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Results: 1 to 20 of 43

1.

Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist EA, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):16995-7002. doi: 10.1073/pnas.1418963111. Epub 2014 Oct 31.

PMID:
25362047
[PubMed - in process]
2.

Genome-wide characterization of light-regulated genes in Neurospora crassa.

Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS.

G3 (Bethesda). 2014 Jul 21;4(9):1731-45. doi: 10.1534/g3.114.012617.

PMID:
25053707
[PubMed - in process]
Free PMC Article
3.

Genomic insights into tuberculosis.

Galagan JE.

Nat Rev Genet. 2014 May;15(5):307-20. doi: 10.1038/nrg3664. Epub 2014 Mar 25. Review.

PMID:
24662221
[PubMed - indexed for MEDLINE]
4.

Resource competition may lead to effective treatment of antibiotic resistant infections.

Gomes AL, Galagan JE, Segrè D.

PLoS One. 2013 Dec 13;8(12):e80775. doi: 10.1371/journal.pone.0080775. eCollection 2013.

PMID:
24349015
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM.

Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE.

PLoS Comput Biol. 2013;9(7):e1003126. doi: 10.1371/journal.pcbi.1003126. Epub 2013 Jul 18.

PMID:
23935467
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The Mycobacterium tuberculosis regulatory network and hypoxia.

Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, Gomes A, Rustad T, Dolganov G, Glotova I, Abeel T, Mahwinney C, Kennedy AD, Allard R, Brabant W, Krueger A, Jaini S, Honda B, Yu WH, Hickey MJ, Zucker J, Garay C, Weiner B, Sisk P, Stolte C, Winkler JK, Van de Peer Y, Iazzetti P, Camacho D, Dreyfuss J, Liu Y, Dorhoi A, Mollenkopf HJ, Drogaris P, Lamontagne J, Zhou Y, Piquenot J, Park ST, Raman S, Kaufmann SH, Mohney RP, Chelsky D, Moody DB, Sherman DR, Schoolnik GK.

Nature. 2013 Jul 11;499(7457):178-83. doi: 10.1038/nature12337. Epub 2013 Jul 3.

PMID:
23823726
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

How accurate can genetic predictions be?

Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF.

BMC Genomics. 2012 Jul 24;13:340. doi: 10.1186/1471-2164-13-340.

PMID:
22827772
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Inferring carbon sources from gene expression profiles using metabolic flux models.

Brandes A, Lun DS, Ip K, Zucker J, Colijn C, Weiner B, Galagan JE.

PLoS One. 2012;7(5):e36947. doi: 10.1371/journal.pone.0036947. Epub 2012 May 14. Erratum in: PLoS One. 2012;7(8). doi: 10.1371/annotation/139857f3-5a05-4a23-9bfe-a77aafbce54d.

PMID:
22606312
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.

D'Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA.

MBio. 2011 Feb 8;2(1):e00342-10. doi: 10.1128/mBio.00342-10. Print 2011.

PMID:
21304167
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

TB database 2010: overview and update.

Galagan JE, Sisk P, Stolte C, Weiner B, Koehrsen M, Wymore F, Reddy TB, Zucker JD, Engels R, Gellesch M, Hubble J, Jin H, Larson L, Mao M, Nitzberg M, White J, Zachariah ZK, Sherlock G, Ball CA, Schoolnik GK.

Tuberculosis (Edinb). 2010 Jul;90(4):225-35. doi: 10.1016/j.tube.2010.03.010. Epub 2010 May 20. Review.

PMID:
20488753
[PubMed - indexed for MEDLINE]
11.

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data.

Lun DS, Sherrid A, Weiner B, Sherman DR, Galagan JE.

Genome Biol. 2009;10(12):R142. doi: 10.1186/gb-2009-10-12-r142. Epub 2009 Dec 22.

PMID:
20028542
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production.

Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE.

PLoS Comput Biol. 2009 Aug;5(8):e1000489. doi: 10.1371/journal.pcbi.1000489. Epub 2009 Aug 28.

PMID:
19714220
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Large-scale identification of genetic design strategies using local search.

Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM.

Mol Syst Biol. 2009;5:296. doi: 10.1038/msb.2009.57. Epub 2009 Aug 18.

PMID:
19690565
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients.

Kuntzen T, Timm J, Berical A, Lennon N, Berlin AM, Young SK, Lee B, Heckerman D, Carlson J, Reyor LL, Kleyman M, McMahon CM, Birch C, Schulze Zur Wiesch J, Ledlie T, Koehrsen M, Kodira C, Roberts AD, Lauer GM, Rosen HR, Bihl F, Cerny A, Spengler U, Liu Z, Kim AY, Xing Y, Schneidewind A, Madey MA, Fleckenstein JF, Park VM, Galagan JE, Nusbaum C, Walker BD, Lake-Bakaar GV, Daar ES, Jacobson IM, Gomperts ED, Edlin BR, Donfield SM, Chung RT, Talal AH, Marion T, Birren BW, Henn MR, Allen TM.

Hepatology. 2008 Dec;48(6):1769-78. doi: 10.1002/hep.22549.

PMID:
19026009
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A high-density single nucleotide polymorphism map for Neurospora crassa.

Lambreghts R, Shi M, Belden WJ, Decaprio D, Park D, Henn MR, Galagan JE, Bastürkmen M, Birren BW, Sachs MS, Dunlap JC, Loros JJ.

Genetics. 2009 Feb;181(2):767-81. doi: 10.1534/genetics.108.089292. Epub 2008 Nov 17.

PMID:
19015548
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

Orsi RH, Borowsky ML, Lauer P, Young SK, Nusbaum C, Galagan JE, Birren BW, Ivy RA, Sun Q, Graves LM, Swaminathan B, Wiedmann M.

BMC Genomics. 2008 Nov 13;9:539. doi: 10.1186/1471-2164-9-539.

PMID:
19014550
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

TB database: an integrated platform for tuberculosis research.

Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK.

Nucleic Acids Res. 2009 Jan;37(Database issue):D499-508. doi: 10.1093/nar/gkn652. Epub 2008 Oct 3.

PMID:
18835847
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Conserved secondary structures in Aspergillus.

McGuire AM, Galagan JE.

PLoS One. 2008 Jul 30;3(7):e2812. doi: 10.1371/journal.pone.0002812.

PMID:
18665251
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Cross-kingdom patterns of alternative splicing and splice recognition.

McGuire AM, Pearson MD, Neafsey DE, Galagan JE.

Genome Biol. 2008;9(3):R50. doi: 10.1186/gb-2008-9-3-r50. Epub 2008 Mar 5.

PMID:
18321378
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Dynamics of Pseudomonas aeruginosa genome evolution.

Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, Koehrsen M, Rokas A, Yandava CN, Engels R, Zeng E, Olavarietta R, Doud M, Smith RS, Montgomery P, White JR, Godfrey PA, Kodira C, Birren B, Galagan JE, Lory S.

Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3100-5. doi: 10.1073/pnas.0711982105. Epub 2008 Feb 19.

PMID:
18287045
[PubMed - indexed for MEDLINE]
Free PMC Article
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