arXiv subjects

Xiaowen Feng

Publications and source records attributed to Xiaowen Feng.

6 recordsLinked to original sources

arXiv2022

Towards complete representation of bacterial contents in metagenomic samples

Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant species we are missing and do not have an approach to recover these species. Results: Here we proposed k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We showed that even with PacBio High-Fidelity (HiFi) reads, abundant species are often not assembled as high strain diversity may lead to fragmented contigs. We developed a novel algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Our algorithm is reference-free and complement to standard metagenome binning. Evaluated on 14 real datasets, it rescued many abundant species that would be missing with existing methods. Conclusions: Our work stresses the importance of metagenome completeness which is often overlooked before. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbiome communities.

q-bio.GN↗

arXiv2022

Electronic Thermal Transport Measurement in Low-Dimensional Materials with Graphene Nonlocal Noise Thermometry

In low-dimensional systems, the combination of reduced dimensionality, strong interactions, and topology has led to a growing number of many-body quantum phenomena. Thermal transport, which is sensitive to all energy-carrying degrees of freedom, provides a discriminating probe of emergent excitations in quantum materials and devices. However, thermal transport measurements in low dimensions are dominated by the phonon contribution of the lattice, requiring an experimental approach to isolate the electronic thermal conductance. Here, we show how the measurement of nonlocal voltage fluctuations in a multiterminal device can reveal the electronic heat transported across a mesoscopic bridge made of low-dimensional materials. By using 2-dimensional graphene as a noise thermometer, we demonstrate quantitative electronic thermal conductance measurements of graphene and carbon nanotubes up to 70 K, achieving a precision of ~1% of the thermal conductance quantum at 5 K. Employing linear and nonlinear thermal transport, we observe signatures of long-range interaction-mediated energy transport in 1-dimensional electron systems, in agreement with a theoretical model. Our versatile nonlocal noise thermometry allows new experiments probing energy transport in emergent states of matter and devices in low dimensions.

cond-mat.mes-hall↗

arXiv2021

Metagenome assembly of high-fidelity long reads with hifiasm-meta

Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome assembler that exploits the high accuracy of recent data. Evaluated on seven empirical datasets, hifiasm-meta reconstructed tens to hundreds of complete circular bacterial genomes per dataset, consistently outperforming other metagenome assemblers.

q-bio.GN↗

arXiv2020

Haplotype-resolved de novo assembly with phased assembly graphs

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a new de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five non-human datasets, including California redwood with a $\sim$30-gigabase hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.

q-bio.GN↗

arXiv2020

The design and construction of reference pangenome graphs

The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists remain an open challenge. Here we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome. We implemented our ideas in the minigraph toolkit and demonstrate that we can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.

q-bio.GN↗

arXiv2017

A Co(II)-based Molecular Magnet with a 6 T Coercive Field

Hard magnets with high coercivity, such as Nd2Fe14B and SmCo5 alloys, can maintain magnetisation under a high reverse external magnetic field and have therefore become irreplaceable parts in many practical applications. Molecular magnets are promising alternatives, owing to their precise and designable chemical structures, tuneable functionalities and controllable synthetic methods. Here, we demonstrate that an unusually large coercive field can be achieved in a single-chain magnet. Systematic characterisations, including magnetic susceptibility, heat capacity and neutron diffraction measurements, show that the observed giant coercive field originates from the spin dynamics along the one-dimensional chain of the compound because of the strong exchange coupling between Co(II) centres and radicals.

physics.chem-ph↗