InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
AddressOne Baylor Plaza
Houston, TX 77030
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    R01GM125650     (IRA, GRZEGORZ A)Jan 1, 2018 - Dec 31, 2021
    Regulation of Initial Steps of Chromosomal Breaks Repair
    Role: Principal Investigator

    R01GM080600     (IRA, GRZEGORZ A)May 1, 2007 - Feb 28, 2025
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Yan Z, Liu L, Pham N, Thakre PK, Malkova A, Ira G. Measuring the contributions of helicases to break-induced replication. Methods Enzymol. 2022; 672:339-368. PMID: 35934483.
    2. Shen J, Zhao Y, Pham NT, Li Y, Zhang Y, Trinidad J, Ira G, Qi Z, Niu H. Deciphering the mechanism of processive ssDNA digestion by the Dna2-RPA ensemble. Nat Commun. 2022 01 18; 13(1):359. PMID: 35042867; PMCID: PMC8766458.
      Citations:    Fields:    Translation:AnimalsCells
    3. Wang X, Dong Y, Zhao X, Li J, Lee J, Yan Z, Yang S, Wu W, Hou X, Liu G, Zhang Y, Song L, Cai G, Li Q, Ira G, Zhang X, Chen X. Rtt105 promotes high-fidelity DNA replication and repair by regulating the single-stranded DNA-binding factor RPA. Proc Natl Acad Sci U S A. 2021 06 22; 118(25). PMID: 34140406; PMCID: PMC8237652.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    4. Pham N, Yan Z, Yu Y, Faria Afreen M, Malkova A, Haber JE, Ira G. Mechanisms restraining break-induced replication at two-ended DNA double-strand breaks. EMBO J. 2021 05 17; 40(10):e104847. PMID: 33844333; PMCID: PMC8126933.
      Citations: 21     Fields:    Translation:HumansCells
    5. Liu L, Yan Z, Osia BA, Twarowski J, Sun L, Kramara J, Lee RS, Kumar S, Elango R, Li H, Dang W, Ira G, Malkova A. Tracking break-induced replication shows that it stalls at roadblocks. Nature. 2021 02; 590(7847):655-659. PMID: 33473214; PMCID: PMC8219245.
      Citations: 17     Fields:    Translation:AnimalsCells
    6. Yan Z, Kumar S, Ira G. Analysis of DNA Double-Strand Break End Resection and Single-Strand Annealing in S. pombe. Methods Mol Biol. 2021; 2153:47-57. PMID: 32840771; PMCID: PMC7647126.
      Citations:    Fields:    Translation:AnimalsCells
    7. Gallagher DN, Pham N, Tsai AM, Janto NV, Choi J, Ira G, Haber JE. A Rad51-independent pathway promotes single-strand template repair in gene editing. PLoS Genet. 2020 10; 16(10):e1008689. PMID: 33057349; PMCID: PMC7591047.
      Citations: 15     Fields:    Translation:AnimalsCells
    8. Yan Z, Xue C, Kumar S, Crickard JB, Yu Y, Wang W, Pham N, Li Y, Niu H, Sung P, Greene EC, Ira G. Rad52 Restrains Resection at DNA Double-Strand Break Ends in Yeast. Mol Cell. 2019 12 05; 76(5):699-711.e6. PMID: 31542296; PMCID: PMC6898758.
      Citations: 14     Fields:    Translation:AnimalsCells
    9. Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. 2019 03 07; 176(6):1310-1324.e10. PMID: 30827684; PMCID: PMC6438178.
      Citations: 29     Fields:    Translation:HumansCells
    10. Klein HL, Bacinskaja G, Che J, Cheblal A, Elango R, Epshtein A, Fitzgerald DM, Khan SR, Kumar S, Leland BA, Mei Q, Piotrowska A, Polleys EJ, Putnam CD, Radchenko EA, Saada AA, Sakofsky CJ, Shim EY, Stracy M, Xia J, Yan Z, Yin Y, Argueso JL, Freudenreich CH, Gasser SM, Gordenin DA, Haber JE, Ira G, Jinks-Robertson S, King MC, Kolodner RD, Kuzminov A, Lambert SA, Lee SE, Miller KM, Mirkin SM, Petes TD, Rosenberg SM, Rothstein R, Symington LS, Zawadzki P, Kim N, Lisby M, Malkova A, G?mez-Gonz?lez B, Marie L, Min?-Hattab J, Aguilera A. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microb Cell. 2019 Jan 07; 6(1):1-64. PMID: 30652105; PMCID: PMC6334234.
      Citations: 15     
    11. Yu Y, Pham N, Xia B, Papusha A, Wang G, Yan Z, Peng G, Chen K, Ira G. Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks. Nature. 2018 12; 564(7735):287-290. PMID: 30518856; PMCID: PMC6346745.
      Citations: 14     Fields:    Translation:AnimalsCells
    12. Zheng S, Li D, Lu Z, Liu G, Wang M, Xing P, Wang M, Dong Y, Wang X, Li J, Zhang S, Peng H, Ira G, Li G, Chen X. Bre1-dependent H2B ubiquitination promotes homologous recombination by stimulating histone eviction at DNA breaks. Nucleic Acids Res. 2018 11 30; 46(21):11326-11339. PMID: 30304473; PMCID: PMC6265479.
      Citations: 11     Fields:    Translation:AnimalsCells
    13. Song X, Beck CR, Du R, Campbell IM, Coban-Akdemir Z, Gu S, Breman AM, Stankiewicz P, Ira G, Shaw CA, Lupski JR. Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements. Genome Res. 2018 08; 28(8):1228-1242. PMID: 29907612; PMCID: PMC6071635.
      Citations: 35     Fields:    Translation:HumansCells
    14. Elango R, Sheng Z, Jackson J, DeCata J, Ibrahim Y, Pham NT, Liang DH, Sakofsky CJ, Vindigni A, Lobachev KS, Ira G, Malkova A. Break-induced replication promotes formation of lethal joint molecules dissolved by Srs2. Nat Commun. 2017 11 27; 8(1):1790. PMID: 29176630; PMCID: PMC5702615.
      Citations: 32     Fields:    Translation:AnimalsCells
    15. Buzovetsky O, Kwon Y, Pham NT, Kim C, Ira G, Sung P, Xiong Y. Role of the Pif1-PCNA Complex in Pol d-Dependent Strand Displacement DNA Synthesis and Break-Induced Replication. Cell Rep. 2017 Nov 14; 21(7):1707-1714. PMID: 29141206; PMCID: PMC5842794.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    16. Jackson J, Quinet A, Brickner JR, Li S, Yazinski S, You Z, Ira G, Zou L, Mosammaparast N, Vindigni A, Lema?on D. MRE11 and EXO1 nucleases degrade reversed forks and elicit MUS81-dependent fork rescue in BRCA2-deficient cells. Nat Commun. 2017 10 16; 8(1):860. PMID: 29038425; PMCID: PMC5643552.
      Citations: 155     Fields:    Translation:HumansCells
    17. Lopez CR, Singh S, Hambarde S, Griffin WC, Gao J, Chib S, Yu Y, Ira G, Raney KD, Kim N. Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA. Nucleic Acids Res. 2017 Jun 02; 45(10):5850-5862. PMID: 28369605; PMCID: PMC5449603.
      Citations: 25     Fields:    Translation:HumansAnimalsCells
    18. Kumar S, Peng X, Daley J, Yang L, Shen J, Nguyen N, Bae G, Niu H, Peng Y, Hsieh HJ, Wang L, Rao C, Stephan CC, Sung P, Ira G, Peng G. Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells. Oncogenesis. 2017 Apr 17; 6(4):e319. PMID: 28414320; PMCID: PMC5520492.
      Citations: 24     
    19. Miller AS, Daley JM, Pham NT, Niu H, Xue X, Ira G, Sung P. A novel role of the Dna2 translocase function in DNA break resection. Genes Dev. 2017 03 01; 31(5):503-510. PMID: 28336516; PMCID: PMC5393064.
      Citations: 24     Fields:    Translation:AnimalsCells
    20. Xue X, Papusha A, Choi K, Bonner JN, Kumar S, Niu H, Kaur H, Zheng XF, Donnianni RA, Lu L, Lichten M, Zhao X, Ira G, Sung P. Differential regulation of the anti-crossover and replication fork regression activities of Mph1 by Mte1. Genes Dev. 2016 03 15; 30(6):687-99. PMID: 26966246; PMCID: PMC4803054.
      Citations: 14     Fields:    Translation:AnimalsCells
    21. Chen X, Niu H, Yu Y, Wang J, Zhu S, Zhou J, Papusha A, Cui D, Pan X, Kwon Y, Sung P, Ira G. Enrichment of Cdk1-cyclins at DNA double-strand breaks stimulates Fun30 phosphorylation and DNA end resection. Nucleic Acids Res. 2016 Apr 07; 44(6):2742-53. PMID: 26801641; PMCID: PMC4824098.
      Citations: 21     Fields:    Translation:AnimalsCells
    22. Sakofsky CJ, Ayyar S, Deem AK, Chung WH, Ira G, Malkova A. Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements. Mol Cell. 2015 Dec 17; 60(6):860-72. PMID: 26669261; PMCID: PMC4688117.
      Citations: 67     Fields:    Translation:HumansAnimalsCells
    23. Mayle R, Campbell IM, Beck CR, Yu Y, Wilson M, Shaw CA, Bjergbaek L, Lupski JR, Ira G. DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science. 2015 Aug 14; 349(6249):742-7. PMID: 26273056; PMCID: PMC4782627.
      Citations: 108     Fields:    Translation:HumansAnimalsCells
    24. Xue X, Choi K, Bonner JN, Szakal B, Chen YH, Papusha A, Saro D, Niu H, Ira G, Branzei D, Sung P, Zhao X. Selective modulation of the functions of a conserved DNA motor by a histone fold complex. Genes Dev. 2015 05 15; 29(10):1000-5. PMID: 25956905; PMCID: PMC4441048.
      Citations: 12     Fields:    Translation:AnimalsCells
    25. Pfundt R, King DA, Lindsay SJ, Zuccherato LW, Macville MV, Liu P, Johnson D, Stankiewicz P, Brown CW, Shaw CA, Hurles ME, Ira G, Hastings PJ, Brunner HG, Lupski JR, Carvalho CM, DDD?Study. Absence of heterozygosity due to template switching during replicative rearrangements. Am J Hum Genet. 2015 Apr 02; 96(4):555-64. PMID: 25799105; PMCID: PMC4385179.
      Citations: 27     Fields:    Translation:HumansCells
    26. Ira G, Nussenzweig A. A new Riff: Rif1 eats its cake and has it too. EMBO Rep. 2014 Jun; 15(6):622-4. PMID: 24769453; PMCID: PMC4197870.
      Citations: 4     Fields:    Translation:AnimalsCells
    27. Wilson MA, Kwon Y, Xu Y, Chung WH, Chi P, Niu H, Mayle R, Chen X, Malkova A, Sung P, Ira G. Pif1 helicase and Pold promote recombination-coupled DNA synthesis via bubble migration. Nature. 2013 Oct 17; 502(7471):393-6. PMID: 24025768; PMCID: PMC3915060.
      Citations: 180     Fields:    Translation:AnimalsCells
    28. Saini N, Ramakrishnan S, Elango R, Ayyar S, Zhang Y, Deem A, Ira G, Haber JE, Lobachev KS, Malkova A. Migrating bubble during break-induced replication drives conservative DNA synthesis. Nature. 2013 Oct 17; 502(7471):389-92. PMID: 24025772; PMCID: PMC3804423.
      Citations: 194     Fields:    Translation:AnimalsCells
    29. Malkova A, Ira G. Break-induced replication: functions and molecular mechanism. Curr Opin Genet Dev. 2013 Jun; 23(3):271-9. PMID: 23790415; PMCID: PMC3915057.
      Citations: 97     Fields:    Translation:HumansCells
    30. Chen X, Cui D, Papusha A, Zhang X, Chu CD, Tang J, Chen K, Pan X, Ira G. The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends. Nature. 2012 Sep 27; 489(7417):576-80. PMID: 22960743; PMCID: PMC3640768.
      Citations: 140     Fields:    Translation:AnimalsCells
    31. Ira G, Hastings PJ. DNA breakage drives nuclear search. Nat Cell Biol. 2012 May 02; 14(5):448-50. PMID: 22552144; PMCID: PMC4495951.
      Citations: 5     Fields:    Translation:Cells
    32. Peng G, Dai H, Zhang W, Hsieh HJ, Pan MR, Park YY, Tsai RY, Bedrosian I, Lee JS, Ira G, Lin SY. Human nuclease/helicase DNA2 alleviates replication stress by promoting DNA end resection. Cancer Res. 2012 Jun 01; 72(11):2802-13. PMID: 22491672; PMCID: PMC3367086.
      Citations: 46     Fields:    Translation:HumansCells
    33. Chen X, Niu H, Chung WH, Zhu Z, Papusha A, Shim EY, Lee SE, Sung P, Ira G. Cell cycle regulation of DNA double-strand break end resection by Cdk1-dependent Dna2 phosphorylation. Nat Struct Mol Biol. 2011 Aug 14; 18(9):1015-9. PMID: 21841787; PMCID: PMC3168961.
      Citations: 104     Fields:    Translation:AnimalsCells
    34. Oum JH, Seong C, Kwon Y, Ji JH, Sid A, Ramakrishnan S, Ira G, Malkova A, Sung P, Lee SE, Shim EY. RSC facilitates Rad59-dependent homologous recombination between sister chromatids by promoting cohesin loading at DNA double-strand breaks. Mol Cell Biol. 2011 Oct; 31(19):3924-37. PMID: 21807899; PMCID: PMC3187356.
      Citations: 30     Fields:    Translation:AnimalsCells
    35. Shim EY, Chung WH, Nicolette ML, Zhang Y, Davis M, Zhu Z, Paull TT, Ira G, Lee SE. Saccharomyces cerevisiae Mre11/Rad50/Xrs2 and Ku proteins regulate association of Exo1 and Dna2 with DNA breaks. EMBO J. 2010 Oct 06; 29(19):3370-80. PMID: 20834227; PMCID: PMC2957216.
      Citations: 141     Fields:    Translation:AnimalsCells
    36. Niu H, Chung WH, Zhu Z, Kwon Y, Zhao W, Chi P, Prakash R, Seong C, Liu D, Lu L, Ira G, Sung P. Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae. Nature. 2010 Sep 02; 467(7311):108-11. PMID: 20811460; PMCID: PMC2955862.
      Citations: 228     Fields:    Translation:AnimalsCells
    37. Chung WH, Zhu Z, Papusha A, Malkova A, Ira G. Defective resection at DNA double-strand breaks leads to de novo telomere formation and enhances gene targeting. PLoS Genet. 2010 May 13; 6(5):e1000948. PMID: 20485519; PMCID: PMC2869328.
      Citations: 112     Fields:    Translation:Cells
    38. Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet. 2009 Aug; 10(8):551-64. PMID: 19597530; PMCID: PMC2864001.
      Citations: 535     Fields:    Translation:Humans
    39. Hastings PJ, Ira G, Lupski JR. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 2009 Jan; 5(1):e1000327. PMID: 19180184; PMCID: PMC2621351.
      Citations: 418     Fields:    Translation:HumansAnimalsCells
    40. Prakash R, Satory D, Papusha A, Kramer W, Krejci L, Klein H, Haber JE, Sung P, Ira G, Dray E, Scheller J. Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination. Genes Dev. 2009 Jan 01; 23(1):67-79. PMID: 19136626; PMCID: PMC2632165.
      Citations: 156     Fields:    Translation:AnimalsCells
    41. Zhu Z, Chung WH, Shim EY, Lee SE, Ira G. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell. 2008 Sep 19; 134(6):981-94. PMID: 18805091; PMCID: PMC2662516.
      Citations: 625     Fields:    Translation:AnimalsCells
    42. Ira G, Satory D, Haber JE. Conservative inheritance of newly synthesized DNA in double-strand break-induced gene conversion. Mol Cell Biol. 2006 Dec; 26(24):9424-9. PMID: 17030630; PMCID: PMC1698534.
      Citations: 37     Fields:    Translation:AnimalsCells
    43. Malkova A, Naylor ML, Yamaguchi M, Ira G, Haber JE. RAD51-dependent break-induced replication differs in kinetics and checkpoint responses from RAD51-mediated gene conversion. Mol Cell Biol. 2005 Feb; 25(3):933-44. PMID: 15657422; PMCID: PMC544012.
      Citations: 104     Fields:    Translation:AnimalsCells
    44. Ira G, Pellicioli A, Balijja A, Wang X, Fiorani S, Carotenuto W, Liberi G, Bressan D, Wan L, Hollingsworth NM, Haber JE, Foiani M. DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature. 2004 Oct 21; 431(7011):1011-7. PMID: 15496928; PMCID: PMC4493751.
      Citations: 391     Fields:    Translation:AnimalsCells
    45. Shroff R, Arbel-Eden A, Pilch D, Ira G, Bonner WM, Petrini JH, Haber JE, Lichten M. Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Curr Biol. 2004 Oct 05; 14(19):1703-11. PMID: 15458641; PMCID: PMC4493763.
      Citations: 226     Fields:    Translation:AnimalsCells
    46. Wang X, Ira G, Holmes AM, Diffley JF, Haber JE, Tercero JA. Role of DNA replication proteins in double-strand break-induced recombination in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Aug; 24(16):6891-9. PMID: 15282291; PMCID: PMC479734.
      Citations: 69     Fields:    Translation:AnimalsCells
    47. Filipski J, Ira G, Kr?l J. Mapping of the hotspots of recombination in human DNA cloned as yeast artificial chromosomes. Methods Mol Biol. 2004; 240:35-52. PMID: 14970404.
      Citations:    Fields:    Translation:HumansCells
    48. Ira G, Malkova A, Liberi G, Foiani M, Haber JE. Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast. Cell. 2003 Nov 14; 115(4):401-11. PMID: 14622595; PMCID: PMC4493758.
      Citations: 354     Fields:    Translation:AnimalsCells
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