D. Zak

发表

Unconventional systems analysis problems in molecular biology: a case study in gene regulatory network modeling

Francis J. Doyle, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli, 2005, Comput. Chem. Eng..

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.

Daniel E. Zak, F. Doyle, G. Gonye, 2003, Genome research.

Continuous-time identification of gene expression models.

Daniel E. Zak, F. Doyle, R. Pearson, 2003, Omics : a journal of integrative biology.

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

Daniel E. Zak, G. Gonye, J. Schwaber, 2003, Omics : a journal of integrative biology.

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

Stephen A. Ramsey, Ilya Shmulevich, Vladimir Litvak, 2010, Bioinform..

Systems biology of innate immunity

Daniel E. Zak, D. Zak, A. Aderem, 2009, Immunological reviews.

Systems-level analysis of innate immunity.

Daniel E. Zak, D. Zak, A. Aderem, 2014, Annual review of immunology.

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

B. Ogunnaike, J. Schwaber, D. Zak, 2006, Genome Biology.

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

Helder I. Nakaya, Tao Dong, Mario Cortese, 2016, Proceedings of the National Academy of Sciences.

Insights From an Identifiability Analysis of an In Silico Network in the Reverse Engineering of Genetic Regulatory Networks : Importance of Input Perturbations and Stochastic Gene Expression data

F. Doyle, G. Gonye, J. Schwaber, 2003 .

The Innate Immune Database (IIDB)

Bin Li, Hamid Bolouri, Vesteinn Thorsson, 2008, BMC Immunology.

Role of the transcription factor C/EBPδ in a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signals

Alistair G. Rust, Stephen A. Ramsey, Ilya Shmulevich, 2009, Nature Immunology.

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

Fergal J. Duffy, D. Zak, S. Kaufmann, 2018, Front. Immunol..

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

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2018, bioRxiv.

Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2022, bioRxiv.

The Ratiometric Transcript Signature MX2/GPR183 Is Consistently Associated With RTS,S-Mediated Protection Against Controlled Human Malaria Infection

R. A. van den Berg, Daniel E. Zak, D. Zak, 2020, Frontiers in Immunology.

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

Daniel E. Zak, D. Zak, A. Aderem, 2012, Proceedings of the National Academy of Sciences.

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

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2019, Front. Immunol..

A prospective blood RNA signature for tuberculosis disease risk

D. Zak, A. Aderem, S. Kaufmann, 2016, Lancet (London, England).

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

Daniel E. Zak, D. Zak, A. Aderem, 2012, Current opinion in HIV and AIDS.

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

Daniel E. Zak, Matthew S. Lewis, D. Zak, 2018, Nature Medicine.

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

D. Zak, M. Hatherill, T. Scriba, 2018, Tuberculosis.

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

D. Zak, Garnet Navarro, A. Aderem, 2016, EBioMedicine.

Metabolite changes in blood predict the onset of tuberculosis

Michel R. Klein, Jane Hughes, Gerhard Walzl, 2018, Nature Communications.

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

Daniel E. Zak, D. Zak, Harukazu Suzuki, 2018, Mucosal Immunology.

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

Eva K. Lee, Bali Pulendran, R. A. van den Berg, 2017, Proceedings of the National Academy of Sciences.

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

Jason A. Skinner, D. Zak, A. Aderem, 2018, The Journal of infectious diseases.

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

David G. Sterling, D. Zak, S. Kaufmann, 2019, PLoS medicine.

RISK6, a universal 6-gene transcriptomic signature of TB disease risk, diagnosis and treatment response

Timothy, Stanley, Daniel E. Zak, 2019 .

Four-Dimensional Organization of Cellular Signal Transduction Cascades

B. Kholodenko, D. Zak, A. Kiyatkin, 2001 .

Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Sandy L. Klemm, Kathleen A. Kennedy, Carrie D. Johnson, 2008, PLoS Computational Biology.

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Bin Li, Jared C. Roach, Alistair G. Rust, 2008, PLoS Comput. Biol..

Caspase-11 Protects Against Bacteria That Escape the Vacuole

Daniel E. Zak, D. Zak, A. Aderem, 2013, Science.

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

Daniel E. Zak, Kylie M. Quinn, A. Folgori, 2015, The Journal of clinical investigation.

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

Daniel E. Zak, Carrie D. Johnson, D. Zak, 2017, Blood advances.

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

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2019, Front. Microbiol..

A systems view of host defense

Daniel E. Zak, Alan Aderem, D. Zak, 2009, Nature Biotechnology.

Cutting Edge: Mouse NAIP1 Detects the Type III Secretion System Needle Protein

Daniel E. Zak, D. Zak, R. Vance, 2013, The Journal of Immunology.

A prospective blood RNA signature for tuberculosis disease risk

Daniel E. Zak, D. Zak, A. Aderem, 2016, The Lancet.

Local identifiability : when can genetic networks be identified from microarray data ?

Francis J. Doyle, Daniel E. Zak, F. Doyle, 2002 .

Experimental Design in Genetic Regulatory Network Identification: Results From In Silico Studies

F. Doyle, R. Pearson, J. Schwaber, 2001 .

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

Daniel E. Zak, Kathleen A. Kennedy, Carrie D. Johnson, 2011, Proceedings of the National Academy of Sciences.

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

Smitha Shankar, Gerhard Walzl, Stefan H E Kaufmann, 2019, PLoS medicine.

Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL.

Daniel E. Zak, D. Zak, A. Aderem, 2008, Immunity.

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

John L. Johnson, David G. Sterling, Daniel E. Zak, 2017, PLoS pathogens.

Type III Secretion System Needle Protein Cutting Edge: Mouse NAIP1 Detects the

D. Zak, R. Vance, E. Miao, 2013 .

Brentuximab Vedotin and Nivolumab for Relapsed or Refractory Classic Hodgkin Lymphoma: Long-Term Follow-up Results from the Single-Arm Phase 1/2 Study

R. Advani, J. Vose, A. LaCasce, 2019, Blood.

T-SIGn tumor reengineering therapy and CAR T cells synergize in combination therapy to clear human lung tumor xenografts and lung metastases in NSG mice

Daniel E. Zak, D. Zak, B. Champion, 2022, Oncoimmunology.

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

D. Zak, Harukazu Suzuki, S. P. Parihar, 2018, Mucosal Immunology.

Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis.

Michael Y. Gerner, Daniel E. Zak, Fergal J. Duffy, 2020, Cell host & microbe.

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

Rachel P. J. Lai, Xinchun Chen, D. Zak, 2015, The Journal of experimental medicine.

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

A Kriete, J S Schwaber, B N Kholodenko, 2006, Systems biology.

Progression to active Tuberculosis among household contacts

Fergal J. Duffy, D. Zak, S. Kaufmann, 2018 .

Systems integration of innate and adaptive immunity.

Daniel E. Zak, D. Zak, A. Aderem, 2015, Vaccine.

RISK6, a universal 6-gene transcriptomic signature of TB disease risk, diagnosis and treatment response

Daniel E. Zak, D. Zak, S. Kaufmann, 2019 .

Four‐Gene Pan‐African Blood Signature Predicts Progression to Tuberculosis

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2018, American journal of respiratory and critical care medicine.

The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2021, Frontiers in Immunology.

Host blood RNA signatures predict the outcome of tuberculosis treatment

Gerard Tromp, David L. Tabb, Smitha Shankar, 2017, Tuberculosis.

RISK6, a 6-gene transcriptomic signature of TB disease risk, diagnosis and treatment response

Daniel E. Zak, D. Zak, G. Schoolnik, 2020, Scientific Reports.

Erratum: 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

D. Zak, S. P. Parihar, T. Scriba, 2017, Mucosal Immunology.

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

Daniel E. Zak, D. Zak, S. P. Parihar, 2017, Mucosal Immunology.

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

D. Zak, Garnet Navarro, A. Aderem, 2016, EBioMedicine.

Interleukin 27 R regulates CD 4 + T cell phenotype and impacts protective immunity during Mycobacterium tuberculosis infection

Rachel P. J. Lai, Xinchun Chen, D. Zak, 2015 .

Considerations for biomarker-targeted intervention strategies for tuberculosis disease prevention

Lindsay N. Carpp, Daniel E. Zak, D. Zak, 2017, Tuberculosis.

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

Thomas Sauter, Babatunde A Ogunnaike, James Schwaber, 2006, Biophysical journal.

Sensitivity analysis of oscillatory (bio)chemical systems

Francis J. Doyle, Jörg Stelling, Daniel E. Zak, 2005, Comput. Chem. Eng..

Stochastic kinetic analysis of transcriptional feedback models for circadian rhythms

Francis J. Doyle, James S. Schwaber, Dionisios G. Vlachos, 2001, Proceedings of the 40th IEEE Conference on Decision and Control (Cat. No.01CH37228).

Simulation Studies for the Identification of Genetic Networks from cDNA Array and Regulatory Activity Data

Francis J. Doyle, Daniel E. Zak, F. Doyle, 2001 .

Predicting tuberculosis risk – Authors’ reply

D. Zak, M. Hatherill, T. Scriba, 2016, The Lancet.