Nature Search

Restoring flowcell type and basecaller configuration from FASTQ files of nanopore sequencing data

Flowcell type and basecaller configuration of nanopore sequencing are crucial for data analysis but are often missing in public datasets, hindering large-scale integrative analysis. Here, the authors present LongBow, which restores this information from FASTQ files.

Jun Mencius
Wenjun Chen
Zhixing Feng
ResearchOpen Access02 May 2025
Nature Communications

Volume: 16, P: 1-19
Correction: Corrigendum: Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

Gang Fang
Diana Munera
Eric E Schadt
Amendments and Corrections10 Jun 2013
Nature Biotechnology

Volume: 31, P: 566
A highly photostable monomeric red fluorescent protein for dual-color 3D STED and time-lapse 3D SIM imaging

mScarlet3-S2 is a red fluorescent protein that is highly photostable and sufficiently bright. It is especially useful for applications such as stimulated emission depletion or structured illumination microscopy imaging with prolonged imaging times.

Ya Ding
Wenting He
Pingyong Xu
ResearchOpen Access26 Nov 2025
Nature Methods

Volume: 23, P: 143-152
Detecting and phasing minor single-nucleotide variants from long-read sequencing data

Cellular genetic heterogeneity is common across biological conditions, yet application of long-read sequencing to this subject is limited by error rates. Here, the authors present iGDA, a tool for detection and phasing of minor variants from long-read sequencing data, allowing accurate reconstruction of haplotypes.

Zhixing Feng
Jose C. Clemente
Eric E. Schadt
ResearchOpen Access24 May 2021
Nature Communications

Volume: 12, P: 1-13
Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics

Efficient and accurate annotation of malignant cells is crucial for single-cell and spatial transcriptomics in cancer. Here, the authors develop Cancer-Finder, a deep-learning algorithm that can identify malignant cells in cancer single-cell and spatial transcriptomics data with speed and precision.

Zhixing Zhong
Junchen Hou
Jia Song
ResearchOpen Access02 Mar 2024
Nature Communications

Volume: 15, P: 1-14
Fully integrated multi-mode optoelectronic memristor array for diversified in-sensor computing

This study reports a fully integrated 128 × 8 optoelectronic memristor array with Si complementary metal–oxide–semiconductor circuits, featuring configurable multi-mode functionality. It demonstrates diversified in-sensor computing tasks and consumes 20 times less energy than GPUs.

Heyi Huang
Xiangpeng Liang
Huaqiang Wu
Research08 Nov 2024
Nature Nanotechnology

Volume: 20, P: 93-103
Deep transfer learning enables lesion tracing of circulating tumor cells

Liquid biopsy offers great promise for noninvasive cancer diagnostics, while the lack of adequate target characterization and analysis hinders its wide application. Here, the authors design a transfer learning-based algorithm to transfer lesion labels from the primary cancer cell atlas to circulating tumor cells.

Xiaoxu Guo
Fanghe Lin
Jia Song
ResearchOpen Access12 Dec 2022
Nature Communications

Volume: 13, P: 1-14
Neural network aided approximation and parameter inference of non-Markovian models of gene expression

Cells are complex systems that make decisions biologists struggle to understand. Here, the authors use neural networks to approximate the solution of mathematical models that capture the history and randomness of biochemical processes in order to understand the principles of transcription control.

Qingchao Jiang
Xiaoming Fu
Ramon Grima
ResearchOpen Access11 May 2021
Nature Communications

Volume: 12, P: 1-12
Mitochondrial dynamics govern whole-body regeneration through stem cell pluripotency and mitonuclear balance

Mitochondrial dynamics in large-scale regeneration remain poorly understood. Here they show that the mitochondrial fusion-fission equilibrium can determine the pluripotency of planarian stem cells and that mitonuclear balance is critical for planarian regeneration.

Xue Pan
Yun Zhao
Kai Lei
ResearchOpen Access13 Dec 2024
Nature Communications

Volume: 15, P: 1-22
Parkin controls dopamine utilization in human midbrain dopaminergic neurons derived from induced pluripotent stem cells

Mutations in parkin, an ubiquitin ligase, cause an inherited form of Parkinson's disease. Here, Jianget al. generate induced pluripotent stem cells from two patients with parkin mutations and find that neurons derived from the stem cells have defects in dopamine release, dopamine uptake and oxidative metabolism.

Houbo Jiang
Yong Ren
Jian Feng
Research07 Feb 2012
Nature Communications

Volume: 3, P: 1-9
Single-handed supramolecular double helix of homochiral bis(N-amidothiourea) supported by double crossed C−I···S halogen bonds

Building an artificial double helix is a compelling challenge, and most strategies rely on the intertwining of two helical strands. Here, in a very different approach, the authors construct a supramolecular double helix from multiple synthetic small molecules chained together by double crossed halogen bonds.

Xiaosheng Yan
Kunshan Zou
Yunbao Jiang
ResearchOpen Access09 Aug 2019
Nature Communications

Volume: 10, P: 1-10
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

Fang et al. generate the first genome-wide, strand-specific, single base–pair resolution map of m6A modifications in Escherichia coli.

Gang Fang
Diana Munera
Eric E Schadt
Research08 Nov 2012
Nature Biotechnology

Volume: 30, P: 1232-1239
Arch dam point cloud segmentation based on deep feature learning and normal vector data optimization

Huokun Li
Yuekang Li
Bo Liu
ResearchOpen Access28 Oct 2024
Scientific Reports

Volume: 14, P: 1-19
10-km passive drone detection using broadband quantum compressed sensing imaging

The dynamic characteristics of drone are detected at the single-photon level.

Shuxiao Wu
Jianyong Hu
Suotang Jia
ResearchOpen Access14 Jul 2025
Light: Science & Applications

Volume: 14, P: 1-12
Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry

Jilei Zhang
Li Chen
Chengming Wang
ResearchOpen Access27 Feb 2018
Scientific Reports

Volume: 8, P: 1-9
Generation of mouse–human chimeric embryos

The authors provide a protocol for generating mouse–human chimeric embryos by injecting naive human pluripotent stem cells converted from the primed state.

Boyang Zhang
Hanqin Li
Jian Feng
Protocols02 Jul 2021
Nature Protocols

Volume: 16, P: 3954-3980
TET1 Deficiency Impairs Morphogen-free Differentiation of Human Embryonic Stem Cells to Neuroectoderm

Hanqin Li
Zhixing Hu
Jian Feng
ResearchOpen Access25 Jun 2020
Scientific Reports

Volume: 10, P: 1-14

Search

Restoring flowcell type and basecaller configuration from FASTQ files of nanopore sequencing data

Correction: Corrigendum: Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

A highly photostable monomeric red fluorescent protein for dual-color 3D STED and time-lapse 3D SIM imaging

Detecting and phasing minor single-nucleotide variants from long-read sequencing data

Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics

Fully integrated multi-mode optoelectronic memristor array for diversified in-sensor computing

Deep transfer learning enables lesion tracing of circulating tumor cells

Neural network aided approximation and parameter inference of non-Markovian models of gene expression

Mitochondrial dynamics govern whole-body regeneration through stem cell pluripotency and mitonuclear balance

Parkin controls dopamine utilization in human midbrain dopaminergic neurons derived from induced pluripotent stem cells

Single-handed supramolecular double helix of homochiral bis(N-amidothiourea) supported by double crossed C−I···S halogen bonds

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

Arch dam point cloud segmentation based on deep feature learning and normal vector data optimization

10-km passive drone detection using broadband quantum compressed sensing imaging

Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry

Generation of mouse–human chimeric embryos

TET1 Deficiency Impairs Morphogen-free Differentiation of Human Embryonic Stem Cells to Neuroectoderm

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