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The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus.

Wu VW, Thieme N, Huberman LB, Dietschmann A, Kowbel DJ, Lee J, Calhoun S, Singan VR, Lipzen A, Xiong Y, Monti R, Blow MJ, O'Malley RC, Grigoriev IV, Benz JP, Glass NL.

Proc Natl Acad Sci U S A. 2020 Mar 17;117(11):6003-6013. doi: 10.1073/pnas.1915611117. Epub 2020 Feb 28.


Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural.

Feldman D, Kowbel DJ, Cohen A, Glass NL, Hadar Y, Yarden O.

Biotechnol Biofuels. 2019 Sep 4;12:210. doi: 10.1186/s13068-019-1550-4. eCollection 2019.


Transcriptional profiling and localization of GUL-1, a COT-1 pathway component, in Neurospora crassa.

Herold I, Kowbel D, Delgado-Álvarez DL, Garduño-Rosales M, Mouriño-Pérez RR, Yarden O.

Fungal Genet Biol. 2019 May;126:1-11. doi: 10.1016/j.fgb.2019.01.010. Epub 2019 Feb 4.


Author Correction: A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus.

Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y.

Sci Rep. 2018 Mar 6;8(1):4213. doi: 10.1038/s41598-018-21904-x.


A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus.

Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y.

Sci Rep. 2017 Nov 6;7(1):14553. doi: 10.1038/s41598-017-15112-2. Erratum in: Sci Rep. 2018 Mar 6;8(1):4213.


Characterization of Greenbeard Genes Involved in Long-Distance Kind Discrimination in a Microbial Eukaryote.

Heller J, Zhao J, Rosenfield G, Kowbel DJ, Gladieux P, Glass NL.

PLoS Biol. 2016 Apr 14;14(4):e1002431. doi: 10.1371/journal.pbio.1002431. eCollection 2016 Apr.


The SEB-1 Transcription Factor Binds to the STRE Motif in Neurospora crassa and Regulates a Variety of Cellular Processes Including the Stress Response and Reserve Carbohydrate Metabolism.

Freitas FZ, Virgilio S, Cupertino FB, Kowbel DJ, Fioramonte M, Gozzo FC, Glass NL, Bertolini MC.

G3 (Bethesda). 2016 May 3;6(5):1327-43. doi: 10.1534/g3.116.028506.


Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan.

Lopez-Moya F, Kowbel D, Nueda MJ, Palma-Guerrero J, Glass NL, Lopez-Llorca LV.

Mol Biosyst. 2016 Feb;12(2):391-403. doi: 10.1039/c5mb00649j.


Transcription profiling of the Neurospora crassa response to a group of synthetic (thio)xanthones and a natural acetophenone.

Pedro Gonçalves A, Silva N, Oliveira C, Kowbel DJ, Glass NL, Kijjoa A, Palmeira A, Sousa E, Pinto M, Videira A.

Genom Data. 2015 Feb 20;4:26-32. doi: 10.1016/j.gdata.2015.02.001. eCollection 2015 Jun.


Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta.

Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW.

Mol Ecol. 2015 Nov;24(22):5657-75. doi: 10.1111/mec.13417. Epub 2015 Nov 11.


Detoxification of 5-hydroxymethylfurfural by the Pleurotus ostreatus lignolytic enzymes aryl alcohol oxidase and dehydrogenase.

Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y.

Biotechnol Biofuels. 2015 Apr 11;8:63. doi: 10.1186/s13068-015-0244-9. eCollection 2015.


Transcriptional interference by antisense RNA is required for circadian clock function.

Xue Z, Ye Q, Anson SR, Yang J, Xiao G, Kowbel D, Glass NL, Crosthwaite SK, Liu Y.

Nature. 2014 Oct 30;514(7524):650-3. doi: 10.1038/nature13671. Epub 2014 Aug 17.


Extracellular calcium triggers unique transcriptional programs and modulates staurosporine-induced cell death in Neurospora crassa.

Gonçalves AP, Monteiro J, Lucchi C, Kowbel DJ, Cordeiro JM, Correia-de-Sá P, Rigden DJ, Glass NL, Videira A.

Microb Cell. 2014 Aug 9;1(9):289-302. doi: 10.15698/mic2014.09.165.


CZT-1 is a novel transcription factor controlling cell death and natural drug resistance in Neurospora crassa.

Gonçalves AP, Hall C, Kowbel DJ, Glass NL, Videira A.

G3 (Bethesda). 2014 Apr 8;4(6):1091-102. doi: 10.1534/g3.114.011312.


Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates.

Ellison CE, Kowbel D, Glass NL, Taylor JW, Brem RB.

mBio. 2014 Apr 1;5(2):e01046-13. doi: 10.1128/mBio.01046-13.


Genome wide association identifies novel loci involved in fungal communication.

Palma-Guerrero J, Hall CR, Kowbel D, Welch J, Taylor JW, Brem RB, Glass NL.

PLoS Genet. 2013;9(8):e1003669. doi: 10.1371/journal.pgen.1003669. Epub 2013 Aug 1.


Population genomics and local adaptation in wild isolates of a model microbial eukaryote.

Ellison CE, Hall C, Kowbel D, Welch J, Brem RB, Glass NL, Taylor JW.

Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2831-6. doi: 10.1073/pnas.1014971108. Epub 2011 Jan 31.


Evolution and diversity of a fungal self/nonself recognition locus.

Hall C, Welch J, Kowbel DJ, Glass NL.

PLoS One. 2010 Nov 19;5(11):e14055. doi: 10.1371/journal.pone.0014055.


Clearance of Pseudomonas aeruginosa from a healthy ocular surface involves surfactant protein D and is compromised by bacterial elastase in a murine null-infection model.

Mun JJ, Tam C, Kowbel D, Hawgood S, Barnett MJ, Evans DJ, Fleiszig SM.

Infect Immun. 2009 Jun;77(6):2392-8. doi: 10.1128/IAI.00173-09. Epub 2009 Apr 6.


Pathogenic phenotype and genotype of Pseudomonas aeruginosa isolates from spontaneous canine ocular infections.

Ledbetter EC, Mun JJ, Kowbel D, Fleiszig SM.

Invest Ophthalmol Vis Sci. 2009 Feb;50(2):729-36. doi: 10.1167/iovs.08-2358. Epub 2008 Oct 3.


Decoding the fine-scale structure of a breast cancer genome and transcriptome.

Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C.

Genome Res. 2006 Mar;16(3):394-404. Epub 2006 Feb 3.


ZNF217 suppresses cell death associated with chemotherapy and telomere dysfunction.

Huang G, Krig S, Kowbel D, Xu H, Hyun B, Volik S, Feuerstein B, Mills GB, Stokoe D, Yaswen P, Collins C.

Hum Mol Genet. 2005 Nov 1;14(21):3219-25. Epub 2005 Oct 3.


Design considerations for array CGH to oligonucleotide arrays.

Baldocchi RA, Glynne RJ, Chin K, Kowbel D, Collins C, Mack DH, Gray JW.

Cytometry A. 2005 Oct;67(2):129-36.


Molecular analysis of WFDC1/ps20 gene in prostate cancer.

Watson JE, Kamkar S, James K, Kowbel D, Andaya A, Paris PL, Simko J, Carroll P, McAlhany S, Rowley D, Collins C.

Prostate. 2004 Oct 1;61(2):192-9.


Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors.

Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H.

Hum Mol Genet. 2004 Jul 1;13(13):1303-13. Epub 2004 May 11.


Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer.

Watson JE, Doggett NA, Albertson DG, Andaya A, Chinnaiyan A, van Dekken H, Ginzinger D, Haqq C, James K, Kamkar S, Kowbel D, Pinkel D, Schmitt L, Simko JP, Volik S, Weinberg VK, Paris PL, Collins C.

Oncogene. 2004 Apr 22;23(19):3487-94.


Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis.

van Dekken H, Paris PL, Albertson DG, Alers JC, Andaya A, Kowbel D, van der Kwast TH, Pinkel D, Schröder FH, Vissers KJ, Wildhagen MF, Collins C.

Genes Chromosomes Cancer. 2004 Mar;39(3):249-56.


Characterization of the novel amplified in breast cancer-1 (NABC1) gene product.

Beardsley DI, Kowbel D, Lataxes TA, Mannino JM, Xin H, Kim WJ, Collins C, Brown KD.

Exp Cell Res. 2003 Nov 1;290(2):402-13.


End-sequence profiling: sequence-based analysis of aberrant genomes.

Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo WL, Magrane G, De Jong P, Gray JW, Collins C.

Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7696-701. Epub 2003 Jun 4.


High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.

Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schröder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H.

Am J Pathol. 2003 Mar;162(3):763-70.


Comprehensive genome sequence analysis of a breast cancer amplicon.

Collins C, Volik S, Kowbel D, Ginzinger D, Ylstra B, Cloutier T, Hawkins T, Predki P, Martin C, Wernick M, Kuo WL, Alberts A, Gray JW.

Genome Res. 2001 Jun;11(6):1034-42.


Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene.

Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, Kowbel D, Kuo WL, Gray JW, Pinkel D.

Nat Genet. 2000 Jun;25(2):144-6.


High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays.

Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG.

Nat Genet. 1998 Oct;20(2):207-11.


Positional cloning of ZNF217 and NABC1: genes amplified at 20q13.2 and overexpressed in breast carcinoma.

Collins C, Rommens JM, Kowbel D, Godfrey T, Tanner M, Hwang SI, Polikoff D, Nonet G, Cochran J, Myambo K, Jay KE, Froula J, Cloutier T, Kuo WL, Yaswen P, Dairkee S, Giovanola J, Hutchinson GB, Isola J, Kallioniemi OP, Palazzolo M, Martin C, Ericsson C, Pinkel D, Albertson D, Li WB, Gray JW.

Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8703-8.


Assignment of protease, serine-like 1 (PRSSL1) to human chromosome 19q13 by in situ hybridization and radiation hybrid mapping.

Polikoff D, Kuo WL, Cochran JF, Wernick M, Kowbel D, Myambo K, Collins CC.

Cytogenet Cell Genet. 1997;79(1-2):147-8. No abstract available.


Mapping of a newly discovered human gene homologous to the apoptosis associated-murine mammary protein, MFG-E8, to chromosome 15q25.

Collins C, Nehlin JO, Stubbs JD, Kowbel D, Kuo WL, Parry G.

Genomics. 1997 Jan 1;39(1):117-8. No abstract available.


Independent amplification and frequent co-amplification of three nonsyntenic regions on the long arm of chromosome 20 in human breast cancer.

Tanner MM, Tirkkonen M, Kallioniemi A, Isola J, Kuukasjärvi T, Collins C, Kowbel D, Guan XY, Trent J, Gray JW, Meltzer P, Kallioniemi OP.

Cancer Res. 1996 Aug 1;56(15):3441-5.


Amplification of chromosomal region 20q13 in invasive breast cancer: prognostic implications.

Tanner MM, Tirkkonen M, Kallioniemi A, Holli K, Collins C, Kowbel D, Gray JW, Kallioniemi OP, Isola J.

Clin Cancer Res. 1995 Dec;1(12):1455-61.


A physical map of chromosome 20 established using fluorescence in situ hybridization and digital image analysis.

Stokke T, Collins C, Kuo WL, Kowbel D, Shadravan F, Tanner M, Kallioniemi A, Kallioniemi OP, Pinkel D, Deaven L, et al.

Genomics. 1995 Mar 1;26(1):134-7.


Increased copy number at 20q13 in breast cancer: defining the critical region and exclusion of candidate genes.

Tanner MM, Tirkkonen M, Kallioniemi A, Collins C, Stokke T, Karhu R, Kowbel D, Shadravan F, Hintz M, Kuo WL, et al.

Cancer Res. 1994 Aug 15;54(16):4257-60.


The human beta-subunit of rod photoreceptor cGMP phosphodiesterase: complete retinal cDNA sequence and evidence for expression in brain.

Collins C, Hutchinson G, Kowbel D, Riess O, Weber B, Hayden MR.

Genomics. 1992 Jul;13(3):698-704.


Isolation and characterization of new highly polymorphic DNA markers from the Huntington disease region.

Weber B, Hedrick A, Andrew S, Riess O, Collins C, Kowbel D, Hayden MR.

Am J Hum Genet. 1992 Feb;50(2):382-93.


Identification of multiple CpG islands and associated conserved sequences in a candidate region for the Huntington disease gene.

Weber B, Collins C, Kowbel D, Riess O, Hayden MR.

Genomics. 1991 Dec;11(4):1113-24.


Genomic organization and complete sequence of the human gene encoding the beta-subunit of the cGMP phosphodiesterase and its localisation to 4p 16.3.

Weber B, Riess O, Hutchinson G, Collins C, Lin BY, Kowbel D, Andrew S, Schappert K, Hayden MR.

Nucleic Acids Res. 1991 Nov 25;19(22):6263-8.


Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus.

Smith MJ, Banfield DK, Doteval K, Gorski S, Kowbel DJ.

J Mol Evol. 1990 Sep;31(3):195-204.


Nucleotide sequence of the apocytochrome B gene in white sturgeon mitochondrial DNA.

Brown JR, Gilbert TL, Kowbel DJ, O'Hara PJ, Buroker NE, Beckenbach AT, Smith MJ.

Nucleic Acids Res. 1989 Jun 12;17(11):4389. No abstract available.


Gene arrangement in sea star mitochondrial DNA demonstrates a major inversion event during echinoderm evolution.

Smith MJ, Banfield DK, Doteval K, Gorski S, Kowbel DJ.

Gene. 1989 Mar 15;76(1):181-5.


The effect of 2-micron DNA on survival and mutagenesis in Saccharomyces cerevisiae.

Nestmann ER, Kowbel DJ, Potter AA.

Can J Genet Cytol. 1986 Feb;28(1):154-60.


Mutagenicity studies in Salmonella: residues of ozonated and/or chlorinated water fulvic acids.

Kowbel DJ, Ramaswamy S, Malaiyandi M, Nestmann ER.

Environ Mutagen. 1986;8(2):253-62.


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