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Items: 1 to 20 of 73

1.

Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans.

Chow EW, Clancey SA, Billmyre RB, Averette AF, Granek JA, Mieczkowski P, Cardenas ME, Heitman J.

PLoS Genet. 2017 Apr 4;13(4):e1006667. doi: 10.1371/journal.pgen.1006667. eCollection 2017 Apr.

2.

Root microbiota drive direct integration of phosphate stress and immunity.

Castrillo G, Teixeira PJ, Paredes SH, Law TF, de Lorenzo L, Feltcher ME, Finkel OM, Breakfield NW, Mieczkowski P, Jones CD, Paz-Ares J, Dangl JL.

Nature. 2017 Mar 23;543(7646):513-518. doi: 10.1038/nature21417. Epub 2017 Mar 15.

3.

Global analysis of genomic instability caused by DNA replication stress in Saccharomyces cerevisiae.

Zheng DQ, Zhang K, Wu XC, Mieczkowski PA, Petes TD.

Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):E8114-E8121. Epub 2016 Nov 28.

4.

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA.

PLoS Genet. 2016 Oct 27;12(10):e1006385. doi: 10.1371/journal.pgen.1006385. eCollection 2016 Oct.

5.

Essential Roles for Polymerase θ-Mediated End Joining in the Repair of Chromosome Breaks.

Wyatt DW, Feng W, Conlin MP, Yousefzadeh MJ, Roberts SA, Mieczkowski P, Wood RD, Gupta GP, Ramsden DA.

Mol Cell. 2016 Aug 18;63(4):662-673. doi: 10.1016/j.molcel.2016.06.020. Epub 2016 Jul 21.

6.

Multiplex amplicon sequencing for microbe identification in community-based culture collections.

Armanhi JS, de Souza RS, de Araújo LM, Okura VK, Mieczkowski P, Imperial J, Arruda P.

Sci Rep. 2016 Jul 12;6:29543. doi: 10.1038/srep29543.

7.

APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication.

Hoopes JI, Cortez LM, Mertz TM, Malc EP, Mieczkowski PA, Roberts SA.

Cell Rep. 2016 Feb 16;14(6):1273-1282. doi: 10.1016/j.celrep.2016.01.021. Epub 2016 Jan 28.

8.

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.

Wu G, Zhao H, Li C, Rajapakse MP, Wong WC, Xu J, Saunders CW, Reeder NL, Reilman RA, Scheynius A, Sun S, Billmyre BR, Li W, Averette AF, Mieczkowski P, Heitman J, Theelen B, Schröder MS, De Sessions PF, Butler G, Maurer-Stroh S, Boekhout T, Nagarajan N, Dawson TL Jr.

PLoS Genet. 2015 Nov 5;11(11):e1005614. doi: 10.1371/journal.pgen.1005614. eCollection 2015 Nov.

9.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R.

N Engl J Med. 2016 Jan 14;374(2):135-45. doi: 10.1056/NEJMoa1505917. Epub 2015 Nov 4.

10.

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers.

Chan K, Roberts SA, Klimczak LJ, Sterling JF, Saini N, Malc EP, Kim J, Kwiatkowski DJ, Fargo DC, Mieczkowski PA, Getz G, Gordenin DA.

Nat Genet. 2015 Sep;47(9):1067-72. doi: 10.1038/ng.3378. Epub 2015 Aug 10.

11.

Essential role for polymerase specialization in cellular nonhomologous end joining.

Pryor JM, Waters CA, Aza A, Asagoshi K, Strom C, Mieczkowski PA, Blanco L, Ramsden DA.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4537-45. doi: 10.1073/pnas.1505805112. Epub 2015 Aug 3.

12.

Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath.

Kasoji SK, Pattenden SG, Malc EP, Jayakody CN, Tsuruta JK, Mieczkowski PA, Janzen WP, Dayton PA.

PLoS One. 2015 Jul 17;10(7):e0133014. doi: 10.1371/journal.pone.0133014. eCollection 2015.

13.

The oncogenic potential of BK-polyomavirus is linked to viral integration into the human genome.

Kenan DJ, Mieczkowski PA, Burger-Calderon R, Singh HK, Nickeleit V.

J Pathol. 2015 Nov;237(3):379-89. doi: 10.1002/path.4584. Epub 2015 Aug 19.

14.

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T Jr, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG Jr, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J.

N Engl J Med. 2015 Jun 25;372(26):2481-98. doi: 10.1056/NEJMoa1402121. Epub 2015 Jun 10.

15.

Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations.

Zhou S, Jones C, Mieczkowski P, Swanstrom R.

J Virol. 2015 Aug;89(16):8540-55. doi: 10.1128/JVI.00522-15. Epub 2015 Jun 3.

16.

Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production.

Carvalho-Netto OV, Carazzolle MF, Mofatto LS, Teixeira PJ, Noronha MF, Calderón LA, Mieczkowski PA, Argueso JL, Pereira GA.

Microb Cell Fact. 2015 Jan 30;14:13. doi: 10.1186/s12934-015-0196-6.

17.

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.

Clausen AR, Lujan SA, Burkholder AB, Orebaugh CD, Williams JS, Clausen MF, Malc EP, Mieczkowski PA, Fargo DC, Smith DJ, Kunkel TA.

Nat Struct Mol Biol. 2015 Mar;22(3):185-91. doi: 10.1038/nsmb.2957. Epub 2015 Jan 26.

18.

Unisexual reproduction drives meiotic recombination and phenotypic and karyotypic plasticity in Cryptococcus neoformans.

Sun S, Billmyre RB, Mieczkowski PA, Heitman J.

PLoS Genet. 2014 Dec 11;10(12):e1004849. doi: 10.1371/journal.pgen.1004849. eCollection 2014 Dec.

19.

Flavonoid supplementation affects the expression of genes involved in cell wall formation and lignification metabolism and increases sugar content and saccharification in the fast-growing eucalyptus hybrid E. urophylla x E. grandis.

Lepikson-Neto J, Nascimento LC, Salazar MM, Camargo EL, Cairo JP, Teixeira PJ, Marques WL, Squina FM, Mieczkowski P, Deckmann AC, Pereira GA.

BMC Plant Biol. 2014 Nov 19;14:301. doi: 10.1186/s12870-014-0301-8.

20.

High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa.

Teixeira PJ, Thomazella DP, Reis O, do Prado PF, do Rio MC, Fiorin GL, José J, Costa GG, Negri VA, Mondego JM, Mieczkowski P, Pereira GA.

Plant Cell. 2014 Nov;26(11):4245-69. doi: 10.1105/tpc.114.130807. Epub 2014 Nov 4.

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