Nature Search

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.

Daniel Taliun
Daniel N. Harris
Gonçalo R. Abecasis
ResearchOpen Access10 Feb 2021
Nature

Volume: 590, P: 290-299
Mapping and characterization of structural variation in 17,795 human genomes

Structural variants in more than 17,000 human genomes are mapped and characterized using whole-genome sequencing, showing how this type of variation contributes to rare deleterious coding and noncoding alleles.

Haley J. Abel
David E. Larson
Ira M. Hall
Research27 May 2020
Nature

Volume: 583, P: 83-89
A large meta-analysis identifies genes associated with anterior uveitis

Anterior Uveitis is a common inflammatory eye disease that can result in vision loss. Here, the authors perform GWAS and whole-exome analyses of Anterior Uveitis to identify the underlying genetics of HLA-B*27 positive and negative forms of the disease.

Sahar Gelfman
Arden Moscati
Giovanni Coppola
ResearchOpen Access11 Nov 2023
Nature Communications

Volume: 14, P: 1-13
Promoting early relational health and resilience in pediatric primary care: a qualitative study

Erin Roby
Lauren K. O’Connell
Rachel S. Gross
Research15 Mar 2026
Pediatric Research

P: 1-11
Patterns of hypermutation shape tumorigenesis and immunotherapy response in mismatch-repair-deficient glioma

The authors analyze 162 primary mismatch-repair-deficient gliomas and identify three subgroups underpinned by distinct somatic mutations in replicative DNA polymerases and IDH1.

Nicholas R. Fernandez
Yuan Chang
Uri Tabori
Research22 Dec 2025
Nature Genetics

Volume: 58, P: 132-142
Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis

Using data from a single time point, passenger-approximated clonal expansion rate (PACER) estimates the fitness of common driver mutations that lead to clonal haematopoiesis and identifies TCL1A activation as a mediator of clonal expansion.

Joshua S. Weinstock
Jayakrishnan Gopakumar
Siddhartha Jaiswal
Research12 Apr 2023
Nature

Volume: 616, P: 755-763
Microbial aerotrophy enables continuous primary production in diverse cave ecosystems

Metabolic strategies of cave microorganisms are poorly studied. Here, the authors show that cave microbes use atmospheric trace gases hydrogen, carbon monoxide and methane as energy and carbon sources, sustaining primary production and revealing how life can thrive in oligotrophic and dark ecosystems.

Sean K. Bay
Gaofeng Ni
Chris Greening
ResearchOpen Access21 Nov 2025
Nature Communications

Volume: 16, P: 1-16
Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Genotype and exome sequencing of 150,000 participants and whole-genome sequencing of 9,950 selected individuals recruited into the Mexico City Prospective Study constitute a valuable, publicly available resource of non-European sequencing data.

Andrey Ziyatdinov
Jason Torres
Roberto Tapia-Conyer
ResearchOpen Access11 Oct 2023
Nature

Volume: 622, P: 784-793
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes

Pamela Feliciano
Xueya Zhou
Wendy K. Chung
ResearchOpen Access23 Aug 2019
npj Genomic Medicine

Volume: 4, P: 1-14
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Microbes play key roles in wastewater treatment. Here, Singleton et al. use long-read and short-read sequencing to recover 1083 high-quality metagenome-assembled genomes from 23 wastewater treatment plants, and combine this information with amplicon data, Raman microspectroscopy and FISH to reveal functionally important lineages.

Caitlin M. Singleton
Francesca Petriglieri
Mads Albertsen
ResearchOpen Access31 Mar 2021
Nature Communications

Volume: 12, P: 1-13
Genome-centric view of carbon processing in thawing permafrost

Analysis of more than 1,500 microbial genomes sheds light on the processing of carbon released as permafrost thaws.

Ben J. Woodcroft
Caitlin M. Singleton
Gene W. Tyson
Research16 Jul 2018
Nature

Volume: 560, P: 49-54
Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Analysis of 97,691 high-coverage human blood DNA-derived whole-genome sequences enabled simultaneous identification of germline and somatic mutations that predispose individuals to clonal expansion of haematopoietic stem cells, indicating that both inherited and acquired mutations are linked to age-related cancers and coronary heart disease.

Alexander G. Bick
Joshua S. Weinstock
Pradeep Natarajan
Research14 Oct 2020
Nature

Volume: 586, P: 763-768
Cardiac angiogenic imbalance leads to peripartum cardiomyopathy

Evidence from mice and humans indicates that peripartum cardiomyopathy (PPCM) is a vascular disease caused by excessive anti-angiogenic signalling in the peripartum period of pregnancy and that pre-eclampsia and multiple gestation are important risk factors for the development of PPCM.

Ian S. Patten
Sarosh Rana
Zoltan Arany
Research09 May 2012
Nature

Volume: 485, P: 333-338
A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum

Currently available platforms to study liver stage of Plasmodium species have limitations. Here, the authors show that primary human hepatocyte cultures in 384-well format support hypnozoite and other liver stage development and are suitable for drug and antibody screens.

Alison Roth
Steven P. Maher
John H. Adams
ResearchOpen Access09 May 2018
Nature Communications

Volume: 9, P: 1-16
Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes

Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.

Joanne B. Emerson
Ruth K. Varner
Virginia I. Rich
ResearchOpen Access05 Oct 2021
Nature Communications

Volume: 12, P: 1-10
Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics

Here, Li et al. show that functional redundancy, which has not previously been quantified at the proteome level, can arise when different microbes play similar roles in the gut microbiome, revealing that proteomes are nested among gut microbes, favoring high functional redundancy.

Leyuan Li
Tong Wang
Daniel Figeys
ResearchOpen Access10 Jun 2023
Nature Communications

Volume: 14, P: 1-14
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats

Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.

Mantas Sereika
Aaron James Mussig
Mads Albertsen
ResearchOpen Access24 Jul 2025
Nature Microbiology

Volume: 10, P: 2018-2030
A genomic view of the reef-building coral Porites lutea and its microbial symbionts

The recovery of metagenome-assembled genomes from the coral Porites lutea, its dinoflagellate symbiont, and its bacterial and archaeal populations, enabled comparative genomic identification of functions important for host–microbe interactions and nutritional associations.

Steven J. Robbins
Caitlin M. Singleton
David G. Bourne
Research23 Sept 2019
Nature Microbiology

Volume: 4, P: 2090-2100
Gene-level analysis of rare variants in 379,066 whole exome sequences identifies an association of GIGYF1 loss of function with type 2 diabetes

Aimee M. Deaton
Margaret M. Parker
Paul Nioi
ResearchOpen Access03 Nov 2021
Scientific Reports

Volume: 11, P: 1-16
Racial and ethnic differences in prenatal exposure to environmental phenols and parabens in the ECHO Cohort

Michael S. Bloom
Sudhi Upadhyaya
Lynne M. Smith
ResearchOpen Access15 Feb 2025
Journal of Exposure Science & Environmental Epidemiology

Volume: 35, P: 992-1002
Parasitic bacteria control foam formation

The search for bacteriophages for the biocontrol of bacteria commonly associated with wastewater foams, such as Gordonia, unexpectedly reveals a new parasitic ultrasmall bacterium with predatory activity against foaming microorganisms.

Per H. Nielsen
Caitlin M. Singleton
News & Views28 May 2021
Nature Microbiology

Volume: 6, P: 701-702
Polymorphisms in CYP2C9 are associated with response to indomethacin among neonates with patent ductus arteriosus

Caitlin J Smith
Kelli K Ryckman
John M Dagle
Research05 Jul 2017
Pediatric Research

Volume: 82, P: 776-780
“Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems

Francesca Petriglieri
Caitlin Singleton
Per H. Nielsen
ResearchOpen Access21 Jun 2021
The ISME Journal

Volume: 15, P: 3605-3614
Host-linked soil viral ecology along a permafrost thaw gradient

The recovery of viral populations from peatland soils across a permafrost thaw gradient provides insights into soil viral diversity, their hosts and the potential impacts on carbon cycling in this environment.

Joanne B. Emerson
Simon Roux
Matthew B. Sullivan
ResearchOpen Access16 Jul 2018
Nature Microbiology

Volume: 3, P: 870-880
Probing the distinct chemosensitivity of Plasmodium vivax liver stage parasites and demonstration of 8-aminoquinoline radical cure activity in vitro

Steven P. Maher
Amélie Vantaux
Dennis E. Kyle
ResearchOpen Access07 Oct 2021
Scientific Reports

Volume: 11, P: 1-18
Composition of the maternal gastrointestinal microbiome as a predictor of neonatal birth weight

Caitlin Dreisbach
Stephanie Prescott
Jeanne Alhusen
Research07 Apr 2023
Pediatric Research

Volume: 94, P: 1158-1165
Use of term reference infants in assessing the developmental outcome of extremely preterm infants: lessons learned in a multicenter study

Charles E. Green
Jon E. Tyson
Kimberlee Weaver-Lewis
ResearchOpen Access04 Aug 2023
Journal of Perinatology

Volume: 43, P: 1398-1405
Variable preterm oral microbiome stabilizes and reflects a full-term infant profile within three months

Caitlin A. Selway
Carmel T. Collins
Laura S. Weyrich
ResearchOpen Access01 Mar 2023
Pediatric Research

P: 1-9
Methanotrophy across a natural permafrost thaw environment

Caitlin M Singleton
Carmody K McCalley
Gene W Tyson
ResearchOpen Access28 Jun 2018
The ISME Journal

Volume: 12, P: 2544-2558
A longitudinal resource for population neuroscience of school-age children and adolescents in China

Xue-Ru Fan
Yin-Shan Wang
Xi-Nian Zuo
ResearchOpen Access21 Aug 2023
Scientific Data

Volume: 10, P: 1-24

Search

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Mapping and characterization of structural variation in 17,795 human genomes

A large meta-analysis identifies genes associated with anterior uveitis

Promoting early relational health and resilience in pediatric primary care: a qualitative study

Patterns of hypermutation shape tumorigenesis and immunotherapy response in mismatch-repair-deficient glioma

Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis

Microbial aerotrophy enables continuous primary production in diverse cave ecosystems

Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Genome-centric view of carbon processing in thawing permafrost

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Cardiac angiogenic imbalance leads to peripartum cardiomyopathy

A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum

Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes

Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

Gene-level analysis of rare variants in 379,066 whole exome sequences identifies an association of GIGYF1 loss of function with type 2 diabetes

Racial and ethnic differences in prenatal exposure to environmental phenols and parabens in the ECHO Cohort

Parasitic bacteria control foam formation

Polymorphisms in CYP2C9 are associated with response to indomethacin among neonates with patent ductus arteriosus

“Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems

Host-linked soil viral ecology along a permafrost thaw gradient

Probing the distinct chemosensitivity of Plasmodium vivax liver stage parasites and demonstration of 8-aminoquinoline radical cure activity in vitro

Composition of the maternal gastrointestinal microbiome as a predictor of neonatal birth weight

Use of term reference infants in assessing the developmental outcome of extremely preterm infants: lessons learned in a multicenter study

Variable preterm oral microbiome stabilizes and reflects a full-term infant profile within three months

Methanotrophy across a natural permafrost thaw environment

A longitudinal resource for population neuroscience of school-age children and adolescents in China

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