Nature Search

Epigenetic alterations facilitate transcriptional and translational programs in hypoxia

Watt, Dauber, Szkop and colleagues find that H3K4me3 remodels 5′UTR selection in hypoxia and that this process is independent of HIF-1 transcriptional mechanisms.

Kathleen Watt
Bianca Dauber
Lynne-Marie Postovit
ResearchOpen Access16 Oct 2025
Nature Cell Biology

Volume: 27, P: 1965-1981
cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions

cellSTAAR advances noncoding rare variant association analysis by integrating single-cell genomics data.

Eric Van Buren
Yi Zhang
Xihong Lin
Research31 Dec 2025
Nature Methods

P: 1-12
Superfoetation of Mice

S. A. BARNETT
KATHLEEN M. H. MUNRO
Research26 Sept 1970
Nature

Volume: 227, P: 1343-1344
Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer

The molecular processes that lead to neuroendocrine prostate cancer after treating prostate adenocarcinoma (PRAD) are not well understood. Here the authors show that regulation by FOXA1 and changes in the epigenomic profile drive the transition from PRAD to a neuroendocrine phenotype.

Sylvan C. Baca
David Y. Takeda
Matthew L. Freedman
ResearchOpen Access30 Mar 2021
Nature Communications

Volume: 12, P: 1-12
Another Doctors' Dilemma

KATHLEEN LONSDALE
Correspondence31 May 1969
Nature

Volume: 222, P: 906
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
Whole-genome sequencing of patients with rare diseases in a national health system

Whole-genome sequencing and phenotype data sharing are introduced in a national health system to streamline diagnosis and to discover coding and non-coding variants that cause rare diseases.

Ernest Turro
William J. Astle
Willem H. Ouwehand
Research24 Jun 2020
Nature

Volume: 583, P: 96-102
Clonal haematopoiesis and risk of chronic liver disease

A study shows that clonal haematopoiesis of indeterminate potential is associated with an increased risk of chronic liver disease specifically through the promotion of liver inflammation and injury.

Waihay J. Wong
Connor Emdin
Pradeep Natarajan
Research12 Apr 2023
Nature

Volume: 616, P: 747-754
A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies

MultiSTAAR provides a general and flexible statistical framework for functionally informed multi-trait rare variant analysis of biobank-scale sequencing studies by jointly analyzing multiple traits and incorporating annotation information.

Xihao Li
Han Chen
Xihong Lin
Research07 Feb 2025
Nature Computational Science

Volume: 5, P: 125-143
Genome sequencing unveils a regulatory landscape of platelet reactivity

Platelet aggregation is associated with myocardial infarction and stroke. Here, the authors have conducted a whole genome sequencing association study on platelet aggregation, discovering a locus in RGS18, where enhancer assays suggest an effect on activity of haematopoeitic lineage transcription factors.

Ali R. Keramati
Ming-Huei Chen
Andrew D. Johnson
ResearchOpen Access15 Jun 2021
Nature Communications

Volume: 12, P: 1-13
Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk

Analyses of genome and exome sequencing data identify rare coding and structural variants associated with atrial fibrillation and highlight genetic links between atrial fibrillation and cardiomyopathies.

Seung Hoan Choi
Sean J. Jurgens
Patrick T. Ellinor
Research06 Mar 2025
Nature Genetics

Volume: 57, P: 548-562
Whole-genome sequencing of a sporadic primary immunodeficiency cohort

Whole-genome sequencing analysis of individuals with primary immunodeficiency identifies new candidate disease-associated genes and shows how the interplay between genetic variants can explain the variable penetrance and complexity of the disease.

James E. D. Thaventhiran
Hana Lango Allen
Kenneth G. C. Smith
Research06 May 2020
Nature

Volume: 583, P: 90-95
Measuring the semantic priming effect across many languages

In this Stage 2 Registered Report, Buchanan et al. show evidence confirming the phenomenon of semantic priming across speakers of 19 diverse languages.

Erin M. Buchanan
Kelly Cuccolo
Savannah C. Lewis
Research24 Sept 2025
Nature Human Behaviour

Volume: 10, P: 182-201
Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma

Radiation-induced high-grade gliomas (RIGs) are an incurable late complication of cranial radiation therapy. In the largest study to date, we report the results of DNA methylation profiling, RNA-Seq and genomic sequencing of 32 RIG tumors, and an in vitro drug screen in two RIG cell lines.

John DeSisto
John T. Lucas Jr.
Adam L. Green
ResearchOpen Access20 Sept 2021
Nature Communications

Volume: 12, P: 1-16
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

Analysis of whole-genome sequences of 25,465 individuals of European ancestry shows that rare variants contribute substantially to the heritability of height and body mass index.

Pierrick Wainschtein
Deepti Jain
Peter M. Visscher
Research07 Mar 2022
Nature Genetics

Volume: 54, P: 263-273
Whole genome sequence analysis of blood lipid levels in >66,000 individuals

Although the common genetic variants contributing to blood lipid levels have been studied, the contribution of rare variants is less understood. Here, the authors perform a rare coding and noncoding variant association study of blood lipid levels using whole genome sequencing data.

Margaret Sunitha Selvaraj
Xihao Li
Pradeep Natarajan
ResearchOpen Access11 Oct 2022
Nature Communications

Volume: 13, P: 1-18
GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Investigation of variation in three cohorts has identified multiple genetic signals associated with the pregnancy-specific liver disorder, intrahepatic cholestasis of pregnancy, giving insight into the disease which can cause preterm birth and stillbirth.

Peter H. Dixon
Adam P. Levine
Catherine Williamson
ResearchOpen Access17 Aug 2022
Nature Communications

Volume: 13, P: 1-18
A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies

STAARpipeline is a comprehensive framework for flexible and scalable rare-variant association analysis using whole-genome sequencing data and annotation information.

Zilin Li
Xihao Li
Xihong Lin
Research27 Oct 2022
Nature Methods

Volume: 19, P: 1599-1611
Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

Pooling participant-level genetic data into a single analysis can result in variance stratification, reducing statistical performance. Here, the authors develop variant-specific inflation factors to assess variance stratification and apply this to pooled individual-level data from whole genome sequencing.

Tamar Sofer
Xiuwen Zheng
Kenneth M. Rice
ResearchOpen Access09 Jun 2021
Nature Communications

Volume: 12, P: 1-14
MNK2 deficiency potentiates β-cell regeneration via translational regulation

MNK2 was identified as the target of a small molecule named CID661578 that can stimulate pancreatic β-cell generation in zebrafish, pig and human organoids. CID661578 prevents MNK2 from binding to eIF4G in the translation initiation complex.

Christos Karampelias
Kathleen Watt
Olov Andersson
ResearchOpen Access13 Jun 2022
Nature Chemical Biology

Volume: 18, P: 942-953
Risk factors for rapid axial length elongation with low concentration atropine for myopia control

Aicun Fu
Fiona Stapleton
Yong Lyu
ResearchOpen Access03 Jun 2021
Scientific Reports

Volume: 11, P: 1-7
Translon: a single term for translated regions

Michał I. Świrski
Jack A. S. Tierney
Pavel V. Baranov
Correspondence01 Sept 2025
Nature Methods

Volume: 22, P: 2002-2006
Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals

Most studies of the genetics of the metabolome have been done in individuals of European descent. Here, the authors integrate genomics and metabolomics in Black individuals, highlighting the value of whole genome sequencing in diverse populations and linking circulating metabolites to human disease.

Usman A. Tahir
Daniel H. Katz
Robert E. Gerszten
ResearchOpen Access22 Aug 2022
Nature Communications

Volume: 13, P: 1-16
Author Correction: Clonal haematopoiesis and risk of chronic liver disease

Waihay J. Wong
Connor Emdin
Pradeep Natarajan
Amendments and Corrections03 Jul 2023
Nature

Volume: 619, P: E47
Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort

James E. D. Thaventhiran
Hana Lango Allen
Kenneth G. C. Smith
Amendments and Corrections17 Jul 2020
Nature

Volume: 584, P: E2
A 130,000-year-old archaeological site in southern California, USA

Evidence of mastodon bone modifications for marrow extraction and/or tool production, found in the presence of hammerstones and anvils that showed use-wear and impact marks, suggest the presence of Homo in North America around 130 thousand years ago.

Steven R. Holen
Thomas A. Deméré
Kathleen A. Holen
Research27 Apr 2017
Nature

Volume: 544, P: 479-483
Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in inflammatory bowel disease patients treated with infliximab and vedolizumab

Vaccination is effective in protecting from COVID-19. Here the authors report immune responses and breakthrough infections in twice-vaccinated patients receiving anti-TNF treatments for inflammatory bowel disease, and find dampened vaccine responses that implicate the need of adapted vaccination schedules for these patients.

Simeng Lin
Nicholas A. Kennedy
Jeannie Bishop
ResearchOpen Access16 Mar 2022
Nature Communications

Volume: 13, P: 1-14
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

This Resource describes data, code and tools developed for the Human Reference Atlas and the Human BioMolecular Atlas Program for building and navigating a multiscale human atlas.

Katy Börner
Philip D. Blood
Bruce W. Herr II
ResearchOpen Access13 Mar 2025
Nature Methods

Volume: 22, P: 845-860
Tailoring 3′ UTRs alters metastatic potential

In cancer, alternative polyadenylation has been shown to lead to altered 3′ UTRs with different regulatory potentials. A study now suggests a mechanism that leads to 3′ UTR lengthening and translational repression of a subset of metastasis-suppressing genes, revealing a new prospective therapeutic vulnerability.

Kathleen Watt
Lynne-Marie Postovit
News & Views08 May 2023
Nature Cell Biology

Volume: 25, P: 805-807
Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

MetaSTAAR enables functionally informed rare variant association analysis in biobank-scale cohorts using an efficient, sparse matrix approach for summary statistic storage.

Xihao Li
Corbin Quick
Xihong Lin
Research23 Dec 2022
Nature Genetics

Volume: 55, P: 154-164
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

A high-resolution reference panel based on whole-genome sequencing data enables accurate imputation of HLA alleles across diverse populations and fine-mapping of HLA association signals for HIV-1 host response.

Yang Luo
Masahiro Kanai
Soumya Raychaudhuri
Research05 Oct 2021
Nature Genetics

Volume: 53, P: 1504-1516
Comparison of visual functions among early and late onset myopia

Salai Dhavamathi Janarthanan
Shonraj Ballae Ganeshrao
Aiswaryah Radhakrishnan
ResearchOpen Access01 Jul 2025
Scientific Reports

Volume: 15, P: 1-9
Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Yang Luo
Masahiro Kanai
Soumya Raychaudhuri
Amendments and Corrections02 Nov 2021
Nature Genetics

Volume: 53, P: 1722
Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data

James H. R. Farmery
Mike L. Smith
Andy G. Lynch
ResearchOpen Access22 Jan 2018
Scientific Reports

Volume: 8, P: 1-17
Kluyveromyces as a Host for Heterologous Gene Expression: Expression and Secretion of Prochymosin

Johan A. van den Berg
Kees J. van der Laken
Jeffrey R. Shuster
Research01 Feb 1990
Bio/Technology

Volume: 8, P: 135-139
Mammographic texture features associated with contralateral breast cancer in the WECARE Study

Gordon P. Watt
Julia A. Knight
Jonine L. Bernstein
ResearchOpen Access29 Nov 2021
npj Breast Cancer

Volume: 7, P: 1-4
4-aminopyridine reverses ataxia and cerebellar firing deficiency in a mouse model of spinocerebellar ataxia type 6

Sriram Jayabal
Hui Ho Vanessa Chang
Alanna J. Watt
ResearchOpen Access06 Jul 2016
Scientific Reports

Volume: 6, P: 1-12
MFRED, 10 second interval real and reactive power for groups of 390 US apartments of varying size and vintage

Christoph J. Meinrenken
Noah Rauschkolb
Patricia J. Culligan
ResearchOpen Access09 Nov 2020
Scientific Data

Volume: 7, P: 1-9
Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis

Debra Van Egeren
Khushi Kohli
Zenta Walther
ResearchOpen Access09 Nov 2022
Scientific Reports

Volume: 12, P: 1-6
Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data

James H. R. Farmery
Mike L. Smith
Andy G. Lynch
Amendments and CorrectionsOpen Access03 Sept 2018
Scientific Reports

Volume: 8, P: 1-4

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