Publications

The following contains an exhaustive list of the publications and preprints which my laboratory and I have participated in. It may be sometimes out-of-date. For the latest updates, please refer to my google scholar profile.

2022

• Miller HE, Ilieva M, Bishop AJR, Uchida S. Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions. Noncoding RNA. 2022 Mar 28;8(2):23. doi: 10.3390/ncrna8020023. PMID: 35447886; PMCID: PMC9025719.
• Ilieva M, Miller HE, Agarwal A, Paulus GK, Madsen JH, Bishop AJR, Kauppinen S, Uchida S. FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis. Noncoding RNA. 2022 Jan 28;8(1):13. doi: 10.3390/ncrna8010013. PMID: 35202087; PMCID: PMC8877069.

2021

• Brown AD, Greenman S, Claybon AB, Bishop AJR. BRCA2 Promotes Spontaneous Homologous Recombination In Vivo. Cancers (Basel). 2021 Jul 21;13(15):3663. doi: 10.3390/cancers13153663. PMID: 34359565; PMCID: PMC8345144.
• Gonçalves RM, Delgobo M, Agnes JP, das Neves RN, Falchetti M, Casagrande T, Garcia APV, Vieira TC, Somensi N, Bruxel MA, Mendes DAGB, Rafacho A, Báfica A, Gelain DP, Moreira JCF, Cassali GD, Bishop AJR, Zanotto-Filho A. COX-2 promotes mammary adipose tissue inflammation, local estrogen biosynthesis, and carcinogenesis in high-sugar/fat diet treated mice. Cancer Lett. 2021 Apr 1;502:44-57. doi: 10.1016/j.canlet.2021.01.003. Epub 2021 Jan 9. PMID: 33429006.
• Sybouts EH, Brown AD, Falcon-Cantrill MG, Thomas MH, DeNapoli T, Voeller J, Chen Y, Tomlinson GE, Bishop AJR. Bloom syndrome in a Mexican American family with rhabdomyosarcoma: evidence of a Mexican founder mutation. Cold Spring Harb Mol Case Stud. 2021 Apr 8;7(2):a005751. doi: 10.1101/mcs.a005751. PMID: 33832920; PMCID: PMC8040734.
• Delgobo M, Gonçalves RM, Delazeri MA, Falchetti M, Zandoná A, Nascimento das Neves R, Almeida K, Fagundes AC, Gelain DP, Fracasso JI, Macêdo GB, Priori L, Bassani N, Bishop AJR, Forcelini CM, Moreira JCF, Zanotto-Filho A. Thioredoxin reductase-1 levels are associated with NRF2 pathway activation and tumor recurrence in non-small cell lung cancer. Free Radic Biol Med. 2021 Oct 19;177:58-71. doi: 10.1016/j.freeradbiomed.2021.10.020. Epub ahead of print. PMID: 34673143.
• Miller HE, Bishop AJR. Correlation AnalyzeR: functional predictions from gene co-expression correlations. BMC Bioinformatics. 2021 Apr 20;22(1):206. doi: 10.1186/s12859-021-04130-7. PMID: 33879054; PMCID: PMC8056587.
• Miller HE, Montemayor D, Abdul J, et al. Quality-controlled R-loop meta-analysis reveals the characteristics of R-Loop consensus regions. bioRxiv; 2021. DOI: 10.1101/2021.11.01.466823.
• Miller HE, Montemayor D, Li J, et al. Exploration and analysis of R-loop mapping data with RLBase. bioRxiv; 2021. DOI: 10.1101/2021.11.01.466854.

2020

• Abraham KJ, Khosraviani N, Chan JNY, Gorthi A, Samman A, Zhao DY, Wang M, Bokros M, Vidya E, Ostrowski LA, Oshidari R, Pietrobon V, Patel PS, Algouneh A, Singhania R, Liu Y, Yerlici VT, De Carvalho DD, Ohh M, Dickson BC, Hakem R, Greenblatt JF, Lee S, Bishop AJR, Mekhail K. Nucleolar RNA polymerase II drives ribosome biogenesis. Nature. 2020 Jul 15. doi: 10.1038/s41586-020-2497-0. Epub ahead of print. PMID: 32669707.
• Pan H, Jin M, Ghadiyaram A, Kaur P, Miller HE, Ta HM, Liu M, Fan Y, Mahn C, Gorthi A, You C, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA. Nucleic Acids Res. 2020 Jun 4;48(10):5639-5655. doi: 10.1093/nar/gkaa284. PMID: 32352519; PMCID: PMC7261166.
• Miller HE, Gorthi A, Bassani N, Lawrence LA, Iskra BS, Bishop AJR. Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility. Cancers (Basel). 2020;12(4):948. Published 2020 Apr 11. doi:10.3390/cancers12040948
• Schafer ES, Rau RE, Berg SL, Liu X, Minard CG, Bishop AJR, Romero JC, Hicks MJ, Nelson MD Jr, Voss S, Reid JM, Fox E, Weigel BJ, Blaney SM. Phase 1/2 trial of talazoparib in combination with temozolomide in children and adolescents with refractory/recurrent solid tumors including Ewing sarcoma: A Children’s Oncology Group Phase 1 Consortium study (ADVL1411). Pediatr Blood Cancer. 2020 Feb;67(2):e28073. doi: 10.1002/pbc.28073. Epub 2019 Nov 14. PubMed PMID: 31724813.

2019

• Lambo S, Gröbner SN, Rausch T, Waszak SM, Schmidt C, Gorthi A, Romero JC, Mauermann M, Brabetz S, Krausert S, Buchhalter I, Koster J, Zwijnenburg DA, Sill M, Hübner JM, Mack N, Schwalm B, Ryzhova M, Hovestadt V, Papillon-Cavanagh S, Chan JA, Landgraf P, Ho B, Milde T, Witt O, Ecker J, Sahm F, Sumerauer D, Ellison DW, Orr BA, Darabi A, Haberler C, Figarella-Branger D, Wesseling P, Schittenhelm J, Remke M, Taylor MD, Gil-da-Costa MJ, Łastowska M, Grajkowska W, Hasselblatt M, Hauser P, Pietsch T, Uro-Coste E, Bourdeaut F, Masliah-Planchon J, Rigau V, Alexandrescu S, Wolf S, Li XN, Schüller U, Snuderl M, Karajannis MA, Giangaspero F, Jabado N, von Deimling A, Jones DTW, Korbel JO, von Hoff K, Lichter P, Huang A, Bishop AJR, Pfister SM, Korshunov A, Kool M. The molecular landscape of ETMR at diagnosis and relapse. Nature. 2019 Dec;576(7786):274-280. doi: 10.1038/s41586-019-1815-x. Epub 2019 Dec 4. PubMed PMID: 31802000; PubMed Central PMCID: PMC6908757.

2018

• Zanotto-Filho A, Rajamanickam S, Loranc E, Masamsetti VP, Gorthi A, Romero JC, Tonapi S, Gonçalves RM, Reddick RL, Benavides R, Kuhn J, Chen Y, Bishop AJR. Sorafenib improves alkylating therapy by blocking induced inflammation, invasion and angiogenesis in breast cancer cells. Cancer Lett. 2018 Jul 1;425:101-115. doi: 10.1016/j.canlet.2018.03.037. Epub 2018 Mar 30. PubMed PMID: 29608984; PubMed Central PMCID: PMC5930000.
• Gorthi A, Bishop AJR. Ewing sarcoma fusion oncogene: At the crossroads of transcription and DNA damage response. Mol Cell Oncol. 2018;5(4):e1465014. doi: 10.1080/23723556.2018.1465014. eCollection 2018. PubMed PMID: 30250915; PubMed Central PMCID: PMC6149845.
• Barron L, Bishop AJ. P53 and HIS-tag Binding. Journal of Proteomics & Bioinformatics. 2018 March; 11(3):62. doi: 10.4172/jpb.1000467.
• Gorthi A, Romero JC, Loranc E, Cao L, Lawrence LA, Goodale E, Iniguez AB, Bernard X, Masamsetti VP, Roston S, Lawlor ER, Toretsky JA, Stegmaier K, Lessnick SL, Chen Y, Bishop AJR. EWS-FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma. Nature. 2018 Mar 15;555(7696):387-391. doi: 10.1038/nature25748. Epub 2018 Mar 7. PubMed PMID: 29513652; PubMed Central PMCID: PMC6318124.
• Countryman P, Fan Y, Gorthi A, Pan H, Strickland J, Kaur P, Wang X, Lin J, Lei X, White C, You C, Wirth N, Tessmer I, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates. J Biol Chem. 2018 Jan 19;293(3):1054-1069. doi: 10.1074/jbc.M117.806406. Epub 2017 Nov 24. PubMed PMID: 29175904; PubMed Central PMCID: PMC5777247.

2017

• Liu R, Gorthi A, Jin Y, Bishop AJ, Chen Y. Computational Tools for Genome-wide R-loops Identification and Characterization. Int. J. of Computational Biology and Drug Design. 2017; 10(2):123. doi: 10.1504/IJCBDD.2017.083883.

2016

• Zanotto-Filho A, Masamsetti VP, Loranc E, Tonapi SS, Gorthi A, Bernard X, Gonçalves RM, Moreira JC, Chen Y, Bishop AJ. Alkylating Agent-Induced NRF2 Blocks Endoplasmic Reticulum Stress-Mediated Apoptosis via Control of Glutathione Pools and Protein Thiol Homeostasis. Mol Cancer Ther. 2016 Dec;15(12):3000-3014. doi: 10.1158/1535-7163.MCT-16-0271. Epub 2016 Sep 16. PubMed PMID: 27638861; PubMed Central PMCID: PMC5136348.
• de Araujo PR, Gorthi A, da Silva AE, Tonapi SS, Vo DT, Burns SC, Qiao M, Uren PJ, Yuan ZM, Bishop AJ, Penalva LO. Musashi1 Impacts Radio-Resistance in Glioblastoma by Controlling DNA-Protein Kinase Catalytic Subunit. Am J Pathol. 2016 Sep;186(9):2271-8. doi: 10.1016/j.ajpath.2016.05.020. Epub 2016 Jul 25. PubMed PMID: 27470713; PubMed Central PMCID: PMC5012509.
• Rajamanickam S, Panneerdoss S, Gorthi A, Timilsina S, Onyeagucha B, Kovalskyy D, Ivanov D, Hanes MA, Vadlamudi RK, Chen Y, Bishop AJ, Arbiser JL, Rao MK. Inhibition of FoxM1-Mediated DNA Repair by Imipramine Blue Suppresses Breast Cancer Growth and Metastasis. Clin Cancer Res. 2016 Jul 15;22(14):3524-36. doi: 10.1158/1078-0432.CCR-15-2535. Epub 2016 Feb 29. PubMed PMID: 26927663; PubMed Central PMCID: PMC4947433.
• Zanotto-Filho A, Dashnamoorthy R, Loranc E, de Souza LH, Moreira JC, Suresh U, Chen Y, Bishop AJ. Combined Gene Expression and RNAi Screening to Identify Alkylation Damage Survival Pathways from Fly to Human. PLoS One. 2016;11(4):e0153970. doi: 10.1371/journal.pone.0153970. eCollection 2016. PubMed PMID: 27100653; PubMed Central PMCID: PMC4839732.

2015

• Zanotto-Filho A, Braganhol E, Klafke K, Figueiró F, Terra SR, Paludo FJ, Morrone M, Bristot IJ, Battastini AM, Forcelini CM, Bishop AJR, Gelain DP, Moreira JCF. Autophagy inhibition improves the efficacy of curcumin/temozolomide combination therapy in glioblastomas. Cancer Lett. 2015 Mar 28;358(2):220-231. doi: 10.1016/j.canlet.2014.12.044. Epub 2014 Dec 24. PubMed PMID: 25542083.
• Zhou T, Chen P, Gu J, Bishop AJ, Scott LM, Hasty P, Rebel VI. Potential relationship between inadequate response to DNA damage and development of myelodysplastic syndrome. Int J Mol Sci. 2015 Jan 5;16(1):966-89. doi: 10.3390/ijms16010966. Review. PubMed PMID: 25569081; PubMed Central PMCID: PMC4307285.

2014

• Brown AD, Sager BW, Gorthi A, Tonapi SS, Brown EJ, Bishop AJ. ATR suppresses endogenous DNA damage and allows completion of homologous recombination repair. PLoS One. 2014;9(3):e91222. doi: 10.1371/journal.pone.0091222. eCollection 2014. PubMed PMID: 24675793; PubMed Central PMCID: PMC3968013.

2013

• Lei C, Tamim S, Bishop AJ, Ruan J. Fully automated protein complex prediction based on topological similarity and community structure. Proteome Sci. 2013 Nov 7;11(Suppl 1):S9. doi: 10.1186/1477-5956-11-S1-S9. Epub 2013 Nov 7. PubMed PMID: 24564887; PubMed Central PMCID: PMC3908383.
• Karia B, Martinez JA, Bishop AJ. Induction of homologous recombination following in utero exposure to DNA-damaging agents. DNA Repair (Amst). 2013 Nov;12(11):912-21. doi: 10.1016/j.dnarep.2013.08.005. Epub 2013 Sep 10. PubMed PMID: 24029142; PubMed Central PMCID: PMC4059048.
• Zhou T, Hasty P, Walter CA, Bishop AJ, Scott LM, Rebel VI. Myelodysplastic syndrome: an inability to appropriately respond to damaged DNA?. Exp Hematol. 2013 Aug;41(8):665-74. doi: 10.1016/j.exphem.2013.04.008. Epub 2013 Apr 30. Review. PubMed PMID: 23643835; PubMed Central PMCID: PMC3729593.
• Kassan M, Choi SK, Galán M, Bishop A, Umezawa K, Trebak M, Belmadani S, Matrougui K. Enhanced NF-κB activity impairs vascular function through PARP-1-, SP-1-, and COX-2-dependent mechanisms in type 2 diabetes. Diabetes. 2013 Jun;62(6):2078-87. doi: 10.2337/db12-1374. Epub 2013 Jan 24. PubMed PMID: 23349490; PubMed Central PMCID: PMC3661639.

2012

• Doderer MS, Anguiano Z, Suresh U, Dashnamoorthy R, Bishop AJ, Chen Y. Pathway Distiller – multisource biological pathway consolidation. BMC Genomics. 2012;13 Suppl 6:S18. doi: 10.1186/1471-2164-13-S6-S18. Epub 2012 Oct 26. PubMed PMID: 23134636; PubMed Central PMCID: PMC3481446.
• Hsu FH, Serpedin E, Hsiao TH, Bishop AJ, Dougherty ER, Chen Y. Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer. BMC Genomics. 2012;13 Suppl 6:S13. doi: 10.1186/1471-2164-13-S6-S13. Epub 2012 Oct 26. PubMed PMID: 23134756; PubMed Central PMCID: PMC3481440.
• Kim TM, Ko JH, Hu L, Kim SA, Bishop AJ, Vijg J, Montagna C, Hasty P. RAD51 mutants cause replication defects and chromosomal instability. Mol Cell Biol. 2012 Sep;32(18):3663-80. doi: 10.1128/MCB.00406-12. Epub 2012 Jul 9. PubMed PMID: 22778135; PubMed Central PMCID: PMC3430192.
• Lee IH, Kawai Y, Fergusson MM, Rovira II, Bishop AJ, Motoyama N, Cao L, Finkel T. Atg7 modulates p53 activity to regulate cell cycle and survival during metabolic stress. Science. 2012 Apr 13;336(6078):225-8. doi: 10.1126/science.1218395. PubMed PMID: 22499945; PubMed Central PMCID: PMC4721513.
• Zimmer SN, Lemieux ME, Karia BP, Day C, Zhou T, Zhou Q, Kung AL, Suresh U, Chen Y, Kinney MC, Bishop AJ, Rebel VI. Mice heterozygous for CREB binding protein are hypersensitive to γ-radiation and invariably develop myelodysplastic/myeloproliferative neoplasm. Exp Hematol. 2012 Apr;40(4):295-306.e5. doi: 10.1016/j.exphem.2011.12.004. Epub 2011 Dec 20. PubMed PMID: 22198154; PubMed Central PMCID: PMC3402047.
• Ravi D, Bishop AJ. Identification of genes required for damage survival using a cell-based RNAi screen against the Drosophila genome. Methods Mol Biol. 2012;920:9-26. doi: 10.1007/978-1-61779-998-3_2. PubMed PMID: 22941593.

2011

• Lin S, Yu L, Yang J, Liu Z, Karia B, Bishop AJ, Jackson J, Lozano G, Copland JA, Mu X, Sun B, Sun LZ. Mutant p53 disrupts role of ShcA protein in balancing Smad protein-dependent and -independent signaling activity of transforming growth factor-β (TGF-β). J Biol Chem. 2011 Dec 23;286(51):44023-34. doi: 10.1074/jbc.M111.265397. Epub 2011 Oct 28. PubMed PMID: 22039050; PubMed Central PMCID: PMC3243540.
• Brown AD, Claybon AB, Bishop AJ. A conditional mouse model for measuring the frequency of homologous recombination events in vivo in the absence of essential genes. Mol Cell Biol. 2011 Sep;31(17):3593-602. doi: 10.1128/MCB.00848-10. Epub 2011 Jun 27. PubMed PMID: 21709021; PubMed Central PMCID: PMC3165555.
• Claybon A, Bishop AJ. Dissection of a mouse eye for a whole mount of the retinal pigment epithelium. J Vis Exp. 2011 Feb 27;(48). doi: 10.3791/2563. PubMed PMID: 21403630; PubMed Central PMCID: PMC3197413.
• Ravi D, Chen Y, Karia B, Brown A, Gu TT, Li J, Carey MS, Hennessy BT, Bishop AJ. 14-3-3 σ expression effects G2/M response to oxygen and correlates with ovarian cancer metastasis. PLoS One. 2011 Jan 10;6(1):e15864. doi: 10.1371/journal.pone.0015864. PubMed PMID: 21249227; PubMed Central PMCID: PMC3018427.

2010

• Claybon A, Karia B, Bruce C, Bishop AJ. PARP1 suppresses homologous recombination events in mice in vivo. Nucleic Acids Res. 2010 Nov;38(21):7538-45. doi: 10.1093/nar/gkq624. Epub 2010 Jul 21. PubMed PMID: 20660013; PubMed Central PMCID: PMC2995050.
• Brown AD, Claybon AB, Bishop AJ. Mouse WRN Helicase Domain Is Not Required for Spontaneous Homologous Recombination-Mediated DNA Deletion. J Nucleic Acids. 2010 Aug 19;2010. doi: 10.4061/2010/356917. PubMed PMID: 20847942; PubMed Central PMCID: PMC2933912.
• Wiles AM, Doderer M, Ruan J, Gu TT, Ravi D, Blackman B, Bishop AJ. Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Biol. 2010 Mar 30;4:36. doi: 10.1186/1752-0509-4-36. PubMed PMID: 20353594; PubMed Central PMCID: PMC2859380.

2009

• Ravi D, Wiles AM, Bhavani S, Ruan J, Leder P, Bishop AJ. A network of conserved damage survival pathways revealed by a genomic RNAi screen. PLoS Genet. 2009 Jun;5(6):e1000527. doi: 10.1371/journal.pgen.1000527. Epub 2009 Jun 19. PubMed PMID: 19543366; PubMed Central PMCID: PMC2688755.

2008

• Wiles AM, Ravi D, Bhavani S, Bishop AJ. An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme. J Biomol Screen. 2008 Sep;13(8):777-84. doi: 10.1177/1087057108323125. Epub 2008 Aug 27. PubMed PMID: 18753689; PubMed Central PMCID: PMC2956424.