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Rembert Pieper, PhD, has 25 years of research experience in molecular biology, biochemistry, and systems biology. His laboratory uses integrated genomics and proteomics as well as computational methods to elucidate disease mechanisms and discover biomarkers for non-communicable and infectious diseases. He pioneered body fluid proteomics technologies and research in his role as a Staff Scientist and later as a Director of Protein Chemistry at Large Scale Biology Corporation from 1999-2003. He had a leading role in NIAID’s Pathogen Functional Genomics Resource Center (PFGRC) based at The Institute of Genomic Research (2003-2006) and the J. Craig Venter Institute (JCVI, 2006-2011) in Rockville, Maryland. Working with the infectious disease scientific community, his team developed functional genomics tools and datasets to advance ways in which systems biology is leveraged to characterize emerging and biodefense threat-related pathogens. In the last six years, his laboratory focused on systems biology research on urinary tract infections (UTI), tuberculosis and diabetes, investigating host-pathogen interactions, host-microbiome interactions, and perturbations of human metabolism and the microbiome. He has directed US government-funded research on type 1 diabetes (NIDDK DP3 grant, 10/2011-6/2016), host-pathogen interactions associated with catheter-associated UTIs (NIGMS R01 grant, since 03/2013), and the genomics/host-pathogen interactions for tuberculosis in Ethiopia (U01 grant in NIH’s H3Africa program, since 03/2014). In addition, he leads a biomarker discovery project for healthy aging (Ruggles Family Foundation grant, since 10/2013). In addition, he has been engaged in systems biology education and training programs over more than 10 years. He has co-organized and evaluated workshops, research fellowships and poster sessions for the H3Africa consortium from 2014-2017. Dr. Pieper is on the editorial board of the journals ‘Proteomics’ and ‘Clinical Proteomics’ and has been a regular participant on NIH study sections since 2003. He is a co-inventor on more than 15 patents and patent applications.

Research Priorities

Protein biomarker discovery for disease onset and progression, drug treatment and toxicity using mass spectrometry and array-based techniques

  • Emphasis on protein biomarkers for diabetes, diseases of the kidneys and urogenital tract and the aging process

Characterization of infectious disease pathogenesis and host-pathogen interactions using systems biology methods

  • Emphasis on urogenital and gastrointestinal infectious diseases and tuberculosis
  • Host-pathogen interactions associated with complex microbial communities (e.g. urethral and urethral catheter biofilms)
  • Role of antibacterial peptides in the innate immune defense

Development of new methods for protein-based clinical diagnostics

  • Emphasis on urine and sputum as a body fluid source for novel clinical diagnostics


  • U.S. Patent, No. US20130178377 (published 7/2013): Metaproteomic method for diagnosis of bacteriuria, urogenital tract and kidney infections from urinary pellet samples
  • Co-inventor U.S. Patent No. 7,342,089 (issued 1/5/10): Immunoaffinity-Based Subtraction Method
  • Co-inventor U.S. Patent No. 6,710,189 B2 (issued 3/24/04): Cell-Free Synthesis of Polyketides
  • Co-inventor U.S. Patent No. 6,066,721 (issued 5/23/00): Method to Produce Novel Polyketides


Select Publications

Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract.
Theranostics. 2017-01-01; 7.10: 238-252.
PMID: 28042331
Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections.
PLoS pathogens. 2017-01-01; 13.1: e1006151.
PMID: 28129394
Evaluation of the GenoType MTBDRplus assay for detection of rifampicin- and isoniazid-resistant Mycobacterium tuberculosis isolates in central Ethiopia.
International journal of mycobacteriology. 2016-12-01; 5.4: 475-481.
PMID: 27931690
Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors.
BMC genomics. 2015-12-29; 16.1106.
PMID: 26714771
Similar Neutrophil-Driven Inflammatory and Antibacterial Responses in Elderly Patients with Symptomatic and Asymptomatic Bacteriuria.
Infection and immunity. 2015-10-01; 83.10: 4142-53.
PMID: 26238715
Diagnosing inflammation and infection in the urinary system via proteomics.
Journal of translational medicine. 2015-04-08; 13.111.
PMID: 25889401
Genetic Diversity of Mycobacterium tuberculosis Complex Isolated from Tuberculosis Patients in Bahir Dar City and Its Surroundings, Northwest Ethiopia.
BioMed research international. 2015-01-01; 2015.174732.
PMID: 26491657
The binary protein-protein interaction landscape of Escherichia coli.
Nature biotechnology. 2014-03-01; 32.3: 285-290.
PMID: 24561554
Analysis of the proteome of intracellular Shigella flexneri reveals pathways important for intracellular growth.
Infection and immunity. 2013-12-01; 81.12: 4635-48.
PMID: 24101689
Novel Burkholderia mallei virulence factors linked to specific host-pathogen protein interactions.
Molecular & cellular proteomics : MCP. 2013-11-01; 12.11: 3036-51.
PMID: 23800426
Proteomic View of Interactions of Shiga Toxin-Producing Escherichia coli with the Intestinal Environment in Gnotobiotic Piglets.
PloS one. 2013-06-19; 8.6: e66462.
PMID: 23840478
Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury.
Journal of translational medicine. 2012-08-28; 10.174.
PMID: 22929533
In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism.
BMC microbiology. 2011-06-24; 11.147.
PMID: 21702961
Genome transplantation in bacteria: changing one species to another.
Science (New York, N.Y.). 2007-08-03; 317.5838: 632-8.
PMID: 17600181
Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots.
Proteomics. 2004-04-01; 4.4: 1159-74.
PMID: 15048996
Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome.
Proteomics. 2003-04-01; 3.4: 422-32.
PMID: 12687610