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Open AccessA mass spectrum-oriented computational method for ion mobility-resolved untargeted metabolomics
Ion mobility (IM) adds a new dimension to liquid chromatography-mass spectrometry-based untargeted metabolomics which significantly enhances coverage, sensitivity, and resolving power for analyzing the metabol...
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Open AccessPublisher Correction: Serum metabolic traits reveal therapeutic toxicities and responses of neoadjuvant chemoradiotherapy in patients with rectal cancer
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Open AccessSerum metabolic traits reveal therapeutic toxicities and responses of neoadjuvant chemoradiotherapy in patients with rectal cancer
Neoadjuvant chemoradiotherapy (nCRT) has become the standard treatment for patients with locally advanced rectal cancer (LARC). Therapeutic efficacy of nCRT is significantly affected by treatment-induced diarr...
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Article
Open AccessMetabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking
Liquid chromatography - mass spectrometry (LC-MS) based untargeted metabolomics allows to measure both known and unknown metabolites in the metabolome. However, unknown metabolite annotation is a major challen...
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Article
Optimization on the multi-period empty container repositioning problem in regional port cluster based upon inventory control strategies
Within the area of regional port clusters, this paper establishes a multi-period mixed integer programming model to optimize the empty container repositioning between public hinterlands and ports, comprehensiv...
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Open AccessGlobal stable-isotope tracing metabolomics reveals system-wide metabolic alternations in aging Drosophila
System-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring th...
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Article
Open AccessUSP1-trap** lesions as a source of DNA replication stress and genomic instability
The deubiquitinase USP1 is a critical regulator of genome integrity through the deubiquitylation of Fanconi Anemia proteins and the DNA replication processivity factor, proliferating cell nuclear antigen (PCNA...
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Open AccessIon mobility-based sterolomics reveals spatially and temporally distinctive sterol lipids in the mouse brain
Aberrant sterol lipid metabolism is associated with physiological dysfunctions in the aging brain and aging-dependent disorders such as neurodegenerative diseases. There is an unmet demand to comprehensively p...
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Open AccessSingle-molecule imaging reveals replication fork coupled formation of G-quadruplex structures hinders local replication stress signaling
Guanine-rich DNA sequences occur throughout the human genome and can transiently form G-quadruplex (G4) structures that may obstruct DNA replication, leading to genomic instability. Here, we apply multi-color ...
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Open AccessIon mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics
The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility – mass spectrometry (IM-MS) has emerged as a ...
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Article
Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors
Damage-induced long non-coding RNAs (dilncRNA) synthesized at DNA double-strand breaks (DSBs) by RNA polymerase II are necessary for DNA-damage-response (DDR) focus formation. We demonstrate that induction of ...
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Advancing untargeted metabolomics using data-independent acquisition mass spectrometry technology
Metabolomics quantitatively measures metabolites in a given biological system and facilitates the understanding of physiological and pathological activities. With the recent advancement of mass spectrometry (M...
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Article
Open AccessMetabolic reaction network-based recursive metabolite annotation for untargeted metabolomics
Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (M...
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Open AccessUltrafast data mining of molecular assemblies in multiplexed high-density super-resolution images
Multicolor single-molecule localization super-resolution microscopy has enabled visualization of ultrafine spatial organizations of molecular assemblies within cells. Despite many efforts, current approaches f...
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Article
XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining
The Ku70–Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that...
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Open AccessSpatiotemporal dynamics of homologous recombination repair at single collapsed replication forks
Homologous recombination (HR) is a crucial pathway for the repair of DNA double-strand breaks. BRCA1/2 breast cancer proteins are key players in HR via their mediation of RAD51 nucleofilament formation and fun...
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Absolute quantitative lipidomics reveals lipidome-wide alterations in aging brain
The absolute quantitation of lipids at the lipidome-wide scale is a challenge but plays an important role in the comprehensive study of lipid metabolism.
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Open AccessA Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy
We introduce the Interaction Factor (IF), a measure for quantifying the interaction of molecular clusters in super-resolution microscopy images. The IF is robust in the sense that it is independent of cluster ...
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Open AccessProbing the Spatial Organization of Molecular Complexes Using Triple-Pair-Correlation
Super-resolution microscopy coupled with multiplexing techniques can resolve specific spatial arrangements of different components within molecular complexes. However, reliable quantification and analysis of s...
