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Daniel E. Zak, Ph.D. - Publications

Affiliations: 
2005 University of Delaware, Newark, DE, United States 
Area:
Civil Engineering
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40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Penn-Nicholson A, Mbandi SK, Thompson E, Mendelsohn SC, Suliman S, Chegou NN, Malherbe ST, Darboe F, Erasmus M, Hanekom WA, Bilek N, Fisher M, Kaufmann SHE, Winter J, Murphy M, ... ... Zak D, et al. RISK6, a 6-gene transcriptomic signature of TB disease risk, diagnosis and treatment response. Scientific Reports. 10: 8629. PMID 32451443 DOI: 10.1038/S41598-020-65043-8  0.34
2020 Du Y, Thompson EG, Muller J, Valvo J, Braun J, Shankar S, van den Berg RA, Jongert E, Dover D, Sadoff J, Hendriks J, Gardner MJ, Ballou WR, Regules JA, van der Most R, ... ... Zak DE, et al. The Ratiometric Transcript Signature MX2/GPR183 Is Consistently Associated With RTS,S-Mediated Protection Against Controlled Human Malaria Infection. Frontiers in Immunology. 11: 669. PMID 32411130 DOI: 10.3389/Fimmu.2020.00669  0.312
2019 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, ... ... Zak DE, et al. Detection of Tuberculosis Recurrence, Diagnosis and Treatment Response by a Blood Transcriptomic Risk Signature in HIV-Infected Persons on Antiretroviral Therapy. Frontiers in Microbiology. 10: 1441. PMID 31297103 DOI: 10.3389/Fmicb.2019.01441  0.32
2019 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, ... ... Zak DE, et al. Discovery and validation of a prognostic proteomic signature for tuberculosis progression: A prospective cohort study. Plos Medicine. 16: e1002781. PMID 30990820 DOI: 10.1371/Journal.Pmed.1002781  0.323
2019 Duffy FJ, Weiner J, 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, ... ... Zak DE, et al. Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome. Frontiers in Immunology. 10: 527. PMID 30967866 DOI: 10.3389/Fimmu.2019.00527  0.37
2018 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, et al. Batf2 differentially regulates tissue immunopathology in Type 1 and Type 2 diseases. Mucosal Immunology. PMID 30542107 DOI: 10.1038/S41385-018-0108-2  0.33
2018 Weiner J, 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, ... ... Zak DE, et al. Metabolite changes in blood predict the onset of tuberculosis. Nature Communications. 9: 5208. PMID 30523338 DOI: 10.1038/S41467-018-07635-7  0.332
2018 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, ... ... Zak DE, et al. Four-gene Pan-African Blood Signature Predicts Progression to Tuberculosis. American Journal of Respiratory and Critical Care Medicine. PMID 29624071 DOI: 10.1164/Rccm.201711-2340Oc  0.342
2018 Fiore-Gartland A, Carpp LN, Naidoo K, Thompson E, Zak DE, Self S, Churchyard G, Walzl G, Penn-Nicholson A, Scriba TJ, Hatherill M. Considerations for biomarker-targeted intervention strategies for tuberculosis disease prevention. Tuberculosis (Edinburgh, Scotland). 109: 61-68. PMID 29559122 DOI: 10.1016/J.Tube.2017.11.009  0.324
2018 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, et al. Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine. Nature Medicine. PMID 29334373 DOI: 10.1038/Nm.4473  0.343
2018 Thompson EG, Shankar S, Gideon HP, Braun J, Valvo J, Skinner J, Aderem A, Flynn JL, Lin PL, Zak DE. Blood RNA signatures prospectively discriminate controllers from progressors early after low-dose M. tuberculosis infection of cynomolgus macaques. The Journal of Infectious Diseases. PMID 29325117 DOI: 10.1093/Infdis/Jiy006  0.366
2017 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, et al. Innate transcriptional effects by adjuvants on the magnitude, quality, and durability of HIV envelope responses in NHPs. Blood Advances. 1: 2329-2342. PMID 29296883 DOI: 10.1182/Bloodadvances.2017011411  0.356
2017 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, ... ... Zak DE, et al. Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease. Plos Pathogens. 13: e1006687. PMID 29145483 DOI: 10.1371/Journal.Ppat.1006687  0.304
2017 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, ... ... Zak DE, et al. Host blood RNA signatures predict the outcome of tuberculosis treatment. Tuberculosis (Edinburgh, Scotland). 107: 48-58. PMID 29050771 DOI: 10.1016/J.Tube.2017.08.004  0.345
2017 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, et al. 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. Mucosal Immunology. PMID 28832027 DOI: 10.1038/Mi.2017.68  0.313
2017 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, et al. Systems analysis of protective immune responses to RTS,S malaria vaccination in humans. Proceedings of the National Academy of Sciences of the United States of America. PMID 28193898 DOI: 10.1073/Pnas.1621489114  0.337
2017 Walzl G, Chegou N, Malherbe S, Hatherill M, Scriba TJ, Zak DE, Barry CE, Kaufmann SHE. Policy-Driven Interventions: Tuberculosis Bmj Global Health. 2. DOI: 10.1136/Bmjgh-2016-000260.5  0.334
2016 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, et al. A blood RNA signature for tuberculosis disease risk: a prospective cohort study. Lancet (London, England). PMID 27017310 DOI: 10.1016/S0140-6736(15)01316-1  0.334
2016 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, et al. Systems biology of immunity to MF59-adjuvanted versus nonadjuvanted trivalent seasonal influenza vaccines in early childhood. Proceedings of the National Academy of Sciences of the United States of America. 113: 1853-8. PMID 26755593 DOI: 10.1073/Pnas.1519690113  0.321
2015 Zak DE, Aderem A. Systems integration of innate and adaptive immunity. Vaccine. 33: 5241-8. PMID 26102534 DOI: 10.1016/J.Vaccine.2015.05.098  0.346
2015 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, et al. Antigen expression determines adenoviral vaccine potency independent of IFN and STING signaling. The Journal of Clinical Investigation. 125: 1129-46. PMID 25642773 DOI: 10.1172/Jci78280  0.354
2014 Zak DE, Tam VC, Aderem A. Systems-level analysis of innate immunity. Annual Review of Immunology. 32: 547-77. PMID 24655298 DOI: 10.1146/Annurev-Immunol-032713-120254  0.357
2014 Quinn K, Zak D, Costa A, Yamamoto A, Nicosia A, Price D, Gall J, Roederer M, Aderem A, Seder R. 152: CD8 T cell responses correlate with antigen but are independent of type I IFN and STING signaling after adenoviral vaccination Cytokine. 70: 64-65. DOI: 10.1016/J.Cyto.2014.07.159  0.329
2012 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, et al. Merck Ad5/HIV induces broad innate immune activation that predicts CD8⁺ T-cell responses but is attenuated by preexisting Ad5 immunity. Proceedings of the National Academy of Sciences of the United States of America. 109: E3503-12. PMID 23151505 DOI: 10.1073/Pnas.1208972109  0.345
2012 Zak DE, Aderem A. Overcoming limitations in the systems vaccinology approach: a pathway for accelerated HIV vaccine development. Current Opinion in Hiv and Aids. 7: 58-63. PMID 22156843 DOI: 10.1097/Coh.0B013E32834Ddd31  0.309
2011 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, et al. Systems analysis identifies an essential role for SHANK-associated RH domain-interacting protein (SHARPIN) in macrophage Toll-like receptor 2 (TLR2) responses. Proceedings of the National Academy of Sciences of the United States of America. 108: 11536-41. PMID 21709223 DOI: 10.1073/Pnas.1107577108  0.343
2009 Zak DE, Aderem A. A systems view of host defense. Nature Biotechnology. 27: 999-1001. PMID 19898453 DOI: 10.1038/Nbt1109-999  0.425
2009 Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A. Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nature Immunology. 10: 437-43. PMID 19270711 DOI: 10.1038/Ni.1721  0.379
2009 Zak DE, Aderem A. Systems biology of innate immunity. Immunological Reviews. 227: 264-82. PMID 19120490 DOI: 10.1111/J.1600-065X.2008.00721.X  0.322
2008 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, et al. Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. Plos Computational Biology. 4: e1000021. PMID 18369420 DOI: 10.1371/Journal.Pcbi.1000021  0.381
2008 Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, et al. The Innate Immune Database (IIDB). Bmc Immunology. 9: 7. PMID 18321385 DOI: 10.1186/1471-2172-9-7  0.357
2006 Yalamanchili N, Zak DE, Ogunnaike BA, Schwaber JS, Kriete A, Kholodenko BN. Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach. Systems Biology. 153: 236-46. PMID 16986625 DOI: 10.1049/ip-syb:20050090  0.498
2006 Zak DE, Hao H, Vadigepalli R, Miller GM, Ogunnaike BA, Schwaber JS. Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling. Genome Biology. 7: R48. PMID 16784547 DOI: 10.1186/Gb-2006-7-6-R48  0.543
2006 Hao H, Zak DE, Sauter T, Schwaber J, Ogunnaike BA. Modeling the VPAC2-activated cAMP/PKA signaling pathway: from receptor to circadian clock gene induction. Biophysical Journal. 90: 1560-71. PMID 16339878 DOI: 10.1529/Biophysj.105.065250  0.502
2005 Zak DE, Vadigepalli R, Gonye GE, Doyle FJ, Schwaber JS, Ogunnaike BA. Unconventional systems analysis problems in molecular biology: A case study in gene regulatory network modeling Computers and Chemical Engineering. 29: 547-563. DOI: 10.1016/J.Compchemeng.2004.08.016  0.527
2005 Zak DE, Hao H, Miller GM, Vadigepalli R, Ogunnaike BA, Schwaber JS. Systems analysis of context-dependent epidermal growth factor receptor signaling in the circadian pacemaker Aiche Annual Meeting, Conference Proceedings. 11675-11676.  0.466
2004 Miller GM, Zak DE, Schwaber JS, Ogunnaike BA. Modeling and identification of the gene regulatory network describing the liver response to corticosteroids Aiche Annual Meeting, Conference Proceedings. 8765-8767.  0.526
2003 Zak DE, Pearson RK, Vadigepalli R, Gonye GE, Schwaber JS, Doyle FJ. Continuous-time identification of gene expression models. Omics : a Journal of Integrative Biology. 7: 373-86. PMID 14683610 DOI: 10.1089/153623103322637689  0.362
2003 Zak DE, Gonye GE, Schwaber JS, Doyle FJ. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Research. 13: 2396-405. PMID 14597654 DOI: 10.1101/Gr.1198103  0.362
2003 Vadigepalli R, Chakravarthula P, Zak DE, Schwaber JS, Gonye GE. PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification. Omics : a Journal of Integrative Biology. 7: 235-52. PMID 14583114 DOI: 10.1089/153623103322452378  0.358
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