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Items: 42

1.

Correction: Discovery and validation of a prognostic proteomic signature for tuberculosis progression: A prospective cohort study.

Penn-Nicholson A, Hraha T, Thompson EG, Sterling D, Mbandi SK, Wall KM, Fisher M, Suliman S, Shankar S, Hanekom WA, Janjic N, Hatherill M, Kaufmann SHE, Sutherland J, Walzl G, De Groote MA, Ochsner U, Zak DE, Scriba TJ; ACS and GC6–74 cohort study groups.

PLoS Med. 2019 Jul 18;16(7):e1002880. doi: 10.1371/journal.pmed.1002880. eCollection 2019 Jul.

2.

Multinomial modelling of TB/HIV co-infection yields a robust predictive signature and generates hypotheses about the HIV+TB+ disease state.

Duffy FJ, Thompson EG, Scriba TJ, Zak DE.

PLoS One. 2019 Jul 15;14(7):e0219322. doi: 10.1371/journal.pone.0219322. eCollection 2019.

3.

Detection of Tuberculosis Recurrence, Diagnosis and Treatment Response by a Blood Transcriptomic Risk Signature in HIV-Infected Persons on Antiretroviral Therapy.

Darboe F, Mbandi SK, Naidoo K, Yende-Zuma N, Lewis L, Thompson EG, Duffy FJ, Fisher M, Filander E, van Rooyen M, Bilek N, Mabwe S, McKinnon LR, Chegou N, Loxton A, Walzl G, Tromp G, Padayatchi N, Govender D, Hatherill M, Karim SA, Zak DE, Penn-Nicholson A, Scriba TJ; SATVI Clinical Immunology Team.

Front Microbiol. 2019 Jun 26;10:1441. doi: 10.3389/fmicb.2019.01441. eCollection 2019.

4.

Discovery and validation of a prognostic proteomic signature for tuberculosis progression: A prospective cohort study.

Penn-Nicholson A, Hraha T, Thompson EG, Sterling D, Mbandi SK, Wall KM, Fisher M, Suliman S, Shankar S, Hanekom WA, Janjic N, Hatherill M, Kaufmann SHE, Sutherland J, Walzl G, De Groote MA, Ochsner U, Zak DE, Scriba TJ; ACS and GC6–74 cohort study groups.

PLoS Med. 2019 Apr 16;16(4):e1002781. doi: 10.1371/journal.pmed.1002781. eCollection 2019 Apr. Erratum in: PLoS Med. 2019 Jul 18;16(7):e1002880.

5.

Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome.

Duffy FJ, Weiner J 3rd, Hansen S, Tabb DL, Suliman S, Thompson E, Maertzdorf J, Shankar S, Tromp G, Parida S, Dover D, Axthelm MK, Sutherland JS, Dockrell HM, Ottenhoff THM, Scriba TJ, Picker LJ, Walzl G, Kaufmann SHE, Zak DE; GC6-74 Consortium.

Front Immunol. 2019 Mar 22;10:527. doi: 10.3389/fimmu.2019.00527. eCollection 2019.

6.

Batf2 differentially regulates tissue immunopathology in Type 1 and Type 2 diseases.

Guler R, Mpotje T, Ozturk M, Nono JK, Parihar SP, Chia JE, Abdel Aziz N, Hlaka L, Kumar S, Roy S, Penn-Nicholson A, Hanekom WA, Zak DE, Scriba TJ, Suzuki H, Brombacher F.

Mucosal Immunol. 2019 Mar;12(2):390-402. doi: 10.1038/s41385-018-0108-2. Epub 2018 Dec 12.

PMID:
30542107
7.

Metabolite changes in blood predict the onset of tuberculosis.

Weiner J 3rd, Maertzdorf J, Sutherland JS, Duffy FJ, Thompson E, Suliman S, McEwen G, Thiel B, Parida SK, Zyla J, Hanekom WA, Mohney RP, Boom WH, Mayanja-Kizza H, Howe R, Dockrell HM, Ottenhoff THM, Scriba TJ, Zak DE, Walzl G, Kaufmann SHE; GC6-74 consortium.

Nat Commun. 2018 Dec 6;9(1):5208. doi: 10.1038/s41467-018-07635-7.

8.

A Serum Circulating miRNA Signature for Short-Term Risk of Progression to Active Tuberculosis Among Household Contacts.

Duffy FJ, Thompson E, Downing K, Suliman S, Mayanja-Kizza H, Boom WH, Thiel B, Weiner Iii J, Kaufmann SHE, Dover D, Tabb DL, Dockrell HM, Ottenhoff THM, Tromp G, Scriba TJ, Zak DE, Walzl G; GC6-74 Consortium.

Front Immunol. 2018 Apr 13;9:661. doi: 10.3389/fimmu.2018.00661. eCollection 2018.

9.

Four-gene Pan-African Blood Signature Predicts Progression to Tuberculosis.

Suliman S, Thompson E, Sutherland J, Weiner Rd J, Ota MOC, Shankar S, Penn-Nicholson A, Thiel B, Erasmus M, Maertzdorf J, Duffy FJ, Hill PC, Hughes EJ, Stanley K, Downing K, Fisher ML, Valvo J, Parida SK, van der Spuy G, Tromp G, Adetifa IMO, Donkor S, Howe R, Mayanja-Kizza H, Boom WH, Dockrell H, Ottenhoff THM, Hatherill M, Aderem A, Hanekom WA, Scriba TJ, Kaufmann SH, Zak DE, Walzl G; GC6-74 and ACS cohort study groups.

Am J Respir Crit Care Med. 2018 Apr 6. doi: 10.1164/rccm.201711-2340OC. [Epub ahead of print]

10.

Considerations for biomarker-targeted intervention strategies for tuberculosis disease prevention.

Fiore-Gartland A, Carpp LN, Naidoo K, Thompson E, Zak DE, Self S, Churchyard G, Walzl G, Penn-Nicholson A, Scriba TJ, Hatherill M.

Tuberculosis (Edinb). 2018 Mar;109:61-68. doi: 10.1016/j.tube.2017.11.009. Epub 2017 Nov 22.

11.

Diagnostic performance of an optimized transcriptomic signature of risk of tuberculosis in cryopreserved peripheral blood mononuclear cells.

Darboe F, Mbandi SK, Thompson EG, Fisher M, Rodo M, van Rooyen M, Filander E, Bilek N, Mabwe S, Hatherill M, Zak DE, Penn-Nicholson A, Scriba TJ; SATVI Clinical Immunology Team.

Tuberculosis (Edinb). 2018 Jan;108:124-126. doi: 10.1016/j.tube.2017.11.001. Epub 2017 Nov 6. No abstract available.

PMID:
29523312
12.

Protein kinase C-delta (PKCδ), a marker of inflammation and tuberculosis disease progression in humans, is important for optimal macrophage killing effector functions and survival in mice.

Parihar SP, Ozturk M, Marakalala MJ, Loots DT, Hurdayal R, Beukes D, Van Reenen M, Zak DE, Mbandi SK, Darboe F, Penn-Nicholson A, Hanekom WA, Leitges M, Scriba TJ, Guler R, Brombacher F.

Mucosal Immunol. 2018 Mar;11(2):579-580. doi: 10.1038/mi.2017.108. Epub 2017 Dec 20.

PMID:
29346346
13.

Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine.

Hansen SG, Zak DE, Xu G, Ford JC, Marshall EE, Malouli D, Gilbride RM, Hughes CM, Ventura AB, Ainslie E, Randall KT, Selseth AN, Rundstrom P, Herlache L, Lewis MS, Park H, Planer SL, Turner JM, Fischer M, Armstrong C, Zweig RC, Valvo J, Braun JM, Shankar S, Lu L, Sylwester AW, Legasse AW, Messerle M, Jarvis MA, Amon LM, Aderem A, Alter G, Laddy DJ, Stone M, Bonavia A, Evans TG, Axthelm MK, Früh K, Edlefsen PT, Picker LJ.

Nat Med. 2018 Feb;24(2):130-143. doi: 10.1038/nm.4473. Epub 2018 Jan 15.

14.

Prospective Discrimination of Controllers From Progressors Early After Low-Dose Mycobacterium tuberculosis Infection of Cynomolgus Macaques using Blood RNA Signatures.

Thompson EG, Shankar S, Gideon HP, Braun J, Valvo J, Skinner JA, Aderem A, Flynn JL, Lin PL, Zak DE.

J Infect Dis. 2018 Mar 28;217(8):1318-1322. doi: 10.1093/infdis/jiy006.

15.

Innate transcriptional effects by adjuvants on the magnitude, quality, and durability of HIV envelope responses in NHPs.

Francica JR, Zak DE, Linde C, Siena E, Johnson C, Juraska M, Yates NL, Gunn B, De Gregorio E, Flynn BJ, Valiante NM, Malyala P, Barnett SW, Sarkar P, Singh M, Jain S, Ackerman M, Alam M, Ferrari G, Salazar A, Tomaras GD, O'Hagan DT, Aderem A, Alter G, Seder RA.

Blood Adv. 2017 Nov 17;1(25):2329-2342. doi: 10.1182/bloodadvances.2017011411. eCollection 2017 Nov 28. Erratum in: Blood Adv. 2018 Mar 13;2(5):516.

16.

Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease.

Scriba TJ, Penn-Nicholson A, Shankar S, Hraha T, Thompson EG, Sterling D, Nemes E, Darboe F, Suliman S, Amon LM, Mahomed H, Erasmus M, Whatney W, Johnson JL, Boom WH, Hatherill M, Valvo J, De Groote MA, Ochsner UA, Aderem A, Hanekom WA, Zak DE; other members of the ACS cohort study team.

PLoS Pathog. 2017 Nov 16;13(11):e1006687. doi: 10.1371/journal.ppat.1006687. eCollection 2017 Nov.

17.

Host blood RNA signatures predict the outcome of tuberculosis treatment.

Thompson EG, Du Y, Malherbe ST, Shankar S, Braun J, Valvo J, Ronacher K, Tromp G, Tabb DL, Alland D, Shenai S, Via LE, Warwick J, Aderem A, Scriba TJ, Winter J, Walzl G, Zak DE; Catalysis TB–Biomarker Consortium.

Tuberculosis (Edinb). 2017 Dec;107:48-58. doi: 10.1016/j.tube.2017.08.004. Epub 2017 Aug 12.

18.

Protein kinase C-delta (PKCδ), a marker of inflammation and tuberculosis disease progression in humans, is important for optimal macrophage killing effector functions and survival in mice.

Parihar SP, Ozturk M, Marakalala MJ, Loots DT, Hurdayal R, Maasdorp DB, Van Reenen M, Zak DE, Darboe F, Penn-Nicholson A, Hanekom WA, Leitges M, Scriba TJ, Guler R, Brombacher F.

Mucosal Immunol. 2018 Mar;11(2):496-511. doi: 10.1038/mi.2017.68. Epub 2017 Aug 9. Erratum in: Mucosal Immunol. 2017 Dec 20;:.

PMID:
28832027
19.

Systems analysis of protective immune responses to RTS,S malaria vaccination in humans.

Kazmin D, Nakaya HI, Lee EK, Johnson MJ, van der Most R, van den Berg RA, Ballou WR, Jongert E, Wille-Reece U, Ockenhouse C, Aderem A, Zak DE, Sadoff J, Hendriks J, Wrammert J, Ahmed R, Pulendran B.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2425-2430. doi: 10.1073/pnas.1621489114. Epub 2017 Feb 13.

20.

Safety and Immunogenicity of the Recombinant BCG Vaccine AERAS-422 in Healthy BCG-naïve Adults: A Randomized, Active-controlled, First-in-human Phase 1 Trial.

Hoft DF, Blazevic A, Selimovic A, Turan A, Tennant J, Abate G, Fulkerson J, Zak DE, Walker R, McClain B, Sadoff J, Scott J, Shepherd B, Ishmukhamedov J, Hokey DA, Dheenadhayalan V, Shankar S, Amon L, Navarro G, Podyminogin R, Aderem A, Barker L, Brennan M, Wallis RS, Gershon AA, Gershon MD, Steinberg S.

EBioMedicine. 2016 May;7:278-86. doi: 10.1016/j.ebiom.2016.04.010. Epub 2016 Apr 19.

21.

A blood RNA signature for tuberculosis disease risk: a prospective cohort study.

Zak DE, Penn-Nicholson A, Scriba TJ, Thompson E, Suliman S, Amon LM, Mahomed H, Erasmus M, Whatney W, Hussey GD, Abrahams D, Kafaar F, Hawkridge T, Verver S, Hughes EJ, Ota M, Sutherland J, Howe R, Dockrell HM, Boom WH, Thiel B, Ottenhoff THM, Mayanja-Kizza H, Crampin AC, Downing K, Hatherill M, Valvo J, Shankar S, Parida SK, Kaufmann SHE, Walzl G, Aderem A, Hanekom WA; ACS and GC6-74 cohort study groups.

Lancet. 2016 Jun 4;387(10035):2312-2322. doi: 10.1016/S0140-6736(15)01316-1. Epub 2016 Mar 24.

22.

Systems biology of immunity to MF59-adjuvanted versus nonadjuvanted trivalent seasonal influenza vaccines in early childhood.

Nakaya HI, Clutterbuck E, Kazmin D, Wang L, Cortese M, Bosinger SE, Patel NB, Zak DE, Aderem A, Dong T, Del Giudice G, Rappuoli R, Cerundolo V, Pollard AJ, Pulendran B, Siegrist CA.

Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1853-8. doi: 10.1073/pnas.1519690113. Epub 2016 Jan 11.

23.

Interleukin 27R regulates CD4+ T cell phenotype and impacts protective immunity during Mycobacterium tuberculosis infection.

Torrado E, Fountain JJ, Liao M, Tighe M, Reiley WW, Lai RP, Meintjes G, Pearl JE, Chen X, Zak DE, Thompson EG, Aderem A, Ghilardi N, Solache A, McKinstry KK, Strutt TM, Wilkinson RJ, Swain SL, Cooper AM.

J Exp Med. 2015 Aug 24;212(9):1449-63. doi: 10.1084/jem.20141520. Epub 2015 Aug 17.

24.

Systems integration of innate and adaptive immunity.

Zak DE, Aderem A.

Vaccine. 2015 Sep 29;33(40):5241-8. doi: 10.1016/j.vaccine.2015.05.098. Epub 2015 Jun 21. Review.

PMID:
26102534
25.

Antigen expression determines adenoviral vaccine potency independent of IFN and STING signaling.

Quinn KM, Zak DE, Costa A, Yamamoto A, Kastenmuller K, Hill BJ, Lynn GM, Darrah PA, Lindsay RW, Wang L, Cheng C, Nicosia A, Folgori A, Colloca S, Cortese R, Gostick E, Price DA, Gall JG, Roederer M, Aderem A, Seder RA.

J Clin Invest. 2015 Mar 2;125(3):1129-46. doi: 10.1172/JCI78280. Epub 2015 Feb 2.

26.

Systems-level analysis of innate immunity.

Zak DE, Tam VC, Aderem A.

Annu Rev Immunol. 2014;32:547-77. doi: 10.1146/annurev-immunol-032713-120254. Review.

27.

Cutting edge: Mouse NAIP1 detects the type III secretion system needle protein.

Rayamajhi M, Zak DE, Chavarria-Smith J, Vance RE, Miao EA.

J Immunol. 2013 Oct 15;191(8):3986-9. doi: 10.4049/jimmunol.1301549. Epub 2013 Sep 16.

28.

Caspase-11 protects against bacteria that escape the vacuole.

Aachoui Y, Leaf IA, Hagar JA, Fontana MF, Campos CG, Zak DE, Tan MH, Cotter PA, Vance RE, Aderem A, Miao EA.

Science. 2013 Feb 22;339(6122):975-8. doi: 10.1126/science.1230751. Epub 2013 Jan 24.

29.

Merck Ad5/HIV induces broad innate immune activation that predicts CD8⁺ T-cell responses but is attenuated by preexisting Ad5 immunity.

Zak DE, Andersen-Nissen E, Peterson ER, Sato A, Hamilton MK, Borgerding J, Krishnamurty AT, Chang JT, Adams DJ, Hensley TR, Salter AI, Morgan CA, Duerr AC, De Rosa SC, Aderem A, McElrath MJ.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):E3503-12. doi: 10.1073/pnas.1208972109. Epub 2012 Nov 14.

30.

Overcoming limitations in the systems vaccinology approach: a pathway for accelerated HIV vaccine development.

Zak DE, Aderem A.

Curr Opin HIV AIDS. 2012 Jan;7(1):58-63. doi: 10.1097/COH.0b013e32834ddd31. Review.

PMID:
22156843
31.

Systems analysis identifies an essential role for SHANK-associated RH domain-interacting protein (SHARPIN) in macrophage Toll-like receptor 2 (TLR2) responses.

Zak DE, Schmitz F, Gold ES, Diercks AH, Peschon JJ, Valvo JS, Niemistö A, Podolsky I, Fallen SG, Suen R, Stolyar T, Johnson CD, Kennedy KA, Hamilton MK, Siggs OM, Beutler B, Aderem A.

Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11536-41. doi: 10.1073/pnas.1107577108. Epub 2011 Jun 27.

32.

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.

Ramsey SA, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I.

Bioinformatics. 2010 Sep 1;26(17):2071-5. doi: 10.1093/bioinformatics/btq405. Epub 2010 Jul 27.

33.

A systems view of host defense.

Zak DE, Aderem A.

Nat Biotechnol. 2009 Nov;27(11):999-1001. doi: 10.1038/nbt1109-999. No abstract available.

34.

Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals.

Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A.

Nat Immunol. 2009 Apr;10(4):437-43. doi: 10.1038/ni.1721. Epub 2009 Mar 8.

35.

Systems biology of innate immunity.

Zak DE, Aderem A.

Immunol Rev. 2009 Jan;227(1):264-82. doi: 10.1111/j.1600-065X.2008.00721.x. Review.

36.

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.

Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I.

PLoS Comput Biol. 2008 Mar 21;4(3):e1000021. doi: 10.1371/journal.pcbi.1000021. Erratum in: PLoS Comput Biol. 2008 Mar;4(3). doi: 10.1371/annotation/1c55be5f-ecd7-49be-91c1-91881be60297. PLoS Comput Biol. 2008 Mar;4(3). doi: 10.1371/annotation/e14ad837-e5ff-4bd5-a5f2-f32e784d75a2.

37.

Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach.

Yalamanchili N, Zak DE, Ogunnaike BA, Schwaber JS, Kriete A, Kholodenko BN.

Syst Biol (Stevenage). 2006 Jul;153(4):236-46.

38.

Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling.

Zak DE, Hao H, Vadigepalli R, Miller GM, Ogunnaike BA, Schwaber JS.

Genome Biol. 2006;7(6):R48.

39.

Modeling the VPAC2-activated cAMP/PKA signaling pathway: from receptor to circadian clock gene induction.

Hao H, Zak DE, Sauter T, Schwaber J, Ogunnaike BA.

Biophys J. 2006 Mar 1;90(5):1560-71. Epub 2005 Dec 9.

40.

Continuous-time identification of gene expression models.

Zak DE, Pearson RK, Vadigepalli R, Gonye GE, Schwaber JS, Doyle FJ 3rd.

OMICS. 2003 Winter;7(4):373-86.

PMID:
14683610
42.

PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification.

Vadigepalli R, Chakravarthula P, Zak DE, Schwaber JS, Gonye GE.

OMICS. 2003 Fall;7(3):235-52.

PMID:
14583114

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