Nature Reviews Genetics2025
Genome scale models in human metabologenomics
Showed how personalised genome scale metabolic models can be built from human multi omic data, the backbone of how we model your biology.
Read the paperScience, our research
LongevityDecoded in the open
Phenome is built on peer reviewed science. Our team and collaborators publish in Longevity, Systems Biology, Genomics and Microbiome research, and the methods behind your reports trace directly back to that work in the world’s leading journals.
- Peer reviewedin Nature Reviews Genetics, Science Signaling and Cell Metabolism
- 10+ yrsof longevity research
- 4 omicsgenome, microbiome, proteome, transcriptome
- 0black boxes, methods are traceable
Published inThe world’s leading journals
A selection of the peer reviewed work our methods build on. The full list follows below.
Science Signaling2020
An atlas of human metabolism
A reference map of human metabolic reactions that underpins how we read and contextualise your metabolic results.
Read the paperCell Metabolism2015
Quantifying diet induced metabolic changes of the human gut microbiome
Demonstrated how diet reshapes the gut microbiome’s metabolism, foundational to our microbiome insights and food first guidance.
Read the paperEvery paper, by method
33 peer reviewed papers from Phenome’s scientific team and collaborators, grouped by the measurement they rest on. Each one opens the original paper.
Genome and multi-omics
7 papers- 2025Longitudinal big biological data in the AI eraMardinoglu et al. · Molecular Systems Biology
- 2025Genome-scale models in human metabologenomicsMardinoglu and Palsson · Nature Reviews Genetics
- 2024Rapid genome sequencing for critically ill infants: an inaugural pilot study from TurkeyGuner Yilmaz et al. · Frontiers in Pediatrics
- 2022Machine Learning Analysis Reveals Biomarkers for the Detection of Neurological DiseasesLam et al. · Frontiers in Molecular Neuroscience
- 2021iNetModels 2.0: an interactive visualization and database of multi-omics dataArif et al. · Nucleic Acids Research
- 2020Integration of molecular profiles in a longitudinal wellness profiling cohortTebani et al. · Nature Communications
- 2020An atlas of human metabolismRobinson et al. · Science Signaling
Transcriptome
8 papers- 2025Integrative proteo-transcriptomic characterization of advanced fibrosis in chronic liver disease across etiologiesYang et al. · Cell Reports Medicine
- 2025The Human Pathology Atlas for deciphering the prognostic features of human cancersYuan et al. · eBioMedicine
- 2021A single cell type transcriptomics map of human tissuesKarlsson et al. · Science Advances
- 2020Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and WomenChapman et al. · Cell Reports
- 2019A genome-wide transcriptomic analysis of protein-coding genes in human blood cellsUhlen et al. · Science
- 2017A pathology atlas of the human cancer transcriptomeUhlen et al. · Science
- 2017Mitochondria-related transcriptional signature is downregulated in adipocytes in obesity: a study of young healthy MZ twinsHeinonen et al. · Diabetologia
- 2016Transcriptomics resources of human tissues and organsUhlén et al. · Molecular Systems Biology
Proteome
5 papers- 2025A human pan-disease blood atlas of the circulating proteomeÁlvez et al. · Science
- 2025Advancing Chronic Liver Disease Diagnoses: Targeted Proteomics for the Non-Invasive Detection of FibrosisVillanueva Raisman et al. · Livers
- 2021Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptomsZhong et al. · eBioMedicine
- 2019Plasma Proteomics Analysis Reveals Dysregulation of Complement Proteins and Inflammation in Acquired Obesity—A Study on Rare BMI-Discordant Monozygotic Twin PairsSahebekhtiari et al. · Proteomics Clinical Applications
- 2015Tissue-based map of the human proteomeUhlén et al. · Science
Metabolome and lipidome
6 papers- 2023Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infectionMikaeloff et al. · eLife
- 2018Elevated Plasma Levels of 3-Hydroxyisobutyric Acid Are Associated With Incident Type 2 DiabetesMardinoglu et al. · eBioMedicine
- 2018Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolomeLovric et al. · Scientific Reports
- 2017Plasma Mannose Levels Are Associated with Incident Type 2 Diabetes and Cardiovascular DiseaseMardinoglu et al. · Cell Metabolism
- 2017Personal model-assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLDMardinoglu et al. · Molecular Systems Biology
- 2016Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin ResistanceLee et al. · Cell Metabolism
Microbiome
7 papers- 2024Global compositional and functional states of the human gut microbiome in health and diseaseLee et al. · Genome Research
- 2024Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer’s diseaseMeng et al. · Alzheimer's Research & Therapy
- 2022Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic SteatosisZeybel et al. · Advanced Science
- 2021Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s diseaseRosario et al. · Cell Reports
- 2019Systems Biology perspective for studying the gut microbiota in human physiology and liver diseasesAltay et al. · eBioMedicine
- 2018An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in HumansMardinoglu et al. · Cell Metabolism
- 2015Quantifying Diet-Induced Metabolic Changes of the Human Gut MicrobiomeShoaie et al. · Cell Metabolism
Where we focus
Systems Biology
Genome scale models that treat your biology as an interacting network, not a list of markers.
Genomics
Turning whole genome data into clinically meaningful, actionable insight.
Microbiome
How the gut and oral microbiome shape metabolism, immunity and longevity.
Metabologenomics
Linking genes and metabolism to explain how your body actually works day to day.
How research reaches you
01Discover
Our team and academic collaborators run studies in Genomics, Microbiome and Systems Biology.
02Validate and publish
Findings are peer reviewed and published before they’re trusted, in journals like Nature Reviews Genetics, Science Signaling and Cell Metabolism.
03Encode into your reports
Validated methods are built into the models and interpretation behind every Phenome result.
Read the science for yourselfRead your own biology.
Explore the Longevity Hub for deep dives, papers and guides.
Every test ships with its methods and references included.