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Items: 1 to 50 of 101

1.

Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements.

Elango R, Osia B, Harcy V, Malc E, Mieczkowski PA, Roberts SA, Malkova A.

Nucleic Acids Res. 2019 Aug 8. pii: gkz651. doi: 10.1093/nar/gkz651. [Epub ahead of print]

PMID:
31392335
2.

Corrigendum to "APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast" [DNA Repair 53 (2017) 4-14].

Saini N, Roberts SA, Sterling JF, Malc EP, Mieczkowski PA, Gordenin DA.

DNA Repair (Amst). 2019 Aug;80:94-95. doi: 10.1016/j.dnarep.2019.05.006. Epub 2019 Jun 7. No abstract available.

PMID:
31182349
3.

Identification of a Locus in Mice that Regulates the Collateral Damage and Lethality of Virus Infection.

Misumi I, Cook KD, Mitchell JE, Lund MM, Vick SC, Lee RH, Uchimura T, Bergmeier W, Mieczkowski P, Pardo-Manuel de Villena F, Ting JPY, Whitmire JK.

Cell Rep. 2019 Apr 30;27(5):1387-1396.e5. doi: 10.1016/j.celrep.2019.04.004.

4.

Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler.

Nascimento LC, Yanagui K, Jose J, Camargo ELO, Grassi MCB, Cunha CP, Bressiani JA, Carvalho GMA, Carvalho CR, Prado PF, Mieczkowski P, Pereira GAG, Carazzolle MF.

DNA Res. 2019 Jun 1;26(3):205-216. doi: 10.1093/dnares/dsz001.

5.

Dengue type 1 viruses circulating in humans are highly infectious and poorly neutralized by human antibodies.

Raut R, Corbett KS, Tennekoon RN, Premawansa S, Wijewickrama A, Premawansa G, Mieczkowski P, Rückert C, Ebel GD, De Silva AD, de Silva AM.

Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):227-232. doi: 10.1073/pnas.1812055115. Epub 2018 Dec 5.

6.

A Case Study of Genomic Instability in an Industrial Strain of Saccharomyces cerevisiae.

Rodrigues-Prause A, Sampaio NMV, Gurol TM, Aguirre GM, Sedam HNC, Chapman MJ, Malc EP, Ajith VP, Chakraborty P, Tizei PA, Pereira GAG, Mieczkowski PA, Nishant KT, Argueso JL.

G3 (Bethesda). 2018 Nov 6;8(11):3703-3713. doi: 10.1534/g3.118.200446.

7.

Intercellular Communication between Airway Epithelial Cells Is Mediated by Exosome-Like Vesicles.

Gupta R, Radicioni G, Abdelwahab S, Dang H, Carpenter J, Chua M, Mieczkowski PA, Sheridan JT, Randell SH, Kesimer M.

Am J Respir Cell Mol Biol. 2019 Feb;60(2):209-220. doi: 10.1165/rcmb.2018-0156OC.

PMID:
30230353
8.

A Mutation in the Borcs7 Subunit of the Lysosome Regulatory BORC Complex Results in Motor Deficits and Dystrophic Axonopathy in Mice.

Snouwaert JN, Church RJ, Jania L, Nguyen M, Wheeler ML, Saintsing A, Mieczkowski P, Manuel de Villena FP, Armao D, Moy SS, Lorenzo DN, Koller BH.

Cell Rep. 2018 Jul 31;24(5):1254-1265. doi: 10.1016/j.celrep.2018.06.118.

9.

RIG-I Detects Kaposi's Sarcoma-Associated Herpesvirus Transcripts in a RNA Polymerase III-Independent Manner.

Zhang Y, Dittmer DP, Mieczkowski PA, Host KM, Fusco WG, Duncan JA, Damania B.

MBio. 2018 Jul 3;9(4). pii: e00823-18. doi: 10.1128/mBio.00823-18.

10.

The two-faced nature of BK polyomavirus: lytic infection or non-lytic large-T-positive carcinoma.

Nickeleit V, Singh HK, Kenan DJ, Mieczkowski PA.

J Pathol. 2018 Sep;246(1):7-11. doi: 10.1002/path.5127. Epub 2018 Jul 31.

11.

Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC).

Molano EPL, Cabrera OG, Jose J, do Nascimento LC, Carazzolle MF, Teixeira PJPL, Alvarez JC, Tiburcio RA, Tokimatu Filho PM, de Lima GMA, Guido RVC, Corrêa TLR, Leme AFP, Mieczkowski P, Pereira GAG.

BMC Genomics. 2018 Jan 17;19(1):58. doi: 10.1186/s12864-018-4440-4.

12.

Whole Genome Sequence Analysis of Mutations Accumulated in rad27Δ Yeast Strains with Defects in the Processing of Okazaki Fragments Indicates Template-Switching Events.

Omer S, Lavi B, Mieczkowski PA, Covo S, Hazkani-Covo E.

G3 (Bethesda). 2017 Nov 6;7(11):3775-3787. doi: 10.1534/g3.117.300262.

13.

Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

Mao P, Brown AJ, Malc EP, Mieczkowski PA, Smerdon MJ, Roberts SA, Wyrick JJ.

Genome Res. 2017 Oct;27(10):1674-1684. doi: 10.1101/gr.225771.117. Epub 2017 Sep 14.

14.

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.

15.

APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast.

Saini N, Roberts SA, Sterling JF, Malc EP, Mieczkowski PA, Gordenin DA.

DNA Repair (Amst). 2017 May;53:4-14. doi: 10.1016/j.dnarep.2017.03.003. Epub 2017 Mar 21. Erratum in: DNA Repair (Amst). 2019 Aug;80:94-95.

16.

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.

17.

Pseudomonas syringae Type III Effector HopBB1 Promotes Host Transcriptional Repressor Degradation to Regulate Phytohormone Responses and Virulence.

Yang L, Teixeira PJ, Biswas S, Finkel OM, He Y, Salas-Gonzalez I, English ME, Epple P, Mieczkowski P, Dangl JL.

Cell Host Microbe. 2017 Feb 8;21(2):156-168. doi: 10.1016/j.chom.2017.01.003. Epub 2017 Jan 26.

18.

BK Polyomavirus Genomic Integration and Large T Antigen Expression: Evolving Paradigms in Human Oncogenesis.

Kenan DJ, Mieczkowski PA, Latulippe E, Côté I, Singh HK, Nickeleit V.

Am J Transplant. 2017 Jun;17(6):1674-1680. doi: 10.1111/ajt.14191. Epub 2017 Feb 21.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus.

Camargo EL, Nascimento LC, Soler M, Salazar MM, Lepikson-Neto J, Marques WL, Alves A, Teixeira PJ, Mieczkowski P, Carazzolle MF, Martinez Y, Deckmann AC, Rodrigues JC, Grima-Pettenati J, Pereira GA.

BMC Plant Biol. 2014 Sep 28;14:256. doi: 10.1186/s12870-014-0256-9.

38.

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA.

Genome Res. 2014 Nov;24(11):1751-64. doi: 10.1101/gr.178335.114. Epub 2014 Sep 12.

39.

Cryptococcus gattii VGIII isolates causing infections in HIV/AIDS patients in Southern California: identification of the local environmental source as arboreal.

Springer DJ, Billmyre RB, Filler EE, Voelz K, Pursall R, Mieczkowski PA, Larsen RA, Dietrich FS, May RC, Filler SG, Heitman J.

PLoS Pathog. 2014 Aug 21;10(8):e1004285. doi: 10.1371/journal.ppat.1004285. eCollection 2014 Aug.

40.

Antifungal drug resistance evoked via RNAi-dependent epimutations.

Calo S, Shertz-Wall C, Lee SC, Bastidas RJ, Nicolás FE, Granek JA, Mieczkowski P, Torres-Martínez S, Ruiz-Vázquez RM, Cardenas ME, Heitman J.

Nature. 2014 Sep 25;513(7519):555-8. doi: 10.1038/nature13575. Epub 2014 Jul 27.

41.

Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution.

Billmyre RB, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo CA, Kronstad JW, Heitman J.

MBio. 2014 Jul 29;5(4):e01494-14. doi: 10.1128/mBio.01494-14.

42.

Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt.

Lee SC, Billmyre RB, Li A, Carson S, Sykes SM, Huh EY, Mieczkowski P, Ko DC, Cuomo CA, Heitman J.

MBio. 2014 Jul 8;5(4):e01390-14. doi: 10.1128/mBio.01390-14.

43.

The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining.

Waters CA, Strande NT, Pryor JM, Strom CN, Mieczkowski P, Burkhalter MD, Oh S, Qaqish BF, Moore DT, Hendrickson EA, Ramsden DA.

Nat Commun. 2014 Jul 3;5:4286. doi: 10.1038/ncomms5286.

44.

Break-induced replication is a source of mutation clusters underlying kataegis.

Sakofsky CJ, Roberts SA, Malc E, Mieczkowski PA, Resnick MA, Gordenin DA, Malkova A.

Cell Rep. 2014 Jun 12;7(5):1640-1648. doi: 10.1016/j.celrep.2014.04.053. Epub 2014 May 29.

45.

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Janbon G, Ormerod KL, Paulet D, Byrnes EJ 3rd, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS.

PLoS Genet. 2014 Apr 17;10(4):e1004261. doi: 10.1371/journal.pgen.1004261. eCollection 2014 Apr.

46.

Evidence for local regulatory control of escape from imprinted X chromosome inactivation.

Mugford JW, Starmer J, Williams RL Jr, Calabrese JM, Mieczkowski P, Yee D, Magnuson T.

Genetics. 2014 Jun;197(2):715-23. doi: 10.1534/genetics.114.162800. Epub 2014 Mar 19.

47.

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

Meinhardt LW, Costa GG, Thomazella DP, Teixeira PJ, Carazzolle MF, Schuster SC, Carlson JE, Guiltinan MJ, Mieczkowski P, Farmer A, Ramaraj T, Crozier J, Davis RE, Shao J, Melnick RL, Pereira GA, Bailey BA.

BMC Genomics. 2014 Feb 27;15:164. doi: 10.1186/1471-2164-15-164.

48.

fourSig: a method for determining chromosomal interactions in 4C-Seq data.

Williams RL Jr, Starmer J, Mugford JW, Calabrese JM, Mieczkowski P, Yee D, Magnuson T.

Nucleic Acids Res. 2014 Apr;42(8):e68. doi: 10.1093/nar/gku156. Epub 2014 Feb 20.

49.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.

Bizon C, Spiegel M, Chasse SA, Gizer IR, Li Y, Malc EP, Mieczkowski PA, Sailsbery JK, Wang X, Ehlers CL, Wilhelmsen KC.

BMC Genomics. 2014 Jan 30;15:85. doi: 10.1186/1471-2164-15-85.

50.

Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.

Ni M, Feretzaki M, Li W, Floyd-Averette A, Mieczkowski P, Dietrich FS, Heitman J.

PLoS Biol. 2013 Sep;11(9):e1001653. doi: 10.1371/journal.pbio.1001653. Epub 2013 Sep 10.

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