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Items: 19

1.

Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients.

Applebaum MA, Jha AR, Kao C, Hernandez KM, DeWane G, Salwen HR, Chlenski A, Dobratic M, Mariani CJ, Godley LA, Prabhakar N, White K, Stranger BE, Cohn SL.

Oncotarget. 2016 Nov 22;7(47):76816-76826. doi: 10.18632/oncotarget.12713.

2.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JT, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D.

Nature. 2016 Oct 13;538(7624):201-206. doi: 10.1038/nature18964. Epub 2016 Sep 21.

3.

Shared Genetic Signals of Hypoxia Adaptation in Drosophila and in High-Altitude Human Populations.

Jha AR, Zhou D, Brown CD, Kreitman M, Haddad GG, White KP.

Mol Biol Evol. 2016 Feb;33(2):501-17. doi: 10.1093/molbev/msv248. Epub 2015 Nov 17.

4.

Global diversity, population stratification, and selection of human copy-number variation.

Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE.

Science. 2015 Sep 11;349(6253):aab3761. doi: 10.1126/science.aab3761. Epub 2015 Aug 6.

5.

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

Jha AR, Miles CM, Lippert NR, Brown CD, White KP, Kreitman M.

Mol Biol Evol. 2015 Oct;32(10):2616-32. doi: 10.1093/molbev/msv136. Epub 2015 Jun 3.

6.

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GB, Cali F, Churnosov M, Cole DE, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J.

Nature. 2014 Sep 18;513(7518):409-13. doi: 10.1038/nature13673.

7.

miR-9a minimizes the phenotypic impact of genomic diversity by buffering a transcription factor.

Cassidy JJ, Jha AR, Posadas DM, Giri R, Venken KJ, Ji J, Jiang H, Bellen HJ, White KP, Carthew RW.

Cell. 2013 Dec 19;155(7):1556-67. doi: 10.1016/j.cell.2013.10.057. Erratum in: Cell. 2014 Apr 24;157(3):753.

8.

Associations between antibodies to a panel of Plasmodium falciparum specific antigens and response to sub-optimal antimalarial therapy in Kampala, Uganda.

Keh CE, Jha AR, Nzarubara B, Lanar DE, Dutta S, Theisen M, Rosenthal PJ, Dorsey G, Nixon DF, Greenhouse B.

PLoS One. 2012;7(12):e52571. doi: 10.1371/journal.pone.0052571. Epub 2012 Dec 19.

9.

Tim-3 marks human natural killer cell maturation and suppresses cell-mediated cytotoxicity.

Ndhlovu LC, Lopez-Vergès S, Barbour JD, Jones RB, Jha AR, Long BR, Schoeffler EC, Fujita T, Nixon DF, Lanier LL.

Blood. 2012 Apr 19;119(16):3734-43. doi: 10.1182/blood-2011-11-392951. Epub 2012 Mar 1.

10.

An Aboriginal Australian genome reveals separate human dispersals into Asia.

Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E.

Science. 2011 Oct 7;334(6052):94-8. doi: 10.1126/science.1211177. Epub 2011 Sep 22.

11.

Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans.

Jha AR, Nixon DF, Rosenberg MG, Martin JN, Deeks SG, Hudson RR, Garrison KE, Pillai SK.

PLoS One. 2011;6(5):e20234. doi: 10.1371/journal.pone.0020234. Epub 2011 May 25.

12.

HTLV-1 tax specific CD8+ T cells express low levels of Tim-3 in HTLV-1 infection: implications for progression to neurological complications.

Ndhlovu LC, Leal FE, Hasenkrug AM, Jha AR, Carvalho KI, Eccles-James IG, Bruno FR, Vieira RG, York VA, Chew GM, Jones RB, Tanaka Y, Neto WK, Sanabani SS, Ostrowski MA, Segurado AC, Nixon DF, Kallas EG.

PLoS Negl Trop Dis. 2011 Apr 26;5(4):e1030. doi: 10.1371/journal.pntd.0001030.

13.

IL-2 immunotherapy to recently HIV-1 infected adults maintains the numbers of IL-17 expressing CD4+ T (T(H)17) cells in the periphery.

Ndhlovu LC, Sinclair E, Epling L, Tan QX, Ho T, Jha AR, Eccles-James I, Tincati C, Levy JA, Nixon DF, Hecht FM, Barbour JD.

J Clin Immunol. 2010 Sep;30(5):681-92. doi: 10.1007/s10875-010-9432-3. Epub 2010 Jun 23.

14.

A novel human CD4+ T-cell inducer subset with potent immunostimulatory properties.

Ndhlovu LC, Leal FE, Eccles-James IG, Jha AR, Lanteri M, Norris PJ, Barbour JD, Wachter DJ, Andersson J, Taskén K, Torheim EA, Aandahl EM, Kallas EG, Nixon DF.

Eur J Immunol. 2010 Jan;40(1):134-41. doi: 10.1002/eji.200939258.

15.

Lower numbers of circulating Natural Killer T (NK T) cells in individuals with human T lymphotropic virus type 1 (HTLV-1) associated neurological disease.

Ndhlovu LC, Snyder-Cappione JE, Carvalho KI, Leal FE, Loo CP, Bruno FR, Jha AR, Devita D, Hasenkrug AM, Barbosa HM, Segurado AC, Nixon DF, Murphy EL, Kallas EG.

Clin Exp Immunol. 2009 Dec;158(3):294-9. doi: 10.1111/j.1365-2249.2009.04019.x. Epub 2009 Sep 2.

16.

Cross-sectional dating of novel haplotypes of HERV-K 113 and HERV-K 115 indicate these proviruses originated in Africa before Homo sapiens.

Jha AR, Pillai SK, York VA, Sharp ER, Storm EC, Wachter DJ, Martin JN, Deeks SG, Rosenberg MG, Nixon DF, Garrison KE.

Mol Biol Evol. 2009 Nov;26(11):2617-26. doi: 10.1093/molbev/msp180. Epub 2009 Aug 10.

17.

Interleukin-10-secreting T cells define a suppressive subset within the HIV-1-specific T-cell population.

Torheim EA, Ndhlovu LC, Pettersen FO, Larsen TL, Jha AR, Torgersen KM, Kvale D, Nixon DF, Taskén K, Aandahl EM.

Eur J Immunol. 2009 May;39(5):1280-7. doi: 10.1002/eji.200839002.

18.

Tim-3 expression defines a novel population of dysfunctional T cells with highly elevated frequencies in progressive HIV-1 infection.

Jones RB, Ndhlovu LC, Barbour JD, Sheth PM, Jha AR, Long BR, Wong JC, Satkunarajah M, Schweneker M, Chapman JM, Gyenes G, Vali B, Hyrcza MD, Yue FY, Kovacs C, Sassi A, Loutfy M, Halpenny R, Persad D, Spotts G, Hecht FM, Chun TW, McCune JM, Kaul R, Rini JM, Nixon DF, Ostrowski MA.

J Exp Med. 2008 Nov 24;205(12):2763-79. doi: 10.1084/jem.20081398. Epub 2008 Nov 10.

19.

Suppression of HIV-1 plasma viral load below detection preserves IL-17 producing T cells in HIV-1 infection.

Ndhlovu LC, Chapman JM, Jha AR, Snyder-Cappione JE, Pagán M, Leal FE, Boland BS, Norris PJ, Rosenberg MG, Nixon DF.

AIDS. 2008 May 11;22(8):990-2. doi: 10.1097/QAD.0b013e3282ff884e.

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