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Items: 1 to 50 of 84

1.

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis.

Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA.

MBio. 2018 May 8;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18.

2.

Microarrays-Enabled Hypothesis Generation: The Suspect Role of FNBP-1 in Neuropsychiatric Pathogenesis Associated with HIV and/or HCV Infection.

Katsounas A, Wilting KR, Lempicki RA, Schlaak JF, Gerken G.

J AIDS Clin Res. 2016 Dec;7(12). pii: 641. doi: 10.4172/2155-6113.1000641. Epub 2016 Dec 7.

3.

Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads.

Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X, Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang DW.

BioData Min. 2016 Apr 5;9:13. doi: 10.1186/s13040-016-0090-8. eCollection 2016.

4.

Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.

Huang DW, Raley C, Jiang MK, Zheng X, Liang D, Rehman MT, Highbarger HC, Jiao X, Sherman B, Ma L, Chen X, Skelly T, Troyer J, Stephens R, Imamichi T, Pau A, Lempicki RA, Tran B, Nissley D, Lane HC, Dewar RL.

J Data Mining Genomics Proteomics. 2016 Jan;7(1). pii: 182. Epub 2015 Nov 8.

5.

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.

Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA.

Nat Commun. 2016 Feb 22;7:10740. doi: 10.1038/ncomms10740.

6.
7.

Characterization of chemokine and chemokine receptor expression during Pneumocystis infection in healthy and immunodeficient mice.

Bishop LR, Lionakis MS, Sassi M, Murphy PM, Hu X, Huang da W, Sherman B, Qiu J, Yang J, Lempicki RA, Kovacs JA.

Microbes Infect. 2015 Sep;17(9):638-50. doi: 10.1016/j.micinf.2015.05.008. Epub 2015 Jun 5.

8.

Hepatitis C-associated mixed cryoglobulinemic vasculitis induces differential gene expression in peripheral mononuclear cells.

Sidharthan S, Kim CW, Murphy AA, Zhang X, Yang J, Lempicki RA, Sneller MC, Kottilil S.

Front Immunol. 2014 May 27;5:248. doi: 10.3389/fimmu.2014.00248. eCollection 2014.

9.

Interferon stimulated exonuclease gene 20 kDa links psychiatric events to distinct hepatitis C virus responses in human immunodeficiency virus positive patients.

Katsounas A, Rasimas JJ, Schlaak JF, Lempicki RA, Rosenstein DL, Kottilil S.

J Med Virol. 2014 Aug;86(8):1323-31. doi: 10.1002/jmv.23956. Epub 2014 Apr 30.

10.

Clearance of Pneumocystis murina infection is not dependent on MyD88.

Ripamonti C, Bishop LR, Yang J, Lempicki RA, Kovacs JA.

Microbes Infect. 2014 Jun;16(6):522-7. doi: 10.1016/j.micinf.2014.03.005. Epub 2014 Mar 25.

11.

Lifespan of effector memory CD4+ T cells determined by replication-incompetent integrated HIV-1 provirus.

Imamichi H, Natarajan V, Adelsberger JW, Rehm CA, Lempicki RA, Das B, Hazen A, Imamichi T, Lane HC.

AIDS. 2014 May 15;28(8):1091-9. doi: 10.1097/QAD.0000000000000223.

PMID:
24492253
12.

Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies.

Migliano AB, Romero IG, Metspalu M, Leavesley M, Pagani L, Antao T, Huang DW, Sherman BT, Siddle K, Scholes C, Hudjashov G, Kaitokai E, Babalu A, Belatti M, Cagan A, Hopkinshaw B, Shaw C, Nelis M, Metspalu E, Mägi R, Lempicki RA, Villems R, Lahr MM, Kivisild T.

Hum Biol. 2013 Feb-Jun;85(1-3):251-84.

PMID:
24297229
13.

A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.

Jiao X, Zheng X, Ma L, Kutty G, Gogineni E, Sun Q, Sherman BT, Hu X, Jones K, Raley C, Tran B, Munroe DJ, Stephens R, Liang D, Imamichi T, Kovacs JA, Lempicki RA, Huang DW.

J Data Mining Genomics Proteomics. 2013 Jul 31;4(3). pii: 16008.

14.

The HIV-1 envelope protein gp120 impairs B cell proliferation by inducing TGF-β1 production and FcRL4 expression.

Jelicic K, Cimbro R, Nawaz F, Huang da W, Zheng X, Yang J, Lempicki RA, Pascuccio M, Van Ryk D, Schwing C, Hiatt J, Okwara N, Wei D, Roby G, David A, Hwang IY, Kehrl JH, Arthos J, Cicala C, Fauci AS.

Nat Immunol. 2013 Dec;14(12):1256-65. doi: 10.1038/ni.2746. Epub 2013 Oct 27.

15.

Interleukin-2 inhibits HIV-1 replication in some human T cell lymphotrophic virus-1-infected cell lines via the induction and incorporation of APOBEC3G into the virion.

Oguariri RM, Dai L, Adelsberger JW, Rupert A, Stevens R, Yang J, Huang D, Lempicki RA, Zhou M, Baseler MW, Lane HC, Imamichi T.

J Biol Chem. 2013 Jun 14;288(24):17812-22. doi: 10.1074/jbc.M113.468975. Epub 2013 May 2.

16.

High interferon-stimulated gene ISG-15 expression affects HCV treatment outcome in patients co-infected with HIV and HCV.

Katsounas A, Hubbard JJ, Wang CH, Zhang X, Dou D, Shivakumar B, Winter S, Schlaak JF, Lempicki RA, Masur H, Polis M, Kottilil S, Osinusi A.

J Med Virol. 2013 Jun;85(6):959-63. doi: 10.1002/jmv.23576.

PMID:
23588721
17.

Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties.

Swaminathan S, Hu X, Zheng X, Kriga Y, Shetty J, Zhao Y, Stephens R, Tran B, Baseler MW, Yang J, Lempicki RA, Huang D, Lane HC, Imamichi T.

Biochem Biophys Res Commun. 2013 May 3;434(2):228-34. doi: 10.1016/j.bbrc.2013.03.046. Epub 2013 Mar 25.

18.

Interleukin-27 is a potent inhibitor of cis HIV-1 replication in monocyte-derived dendritic cells via a type I interferon-independent pathway.

Chen Q, Swaminathan S, Yang D, Dai L, Sui H, Yang J, Hornung RL, Wang Y, Huang da W, Hu X, Lempicki RA, Imamichi T.

PLoS One. 2013;8(3):e59194. doi: 10.1371/journal.pone.0059194. Epub 2013 Mar 20.

19.

IL-27 inhibits HIV-1 infection in human macrophages by down-regulating host factor SPTBN1 during monocyte to macrophage differentiation.

Dai L, Lidie KB, Chen Q, Adelsberger JW, Zheng X, Huang D, Yang J, Lempicki RA, Rehman T, Dewar RL, Wang Y, Hornung RL, Canizales KA, Lockett SJ, Lane HC, Imamichi T.

J Exp Med. 2013 Mar 11;210(3):517-34. doi: 10.1084/jem.20120572. Epub 2013 Mar 4.

20.

Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis.

Ma L, Huang DW, Cuomo CA, Sykes S, Fantoni G, Das B, Sherman BT, Yang J, Huber C, Xia Y, Davey E, Kutty G, Bishop L, Sassi M, Lempicki RA, Kovacs JA.

FASEB J. 2013 May;27(5):1962-72. doi: 10.1096/fj.12-224444. Epub 2013 Feb 7.

21.

Distinct and overlapping genomic profiles and antiviral effects of Interferon-λ and -α on HCV-infected and noninfected hepatoma cells.

Kohli A, Zhang X, Yang J, Russell RS, Donnelly RP, Sheikh F, Sherman A, Young H, Imamichi T, Lempicki RA, Masur H, Kottilil S.

J Viral Hepat. 2012 Dec;19(12):843-53. doi: 10.1111/j.1365-2893.2012.01610.x. Epub 2012 May 27.

22.

Differential gene and microRNA expression between etoposide resistant and etoposide sensitive MCF7 breast cancer cell lines.

Moitra K, Im K, Limpert K, Borsa A, Sawitzke J, Robey R, Yuhki N, Savan R, Huang da W, Lempicki RA, Bates S, Dean M.

PLoS One. 2012;7(9):e45268. doi: 10.1371/journal.pone.0045268. Epub 2012 Sep 18.

23.

The CD8+ HLA-DR+ T cells expanded in HIV-1 infection are qualitatively identical to those from healthy controls.

Imamichi H, Lempicki RA, Adelsberger JW, Hasley RB, Rosenberg A, Roby G, Rehm CA, Nelson A, Krishnan S, Pavlick M, Woods CJ, Baseler MW, Lane HC.

Eur J Immunol. 2012 Oct;42(10):2608-20. doi: 10.1002/eji.201142046. Epub 2012 Aug 6.

24.

Gene expression profiles predict emergence of psychiatric adverse events in HIV/HCV-coinfected patients on interferon-based HCV therapy.

Rasimas J, Katsounas A, Raza H, Murphy AA, Yang J, Lempicki RA, Osinusi A, Masur H, Polis M, Kottilil S, Rosenstein D.

J Acquir Immune Defic Syndr. 2012 Jul 1;60(3):273-81. doi: 10.1097/QAI.0b013e31824c17c4. Erratum in: J Acquir Immune Defic Syndr. 2012 Aug 15;60(5):e122.

25.

Cytokine/chemokine patterns connect host and viral characteristics with clinics during chronic hepatitis C.

Katsounas A, Trippler M, Kottilil S, Lempicki RA, Gerken G, Schlaak JF.

Eur J Med Res. 2012 May 11;17:9. doi: 10.1186/2047-783X-17-9.

26.

DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

Jiao X, Sherman BT, Huang da W, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Bioinformatics. 2012 Jul 1;28(13):1805-6. doi: 10.1093/bioinformatics/bts251. Epub 2012 Apr 27.

27.

HIV infection and antiretroviral therapy have divergent effects on mitochondria in adipose tissue.

Morse CG, Voss JG, Rakocevic G, McLaughlin M, Vinton CL, Huber C, Hu X, Yang J, Huang da W, Logun C, Danner RL, Rangel ZG, Munson PJ, Orenstein JM, Rushing EJ, Lempicki RA, Dalakas MC, Kovacs JA.

J Infect Dis. 2012 Jun 15;205(12):1778-87. doi: 10.1093/infdis/jis101. Epub 2012 Apr 3.

28.

Host gene expression changes correlating with anti-HIV-1 effects in human subjects after treatment with peginterferon Alfa-2a.

Hubbard JJ, Greenwell-Wild T, Barrett L, Yang J, Lempicki RA, Wahl SM, Asmuth DM, Murphy RL, Pollard RB, Kottilil S.

J Infect Dis. 2012 May 1;205(9):1443-7. doi: 10.1093/infdis/jis211. Epub 2012 Mar 26.

29.

CCL5 mRNA is a marker for early fibrosis in chronic hepatitis C and is regulated by interferon-α therapy and toll-like receptor 3 signalling.

Katsounas A, Trippler M, Wang B, Polis M, Lempicki RA, Kottilil S, Gerken G, Schlaak JF.

J Viral Hepat. 2012 Feb;19(2):128-37. doi: 10.1111/j.1365-2893.2011.01503.x. Epub 2011 Nov 21.

PMID:
22239502
30.

Interleukin-27 induces interferon-inducible genes: analysis of gene expression profiles using Affymetrix microarray and DAVID.

Imamichi T, Yang J, Huang da W, Sherman B, Lempicki RA.

Methods Mol Biol. 2012;820:25-53. doi: 10.1007/978-1-61779-439-1_3.

PMID:
22131024
31.

CCL5: a double-edged sword in host defense against the hepatitis C virus.

Katsounas A, Schlaak JF, Lempicki RA.

Int Rev Immunol. 2011 Oct-Dec;30(5-6):366-78. doi: 10.3109/08830185.2011.593105. Review.

PMID:
22053974
32.

LIM kinase 1 - dependent cofilin 1 pathway and actin dynamics mediate nuclear retinoid receptor function in T lymphocytes.

Ishaq M, Lin BR, Bosche M, Zheng X, Yang J, Huang D, Lempicki RA, Aguilera-Gutierrez A, Natarajan V.

BMC Mol Biol. 2011 Sep 16;12:41. doi: 10.1186/1471-2199-12-41. Erratum in: BMC Mol Biol. 2012;13:14. Aguilera-Gutierrez, Angelica [added].

33.

Altered expression of SHIP, a Toll-like receptor pathway inhibitor, is associated with the severity of liver fibrosis in chronic hepatitis C virus infection.

Katsounas A, Trippler M, Kottilil S, Lempicki RA, Gerken G, Schlaak JF.

J Infect Dis. 2011 Oct 15;204(8):1181-5. doi: 10.1093/infdis/jir500.

34.

Twice-weekly pegylated interferon-α-2a and ribavirin results in superior viral kinetics in HIV/hepatitis C virus co-infected patients compared to standard therapy.

Murphy AA, Herrmann E, Osinusi AO, Wu L, Sachau W, Lempicki RA, Yang J, Chung TL, Wood BJ, Haagmans BL, Kottilil S, Polis MA.

AIDS. 2011 Jun 1;25(9):1179-87. doi: 10.1097/QAD.0b013e3283471d53. Erratum in: AIDS. 2011 Nov 13;25(17):2195. Chung, Tei L [corrected to Chung, Tje L].

35.

Differential effects of HIV viral load and CD4 count on proliferation of naive and memory CD4 and CD8 T lymphocytes.

Srinivasula S, Lempicki RA, Adelsberger JW, Huang CY, Roark J, Lee PI, Rupert A, Stevens R, Sereti I, Lane HC, Di Mascio M, Kovacs JA.

Blood. 2011 Jul 14;118(2):262-70. doi: 10.1182/blood-2011-02-335174. Epub 2011 May 11.

36.

Cutting edge: Ku70 is a novel cytosolic DNA sensor that induces type III rather than type I IFN.

Zhang X, Brann TW, Zhou M, Yang J, Oguariri RM, Lidie KB, Imamichi H, Huang DW, Lempicki RA, Baseler MW, Veenstra TD, Young HA, Lane HC, Imamichi T.

J Immunol. 2011 Apr 15;186(8):4541-5. doi: 10.4049/jimmunol.1003389. Epub 2011 Mar 11.

37.

Gene duplications in prokaryotes can be associated with environmental adaptation.

Bratlie MS, Johansen J, Sherman BT, Huang da W, Lempicki RA, Drabløs F.

BMC Genomics. 2010 Oct 20;11:588. doi: 10.1186/1471-2164-11-588.

38.

Pre-gastrula expression of zebrafish extraembryonic genes.

Hong SK, Levin CS, Brown JL, Wan H, Sherman BT, Huang da W, Lempicki RA, Feldman B.

BMC Dev Biol. 2010 Apr 27;10:42. doi: 10.1186/1471-213X-10-42.

39.

Safety, tolerability, and mechanisms of antiretroviral activity of pegylated interferon Alfa-2a in HIV-1-monoinfected participants: a phase II clinical trial.

Asmuth DM, Murphy RL, Rosenkranz SL, Lertora JJ, Kottilil S, Cramer Y, Chan ES, Schooley RT, Rinaldo CR, Thielman N, Li XD, Wahl SM, Shore J, Janik J, Lempicki RA, Simpson Y, Pollard RB; AIDS Clinical Trials Group A5192 Team.

J Infect Dis. 2010 Jun 1;201(11):1686-96. doi: 10.1086/652420.

40.

Defective plasmacytoid dendritic cell-NK cell cross-talk in HIV infection.

Reitano KN, Kottilil S, Gille CM, Zhang X, Yan M, O'Shea MA, Roby G, Hallahan CW, Yang J, Lempicki RA, Arthos J, Fauci AS.

AIDS Res Hum Retroviruses. 2009 Oct;25(10):1029-37. doi: 10.1089/aid.2008.0311.

41.

Altered regulation of extrinsic apoptosis pathway in HCV-infected HCC cells enhances susceptibility to mapatumumab-induced apoptosis.

Zhang X, Frank AC, Gille CM, Daucher M, Kabat J, Becker S, Lempicki RA, Cortez KJ, Polis MA, Subramanian GM, Kottilil S.

Hepatol Res. 2009 Dec;39(12):1178-89. doi: 10.1111/j.1872-034X.2009.00568.x. Epub 2009 Sep 25.

PMID:
19788693
42.

Extracting biological meaning from large gene lists with DAVID.

Huang da W, Sherman BT, Zheng X, Yang J, Imamichi T, Stephens R, Lempicki RA.

Curr Protoc Bioinformatics. 2009 Sep;Chapter 13:Unit 13.11. doi: 10.1002/0471250953.bi1311s27.

PMID:
19728287
43.

Association of interleukin-15-induced peripheral immune activation with hepatic stellate cell activation in persons coinfected with hepatitis C virus and HIV.

Allison RD, Katsounas A, Koziol DE, Kleiner DE, Alter HJ, Lempicki RA, Wood B, Yang J, Fullmer B, Cortez KJ, Polis MA, Kottilil S.

J Infect Dis. 2009 Aug 15;200(4):619-23. doi: 10.1086/600107.

44.

Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients.

García-Piñeres AJ, Hildesheim A, Dodd L, Kemp TJ, Yang J, Fullmer B, Harro C, Lowy DR, Lempicki RA, Pinto LA.

J Immunol. 2009 Feb 1;182(3):1706-29.

45.

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Huang da W, Sherman BT, Lempicki RA.

Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.

PMID:
19131956
46.

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Huang da W, Sherman BT, Lempicki RA.

Nucleic Acids Res. 2009 Jan;37(1):1-13. doi: 10.1093/nar/gkn923. Epub 2008 Nov 25.

47.

DAVID gene ID conversion tool.

Huang da W, Sherman BT, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Bioinformation. 2008 Jul 30;2(10):428-30.

48.

CD4 T cell survival after intermittent interleukin-2 therapy is predictive of an increase in the CD4 T cell count of HIV-infected patients.

Read SW, Lempicki RA, Di Mascio M, Srinivasula S, Burke R, Sachau W, Bosche M, Adelsberger JW, Sereti I, Davey RT Jr, Tavel JA, Huang CY, Issaq HJ, Fox SD, Lane H, Kovacs JA.

J Infect Dis. 2008 Sep 15;198(6):843-50. doi: 10.1086/591250.

49.

Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach.

Suzman DL, McLaughlin M, Hu Z, Kleiner DE, Wood B, Lempicki RA, Mican JM, Suffredini A, Masur H, Polis MA, Kottilil S.

AIDS. 2008 Jul 31;22(12):1433-9. doi: 10.1097/QAD.0b013e328304dfe7.

50.

HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells.

Arthos J, Cicala C, Martinelli E, Macleod K, Van Ryk D, Wei D, Xiao Z, Veenstra TD, Conrad TP, Lempicki RA, McLaughlin S, Pascuccio M, Gopaul R, McNally J, Cruz CC, Censoplano N, Chung E, Reitano KN, Kottilil S, Goode DJ, Fauci AS.

Nat Immunol. 2008 Mar;9(3):301-9. doi: 10.1038/ni1566. Epub 2008 Feb 10.

PMID:
18264102

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