Evidence map›Paper›PMID 30561547›Full record

ArticleBioinformatics (Oxford, England)2019

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

Mohammad Sajjad Ghaemi, Daniel B DiGiulio, Kévin Contrepois, Benjamin Callahan, Thuy T M Ngo, Brittany Lee-McMullen, Benoit Lehallier, Anna Robaczewska, David Mcilwain, Yael Rosenberg-Hasson and 33 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.

0numbers the graph read from it
0cells of the map it votes in
127citing papers in PubMed
16.2field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

127 citing papers in PubMed, 192 citations in OpenAlex.

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  14. Towards a new taxonomy of preterm birth.Journal of perinatology : official journal of the California Perinatal Association · 2025
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67 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

43 authors at 7 institutions in 2 countries.

Mohammad Sajjad GhaemiDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Daniel B DiGiulioDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Kévin ContrepoisDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Benjamin CallahanDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Thuy T M NgoDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Brittany Lee-McMullenDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Benoit LehallierDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
Anna RobaczewskaDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
David McilwainDepartment of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Yael Rosenberg-HassonInstitute for Immunity, Transplantation and Infection, Human Immune Monitoring Center Stanford, CA, USA.
Ronald J WongDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Cecele QuaintanceDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Anthony CulosDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Natalie StanleyDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Athena TanadaDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Amy TsaiDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Dyani GaudilliereDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Edward GanioDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Xiaoyuan HanDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Kazuo AndoDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Leslie McNeilDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Martha TingleDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Paul WiseDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Ivana MaricDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Marina SirotaInstitute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA.
Tony Wyss-CorayDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
Virginia D WinnDepartment of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA.
Maurice L DruzinDepartment of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA.
Ronald GibbsDepartment of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA.
Gary L DarmstadtDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
David B LewisDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Vahid Partovi NiaDépartement de Mathématiques et de Génie Industriel, École Polytechnique de Montréal, QC, Canada.
Bruno AgardDépartement de Mathématiques et de Génie Industriel, École Polytechnique de Montréal, QC, Canada.
Robert TibshiraniDepartments of Biomedical Data Sciences and Statistics, Stanford University, Stanford, CA, USA.
Garry NolanDepartment of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Michael P SnyderDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
David A RelmanDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Stephen R QuakeDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Gary M ShawDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
David K StevensonDivision of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Martin S AngstDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Brice GaudilliereDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Nima AghaeepourDepartment of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Stanford University · USVA Palo Alto Health Care System · USTransport Canada · CAGroup for Research in Decision Analysis · CANorth Carolina State University · USOregon Health & Science University · USUniversity of California, San Francisco · US

Funding

Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5M
Stanford Islet Research CoreP30DK116074 · NIDDK · STANFORD UNIVERSITY · PI Seung K Kim · 2017 to 2026
$19.5M
Preeclampsia to cardiovascular disease: Life course analysis of biomarkers and riskR01HL139844 · NHLBI · STANFORD UNIVERSITY · PI HLATKY, MARK A., WINN, VIRGINIA D · 2018 to 2021
$9.0M
Machine Learning for Integrative Modeling of the Immune System in Clinical SettingsR35GM138353 · NIGMS · STANFORD UNIVERSITY · PI AGHAEEPOUR, NIMA · 2020 to 2024
$2.2M
Stanford Career Development Program in Omics of Lung DiseasesK12HL120001 · NHLBI · STANFORD UNIVERSITY · PI NICOLLS, MARK ROBERT, RABINOVITCH, MARLENE · 2013 to 2017
$1.3M
Elucidating the Role of the Genetic and Environmental Determinants of Preterm Birth Using Integrative Computational ApproachesK01LM012381 · NLM · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SIROTA, MARINA · 2016 to 2018
$531k
NHLBI NIH HHS K12 HL120001NHLBI NIH HHS R01 HL139844NIAID NIH HHS U19 AI057229NIDDK NIH HHS P30 DK116074NIGMS NIH HHS R35 GM138353NLM NIH HHS K01 LM012381Wellcome Trust
6 · The paper itself

Abstract

Motivation: Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. Results: We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified. Availability and implementation: Datasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/. Supplementary information: Supplementary data are available at Bioinformatics online.

Indexed as

MetabolomeMicrobiotaPregnancyProteomeTranscriptomeComputational BiologyFemaleHumansProteome

Identifiers

PMID30561547
PMCPMC6298056
OpenAlexW2809990446

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.