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Items: 41


neoepiscope improves neoepitope prediction with multi-variant phasing.

Wood MA, Nguyen A, Struck A, Ellrott K, Nellore A, Thompson RF.

Bioinformatics. 2019 Aug 19. pii: btz653. doi: 10.1093/bioinformatics/btz653. [Epub ahead of print]


Letter to the Editor.

Nellore A, Mannon RB, Limaye AP.

Clin Infect Dis. 2019 Jul 25. pii: ciz495. doi: 10.1093/cid/ciz495. [Epub ahead of print] No abstract available.


Carbapenem-Resistant Enterobacteriaceae in Solid Organ Transplantation: Management Principles.

Smibert O, Satlin MJ, Nellore A, Peleg AY.

Curr Infect Dis Rep. 2019 Jun 10;21(7):26. doi: 10.1007/s11908-019-0679-4. Review.


IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiation.

Zumaquero E, Stone SL, Scharer CD, Jenks SA, Nellore A, Mousseau B, Rosal-Vela A, Botta D, Bradley JE, Wojciechowski W, Ptacek T, Danila MI, Edberg JC, Bridges SL Jr, Kimberly RP, Chatham WW, Schoeb TR, Rosenberg AF, Boss JM, Sanz I, Lund FE.

Elife. 2019 May 15;8. pii: e41641. doi: 10.7554/eLife.41641.


Vancomycin-resistant Enterococcus in solid organ transplant recipients: Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice.

Nellore A, Huprikar S; AST ID Community of Practice.

Clin Transplant. 2019 Mar 26:e13549. doi: 10.1111/ctr.13549. [Epub ahead of print]


Infections after xenotransplantation.

Nellore A.

Curr Opin Organ Transplant. 2018 Dec;23(6):628-632. doi: 10.1097/MOT.0000000000000580.


Donor-derived infections and infectious risk in xenotransplantation and allotransplantation.

Nellore A, Fishman JA.

Xenotransplantation. 2018 Jul;25(4):e12423. doi: 10.1111/xen.12423. Review.


Management of Strongyloides in Solid Organ Transplant Recipients.

Hayes J, Nellore A.

Infect Dis Clin North Am. 2018 Sep;32(3):749-763. doi: 10.1016/j.idc.2018.04.012. Review.


Moving Career Development Upstream: Evaluation of a Course for Internal Medicine Trainees Contemplating Career Pathways in Academic Medicine.

Kraemer RR, Wakelee JF, Hites L, Frank SJ, Saag K, Rogers DA, Nellore A, Erdmann N, Nichols AC, Merlin JS.

South Med J. 2018 Aug;111(8):471-475. doi: 10.14423/SMJ.0000000000000844.


Two Cases and a Review of Graft-Versus-Host Disease and the Role of Hepatitis C Treatment in Liver Transplant Patients.

Advani SD, Nellore A, Hadjivassiliou G, Eckhoff DE, Salzman D, Lavie D, Pavlidakey P, Baddley JW.

Prog Transplant. 2018 Sep;28(3):267-270. doi: 10.1177/1526924818781558. Epub 2018 Jun 28.


Population-level distribution and putative immunogenicity of cancer neoepitopes.

Wood MA, Paralkar M, Paralkar MP, Nguyen A, Struck AJ, Ellrott K, Margolin A, Nellore A, Thompson RF.

BMC Cancer. 2018 Apr 13;18(1):414. doi: 10.1186/s12885-018-4325-6.


Cloud computing for genomic data analysis and collaboration.

Langmead B, Nellore A.

Nat Rev Genet. 2018 May;19(5):325. doi: 10.1038/nrg.2018.8. Epub 2018 Feb 12.


Cloud computing for genomic data analysis and collaboration.

Langmead B, Nellore A.

Nat Rev Genet. 2018 Apr;19(4):208-219. doi: 10.1038/nrg.2017.113. Epub 2018 Jan 30. Review. Erratum in: Nat Rev Genet. 2018 Feb 12;:.


recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.

Collado-Torres L, Nellore A, Jaffe AE.

F1000Res. 2017 Aug 24;6:1558. doi: 10.12688/f1000research.12223.1. eCollection 2017.


Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.

Wilks C, Gaddipati P, Nellore A, Langmead B.

Bioinformatics. 2018 Jan 1;34(1):114-116. doi: 10.1093/bioinformatics/btx547.


qSVA framework for RNA quality correction in differential expression analysis.

Jaffe AE, Tao R, Norris AL, Kealhofer M, Nellore A, Shin JH, Kim D, Jia Y, Hyde TM, Kleinman JE, Straub RE, Leek JT, Weinberger DR.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7130-7135. doi: 10.1073/pnas.1617384114. Epub 2017 Jun 20.


Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.


Rhodococcus Infection in Solid Organ and Hematopoietic Stem Cell Transplant Recipients1.

Vergidis P, Ariza-Heredia EJ, Nellore A, Kotton CN, Kaul DR, Morris MI, Kelesidis T, Shah H, Park SY, Nguyen MH, Razonable RR.

Emerg Infect Dis. 2017 Mar;23(3):510-512. doi: 10.3201/eid2303.160633.


Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT.

Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.


Narcolepsy and influenza vaccination-the inappropriate awakening of immunity.

Nellore A, Randall TD.

Ann Transl Med. 2016 Oct;4(Suppl 1):S29. No abstract available.


Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.


Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B.

Bioinformatics. 2017 Dec 15;33(24):4033-4040. doi: 10.1093/bioinformatics/btw575.


Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B.

Bioinformatics. 2016 Aug 15;32(16):2551-3. doi: 10.1093/bioinformatics/btw177. Epub 2016 Apr 21.


The Microbiome, Systemic Immune Function, and Allotransplantation.

Nellore A, Fishman JA.

Clin Microbiol Rev. 2016 Jan;29(1):191-9. doi: 10.1128/CMR.00063-15. Review.


Loss of Vancomycin-Resistant Enterococcus Fecal Dominance in an Organ Transplant Patient With Clostridium difficile Colitis After Fecal Microbiota Transplant.

Stripling J, Kumar R, Baddley JW, Nellore A, Dixon P, Howard D, Ptacek T, Lefkowitz EJ, Tallaj JA, Benjamin WH Jr, Morrow CD, Rodriguez JM.

Open Forum Infect Dis. 2015 Jun 3;2(2):ofv078. doi: 10.1093/ofid/ofv078. eCollection 2015 Apr.


Long-term Outcomes After Liver Transplantation Among Human Immunodeficiency Virus-Infected Recipients.

Locke JE, Durand C, Reed RD, MacLennan PA, Mehta S, Massie A, Nellore A, DuBay D, Segev DL.

Transplantation. 2016 Jan;100(1):141-6. doi: 10.1097/TP.0000000000000829.


A National Study of Outcomes among HIV-Infected Kidney Transplant Recipients.

Locke JE, Mehta S, Reed RD, MacLennan P, Massie A, Nellore A, Durand C, Segev DL.

J Am Soc Nephrol. 2015 Sep;26(9):2222-9. doi: 10.1681/ASN.2014070726. Epub 2015 Mar 19.


The cyclin dependent kinase inhibitor (R)-roscovitine mediates selective suppression of alloreactive human T cells but preserves pathogen-specific and leukemia-specific effectors.

Nellore A, Liu B, Patsoukis N, Boussiotis VA, Li L.

Clin Immunol. 2014 May-Jun;152(1-2):48-57. doi: 10.1016/j.clim.2014.02.015. Epub 2014 Mar 12.


Prostaglandin E2 promotes survival of naive UCB T cells via the Wnt/β-catenin pathway and alters immune reconstitution after UCBT.

Li L, Kim HT, Nellore A, Patsoukis N, Petkova V, McDonough S, Politikos I, Nikiforow S, Soiffer R, Antin JH, Ballen K, Cutler C, Ritz J, Boussiotis VA.

Blood Cancer J. 2014 Jan 17;4:e178. doi: 10.1038/bcj.2013.75.


Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.

Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA.

Cell Stem Cell. 2013 May 2;12(5):616-28. doi: 10.1016/j.stem.2013.03.003. Epub 2013 Apr 11.


Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF.

Haq R, Shoag J, Andreu-Perez P, Yokoyama S, Edelman H, Rowe GC, Frederick DT, Hurley AD, Nellore A, Kung AL, Wargo JA, Song JS, Fisher DE, Arany Z, Widlund HR.

Cancer Cell. 2013 Mar 18;23(3):302-15. doi: 10.1016/j.ccr.2013.02.003. Epub 2013 Mar 7.


NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data.

Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song JS.

Front Genet. 2013 Jan 11;3:320. doi: 10.3389/fgene.2012.00320. eCollection 2012.


Screening strategies for tuberculosis in children with kidney disease: what is cost-effective?

Nellore A, Kotton CN.

Am J Kidney Dis. 2013 Jan;61(1):3-5. doi: 10.1053/j.ajkd.2012.10.003. No abstract available.


CHANCE: comprehensive software for quality control and validation of ChIP-seq data.

Diaz A, Nellore A, Song JS.

Genome Biol. 2012 Oct 15;13(10):R98. doi: 10.1186/gb-2012-13-10-r98.


The risk of tuberculosis in transplant candidates and recipients: a TBNET consensus statement.

Bumbacea D, Arend SM, Eyuboglu F, Fishman JA, Goletti D, Ison MG, Jones CE, Kampmann B, Kotton CN, Lange C, Ljungman P, Milburn H, Morris MI, Muller E, Muñoz P, Nellore A, Rieder HL, Sester U, Theodoropoulos N, Wagner D, Sester M.

Eur Respir J. 2012 Oct;40(4):990-1013. Epub 2012 Apr 10. Review.


NK cells, innate immunity and hepatitis C infection after liver transplantation.

Nellore A, Fishman JA.

Clin Infect Dis. 2011 Feb 1;52(3):369-77. doi: 10.1093/cid/ciq156. Review.


Pandemic Swine flu 2009.

Nellore A, Fishman J.

Xenotransplantation. 2009 Nov-Dec;16(6):463-5. doi: 10.1111/j.1399-3089.2009.00559.x. No abstract available.


Loss of Rap1GAP in papillary thyroid cancer.

Nellore A, Paziana K, Ma C, Tsygankova OM, Wang Y, Puttaswamy K, Iqbal AU, Franks SR, Lv Y, Troxel AB, Feldman MD, Meinkoth JL, Brose MS.

J Clin Endocrinol Metab. 2009 Mar;94(3):1026-32. doi: 10.1210/jc.2008-1042. Epub 2008 Dec 9.


Thermodynamics and bulk viscosity of approximate black hole duals to finite temperature quantum chromodynamics.

Gubser SS, Nellore A, Pufu SS, Rocha FD.

Phys Rev Lett. 2008 Sep 26;101(13):131601. Epub 2008 Sep 23.


Phase II trial of sorafenib in advanced thyroid cancer.

Gupta-Abramson V, Troxel AB, Nellore A, Puttaswamy K, Redlinger M, Ransone K, Mandel SJ, Flaherty KT, Loevner LA, O'Dwyer PJ, Brose MS.

J Clin Oncol. 2008 Oct 10;26(29):4714-9. doi: 10.1200/JCO.2008.16.3279. Epub 2008 Jun 9.


Delayed migration of a catheter fragment from the left to the right pulmonary artery.

Nellore A, Trerotola SO.

J Vasc Interv Radiol. 2004 May;15(5):497-9.


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