Pathogen Strain Identification Professors and Supervisors

Côme Thieulentمشاهده پروفایل

استادیار

Louisiana State UniversityUnited States

Côme Thieulent is an Assistant Research Professor in the Department of Pathobiological Sciences at the LSU School of Veterinary Medicine, Louisiana State University. He joined the faculty in December 2023, bringing expertise in molecular virology and infectious disease diagnostics with applications spanning animal and human health. Dr. Thieulent's educational background includes: PhD in Virology from ComUE Normandie Université, France (2020) MSc in Molecular Biology from University of Caen Normandie, France (2016) BSc in Biology from University of Caen Normandie, France (2014) His research program centers on viral pathogenesis, host-pathogen interactions, and innovative diagnostic development. Using advanced techniques including bulk and single-cell RNA sequencing, he investigates pathogens such as equine herpesviruses, equine infectious anemia virus, and SARS-CoV-2. His work bridges veterinary and human medicine through a One Health approach, focusing on how host factors influence viral replication and immune responses. Analysis of his 15 most recent publications reveals a strong thematic focus on equine viral diseases (EHV-1, EIAV) and emerging pathogens like SARS-CoV-2, with significant emphasis on developing multiplex molecular diagnostic assays for respiratory pathogens in companion animals. The research demonstrates consistent translational output with practical applications in veterinary diagnostics and antiviral development. Dr. Thieulent's achievements have been recognized through: Best Poster Presentation Award, Society of Phi Zeta, LSU School of Veterinary Medicine (2023) Best Poster Award, 4th Conference on Impedance-Based Cellular Assays, Edinburgh, Scotland (2018) Second place, French national competition 'My thesis in 180 seconds' (horse industry section), Paris, France (2018) His active research program is supported by multiple grants: Modulation of canine airway epithelial responses by Mycoplasma spp. and coronavirus co-infection (VTSA, $10,000, 2024-2025) Tropism and transcriptional profiling of Equine Infectious Anemia Virus (USDA, $9,615, 2024-2025) Rapid detection of latent equine herpesviruses (EHSP Charles V. Cusimano Grant, $12,000, 2023-2024) These projects drive his team's work on respiratory and viral diseases in horses and companion animals. While no formal lab name is specified, his research group operates within LSU's Department of Pathobiological Sciences, utilizing state-of-the-art molecular facilities to investigate viral infections and develop diagnostic solutions.

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Stéphane Bonacorsiمشاهده پروفایل

استاد

Centre for Research in Epidemiology and Statistics (CRESS)France

Paediatric Infectious Diseases
Molecular Epidemiology of Bacterial Infections
Antibiotic Resistance
+۳ مورد دیگر

Stéphane Bonacorsi is a Professor (PU-PH) at Université Paris Cité, conducting research through IAME (Institut de Recherche en Infectiologie de Paris) where he leads the EVREST team. His work bridges academic microbiology and pediatric clinical practice, focusing on severe bacterial infections in children. Affiliation: Université Paris Cité, IAME Research Institute Research Unit: EVREST team specializing in pediatric bacterial pathogenesis His research centers on pediatric E. coli infections , with emphasis on meningitis, urinary tract infections, and hemolytic uremic syndrome. He investigates molecular epidemiology, virulence mechanisms, and antibiotic resistance evolution using genomic approaches. Key areas include: Hybrid pathotypes (e.g., STEC/ESBL-producing E. coli O80) Neonatal meningitis pathogenesis European surveillance of emerging resistant strains Therapeutic target identification via sequencing Analysis of his 15 most recent publications (2014-2025) reveals dominant focus on E. coli molecular epidemiology in children, with 73% addressing antibiotic resistance mechanisms and 40% involving genomic characterization of hybrid virulence/resistance traits. Over half specifically study meningitis or UTIs in pediatric populations. His scientific contributions include: Defining characteristics of emerging E. coli clones (ST301, O80:H2) Mechanistic studies of virulence factors (e.g., ssbL gene in meningitis) Population-based sepsis surveillance in neonates Therapeutic evaluations for resistant infections Bonacorsi's work demonstrates strong clinical translation, with studies directly informing pediatric infection management. His EVREST team maintains active surveillance of pathogen evolution in French hospitals, generating genomic resources for tracking resistance spread and identifying novel treatment approaches for life-threatening childhood infections.

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Christophe Solaمشاهده پروفایل

پژوهشگر

Centre for Research in Epidemiology and Statistics (CRESS)France

Christophe Sola is a Permanent Researcher at University Paris-Saclay, France, affiliated with the Institute for Integrative Biology of the Cell and the EVREST team within the Infectious Agents and Public Health unit (IAME). His research focuses on the molecular epidemiology and genetics of Mycobacterium tuberculosis, with particular expertise in strain typing methods and evolutionary analysis across global populations. Dr. Sola's research interests span several key areas in tuberculosis research: Molecular epidemiology of Mycobacterium tuberculosis lineages Development and application of spoligotyping methods using Luminex technology CRISPR-based analysis of TB strains through tools like CRISPRbuilder-TB Genetic diversity and evolution of TB lineages across geographical regions Historical spread patterns of tuberculosis, including connections to the slave trade Drug resistance mechanisms and detection in Mycobacterium tuberculosis His publication record demonstrates consistent contributions to understanding TB transmission across five continents, with particular focus on connections between African, Asian, and American strains. Recent work has examined tuberculosis trends in Paris hotspots, strain diversity in Lebanon, Papua New Guinea, and Brazil, revealing significant findings such as the shared SIT129 spoligotype between Pará/Brazil and Malawi/Mozambique regions, suggesting historical transmission routes. Dr. Sola has published extensively in high-impact journals including Nature Genetics, PLoS Computational Biology, Emerging Infectious Diseases, and Infection, Genetics and Evolution. His methodological papers on spoligotyping and CRISPR analysis have been particularly influential in standardizing TB strain identification techniques used in laboratories worldwide. As a researcher, Dr. Sola maintains extensive international collaborations across multiple continents, working with institutions in Lebanon, Brazil, Madagascar, Peru, Mozambique, and Papua New Guinea. These collaborations focus on comparative studies of TB strains to understand global transmission patterns, evolutionary history, and the development of region-specific diagnostic approaches. His EVREST team at University Paris-Saclay serves as the central hub for this international research network focused on tuberculosis genetics and epidemiology.

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Nicholas Oberliesمشاهده پروفایل

استاد

University of North Carolina at GreensboroUnited States

Nicholas Oberlies serves as the Patricia A. Sullivan Distinguished Professor of Chemistry and Graduate Director for MS and PhD programs in the Department of Chemistry and Biochemistry at the University of North Carolina at Greensboro (UNCG). With an extensive research program and numerous publications, Dr. Oberlies has established himself as a leading researcher in natural products chemistry and drug discovery from natural sources. Dr. Oberlies received his B.S. in Chemistry from Miami University in 1992 and completed his Ph.D. in Medicinal Chemistry and Pharmacognosy from Purdue University in 1997. His educational background provided the foundation for his research career focused on the chemistry of natural products. Dr. Oberlies leads a dynamic research group that focuses on the isolation and structure elucidation of bioactive compounds from natural sources, particularly from fungal cultures and plants. His work spans two primary areas: natural products drug discovery and herbal drug research. In drug discovery, his team examines filamentous fungi for new anticancer leads as part of a National Cancer Institute Program Project, having examined over 1000 fungal cultures and isolated more than 300 compounds. In the herbal drug arena, Dr. Oberlies applies similar methodologies to better understand and standardize herbal products, with significant work on milk thistle (Silybum marianum) and its extract silymarin. His group also investigates mechanisms underlying drug-diet interactions, particularly those involving herbal products. The research output from Dr. Oberlies' laboratory demonstrates a consistent focus on natural products chemistry with applications across multiple therapeutic areas. His recent publications show strong interdisciplinary collaboration across fields including genomics, pharmacology, oncology, and analytical chemistry. The work spans from basic chemical characterization of novel compounds to preclinical studies evaluating therapeutic potential, particularly in cancer treatment. Notably, his group has developed expertise in 3D printing applications for laboratory equipment, designing and sharing various useful tools that enhance research efficiency. As Graduate Director for MS and PhD programs in Chemistry and Biochemistry, Dr. Oberlies mentors numerous graduate students. His research is supported by significant funding, notably from the National Cancer Institute for his fungal anticancer drug discovery program. He has established productive collaborations with researchers at institutions including Washington State University and the University of North Carolina at Chapel Hill. Dr. Oberlies leads the Oberlies Research Group, which takes a team-oriented approach to studying bioactive compounds from nature. The group collaborates with scientists across diverse disciplines including pharmacology, virology, ecology, and metabolism to reveal the biological potential of natural compounds. Their innovative approach to laboratory work, including 3D printing applications for research tools, demonstrates a commitment to advancing methodology alongside scientific discovery.

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Jakub Sawickiمشاهده پروفایل

استاد

University of Warmia and Mazury in OlsztynPoland

Jakub Sawicki , a Professor at the University of Warmia and Mazury in Olsztyn , is affiliated with the Faculty of Biology and Biotechnology and the Department of Botany and Nature Conservation . His research focuses on plant genetics, particularly the genomic and molecular mechanisms in bryophytes. Specializes in genomic adaptation of liverworts to aquatic habitats Investigates sex determination mechanisms in thallose liverworts Utilizes organellar genome sequencing and DNA barcoding for species discrimination Secured funding via the OPUS Project for genomic research His work emphasizes evolutionary biology and conservation genetics, leveraging advanced sequencing techniques to address cryptic speciation and adaptive traits in endangered plant species.

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Abdolrahman Khezriمشاهده پروفایل

دانشیار

Inland Norway University of Applied SciencesNorway

Dr. Abdolrahman Khezri is an Associate Professor at the University of Inland Norway , affiliated with the Faculty of Applied Ecology, Agricultural Sciences and Biotechnology and the Department of Biotechnology . His research focuses on reproductive biotechnology, antimicrobial resistance, and pathogen diagnostics in livestock and aquatic species. Key research areas include: DNA methylation and epigenetic markers in fertility regulation Development of rapid diagnostic tools (e.g., SERS nanowire chips, whole genome sequencing) Investigating antimicrobial resistance mechanisms in bacterial infections Cryopreservation and cold-storage impacts on sperm quality Recent publications highlight interdisciplinary work merging biotechnology with machine learning and advanced microscopy techniques for infection detection. No awards or student advisement details are currently available.

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Travis Glareمشاهده پروفایل

استاد

Lincoln UniversityNew Zealand

Professor Travis Glare serves as Director of Lincoln Agritech at Lincoln University, New Zealand, and previously directed the Bio-Protection Research Centre (2013-2022). He is a member of the Senior Management Team, Professional Forum, and Deans and Directors Group at Lincoln University, demonstrating his significant institutional leadership. Director, Lincoln University Research Management Office (2021-present) Director, Bio-Protection Research Centre (2013-2022) Council member, B3 Science Solutions for Better Border Biosecurity (2016-present) Member, Industry Advisory Group, Seed Research Centre (2014-present) His research focuses on entomopathogenic microbes as biocontrol agents, with particular emphasis on Beauveria, Metarhizium, and Brevibacillus species. His work spans from genomic studies to field applications, investigating both fundamental mechanisms and practical implementations of microbial pesticides. Analysis of his recent publications reveals a strong focus on microbial genomics, plant-microbe-insect interactions, and practical biocontrol applications. His research group is particularly active in studying endophytic capabilities of entomopathogenic fungi, mechanisms of pathogenicity, and developing effective biopesticide formulations through fermentation technology. Editorial Board member for Insects and AIMS Bioengineering journals Associate editor for Journal of Biopesticides Member of New Zealand Plant Protection Society Member of Society for Invertebrate Pathology Professor Glare actively supervises graduate students (currently 7 PhD and 2 MSc candidates) and has successfully completed 25 postgraduate supervisions. His research group explores diverse topics including genomic drivers of entomopathogenic evolution, microbiome effects on pest control, and practical applications of microbial biocontrol in Pacific Island ecosystems. He also contributes to fermentation technology development for mass production of biocontrol agents.

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Rachel Bleichمشاهده پروفایل

استادیار

Appalachian State UniversityUnited States

Rachel Bleich is an Assistant Professor in the Department of Biology at Appalachian State University, where she has conducted research on gut microbiome dynamics in inflammatory bowel disease (IBD) since 2020. Her work focuses on Crohn's-associated $$E. coli$$ strains and their impact on host-microbe interactions using molecular barcoding technology. Education: Ph.D. in Pharmaceutical Sciences, University of North Carolina at Chapel Hill (2017) B.S. in Chemistry, Western Carolina University (2012) Dr. Bleich's research investigates how strain-specific bacterial features and specialized metabolites shape microbial community structure and influence host health in IBD. Her laboratory employs molecular barcoding to overcome limitations of traditional 16S rRNA sequencing, enabling precise identification of functionally distinct $$E. coli$$ strains within complex microbiota. Key questions explore bacterial communication mechanisms, metabolite-mediated interactions, and their downstream effects on inflammatory pathways. Her publication record shows a clear trajectory from bacterial physiology studies (2015-2017) toward microbiome-disease connections, with recent high-impact contributions examining microbiome roles in cancer development and IBD pathogenesis. The 2021 $$Annual Review of Medicine$$ article synthesizes evidence for microbiota involvement across all carcinogenesis stages, while her $$Science$$ perspective highlights emerging microbial carcinogen research. Dr. Bleich actively mentors undergraduate and graduate students in laboratory research, providing hands-on training in microbiological and molecular techniques. Her work receives institutional support through Appalachian State University resources, though specific grant details aren't provided in source materials. She maintains an active research laboratory in Rankin Science West, where her team investigates host-microbe dynamics with potential therapeutic applications for IBD treatment.

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Geert-Jan Boonsمشاهده پروفایل

استاد

University of GeorgiaUnited States

Geert-Jan Boons serves as the UGA Foundation Distinguished Professor in Biochemical Sciences at the University of Georgia's Department of Chemistry and Complex Carbohydrate Research Center (CCRC), while also holding a secondary appointment as Professor and Chair of the Department of Medicinal and Biological Chemistry at Utrecht University (Netherlands). His educational background includes a First Degree (equivalent to M.S.) in Chemistry from Leiden University (1987), followed by a Ph.D. in Synthetic Carbohydrate Chemistry from the same institution (1991) under Prof. J.H. van Boom. Postdoctoral training was completed at Imperial College London and the University of Cambridge with Prof. S.V. Ley. Boons' research focuses on overcoming glycoscience limitations through chemical and chemoenzymatic synthesis of complex oligosaccharides and glycoconjugates. His laboratory develops innovative methodologies using minimal building blocks for efficient assembly of N- and O-glycans, ganglio-oligosaccharides, heparan sulfates, tumor-associated antigens, and bacterial capsular polysaccharides. A hallmark of his work involves applying synthesized glycans to study infectious, immunological, and inflammatory processes at the molecular level, leading to therapeutic applications including fully synthetic immuno-modulators, vaccines for epithelial cancers, and glycomimetic drugs. Analysis of his recent publications reveals dominant themes in virology (particularly SARS-CoV-2 and influenza receptor mechanisms), autoimmune disorder research (Guillain-Barré syndrome), and technological advances in automated glycan synthesis platforms. His work consistently bridges chemical synthesis with biomedical applications, emphasizing glycan roles in disease mechanisms and therapeutic development. Creativity in Carbohydrate Science Award (European Carbohydrate Association, 2003) Horace Isbell Award (American Chemical Society, 2004) Roy L. Whistler International Award (International Carbohydrate Organization, 2014) Hudson Award (2015) Cope Mid-Career Scholar Award (ACS, 2016) Boons maintains an active research group with five graduate students and leads multiple laboratory spaces at CCRC (rooms 1014, 1023, 1095, 1101, 3044). His work is supported by significant grant funding enabling the development of glycan microarrays, vaccine candidates, and visualization techniques for glycoconjugates in living cells. The Boons Group website details ongoing projects in glycomimetic drug development and chemoenzymatic synthesis automation.

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Lidiya Dubytskaمشاهده پروفایل

دانشیار

Southern University and A&M CollegeUnited States

Dr. Lidiya Dubytska serves as Associate Professor of Biology at Southern University and Agricultural and Mechanical College, Baton Rouge, where she established new research directions in microbiology and pathogen-host interactions since joining in 2017. Her work focuses on bacterial virulence mechanisms and translational applications for disease control, with extensive contributions to understanding Edwardsiella ictaluri and Borrelia burgdorferi pathogenesis. Her academic training includes: MS in Biochemistry from Ivan Franko State University of L'viv, Ukraine, researching TGF-beta effects on fibroblast collagen gel contraction Ph.D. in Molecular Genetics from Ukraine's National Academy of Science (2003), developing Streptomyces strains for anticancer drug production Dr. Dubytska's research examines global virulence regulation through Type Three Secretion Systems, alternative sigma factors, and two-component systems. She investigates how pathogens like Edwardsiella modulate host organelle trafficking and immune responses, with implications for vaccine development and therapeutic interventions against bacterial infections. Publication analysis reveals consistent interdisciplinary work bridging bacterial genomics, host-pathogen dynamics, and molecular pathogenesis. Her recent output emphasizes aquaculture pathogens and spirochetal diseases, demonstrating technical expertise in genome annotation, effector protein characterization, and virulence gene regulation across diverse bacterial systems. Key recognition includes: National Academy of Science of Ukraine prize for best scientific presentation (2002) She has mentored undergraduate researchers like Demetrius McAtee (2nd place biology poster competition, 2019) and secured research funding including an LSU/USDA grant as Co-PI and CEIDER support. Her collaborative network spans Ukrainian institutions, New York Medical College, and Louisiana State University. Dr. Dubytska's laboratory has annotated multiple Edwardsiella genomes and plasmids, contributing to GenBank submissions. She maintains active editorial roles with Advances in Microbiology and BMC Microbiology while advising on microbiological applications textbooks.

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Jose Hernandezمشاهده پروفایل

استاد

Midwestern UniversityUnited States

Metals Biology
Nitrogen Metabolism in Diazotrophic Bacteria
Bacterial Metal-Dependent Transcriptional Regulators
+۲ مورد دیگر

Jose Hernandez, Ph.D., serves as Professor and Chair of Biochemistry and Molecular Genetics at Midwestern University's College of Graduate Studies in Arizona. His academic leadership spans biochemical research, graduate education, and departmental administration within the institution's health sciences framework. His educational background includes a Ph.D. and M.S. from the University of Zaragoza (Spain), followed by postdoctoral training at the University of California, Berkeley. Hernandez maintains active teaching responsibilities in biochemistry courses including Biochemistry I (BIOCG 1511/1512) and Biochemistry II (BIOCG 1522/1523), with scheduled instruction through 2025. Hernandez's research centers on microbial metal biology, with two primary thrusts: (1) Metal-responsive transcription factors (Fur, Zur, PerR families) in Klebsiella sp. pathogenesis and antibiotic resistance development, and (2) Metallochaperone mechanisms in nitrogenase iron-molybdenum cofactor assembly using Azotobacter vinelandii models. His work integrates genetic, microbiological, and biochemical approaches to investigate metal homeostasis in pathogens and nitrogen-fixing bacteria. Analysis of his 15 most recent publications reveals consistent focus on nitrogenase biochemistry (7 papers), metal cofactor assembly (5 papers), and vector-borne disease mechanisms (4 papers), demonstrating interdisciplinary expertise bridging inorganic chemistry, microbiology, and infectious disease research. His work appears in high-impact journals including Nature Communications (120 citations) and PNAS (62 citations). Professional activities include teaching core biochemistry curriculum for multiple health science programs including Doctor of Osteopathic Medicine (D.O.), Master of Biomedical Sciences (M.B.S.), and Doctor of Pharmacy (Pharm.D.). His laboratory investigations target therapeutic applications against infectious diseases through manipulation of metal-dependent bacterial pathways.

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Antoine Hugueninمشاهده پروفایل

مدرس

University of Reims Champagne-ArdenneFrance

Antoine Huguenin is a Lecturer and Hospital Practitioner affiliated with the University of Reims Champagne-Ardenne. He is associated with the research unit UR 7510 ESCAPE, where he completed his university thesis in September 2022 titled "Contribution of MALDI-TOF mass spectrometry in the characterization of pathogenic agents in Parasitology-Mycology" . His research focuses on applying innovative technologies such as MALDI-TOF Mass Spectrometry, High-throughput Sequencing, and Machine Learning to epidemiological studies of pathogenic eukaryotes, particularly fungi, helminths, and diptera. This work emphasizes specific identification and strain typing methodologies.

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Weigang Qiuمشاهده پروفایل

استاد

City University of New YorkUnited States

Weigang Qiu is a Professor in the Department of Biological Sciences at Hunter College, part of the City University of New York (CUNY). His research focuses on the population genomics of microbial pathogens, particularly the Lyme disease bacterium Borrelia burgdorferi . Dr. Qiu received his educational training from: BS in Biochemistry from Fudan University, China (1986) PhD in Ecology and Evolution from State University of New York at Stony Brook (1999) Postdoctoral training in Bioinformatics at University of Maryland Biotechnology Institute (2002) Dr. Qiu's research interests center on evolutionary bioinformatics and pathogen variability. His lab specializes in comparative analysis of multiple genomes of the Lyme disease pathogen, reconstructing the history of worldwide diversification of Lyme disease bacteria, understanding mechanisms of genome evolution (particularly roles of recombination and natural selection), and inference of gene and genome functions. His approach is primarily bioinformatics-based, focusing on computational and statistical testing of evolutionary hypotheses. Students in his lab learn modern computational tools including relational databases/SQL, Perl/BioPerl, and statistical computing with R. Analysis of Dr. Qiu's publication record shows a consistent focus on Lyme disease pathogens and bacterial evolution, with recent work expanding into cancer biology and thyroid cancer research. His research demonstrates interdisciplinary connections between evolutionary biology, microbiology, and medical applications, highlighting how evolutionary principles can inform our understanding of disease mechanisms. Dr. Qiu teaches several courses including Molecular Evolution (BIOL 375), Computational Molecular Biology (BIOL 425), Bioinformatics Summer Workshop (BIOL 470), and Microbiology (BIOL 230). He is also involved in the QuBi Project for curricular improvement in quantitative biology. Dr. Qiu leads the Qiu Lab, which focuses on bioinformatics tools development for bacterial genomics research. The lab has developed several specialized tools including: Borrelia Ortholog Retriever: For obtaining ortholog alignments from 23 Borrelia spp genomes SimBac: A package for simulating bacterial genome evolution DNATweezer: A Perl wrapper of BioPerl modules The Bio::Align::Graphics module

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Rabaab Zahraمشاهده پروفایل

استاد

Quaid-i-Azam UniversityPakistan

Dr. Rabaab Zahra serves as a Professor in the Department of Microbiology at Quaid-i-Azam University, Islamabad, Pakistan, actively contributing to antimicrobial resistance research with a focus on public health implications in South Asia. Her academic credentials include a B.Sc. in Medical Laboratory Technology, M.Sc. in Biotechnology, and Ph.D. in Cell & Molecular Biology, establishing her expertise in molecular mechanisms of infectious diseases. Dr. Zahra's research centers on antibiotic resistance epidemiology , investigating transmission dynamics between clinical and environmental reservoirs in Pakistan. She specializes in neonatal infection outcomes, hospital-community resistance transmission links, and environmental persistence of resistant pathogens, with particular emphasis on Enterobacteriaceae and Staphylococcus aureus mechanisms. Analysis of her 15 most recent publications reveals dominant themes in carbapenemase-producing organisms (NDM-1, OXA-181), molecular epidemiology of pathogens across human-animal-environment interfaces, and virological surveillance for diseases like Foot and Mouth and PPRV. Over 60% of her work addresses Pakistan-specific public health challenges in vulnerable neonatal populations. No scientific awards were documented in the provided materials. As Principal Investigator, she directs major funded projects including the Bill & Melinda Gates Foundation's BARNARDS initiative on neonatal resistance burden, HEC Pakistan grants on MRSA resistance mechanisms, and international collaborations with Cardiff University on environmental reservoirs and genomic epidemiology of carbapenem-resistant Enterobacteriaceae. 2011-2012: agr system/autophagy in MRSA resistance (HEC Pakistan) 2013-2016: S. aureus autophagy/resistance mechanisms (HEC Pakistan) 2015-2018: BARNARDS neonatal resistance project (Gates Foundation) 2015: Gram-negative neonatal infection genetics (UK-Cardiff) 2016-2018: BARNARDS Community Project (Gates Foundation) 2016-2017: E. coli environmental sequence typing (Commonwealth Fellowship) 2017-2020: CPE genomic comparison (Pak-France PERIDOT) She leads a multidisciplinary research team at QAU collaborating with the BARNARDS Network and European antimicrobial resistance initiatives (https://antimicrobialresistance.eu/team/), with laboratory facilities focused on molecular characterization of resistant pathogens and environmental sampling methodologies.

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