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Items: 19

1.

Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic.

Grubaugh ND, Saraf S, Gangavarapu K, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW 4th, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH; GeoSentinel Surveillance Network, Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG.

Cell. 2019 Aug 22;178(5):1057-1071.e11. doi: 10.1016/j.cell.2019.07.018.

PMID:
31442400
2.

Comparison of SureSelect and Nextera Exome Capture Performance in Single-Cell Sequencing.

Huss WJ, Hu Q, Glenn ST, Gangavarapu KJ, Wang J, Luce JD, Quinn PK, Brese EA, Zhan F, Conroy JM, Paragh G, Foster BA, Morrison CD, Liu S, Wei L.

Hum Hered. 2018;83(3):153-162. doi: 10.1159/000490506. Epub 2019 Jan 22.

3.

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG.

Genome Biol. 2019 Jan 8;20(1):8. doi: 10.1186/s13059-018-1618-7.

4.

Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection.

Saphire EO, Schendel SL, Fusco ML, Gangavarapu K, Gunn BM, Wec AZ, Halfmann PJ, Brannan JM, Herbert AS, Qiu X, Wagh K, He S, Giorgi EE, Theiler J, Pommert KBJ, Krause TB, Turner HL, Murin CD, Pallesen J, Davidson E, Ahmed R, Aman MJ, Bukreyev A, Burton DR, Crowe JE Jr, Davis CW, Georgiou G, Krammer F, Kyratsous CA, Lai JR, Nykiforuk C, Pauly MH, Rijal P, Takada A, Townsend AR, Volchkov V, Walker LM, Wang CI, Zeitlin L, Doranz BJ, Ward AB, Korber B, Kobinger GP, Andersen KG, Kawaoka Y, Alter G, Chandran K, Dye JM; Viral Hemorrhagic Fever Immunotherapeutic Consortium.

Cell. 2018 Aug 9;174(4):938-952.e13. doi: 10.1016/j.cell.2018.07.033.

5.

A Role for Fc Function in Therapeutic Monoclonal Antibody-Mediated Protection against Ebola Virus.

Gunn BM, Yu WH, Karim MM, Brannan JM, Herbert AS, Wec AZ, Halfmann PJ, Fusco ML, Schendel SL, Gangavarapu K, Krause T, Qiu X, He S, Das J, Suscovich TJ, Lai J, Chandran K, Zeitlin L, Crowe JE Jr, Lauffenburger D, Kawaoka Y, Kobinger GP, Andersen KG, Dye JM, Saphire EO, Alter G.

Cell Host Microbe. 2018 Aug 8;24(2):221-233.e5. doi: 10.1016/j.chom.2018.07.009.

6.

Analysis of CD8+ T cell response during the 2013-2016 Ebola epidemic in West Africa.

Sakabe S, Sullivan BM, Hartnett JN, Robles-Sikisaka R, Gangavarapu K, Cubitt B, Ware BC, Kotliar D, Branco LM, Goba A, Momoh M, Sandi JD, Kanneh L, Grant DS, Garry RF, Andersen KG, de la Torre JC, Sabeti PC, Schieffelin JS, Oldstone MBA.

Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):E7578-E7586. doi: 10.1073/pnas.1806200115. Epub 2018 Jul 23.

7.

Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas.

Gardner LM, Bóta A, Gangavarapu K, Kraemer MUG, Grubaugh ND.

PLoS Negl Trop Dis. 2018 Jan 18;12(1):e0006194. doi: 10.1371/journal.pntd.0006194. eCollection 2018 Jan.

8.

Ontogeny of the B- and T-cell response in a primary Zika virus infection of a dengue-naïve individual during the 2016 outbreak in Miami, FL.

Ricciardi MJ, Magnani DM, Grifoni A, Kwon YC, Gutman MJ, Grubaugh ND, Gangavarapu K, Sharkey M, Silveira CGT, Bailey VK, Pedreño-Lopez N, Gonzalez-Nieto L, Maxwell HS, Domingues A, Martins MA, Pham J, Weiskopf D, Altman J, Kallas EG, Andersen KG, Stevenson M, Lichtenberger P, Choe H, Whitehead SS, Sette A, Watkins DI.

PLoS Negl Trop Dis. 2017 Dec 21;11(12):e0006000. doi: 10.1371/journal.pntd.0006000. eCollection 2017 Dec.

9.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ.

Nat Protoc. 2017 Jun;12(6):1261-1276. doi: 10.1038/nprot.2017.066. Epub 2017 May 24.

10.

Zika virus evolution and spread in the Americas.

Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC.

Nature. 2017 Jun 15;546(7658):411-415. doi: 10.1038/nature22402. Epub 2017 May 24.

11.

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG.

Nature. 2017 Jun 15;546(7658):401-405. doi: 10.1038/nature22400. Epub 2017 May 24.

12.

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL.

Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. No abstract available.

13.
14.

Branch: an interactive, web-based tool for testing hypotheses and developing predictive models.

Gangavarapu K, Babji V, Meißner T, Su AI, Good BM.

Bioinformatics. 2016 Jul 1;32(13):2072-2074. doi: 10.1093/bioinformatics/btw117. Epub 2016 Mar 7.

15.

Impact of devascularization and tissue procurement on cell number and RNA integrity in prostatectomy tissue.

Payne Ondracek R, Cheng J, Gangavarapu KJ, Azabdaftari G, Woltz J, Brese E, Omilian A, Bshara W, Huss WJ, Mohler JL, Marshall JR.

Prostate. 2015 Dec;75(16):1910-5. doi: 10.1002/pros.23087. Epub 2015 Sep 9.

16.
17.

Interleukin-6 and JAK2/STAT3 signaling mediate the reversion of dexamethasone resistance after dexamethasone withdrawal in 7TD1 multiple myeloma cells.

Liu T, Fei Z, Gangavarapu KJ, Agbenowu S, Bhushan A, Lai JC, Daniels CK, Cao S.

Leuk Res. 2013 Oct;37(10):1322-8. doi: 10.1016/j.leukres.2013.06.026. Epub 2013 Jul 18.

18.

Human prostate side population cells demonstrate stem cell properties in recombination with urogenital sinus mesenchyme.

Foster BA, Gangavarapu KJ, Mathew G, Azabdaftari G, Morrison CD, Miller A, Huss WJ.

PLoS One. 2013;8(1):e55062. doi: 10.1371/journal.pone.0055062. Epub 2013 Jan 31.

19.

Apoptotic resistance exhibited by dexamethasone-resistant murine 7TD1 cells is controlled independently of interleukin-6 triggered signaling.

Gangavarapu KJ, Olbertz JL, Bhushan A, Lai JC, Daniels CK.

Apoptosis. 2008 Nov;13(11):1394-400. doi: 10.1007/s10495-008-0265-y.

PMID:
18819004

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