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Items: 1 to 50 of 419

1.

HIV-1 Vif Triggers Cell Cycle Arrest by Degrading Cellular PPP2R5 Phospho-regulators.

Salamango DJ, Ikeda T, Moghadasi SA, Wang J, McCann JL, Serebrenik AA, Ebrahimi D, Jarvis MC, Brown WL, Harris RS.

Cell Rep. 2019 Oct 29;29(5):1057-1065.e4. doi: 10.1016/j.celrep.2019.09.057.

2.

The Role of RNA in HIV-1 Vif-Mediated Degradation of APOBEC3H.

Wang J, Becker JT, Shi K, Lauer KV, Salamango DJ, Aihara H, Shaban NM, Harris RS.

J Mol Biol. 2019 Oct 16. pii: S0022-2836(19)30569-8. doi: 10.1016/j.jmb.2019.09.014. [Epub ahead of print]

PMID:
31628948
3.

The deaminase APOBEC3B triggers the death of cells lacking uracil DNA glycosylase.

Serebrenik AA, Starrett GJ, Leenen S, Jarvis MC, Shaban NM, Salamango DJ, Nilsen H, Brown WL, Harris RS.

Proc Natl Acad Sci U S A. 2019 Oct 29;116(44):22158-22163. doi: 10.1073/pnas.1904024116. Epub 2019 Oct 14.

PMID:
31611371
4.

A Rabbit Monoclonal Antibody against the Antiviral and Cancer Genomic DNA Mutating Enzyme APOBEC3B.

Brown WL, Law EK, Argyris PP, Carpenter MA, Levin-Klein R, Ranum AN, Molan AM, Forster CL, Anderson BD, Lackey L, Harris RS.

Antibodies (Basel). 2019 Sep 10;8(3). pii: E47. doi: 10.3390/antib8030047.

5.

A Conserved Mechanism of APOBEC3 Relocalization by Herpesviral Ribonucleotide Reductase Large Subunits.

Cheng AZ, Moraes SN, Attarian C, Yockteng-Melgar J, Jarvis MC, Biolatti M, Galitska G, Dell'Oste V, Frappier L, Bierle CJ, Rice SA, Harris RS.

J Virol. 2019 Nov 13;93(23). pii: e01539-19. doi: 10.1128/JVI.01539-19. Print 2019 Dec 1.

PMID:
31534038
6.

Improved representation of sequence Bloom trees.

Harris RS, Medvedev P.

Bioinformatics. 2019 Aug 22. pii: btz662. doi: 10.1093/bioinformatics/btz662. [Epub ahead of print]

PMID:
31504157
7.

Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data.

Harris RS, Cechova M, Makova KD.

Bioinformatics. 2019 Nov 1;35(22):4809-4811. doi: 10.1093/bioinformatics/btz484.

PMID:
31290946
8.

High satellite repeat turnover in great apes studied with short- and long-read technologies.

Cechova M, Harris RS, Tomaszkiewicz M, Arbeithuber B, Chiaromonte F, Makova KD.

Mol Biol Evol. 2019 Jul 2. pii: msz156. doi: 10.1093/molbev/msz156. [Epub ahead of print]

9.

A phase 3 study of tezacaftor in combination with ivacaftor in children aged 6 through 11 years with cystic fibrosis.

Walker S, Flume P, McNamara J, Solomon M, Chilvers M, Chmiel J, Harris RS, Haseltine E, Stiles D, Li C, Ahluwalia N, Zhou H, Owen CA, Sawicki G; VX15-661-113 Investigator Group.

J Cyst Fibros. 2019 Sep;18(5):708-713. doi: 10.1016/j.jcf.2019.06.009. Epub 2019 Jun 26.

10.

The DNA deaminase APOBEC3B interacts with the cell-cycle protein CDK4 and disrupts CDK4-mediated nuclear import of Cyclin D1.

McCann JL, Klein MM, Leland EM, Law EK, Brown WL, Salamango DJ, Harris RS.

J Biol Chem. 2019 Aug 9;294(32):12099-12111. doi: 10.1074/jbc.RA119.008443. Epub 2019 Jun 19.

PMID:
31217276
11.

Retrovirus insertion site analysis of LGL leukemia patient genomes.

Li W, Yang L, Harris RS, Lin L, Olson TL, Hamele CE, Feith DJ, Loughran TP Jr, Poss M.

BMC Med Genomics. 2019 Jun 17;12(1):88. doi: 10.1186/s12920-019-0549-9.

12.

HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1.

Ikeda T, Molan AM, Jarvis MC, Carpenter MA, Salamango DJ, Brown WL, Harris RS.

J Gen Virol. 2019 Jul;100(7):1140-1152. doi: 10.1099/jgv.0.001276. Epub 2019 May 30.

PMID:
31145054
13.

Suboptimal T-cell Therapy Drives a Tumor Cell Mutator Phenotype That Promotes Escape from First-Line Treatment.

Evgin L, Huff AL, Kottke T, Thompson J, Molan AM, Driscoll CB, Schuelke M, Shim KG, Wongthida P, Ilett EJ, Smith KK, Harris RS, Coffey M, Pulido JS, Pandha H, Selby PJ, Harrington KJ, Melcher A, Vile RG.

Cancer Immunol Res. 2019 May;7(5):828-840. doi: 10.1158/2326-6066.CIR-18-0013. Epub 2019 Apr 2.

PMID:
30940643
14.

Quantitative assessment of airway remodelling and response to allergen in asthma.

Adams DC, Miller AJ, Applegate MB, Cho JL, Hamilos DL, Chee A, Holz JA, Szabari MV, Hariri LP, Harris RS, Griffith JW, Luster AD, Medoff BD, Suter MJ.

Respirology. 2019 Nov;24(11):1073-1080. doi: 10.1111/resp.13521. Epub 2019 Mar 7.

PMID:
30845351
15.

Perfusion Imaging Distinguishes Exercise Pulmonary Arterial Hypertension at Rest.

Kohli P, Kelly VJ, Kehl EG, Rodriguez-Lopez J, Hibbert KA, Kone M, Systrom DM, Waxman AB, Venegas JG, Channick R, Winkler T, Harris RS.

Am J Respir Crit Care Med. 2019 Jun 1;199(11):1438-1441. doi: 10.1164/rccm.201810-1899LE. No abstract available.

PMID:
30811948
16.

Evolved Proteins Inhibit Entry of Enfuvirtide-Resistant HIV-1.

Ikeda T, Tennyson RL, Walker SN, Harris RS, McNaughton BR.

ACS Infect Dis. 2019 Apr 12;5(4):634-640. doi: 10.1021/acsinfecdis.8b00362. Epub 2019 Mar 12.

PMID:
30811933
17.

Polyomavirus T Antigen Induces APOBEC3B Expression Using an LXCXE-Dependent and TP53-Independent Mechanism.

Starrett GJ, Serebrenik AA, Roelofs PA, McCann JL, Verhalen B, Jarvis MC, Stewart TA, Law EK, Krupp A, Jiang M, Martens JWM, Cahir-McFarland E, Span PN, Harris RS.

MBio. 2019 Feb 5;10(1). pii: e02690-18. doi: 10.1128/mBio.02690-18.

18.

A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes.

Martin AS, Salamango DJ, Serebrenik AA, Shaban NM, Brown WL, Harris RS.

Sci Rep. 2019 Jan 24;9(1):497. doi: 10.1038/s41598-018-36739-9.

19.

Quantification of the Pulmonary Vascular Response to Inhaled Nitric Oxide Using Noncontrast Computed Tomography Imaging.

Rahaghi FN, Winkler T, Kohli P, Nardelli P, Martí-Fuster B, Ross JC, Radhakrishnan R, Blackwater T, Ash SY, de La Bruere I, Diaz AA, Channick RN, Harris RS, Washko GR, San José Estépar R.

Circ Cardiovasc Imaging. 2019 Dec;12(1):e008338. doi: 10.1161/CIRCIMAGING.118.008338. No abstract available.

PMID:
30632391
20.

A lentivirus-based system for Cas9/gRNA expression and subsequent removal by Cre-mediated recombination.

Carpenter MA, Law EK, Serebrenik A, Brown WL, Harris RS.

Methods. 2019 Mar 1;156:79-84. doi: 10.1016/j.ymeth.2018.12.006. Epub 2018 Dec 19.

PMID:
30578845
21.

Elevation in lung volume and preventing catastrophic airway closure in asthmatics during bronchoconstriction.

Osorio-Valencia JS, Wongviriyawong C, Winkler T, Kelly VJ, Harris RS, Venegas JG.

PLoS One. 2018 Dec 19;13(12):e0208337. doi: 10.1371/journal.pone.0208337. eCollection 2018.

22.

Natural APOBEC3C variants can elicit differential HIV-1 restriction activity.

Anderson BD, Ikeda T, Moghadasi SA, Martin AS, Brown WL, Harris RS.

Retrovirology. 2018 Dec 17;15(1):78. doi: 10.1186/s12977-018-0459-5.

23.

A phase I trial of low-dose inhaled carbon monoxide in sepsis-induced ARDS.

Fredenburgh LE, Perrella MA, Barragan-Bradford D, Hess DR, Peters E, Welty-Wolf KE, Kraft BD, Harris RS, Maurer R, Nakahira K, Oromendia C, Davies JD, Higuera A, Schiffer KT, Englert JA, Dieffenbach PB, Berlin DA, Lagambina S, Bouthot M, Sullivan AI, Nuccio PF, Kone MT, Malik MJ, Porras MAP, Finkelsztein E, Winkler T, Hurwitz S, Serhan CN, Piantadosi CA, Baron RM, Thompson BT, Choi AM.

JCI Insight. 2018 Dec 6;3(23). pii: 124039. doi: 10.1172/jci.insight.124039.

24.

Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity.

Cheng AZ, Yockteng-Melgar J, Jarvis MC, Malik-Soni N, Borozan I, Carpenter MA, McCann JL, Ebrahimi D, Shaban NM, Marcon E, Greenblatt J, Brown WL, Frappier L, Harris RS.

Nat Microbiol. 2019 Jan;4(1):78-88. doi: 10.1038/s41564-018-0284-6. Epub 2018 Nov 12.

25.

Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2'-Deoxyzebularine Analogues.

Kvach MV, Barzak FM, Harjes S, Schares HAM, Jameson GB, Ayoub AM, Moorthy R, Aihara H, Harris RS, Filichev VV, Harki DA, Harjes E.

Biochemistry. 2019 Feb 5;58(5):391-400. doi: 10.1021/acs.biochem.8b00858. Epub 2018 Nov 28.

26.

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate.

Guiblet WM, Cremona MA, Cechova M, Harris RS, Kejnovská I, Kejnovsky E, Eckert K, Chiaromonte F, Makova KD.

Genome Res. 2018 Dec;28(12):1767-1778. doi: 10.1101/gr.241257.118. Epub 2018 Nov 6.

27.

Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease.

Ebrahimi D, Richards CM, Carpenter MA, Wang J, Ikeda T, Becker JT, Cheng AZ, McCann JL, Shaban NM, Salamango DJ, Starrett GJ, Lingappa JR, Yong J, Brown WL, Harris RS.

Nat Commun. 2018 Oct 8;9(1):4137. doi: 10.1038/s41467-018-06594-3.

28.

APOBEC3 Mediates Resistance to Oncolytic Viral Therapy.

Huff AL, Wongthida P, Kottke T, Thompson JM, Driscoll CB, Schuelke M, Shim KG, Harris RS, Molan A, Pulido JS, Selby PJ, Harrington KJ, Melcher A, Evgin L, Vile RG.

Mol Ther Oncolytics. 2018 Aug 29;11:1-13. doi: 10.1016/j.omto.2018.08.003. eCollection 2018 Dec 21.

29.

Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template.

Aird EJ, Lovendahl KN, St Martin A, Harris RS, Gordon WR.

Commun Biol. 2018 May 31;1:54. doi: 10.1038/s42003-018-0054-2. eCollection 2018.

30.

APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction.

Salamango DJ, Becker JT, McCann JL, Cheng AZ, Demir Ö, Amaro RE, Brown WL, Shaban NM, Harris RS.

Mol Cell Biol. 2018 Nov 13;38(23). pii: e00356-18. doi: 10.1128/MCB.00356-18. Print 2018 Dec 1.

31.

Lobular Carcinomas In Situ Display Intralesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Lobular Carcinoma.

Lee JY, Schizas M, Geyer FC, Selenica P, Piscuoglio S, Sakr RA, Ng CKY, Carniello JVS, Towers R, Giri DD, de Andrade VP, Papanastasiou AD, Viale A, Harris RS, Solit DB, Weigelt B, Reis-Filho JS, King TA.

Clin Cancer Res. 2019 Jan 15;25(2):674-686. doi: 10.1158/1078-0432.CCR-18-1103. Epub 2018 Sep 5.

PMID:
30185420
32.

Determinants of Oligonucleotide Selectivity of APOBEC3B.

Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE.

J Chem Inf Model. 2019 May 28;59(5):2264-2273. doi: 10.1021/acs.jcim.8b00427. Epub 2018 Sep 10.

PMID:
30130104
33.

The effect of emphysema on readmission and survival among smokers with heart failure.

Kohli P, Staziaki PV, Janjua SA, Addison DA, Hallett TR, Hennessy O, Takx RAP, Lu MT, Fintelmann FJ, Semigran M, Harris RS, Celli BR, Hoffmann U, Neilan TG.

PLoS One. 2018 Jul 30;13(7):e0201376. doi: 10.1371/journal.pone.0201376. eCollection 2018.

34.

Mutation Signatures Including APOBEC in Cancer Cell Lines.

Jarvis MC, Ebrahimi D, Temiz NA, Harris RS.

JNCI Cancer Spectr. 2018 Jan;2(1). pii: pky002. doi: 10.1093/jncics/pky002. Epub 2018 Mar 17.

35.

APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces.

Salamango DJ, McCann JL, Demir Ö, Brown WL, Amaro RE, Harris RS.

J Mol Biol. 2018 Aug 17;430(17):2695-2708. doi: 10.1016/j.jmb.2018.04.044. Epub 2018 May 19.

36.

Deterioration of Regional Lung Strain and Inflammation during Early Lung Injury.

Motta-Ribeiro GC, Hashimoto S, Winkler T, Baron RM, Grogg K, Paula LFSC, Santos A, Zeng C, Hibbert K, Harris RS, Bajwa E, Vidal Melo MF.

Am J Respir Crit Care Med. 2018 Oct 1;198(7):891-902. doi: 10.1164/rccm.201710-2038OC.

37.

Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution.

Peretti A, Geoghegan EM, Pastrana DV, Smola S, Feld P, Sauter M, Lohse S, Ramesh M, Lim ES, Wang D, Borgogna C, FitzGerald PC, Bliskovsky V, Starrett GJ, Law EK, Harris RS, Killian JK, Zhu J, Pineda M, Meltzer PS, Boldorini R, Gariglio M, Buck CB.

Cell Host Microbe. 2018 May 9;23(5):628-635.e7. doi: 10.1016/j.chom.2018.04.005.

38.

A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC-Cas9 or cleavage by Cas9 in living cells.

St Martin A, Salamango D, Serebrenik A, Shaban N, Brown WL, Donati F, Munagala U, Conticello SG, Harris RS.

Nucleic Acids Res. 2018 Aug 21;46(14):e84. doi: 10.1093/nar/gky332.

39.

HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G.

Ikeda T, Symeonides M, Albin JS, Li M, Thali M, Harris RS.

PLoS Pathog. 2018 Apr 20;14(4):e1007010. doi: 10.1371/journal.ppat.1007010. eCollection 2018 Apr.

40.

AllSome Sequence Bloom Trees.

Sun C, Harris RS, Chikhi R, Medvedev P.

J Comput Biol. 2018 May;25(5):467-479. doi: 10.1089/cmb.2017.0258. Epub 2018 Apr 5.

PMID:
29620920
41.

Simian Immunodeficiency Virus Vif and Human APOBEC3B Interactions Resemble Those between HIV-1 Vif and Human APOBEC3G.

Wang J, Shaban NM, Land AM, Brown WL, Harris RS.

J Virol. 2018 May 29;92(12). pii: e00447-18. doi: 10.1128/JVI.00447-18. Print 2018 Jun 15.

42.

Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity.

Hayward JA, Tachedjian M, Cui J, Cheng AZ, Johnson A, Baker ML, Harris RS, Wang LF, Tachedjian G.

Mol Biol Evol. 2018 Jul 1;35(7):1626-1637. doi: 10.1093/molbev/msy048.

43.

Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution.

Venkatesan S, Rosenthal R, Kanu N, McGranahan N, Bartek J, Quezada SA, Hare J, Harris RS, Swanton C.

Ann Oncol. 2018 Mar 1;29(3):563-572. doi: 10.1093/annonc/mdy003. Review.

44.

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism.

Shaban NM, Shi K, Lauer KV, Carpenter MA, Richards CM, Salamango D, Wang J, Lopresti MW, Banerjee S, Levin-Klein R, Brown WL, Aihara H, Harris RS.

Mol Cell. 2018 Jan 4;69(1):75-86.e9. doi: 10.1016/j.molcel.2017.12.010. Epub 2017 Dec 28.

45.

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.

Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H.

Sci Rep. 2017 Dec 12;7(1):17415. doi: 10.1038/s41598-017-17694-3.

46.

Computational Model and Dynamics of Monomeric Full-Length APOBEC3G.

Gorle S, Pan Y, Sun Z, Shlyakhtenko LS, Harris RS, Lyubchenko YL, Vuković L.

ACS Cent Sci. 2017 Nov 22;3(11):1180-1188. doi: 10.1021/acscentsci.7b00346. Epub 2017 Oct 20.

47.

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.

Rangavittal S, Harris RS, Cechova M, Tomaszkiewicz M, Chikhi R, Makova KD, Medvedev P.

Bioinformatics. 2018 Apr 1;34(7):1125-1131. doi: 10.1093/bioinformatics/btx771.

48.

APOBEC Enzymes as Targets for Virus and Cancer Therapy.

Olson ME, Harris RS, Harki DA.

Cell Chem Biol. 2018 Jan 18;25(1):36-49. doi: 10.1016/j.chembiol.2017.10.007. Epub 2017 Nov 16. Review.

50.

Correction: HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation.

Nakano Y, Misawa N, Juarez-Fernandez G, Moriwaki M, Nakaoka S, Funo T, Yamada E, Soper A, Yoshikawa R, Ebrahimi D, Tachiki Y, Iwami S, Harris RS, Koyanagi Y, Sato K.

PLoS Pathog. 2017 Sep 7;13(9):e1006606. doi: 10.1371/journal.ppat.1006606. eCollection 2017 Sep.

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