Nature Search

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth.

Michael J Ziller
Kasper D Hansen
Martin J Aryee
Research02 Nov 2014
Nature Methods

Volume: 12, P: 230-232
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

The spatial organization of cells in solid tumors is considered to be important for immune response and response to therapy. Here the authors use multiomics including spatial transcriptomics of human lung tumors prior to patients being treated and show among other things an association of stem-immunity hubs rich in stem-like CD8⁺ T cells with positive response to anti-PD-1 therapy.

Jonathan H. Chen
Linda T. Nieman
Nir Hacohen
Research19 Mar 2024
Nature Immunology

Volume: 25, P: 644-658
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Single-nucleus and spatial, whole-transcriptome profiling of 43 pancreatic adenocarcinomas provides a refined molecular and cellular classification, highlighting a new neoadjuvant treatment-associated neural-like progenitor tumor cell state.

William L. Hwang
Karthik A. Jagadeesh
Aviv Regev
Research28 Jul 2022
Nature Genetics

Volume: 54, P: 1178-1191
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

Combining droplet-based ATAC-seq and mitochondrial DNA sequencing reveals clonal variation in human cells and tissues.

Caleb A. Lareau
Leif S. Ludwig
Vijay G. Sankaran
Research12 Aug 2020
Nature Biotechnology

Volume: 39, P: 451-461
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

Combining microfluidics with combinatorial indexing enables rapid mapping of genome accessibility in hundreds of thousands of single cells.

Caleb A. Lareau
Fabiana M. Duarte
Jason D. Buenrostro
Research24 Jun 2019
Nature Biotechnology

Volume: 37, P: 916-924
Smart-RRBS for single-cell methylome and transcriptome analysis

This is a protocol for profiling the methylome and transcriptome of a single cell by using Smart-seq2 and reduced representation bisulfite sequencing.

Hongcang Gu
Ayush T. Raman
Andreas Gnirke
Protocols09 Jul 2021
Nature Protocols

Volume: 16, P: 4004-4030
Spike-antibody responses to COVID-19 vaccination by demographic and clinical factors in a prospective community cohort study

Vaccination can provide reliable and long-lasting protection against COVID-19, however the immune response to vaccination can vary between individuals and can decline over time, leading to differences in protective effects. Here the authors assess the immune response to COVID-19 vaccination across a large cohort of previously uninfected adults and demonstrate lower post-vaccination antibody levels amongst those with immune-suppressing conditions and medications, as well as those with several other more common chronic conditions.

Madhumita Shrotri
Ellen Fragaszy
Robert W. Aldridge
ResearchOpen Access02 Oct 2022
Nature Communications

Volume: 13, P: 1-10
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

The increasing accessibility of single cell omics technologies beyond transcriptomics demands parallel advances in analysis. Here, the authors introduce STREAM, a pipeline for reconstruction and visualization of differentiation trajectories from both single-cell RNA-seq and ATAC-seq data.

Huidong Chen
Luca Albergante
Luca Pinello
ResearchOpen Access23 Apr 2019
Nature Communications

Volume: 10, P: 1-14
Reversible switching between epigenetic states in honeybee behavioral subcastes

This paper reports that there are substantial differences in DNA methylation patterns between nurses and forager caste phenotypes in honeybees, and that reverting foragers back to nurses reestablishes methylation levels for a majority of genes.

Brian R Herb
Florian Wolschin
Andrew P Feinberg
Research16 Sept 2012
Nature Neuroscience

Volume: 15, P: 1371-1373
Interrogation of human hematopoiesis at single-cell and single-variant resolution

Fine-mapping of blood cell traits in the UK Biobank identifies putative causal variants and enrichment of fine-mapped variants in accessible chromatin of hematopoietic progenitor cells. The study provides an analytical framework for single-variant and single-cell analyses of genetic associations.

Jacob C. Ulirsch
Caleb A. Lareau
Vijay G. Sankaran
Research11 Mar 2019
Nature Genetics

Volume: 51, P: 683-693
GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins

The evolutionarily conserved RNA-binding protein GTSF1 and its homologues interact with members of the PIWI class of Argonaute proteins, increasing the efficiency of the RNA-cleaving activity of PIWI proteins, an essential function across the animal kingdom.

Amena Arif
Shannon Bailey
Phillip D. Zamore
ResearchOpen Access30 Jun 2022
Nature

Volume: 608, P: 618-625
Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

A single-cell approach is used to follow the heritable stochastic changes to DNA methylation that occur in primary chronic lymphocytic leukaemia and healthy B cells, allowing the tracing of cell lineage histories and evolution during treatment with ibrutinib.

Federico Gaiti
Ronan Chaligne
Dan A. Landau
Research15 May 2019
Nature

Volume: 569, P: 576-580
Examining the nexus between servant leadership and employee task performance: the moderation mediation model

Muhammad Zada
Jawad Khan
Shagufta Zada
ResearchOpen Access17 Nov 2024
Humanities and Social Sciences Communications

Volume: 11, P: 1-12
O-GlcNAcylation is involved in the transcriptional activity of EWS-FLI1 in Ewing's sarcoma

R Bachmaier
D N T Aryee
H Kovar
Research19 Jan 2009
Oncogene

Volume: 28, P: 1280-1284
Inhibition of apoptosis by normal and aberrant Fli-1 and erg proteins involved in human solid tumors and leukemias

Ho-keun Yi
Yasuo Fujimura
E Shyam P Reddy
Research20 Mar 1997
Oncogene

Volume: 14, P: 1259-1268
Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case–control study

Pierre-Antoine Dugué
Maree T Brinkman
Graham G Giles
ResearchOpen Access04 Aug 2016
British Journal of Cancer

Volume: 115, P: 664-673
In vivo CRISPR editing with no detectable genome-wide off-target mutations

A strategy developed to define off-target effects of gene-editing nucleases in whole organisms is validated and leveraged to show that CRISPR–Cas9 nucleases can be used effectively in vivo without inducing detectable off-target mutations.

Pinar Akcakaya
Maggie L. Bobbin
J. Keith Joung
Research12 Sept 2018
Nature

Volume: 561, P: 416-419
Delineation of a 6 cM commonly deleted region in childhood acute lymphoblastic leukemia on the 6q chromosomal arm

B Gérard
H Cavé
B Grandchamp
Research01 Feb 1997
Leukemia

Volume: 11, P: 228-232
Variability in functional p53 reactivation by PRIMA-1^Met/APR-246 in Ewing sarcoma

D N T Aryee
S Niedan
H Kovar
ResearchOpen Access15 Oct 2013
British Journal of Cancer

Volume: 109, P: 2696-2704
Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

Region Capture Micro-C (RCMC) combines MNase-based 3C with a tiling region-capture method. Profiling mouse embryonic stem cells with RCMC identifies nested microcompartments, which connect enhancers and promoters.

Viraat Y. Goel
Miles K. Huseyin
Anders S. Hansen
Research08 May 2023
Nature Genetics

Volume: 55, P: 1048-1056
Comprehensive methylome map of lineage commitment from haematopoietic progenitors

During haematopoiesis, multipotent progenitors differentiate into progressively restricted myeloid or lymphoid progenitors. A comprehensive genome-wide DNA methylation analysis of haematopoietic cell populations with well-characterized differentiation potentials reveals remarkable epigenetic plasticity during lymphoid and myeloid restriction.

Hong Ji
Lauren I. R. Ehrlich
Andrew P. Feinberg
Research15 Aug 2010
Nature

Volume: 467, P: 338-342
First report on the presence of huanglongbing vectors (Diaphorina citri and Trioza erytreae) in Ghana

Owusu F. Aidoo
Fred K. Ablormeti
Mamoudou Sétamou
ResearchOpen Access13 Jul 2023
Scientific Reports

Volume: 13, P: 1-10
Hsa-mir-145 is the top EWS-FLI1-repressed microRNA involved in a positive feedback loop in Ewing's sarcoma

J Ban
G Jug
H Kovar
Research10 Jan 2011
Oncogene

Volume: 30, P: 2173-2180
Suppression of KCMF1 by constitutive high CD99 expression is involved in the migratory ability of Ewing's sarcoma cells

M Kreppel
D N T Aryee
H Kovar
Research12 Dec 2005
Oncogene

Volume: 25, P: 2795-2800
Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in human osteosarcoma

Christopher Lietz et al. examined genome-wide methylation in patient cohorts of primary osteosarcoma. Their results suggest that genomic hypomethylation is predictive of response to standard chemotherapy, and provide further insight into clinical implications of methylation patterns.

Christopher E. Lietz
Erik T. Newman
Dimitrios Spentzos
ResearchOpen Access08 Mar 2022
Communications Biology

Volume: 5, P: 1-20
Magnetic Resonance Spectroscopy-based Metabolomic Biomarkers for Typing, Staging, and Survival Estimation of Early-Stage Human Lung Cancer

Yannick Berker
Lindsey A. Vandergrift
Leo L. Cheng
ResearchOpen Access16 Jul 2019
Scientific Reports

Volume: 9, P: 1-12
Suppression of FOXO1 is responsible for a growth regulatory repressive transcriptional sub-signature of EWS-FLI1 in Ewing sarcoma

S Niedan
M Kauer
H Kovar
ResearchOpen Access02 Sept 2013
Oncogene

Volume: 33, P: 3927-3938
Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa

Samuel Terkper Ahuno
Anna-Lisa Doebley
Richard Biritwum
ResearchOpen Access17 Sept 2021
npj Precision Oncology

Volume: 5, P: 1-8
CD99 regulates neural differentiation of Ewing sarcoma cells through miR-34a-Notch-mediated control of NF-κB signaling

S Ventura
D N T Aryee
K Scotlandi
Research30 Nov 2015
Oncogene

Volume: 35, P: 3944-3954
EWS-FLI1 perturbs MRTFB/YAP-1/TEAD target gene regulation inhibiting cytoskeletal autoregulatory feedback in Ewing sarcoma

A M Katschnig
M O Kauer
H Kovar
ResearchOpen Access03 Jul 2017
Oncogene

Volume: 36, P: 5995-6005

Search

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

Smart-RRBS for single-cell methylome and transcriptome analysis

Spike-antibody responses to COVID-19 vaccination by demographic and clinical factors in a prospective community cohort study

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

Reversible switching between epigenetic states in honeybee behavioral subcastes

Interrogation of human hematopoiesis at single-cell and single-variant resolution

GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

Examining the nexus between servant leadership and employee task performance: the moderation mediation model

O-GlcNAcylation is involved in the transcriptional activity of EWS-FLI1 in Ewing's sarcoma

Inhibition of apoptosis by normal and aberrant Fli-1 and erg proteins involved in human solid tumors and leukemias

Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case–control study

In vivo CRISPR editing with no detectable genome-wide off-target mutations

Delineation of a 6 cM commonly deleted region in childhood acute lymphoblastic leukemia on the 6q chromosomal arm

Variability in functional p53 reactivation by PRIMA-1^Met/APR-246 in Ewing sarcoma

Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

First report on the presence of huanglongbing vectors (Diaphorina citri and Trioza erytreae) in Ghana

Hsa-mir-145 is the top EWS-FLI1-repressed microRNA involved in a positive feedback loop in Ewing's sarcoma

Suppression of KCMF1 by constitutive high CD99 expression is involved in the migratory ability of Ewing's sarcoma cells

Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in human osteosarcoma

Magnetic Resonance Spectroscopy-based Metabolomic Biomarkers for Typing, Staging, and Survival Estimation of Early-Stage Human Lung Cancer

Suppression of FOXO1 is responsible for a growth regulatory repressive transcriptional sub-signature of EWS-FLI1 in Ewing sarcoma

Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa

CD99 regulates neural differentiation of Ewing sarcoma cells through miR-34a-Notch-mediated control of NF-κB signaling

EWS-FLI1 perturbs MRTFB/YAP-1/TEAD target gene regulation inhibiting cytoskeletal autoregulatory feedback in Ewing sarcoma

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