Campen S, Simmons BA, Baker SE, Gladden JM, Magnuson JK.

Methods Mol Biol. 2018;1796:123-133. doi: 10.1007/978-1-4939-7877-9_10. Erratum in: Methods Mol Biol. 2018;1796:E1.

PMID:
29856051
10.

Draft Genome Sequence of Aspergillus oryzae ATCC 12892.

Deng S, Pomraning KR, Bohutskyi P, Magnuson JK.

Genome Announc. 2018 May 3;6(18). pii: e00251-18. doi: 10.1128/genomeA.00251-18.

11.

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.

Kjærbølling I, Vesth TC, Frisvad JC, Nybo JL, Theobald S, Kuo A, Bowyer P, Matsuda Y, Mondo S, Lyhne EK, Kogle ME, Clum A, Lipzen A, Salamov A, Ngan CY, Daum C, Chiniquy J, Barry K, LaButti K, Haridas S, Simmons BA, Magnuson JK, Mortensen UH, Larsen TO, Grigoriev IV, Baker SE, Andersen MR.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E753-E761. doi: 10.1073/pnas.1715954115. Epub 2018 Jan 9.

12.

Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger.

Reilly MC, Kim J, Lynn J, Simmons BA, Gladden JM, Magnuson JK, Baker SE.

Appl Microbiol Biotechnol. 2018 Feb;102(4):1797-1807. doi: 10.1007/s00253-017-8717-3. Epub 2018 Jan 6.

13.

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger.

Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, Gladden JM.

PLoS One. 2017 Dec 27;12(12):e0189604. doi: 10.1371/journal.pone.0189604. eCollection 2017.

14.

Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts.

Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, Singer SW, Magnuson JK, Arkin AP, Skerker JM, Gladden JM.

Biotechnol Biofuels. 2017 Oct 23;10:241. doi: 10.1186/s13068-017-0927-5. eCollection 2017.

15.

Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12.

Gaskell J, Kersten P, Larrondo LF, Canessa P, Martinez D, Hibbett D, Schmoll M, Kubicek CP, Martinez AT, Yadav J, Master E, Magnuson JK, Yaver D, Berka R, Lail K, Chen C, LaButti K, Nolan M, Lipzen A, Aerts A, Riley R, Barry K, Henrissat B, Blanchette R, Grigoriev IV, Cullen D.

Genom Data. 2017 Aug 10;14:21-23. doi: 10.1016/j.gdata.2017.08.003. eCollection 2017 Dec. No abstract available.

16.

Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species.

Dai Z, Deng S, Culley DE, Bruno KS, Magnuson JK.

Appl Microbiol Biotechnol. 2017 Aug;101(15):6099-6110. doi: 10.1007/s00253-017-8357-7. Epub 2017 Jun 19.

PMID:
28631219
17.

Fungal Ligninolytic Enzymes and Their Applications.

Mäkelä MR, Bredeweg EL, Magnuson JK, Baker SE, de Vries RP, Hildén K.

Microbiol Spectr. 2016 Dec;4(6). doi: 10.1128/microbiolspec.FUNK-0017-2016. Review.

PMID:
28087936
18.

Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger.

Dai Z, Aryal UK, Shukla A, Qian WJ, Smith RD, Magnuson JK, Adney WS, Beckham GT, Brunecky R, Himmel ME, Decker SR, Ju X, Zhang X, Baker SE.

Fungal Genet Biol. 2013 Dec;61:120-32. doi: 10.1016/j.fgb.2013.09.004. Epub 2013 Sep 25.

PMID:
24076077
19.

Post-genomic approaches to understanding interactions between fungi and their environment.

de Vries RP, Benoit I, Doehlemann G, Kobayashi T, Magnuson JK, Panisko EA, Baker SE, Lebrun MH.

IMA Fungus. 2011 Jun;2(1):81-6. doi: 10.5598/imafungus.2011.02.01.11. Epub 2011 May 24.

20.

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.

Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5458-63. doi: 10.1073/pnas.1119912109. Epub 2012 Mar 20. Erratum in: Proc Natl Acad Sci U S A. 2012 May 22;109(21):8352. San, Ryu Jae [corrected to Ryu, Jae San].

21.

Proteomic and functional analysis of the cellulase system expressed by Postia placenta during brown rot of solid wood.

Ryu JS, Shary S, Houtman CJ, Panisko EA, Korripally P, St John FJ, Crooks C, Siika-Aho M, Magnuson JK, Hammel KE.

Appl Environ Microbiol. 2011 Nov;77(22):7933-41. doi: 10.1128/AEM.05496-11. Epub 2011 Sep 23.

22.

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.

Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE.

Genome Res. 2011 Jun;21(6):885-97. doi: 10.1101/gr.112169.110. Epub 2011 May 4.

23.

Genome sequence of the model mushroom Schizophyllum commune.

Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wösten HA.

Nat Biotechnol. 2010 Sep;28(9):957-63. doi: 10.1038/nbt.1643. Epub 2010 Jul 11.

PMID:
20622885
24.

The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA.

Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JE.

BMC Plant Biol. 2010 May 7;10:83. doi: 10.1186/1471-2229-10-83.

25.

Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing.

Le Crom S, Schackwitz W, Pennacchio L, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16151-6. doi: 10.1073/pnas.0905848106. Epub 2009 Sep 2.

26.

Proteomics for validation of automated gene model predictions.

Zhou K, Panisko EA, Magnuson JK, Baker SE, Grigoriev IV.

Methods Mol Biol. 2009;492:447-52. doi: 10.1007/978-1-59745-493-3_27.

PMID:
19241050
27.

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion.

Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavín JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kües U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D.

Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1954-9. doi: 10.1073/pnas.0809575106. Epub 2009 Feb 4.

28.

Differential expression in Phanerochaete chrysosporium of membrane-associated proteins relevant to lignin degradation.

Shary S, Kapich AN, Panisko EA, Magnuson JK, Cullen D, Hammel KE.

Appl Environ Microbiol. 2008 Dec;74(23):7252-7. doi: 10.1128/AEM.01997-08. Epub 2008 Oct 10.

29.

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).

Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS.

Nat Biotechnol. 2008 May;26(5):553-60. doi: 10.1038/nbt1403. Epub 2008 May 4. Erratum in: Nat Biotechnol. 2008 Oct;26(10):1193.. Barbote, Ravi [corrected to Barabote, Ravi].

PMID:
18454138
30.

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.

Cuomo CA, Güldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, Walton JD, Ma LJ, Baker SE, Rep M, Adam G, Antoniw J, Baldwin T, Calvo S, Chang YL, Decaprio D, Gale LR, Gnerre S, Goswami RS, Hammond-Kosack K, Harris LJ, Hilburn K, Kennell JC, Kroken S, Magnuson JK, Mannhaupt G, Mauceli E, Mewes HW, Mitterbauer R, Muehlbauer G, Münsterkötter M, Nelson D, O'donnell K, Ouellet T, Qi W, Quesneville H, Roncero MI, Seong KY, Tetko IV, Urban M, Waalwijk C, Ward TJ, Yao J, Birren BW, Kistler HC.

Science. 2007 Sep 7;317(5843):1400-2.

31.

Characterization of functionalized nanoporous supports for protein confinement.

Lei C, Shin Y, Magnuson JK, Fryxell G, Lasure LL, Elliott DC, Liu J, Ackerman EJ.

Nanotechnology. 2006 Nov 28;17(22):5531-8. doi: 10.1088/0957-4484/17/22/001. Epub 2006 Oct 25.

PMID:
21727320
32.

Characterization of Pseudomonas putida genes responsive to nutrient limitation.

Syn CK, Magnuson JK, Kingsley MT, Swarup S.

Microbiology. 2004 Jun;150(Pt 6):1661-9.

PMID:
15184552
33.
34.

A green nonsulfur bacterium, Dehalococcoides ethenogenes, with the LexA binding sequence found in gram-positive organisms.

Fernández de Henestrosa AR, Cuñé J, Erill I, Magnuson JK, Barbé J.

J Bacteriol. 2002 Nov;184(21):6073-80.

35.

Trichloroethene reductive dehalogenase from Dehalococcoides ethenogenes: sequence of tceA and substrate range characterization.

Magnuson JK, Romine MF, Burris DR, Kingsley MT.

Appl Environ Microbiol. 2000 Dec;66(12):5141-7.

36.

Reductive dechlorination of tetrachloroethene to ethene by a two-component enzyme pathway.

Magnuson JK, Stern RV, Gossett JM, Zinder SH, Burris DR.

Appl Environ Microbiol. 1998 Apr;64(4):1270-5.

37.

Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR.

Blake PR, Park JB, Bryant FO, Aono S, Magnuson JK, Eccleston E, Howard JB, Summers MF, Adams MW.

Biochemistry. 1991 Nov 12;30(45):10885-95.

PMID:
1932012
38.

Teichuronic acid reducing terminal N-acetylglucosamine residue linked by phosphodiester to peptidoglycan of Micrococcus luteus.

Gassner GT, Dickie JP, Hamerski DA, Magnuson JK, Anderson JS.

J Bacteriol. 1990 May;172(5):2273-9.

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