Karen E. Nelson, PhD is the President of the J. Craig Venter Institute (JCVI). Prior to being appointed President, she held a number of other positions at the Institute, including Director of JCVI's Rockville Campus, and Director of Human Microbiology and Metagenomics in the Department of Human Genomic Medicine at JCVI. Dr. Nelson received her undergraduate degree from the University of the West Indies, and her PhD from Cornell University. She has authored or co-authored over 200 peer reviewed publications, edited three books, and is currently Editor-in-Chief of the journal Microbial Ecology.

Dr. Nelson is an elected member of the National Academy of Sciences. Other honors include being named ARCS Scientist of the Year 2017; a Fellow of the American Academy of Microbiology; being inducted into the Indian National Academy of Sciences in 2018; and being appointed an Honorary Professor at the University of the West Indies as well as a Helmholtz International Fellow.

Dr. Nelson has extensive experience in microbial ecology, microbial genomics, microbial physiology and metagenomics. Dr. Nelson has led several genomic and metagenomic efforts, and led the first human metagenomics study that was published in 2006. Additional ongoing studies in her group include metagenomic approaches to study the ecology of the gastrointestinal tract of humans and animals, studies on the relationship between the microbiome and various human and animal disease conditions, reference genome sequencing and analysis primarily for the human body, and other -omics studies.

Research Priorities

Microbiome in health and disease
  • Interrogating microbiome profiles and host microbe interactions
Emergence of Antimicrobial Resistance
  • Understanding the intricate play between infectious species, gene transfer and the emergence of resistance
Understanding Resistance mechanisms in microbial species
  • Deep investigations into how microbes respond to different types of drugs
Identification of novel species
  • In different environments including the oral cavity, plants, and artic sediments

Publications

Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort.
GeroScience. 2020-09-24;
PMID: 32974878
Inflammatory Networks Linking Oral Microbiome with Systemic Health and Disease.
Journal of dental research. 2020-09-01; 99.10: 1131-1139.
PMID: 32459164
Predictive Signatures of 19 Antibiotic-Induced Escherichia coli Proteomes.
ACS infectious diseases. 2020-08-14; 6.8: 2120-2129.
PMID: 32673475
Applications of weighted association networks applied to compositional data in biology.
Environmental microbiology. 2020-08-01; 22.8: 3020-3038.
PMID: 32436334
Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.
Nature communications. 2020-06-16; 11.1: 3132.
PMID: 32546784
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.
Nature communications. 2020-05-21; 11.1: 2537.
PMID: 32439901
Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance.
Microbial ecology. 2020-05-21;
PMID: 32440698
Longitudinal Study of Oral Microbiome Variation in Twins.
Scientific reports. 2020-05-14; 10.1: 7954.
PMID: 32409670
Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy.
Microbial ecology. 2020-05-01; 79.4: 1034-1043.
PMID: 31754744
Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth.
The Journal of infectious diseases. 2020-04-02;
PMID: 32239170
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
PMID: 31907190
An unsupervised learning approach to identify novel signatures of health and disease from multimodal data.
Genome medicine. 2020-01-10; 12.1: 7.
PMID: 31924279
Long-term impact of oral surgery with or without amoxicillin on the oral microbiome-A prospective cohort study.
Scientific reports. 2019-12-10; 9.1: 18761.
PMID: 31822712
Gastro-intestinal and oral microbiome signatures associated with healthy aging.
GeroScience. 2019-12-01; 41.6: 907-921.
PMID: 31620923
Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis.
Frontiers in immunology. 2019-11-12; 10.2602.
PMID: 31781106
Interplay between the human gut microbiome and host metabolism.
Nature communications. 2019-10-03; 10.1: 4505.
PMID: 31582752
Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants.
Scientific reports. 2019-07-23; 9.1: 10635.
PMID: 31337807
Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors.
American journal of physical anthropology. 2019-07-01; 169.3: 575-585.
PMID: 31025322
Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery.
Journal of proteome research. 2019-04-05; 18.4: 1907-1915.
PMID: 30848925
Co-occurrence of Anaerobes in Human Chronic Wounds.
Microbial ecology. 2019-04-01; 77.3: 808-820.
PMID: 30141127
A novel approach for the identification and phylogenetic delineation of human Mycoplasma species and strains using genomic segment sequence analysis.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2019-03-01; 68.68-76.
PMID: 30529087
OMeta: an ontology-based, data-driven metadata tracking system.
BMC bioinformatics. 2019-01-07; 20.1: 8.
PMID: 30612540
Xylitol and sorbitol effects on the microbiome of saliva and plaque.
Journal of oral microbiology. 2019-01-01; 11.1: 1536181.
PMID: 30598728
The Airplane Cabin Microbiome.
Microbial ecology. 2019-01-01; 77.1: 87-95.
PMID: 29876609
Papio spp. Colon microbiome and its link to obesity in pregnancy.
Journal of medical primatology. 2018-12-01; 47.6: 393-401.
PMID: 30039863
Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.
mBio. 2018-11-27; 9.6:
PMID: 30482830
Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy.
The Journal of allergy and clinical immunology. 2018-11-01; 142.5: 1447-1456.e9.
PMID: 29330010
Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas.
Frontiers in microbiology. 2018-06-15; 9.1202.
PMID: 29963018
Spatial and Environmental Variation of the Human Hair Microbiota.
Scientific reports. 2018-06-13; 8.1: 9017.
PMID: 29899411
Microbial metagenome of urinary tract infection.
Scientific reports. 2018-03-12; 8.1: 4333.
PMID: 29531289
Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality.
The Journal of animal ecology. 2018-03-01; 87.2: 388-399.
PMID: 29205327
Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques.
Microbial ecology. 2018-02-01; 75.2: 303-309.
PMID: 29080910
Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.
Clinical and translational gastroenterology. 2018-01-18; 9.1: e132.
PMID: 29345635
Impact of stress on the gut microbiome of free-ranging western lowland gorillas.
Microbiology (Reading, England). 2018-01-01; 164.1: 40-44.
PMID: 29205130
Comparative genomics of four Mycoplasma species of the human urogenital tract: Analysis of their core genomes and virulence genes.
International journal of medical microbiology : IJMM. 2017-12-01; 307.8: 508-520.
PMID: 28927691
A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation.
Genes. 2017-11-09; 8.11:
PMID: 29120399
The Threat of Antimicrobial Resistance on the Human Microbiome.
Microbial ecology. 2017-11-01; 74.4: 1001-1008.
PMID: 28492988
Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.
Nature communications. 2017-10-16; 8.1: 837.
PMID: 29038503
Integrating the microbiome as a resource in the forensics toolkit.
Forensic science international. Genetics. 2017-09-01; 30.141-147.
PMID: 28728057
Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.
Theranostics. 2017-07-07; 7.10: 2704-2717.
PMID: 28819457
Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate.
Microbial ecology. 2017-07-01; 74.1: 250-258.
PMID: 28124727
Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.
Cell metabolism. 2017-05-02; 25.5: 1054-1062.e5.
PMID: 28467925
Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.
BMC genomics. 2017-04-13; 18.1: 296.
PMID: 28407798
Reducing the Bottleneck in Discovery of Novel Antibiotics.
Microbial ecology. 2017-04-01; 73.3: 658-667.
PMID: 27896376
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences.
Journal of neurovirology. 2017-04-01; 23.2: 171-185.
PMID: 27739035
The Human Microbiome and Cancer.
Cancer prevention research (Philadelphia, Pa.). 2017-04-01; 10.4: 226-234.
PMID: 28096237
The blood DNA virome in 8,000 humans.
PLoS pathogens. 2017-03-22; 13.3: e1006292.
PMID: 28328962
The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.
Microbial ecology. 2017-02-01; 73.2: 492-503.
PMID: 27628595
Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections.
PLoS pathogens. 2017-01-27; 13.1: e1006151.
PMID: 28129394
Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.
Microbial ecology. 2017-01-01; 73.1: 91-100.
PMID: 27815589
Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract.
Theranostics. 2017-01-01; 7.2: 238-252.
PMID: 28042331
Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy.
The Journal of infectious diseases. 2016-12-15; 214.12: 1924-1928.
PMID: 27923952
Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla).
Microbial ecology. 2016-11-01; 72.4: 943-954.
PMID: 26984253
Shared genetic effects between hepatic steatosis and fibrosis: A prospective twin study.
Hepatology (Baltimore, Md.). 2016-11-01; 64.5: 1547-1558.
PMID: 27315352
A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.
Scientific reports. 2016-08-25; 6.31731.
PMID: 27558918
Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.
BMC genomics. 2016-08-15; 17.1: 635.
PMID: 27527070
Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta).
American journal of primatology. 2016-08-01; 78.8: 883-92.
PMID: 27177345
Microbial diversity in individuals and their household contacts following typical antibiotic courses.
Microbiome. 2016-07-30; 4.1: 39.
PMID: 27473422
Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk.
American journal of respiratory and critical care medicine. 2016-05-15; 193.10: 1180-3.
PMID: 27174483
Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns.
Cell reports. 2016-03-08; 14.9: 2142-2153.
PMID: 26923597
Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species.
Oecologia. 2016-03-01; 180.3: 717-33.
PMID: 26597549
Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.
The ISME journal. 2016-02-01; 10.2: 514-26.
PMID: 26315972
Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery.
Microbial ecology. 2016-01-01; 71.1: 233-42.
PMID: 26370110
Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism.
The ISME journal. 2015-12-01; 9.12: 2605-19.
PMID: 26023872
Heritability of Hepatic Fibrosis and Steatosis Based on a Prospective Twin Study.
Gastroenterology. 2015-12-01; 149.7: 1784-93.
PMID: 26299412
Variable responses of human and non-human primate gut microbiomes to a Western diet.
Microbiome. 2015-11-16; 3.53.
PMID: 26568112
Library preparation methodology can influence genomic and functional predictions in human microbiome research.
Proceedings of the National Academy of Sciences of the United States of America. 2015-11-10; 112.45: 14024-9.
PMID: 26512100
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
Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.
BMC genomics. 2015-08-22; 16.631.
PMID: 26296559
Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes.
Journal of proteome research. 2015-08-07; 14.8: 3123-35.
PMID: 26143644
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae.
Standards in genomic sciences. 2015-07-18; 10.37.
PMID: 26221418
Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology.
Molecular ecology. 2015-05-01; 24.10: 2551-65.
PMID: 25846719
Diagnosing inflammation and infection in the urinary system via proteomics.
Journal of translational medicine. 2015-04-08; 13.111.
PMID: 25889401
Where next for microbiome research?
PLoS biology. 2015-01-20; 13.1: e1002050.
PMID: 25602283
An Update on the Status of Current Research on the Mammalian Microbiome.
ILAR journal. 2015-01-01; 56.2: 163-8.
PMID: 26323626
Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice.
Gastroenterology. 2015-01-01; 148.1: 203-214.e16.
PMID: 25239591
Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces.
Genome announcements. 2013-02-21; 1.1:
PMID: 23469340
Microbiome in human health and disease.
Science progress. 2013-01-01; 96.Pt 2: 153-70.
PMID: 23901633
Microbiome analysis of stool samples from African Americans with colon polyps.
PloS one. 2013-01-01; 8.12: e81352.
PMID: 24376500
Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.
Proceedings of the National Academy of Sciences of the United States of America. 2012-06-19; 109.25: 9692-8.
PMID: 22615407
Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease.
Journal of hepatology. 2012-06-01; 56.6: 1283-92.
PMID: 22326468
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.
BMC bioinformatics. 2012-03-19; 13.42.
PMID: 22429538
Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.
BMC genomics. 2010-09-07; 11.488.
PMID: 20819230
Bacterial diversity in the oral cavity of 10 healthy individuals.
The ISME journal. 2010-08-01; 4.8: 962-74.
PMID: 20336157
Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.
Journal of bacteriology. 2008-08-01; 190.15: 5455-63.
PMID: 18556790
Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy.
Infection and immunity. 2008-05-01; 76.5: 1889-96.
PMID: 18316382
Metagenomic analysis of the human distal gut microbiome.
Science (New York, N.Y.). 2006-06-02; 312.5778: 1355-9.
PMID: 16741115
Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences.
Journal of bacteriology. 2006-04-01; 188.7: 2364-74.
PMID: 16547022
Molecular analysis of the bacterial microbiota in the human stomach.
Proceedings of the National Academy of Sciences of the United States of America. 2006-01-17; 103.3: 732-7.
PMID: 16407106
Diversity of the human intestinal microbial flora.
Science (New York, N.Y.). 2005-06-10; 308.5728: 1635-8.
PMID: 15831718
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.
PLoS biology. 2005-01-01; 3.1: e15.
PMID: 15660156

Identifying Healthy Aging Biomarkers

This study aims to identify specific biomarkers that correlate with longevity and healthy aging using genomics and proteomics approaches.

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Characterizing the Microbial Communities in Caribbean Environments

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Gut Microbiome Sysbiosis in Childhood Acute Lymphoblastic Leukemia (ALL) Patients

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Effect of Xylitol Consumption on the Oral Microbiome

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Leonardo da Vinci DNA Project

This project utilizes genomics approaches to confirm the identity of the remains purported to be that of Leonardo da Vinci as well as to characterize the microbial population on aging artwork.

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Relationship Between the Oral Microbiome and Caries Status of Young Twins

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Proteomics for UTI diagnosis

Understanding host-pathogen interactions is critical when it comes to improving diagnostic approaches to urinary tract infections. 

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Human Microbiome Project

The Human Microbiome Project involves characterizing human microbial isolates using whole genome shotgun sequencing.

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Understanding Dissemination Routes of Antibiotic Resistance During Early Life

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Zoo in You Traveling Exhibition

Our bodies are home to trillions of bacteria. This project provides an education resource to middle and high school aged children who are interested in science and medicine.

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Signature Infiltration and Maintenance on Plasmid Elements creating a Forensic Microbial System (SIMPLE-FMS)

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Human Hair Microbiota

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Comprehensive Genome Sequencing of Nontyphoidal Salmonellae

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Genome Sequencing of Atypical Disease-associated and Emerging Infectious Disease Isolates of C. Jejuni, and Related Species

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The Nasopharynx Microbiome and Pneumococcal Vaccination in Filipino and South African Infants

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Gut Microbiome-Based Metagenomic Signature for Detection of Advanced Fibrosis in Nonalcoholic Fatty Liver Disease

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Progression of Esophageal Cancer

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Seasonal Succession in the High Arctic

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Transmission Kinetics of RSV Infection

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Howler Monkey Microbiome

Gastrointestinal microbial community composition and habitat structure in howler monkeys (Alouatta pigra).

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Vervet Microbiome

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Western Lowland Gorilla Microbiome

The gastrointestinal microbiota composition and function of free range wild Western Lowland Gorillas mirrors macro-ecological patterns.

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Vaginal Microbiome Project

A metagenomics approach to understanding the relationship between the vaginal microbiome, bacterial vaginosis, vaginal health and preterm birth.

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Mouse Microbiome

Enteric dysbiosis associated with a mouse model of alcoholic liver disease. The translocation of bacteria and bacterial products into the circulation contributes to alcoholic liver disease.

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Bovine Rumen Microbiome

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The Montastraea faveolata Microbiome

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Coral Pathogen Vibrio coralliilyticus

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Bottlenose Dolphin Microbiome

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Chicken Cecum Microbiome

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TEDxIEMadrid — Karen Nelson: We are not alone: The depths of the human superorganism
Salk Institute Lecture — Karen Nelson on overcoming the challenges in a scientific career
Precision Medicine Leaders Summit — The Invisible Ecosystem – Illuminating the Microbiome with Precision Medicine
Science — Harnessing the Power of Metagenomics: Applications, Methods, and Real World Examples
18-Jun-2020
Press Release

Biology in Art: Genetic Detectives ID Microbes Suspected of Slowly Ruining Humanity’s Treasures

DNA science may help restore, preserve historic works, unmask counterfeits

The trait elite baseball hitters share with Leonardo da Vinci: A “quick eye” with higher “frames per second.” A function of training, genetics, or both?

26-May-2020
Press Release

Maintaining a Healthy Upper Respiratory Tract Microbiome May Help Prevent Secondary Infections in Influenza A Patients

An influenza-impacted upper respiratory tract microbiome may invite opportunistic bacterial pathogens

13-Nov-2019
The San Diego Union-Tribune

Pink shoes and a lab jacket: Finding your way as a female scientist

Women in science tell high school girls they, too, can change the world

22-Aug-2019
Workshop Alert

JCVI/AADR Fall Focused Symposium

Integrating Omic Datasets Towards Translation

02-May-2018
Blog

BioVision Alexandria 2018