bioRxiv Science⌕ Search

Biology subjects

Liang, Z.

Publications and source records attributed to Liang, Z..

At least 109 records · Page 6Linked to original sources

Upregulation of the AMPK-FOXO1-PDK4 pathway is a primary mechanism of pyruvate dehydrogenase activity reduction and leads to increased glucose uptake in tafazzin-deficient cells

Barth syndrome (BTHS) is a rare disorder caused by mutations in the TAFAZZIN gene. Previous studies from both patients and model systems have established metabolic dysregulation as a core component of BTHS pathology. In particular, features such as lactic acidosis, pyruvate dehydrogenase (PDH) deficiency, and aberrant fatty acid and glucose oxidation have been identified. However, the lack of a mechanistic understanding of what causes these conditions in the context of BTHS remains a significant knowledge gap, and this has hindered the development of effective therapeutic strategies for treating the associated metabolic problems. In the current study, we utilized tafazzin-knockout C2C12 mouse myoblasts (TAZ-KO) and cardiac and skeletal muscle tissue from tafazzin-knockout mice to identify an upstream mechanism underlying impaired PDH activity in BTHS. This mechanism centers around robust upregulation of pyruvate dehydrogenase kinase 4 (PDK4), resulting from hyperactivation of AMP-activated protein kinase (AMPK) and subsequent transcriptional upregulation by forkhead box protein O1 (FOXO1). Upregulation of PDK4 in tafazzin-deficient cells causes direct phospho-inhibition of PDH activity accompanied by increased glucose uptake and elevated intracellular glucose concentration. Collectively, our findings provide a novel mechanistic framework whereby impaired tafazzin function ultimately results in robust PDK4 upregulation, leading to impaired PDH activity and likely linked to dysregulated metabolic substrate utilization. This mechanism may underlie previously reported findings of BTHS-associated metabolic dysregulation.

cell biology↗

Chromosome segment scanning for gain- or loss-of-function screening (CHASING) and its application in metabolic engineering

Constructing a library of thousands of single-gene knockout or interference strains is a powerful tool to understand the relation between genotype and phenotype, but it is labor and cost intensive. Powered by the computer-aided gene annotation and functional grouping of non-essential genes, we showed that targeting a single gene directly to a specific observed phenotype could be quickly achieved for a specific microorganism via constructing a library of strains containing single chromosome-segment-deletion per strain. As a proof-of-concept, a genome-scale library consisting of 70 chromosome-segment-deletion strains for B. subtilis was constructed by CRISPR-based methods and strains with six loss-of- and gain-of-function phenotypes were screened out. To facilitate the rapid genotyping, we developed a web tool to visualize the potential targets of each chromosome segment associated with a particular function, successfully identifying the genes for valuable representative phenotypes. To apply the library to metabolic engineering, the hosts with improved production capacity of acetoin and lycopene were screened in the presence of pathway genes. This work demonstrated the significance of our strategy of chromosome segment scanning for gain- or loss-of-function screening (CHASING) on functional genomics investigation, robust chassis engineering, and chemical overproduction. O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/578163v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@19b4938org.highwire.dtl.DTLVardef@1e41d2eorg.highwire.dtl.DTLVardef@137d4b3org.highwire.dtl.DTLVardef@6d4bfc_HPS_FORMAT_FIGEXP M_FIG TOC C_FIG

bioengineering↗

Explorations of using a convolutional neural network to understand brain activations during movie watching

Neuroimaging studies increasingly use naturalistic stimuli like video clips to trigger complex brain activations, but the complexity of such stimuli makes it difficult to assign specific functions to the resulting brain activations, particularly for higher-level content like social interactions. To address this challenge, researchers have turned to deep neural networks, e.g., convolutional neural networks (CNNs). CNNs have shown success in image recognition due to their different levels of features enabling high performance. In this study, we used pre-trained VGG-16, a popular CNN model, to analyze video data and extract hierarchical features from low-level shallow layers to high-level deeper layers, linking these activations to different levels of activation of the human brain. We hypothesized that activations in different layers of VGG-16 would be associated with different levels of brain activation and visual processing hierarchy in the brain. We were also curious about which brain regions would be associated with deeper convolutional layers in VGG-16. The study analyzed a functional MRI (fMRI) dataset where participants watched the cartoon movie Partly Cloudy. Frames of the videos were fed into VGG-16, and activation maps from different kernels and layers were extracted. Time series of the average activation patterns for each kernel were created and fed into a voxel-wise model to study brain activations. Results showed that lower convolutional layers (1st convolutional layer) were mostly associated with lower visual regions, but some kernels (6, 19, 24, 42, 55, and 58) surprisingly showed associations with activations in the posterior cingulate cortex, part of the default mode network. Deeper convolutional layers were associated with more anterior and lateral portions of the visual cortex (e.g., the lateral occipital complex) and the supramarginal gyrus. Analyzing activation features associated with different brain regions showed the promise and limitations of using CNNs to link video content to brain functions.

neuroscience↗

Cerebral Blood Volume Modulates Glymphatic Influx Through Extra-ventricular Cerebrospinal Fluid Volume

The glymphatic system facilitates waste removal via cerebrospinal fluid (CSF) influx alongside perivascular spaces throughout the brain. Vasomotion, the slow motion of blood vessel (0.1-0.3 Hz), has been found to be one of the driving forces for perivascular clearance, but it is not clear whether more chronical change of vessel diameter, as reflected by macroscopic cerebral blood volume (CBV), has any impact on glymphatic function. Combining multimodal mouse MRI techniques, we investigated the relationship among glymphatic influx, CBV, CSF volume and EEG power under six different conditions (awake, dexmedetomidine, isoflurane, isoflurane/dexmedetomidine, ketamine/xylazine and awake with caffeine). We found dexmedetomidine and caffeine enhanced glymphatic influx, while isoflurane reduced it compared with awake condition. Quantitative CBV imaging revealed that glymphatic influx was negatively correlated to CBV across the above conditions. Furthermore, such negative correlation was found to be mediated in part by changes of extra-ventricular CSF volume, which was quantified using T1 MRI. Taken together, our results suggest that CBV is a consciousness independent modulator of glymphatic function and modulates glymphatic influx through extra-ventricular CSF volume. This new finding opens potential avenues to enhance brain waste clearance by regulating CBV, which could be beneficial for protein deposition related neurological diseases. TeaserCBV is a consciousness independent modulator of glymphatic function and modulates glymphatic influx through extra-ventricular CSF volume.

neuroscience↗

Auditory High Entropy Response (A-HER): A Novel Paradigm for Studying Brain Processing of Uncertain Information

This paper introduces a novel experimental paradigm - Auditory High Entropy Response (A-HER), which maximizes the information entropy of auditory stimulus sequences. This allows us to study how the brain processes complex information, rather than isolated individual events. Our analysis of the frequency response of the frontal theta rhythm induced by A-HER indicated a significant increase in signal-to-noise ratio and repeatability compared to zero-entropy Auditory Steady-State Response (A-SSR) and low-entropy mismatch negativity (MMN). We further investigated whether the A-HER response was induced by stimulus sequence differences or uncertainty, and studied its propagation rules. Different principles between evoked and entrained were found in A-HER and A-SSR. In conclusion, the A-HER paradigm, by maximizing stimulus sequence uncertainty, offers a new approach to analyzing how the brain processes uncertain information. It has potential for diagnosing and researching neurological and mental diseases, and for brain-computer interfaces, thus potentially impacting neuroscience, cognitive science, and psychology.

bioengineering↗

The Effects of Different Fatigue Types on Action Anticipation and Physical Performance in High-level Volleyball Players

This study examined the effects of different fatigue types on action anticipation and physical performance in high-level volleyball players. Twenty-four participants underwent four counterbalanced conditions: 60-min of cycling at 60% peak power output, 60-min Stroop task, 60-min cycling at 60% peak power output with Stroop task and 60-min neutral documentary to induce physical fatigue (PF), mental fatigue (MF), dual fatigue (DF) and control group (CG), respectively. Action anticipation (anticipation test and visual search test) and physical performance (countermovement jump, T-test, and spike test) were conducted at baseline, immediately after (Post1), and 40-min after fatigue intervention (Post2). DF and PF led to significantly lower jump height, T-test completion time, and spiking speed at Post1 and Post2 compared with CG and MF. Compared with PF, DF led to a significant decline in jumping, agility, and spiking performance at Post1 and decreased jumping performance at Post2. MF significantly decreased reaction time in the anticipation test at Post1 compared with CG. Reaction times in the visual search test were significantly lower with DF and MF at Post2 compared with CG. PF led to a greater decline in physical performance and this was exacerbated in DF, yet anticipation performance remained lesser impact.

physiology↗

Microglia Depletion Reduces Human Neuronal APOE4-Driven Pathologies in a Chimeric Alzheimer's Disease Model

Despite strong evidence supporting the involvement of both apolipoprotein E4 (APOE4) and microglia in Alzheimers Disease (AD) pathogenesis, the effects of microglia on neuronal APOE4-driven AD pathogenesis remain elusive. Here, we examined such effects utilizing microglial depletion in a chimeric model with human neurons in mouse hippocampus. Specifically, we transplanted homozygous APOE4, isogenic APOE3, and APOE-knockout (APOE-KO) induced pluripotent stem cell (iPSC)-derived human neurons into the hippocampus of human APOE3 or APOE4 knock-in mice, and depleted microglia in half the chimeric mice. We found that both neuronal APOE and microglial presence were important for the formation of A{beta} and tau pathologies in an APOE isoform-dependent manner (APOE4 > APOE3). Single-cell RNA-sequencing analysis identified two pro-inflammatory microglial subtypes with high MHC-II gene expression that are enriched in chimeric mice with human APOE4 neuron transplants. These findings highlight the concerted roles of neuronal APOE, especially APOE4, and microglia in AD pathogenesis. HIGHLIGHTSO_LITransplanted human APOE4 neurons generate A{beta} and p-tau aggregates in APOE4-KI mouse hippocampus. C_LIO_LIHuman neuronal APOE4 promotes the formation of dense-core A{beta} plaques and p-tau aggregates. C_LIO_LIMicroglia is required for human neuronal APOE4-driven formation of p-tau aggregates. C_LIO_LIscRNA-seq reveals enrichment of MHC-II microglia in mice with human APOE4 neuron transplants. C_LI

neuroscience↗

High-throughput and in-depth analysis of plasma proteome by UV-assisted protein digestion, 5-plex labeling and MS-based high abundance protein removal method

Human plasma contains various proteins, some of which reflect individuals physiological health state or predict diseases. Therefore, plasma analysis can provide a wealth of information on novel biomarkers for clinical diagnosis and prognosis. The use of mass spectrometry (MS) for high-throughput and in-depth quantitative proteomic analysis of plasma allows for highly specific and quantitative readout, but is challenging because of the high dynamic range of protein abundances. Here, we introduce a robust, high-throughput, and in-depth workflow for plasma proteome analysis based on UV-assisted rapid protein digestion, 5-plex dimethyl labeling, and MS-based high abundance protein removal. UV-assisted protein digestion could quantify the same protein numbers as traditional enzymatic hydrolysis and achieve a low miss-cleavage rate in only 20 minutes. And the MS-based high abundance protein removed 5-plex DIA method, which does not require extra protein depletion procedures, enables quantitative analysis of more than 600 proteins using an equivalent MS analysis time of 30 minutes per sample. The average relative error was 6.9%. We believe the method is beneficial for analyzing large numbers of trace-level clinical samples and broaden a vision for the discovery of low abundance protein markers.

biochemistry↗

Instant Assembly of Collagen for Scaffolding, Tissue Engineering, and Bioprinting

Controllable assembly of cells and tissues offers potential for advancing disease and development modeling and regenerative medicine. The bodys natural scaffolding material is the extracellular matrix, composed largely of collagen I. However, challenges in precisely controlling collagen assembly limit collagens applicability as a primary bioink or glue for biofabrication. Here, we introduce a set of biopatterning methods, termed Tunable Rapid Assembly of Collagenous Elements (TRACE), that enables instant gelation and rapid patterning of collagen I solutions with wide range of concentrations. Our methods are based on accelerating the gelation of collagen solutions to instantaneous speeds via macromolecular crowding, allowing versatile patterning of both cell-free and cell-laden collagen-based bioinks. We demonstrate notable applications, including macroscopic organoid engineering, rapid free-form 3D bioprinting, contractile cardiac ventricle model, and patterning of high-resolution (below 5 (m) collagen filament. Our findings enable more controllable and versatile applications for multi-scale collagen-based biofabrication.

bioengineering↗

Nitric Oxide controls shoot meristem activity via regulation of DNA methylation

Despite the importance of Nitric Oxide (NO) as signaling molecule in both plant and animal development1-7, the regulatory mechanisms downstream of NO remain largely unclear. Here, we show that NO is involved in Arabidopsis shoot stem cell control via modifying expression and activity of ARGONAUTE 4 (AGO4), a core component of the RNA directed DNA Methylation (RdDM) pathway. Mutations in components of the RdDM pathway cause meristematic defects, and reduce responses of the stem cell system to NO signaling. Importantly, we found that the stem cell inducing WUSCHEL transcription factor directly interacts with AGO4 in an NO dependent manner, explaining how these two signaling systems may converge to modify DNA methylation patterns. Taken together, our results reveal that NO signaling plays an important role in controlling plant stem cell homeostasis via the regulation of de novo DNA methylation.

plant biology↗

Proximity proteomics reveals UCH-L1 as an essential regulator of NLRP3 mediated IL-1β production in human macrophages and microglia

Activation of the NACHT, LRR family pyrin domain containing 3 (NLRP3) inflammasome complex is an essential innate immune signalling mechanism. To reveal how human NLRP3 inflammasome assembly and activation are controlled, in particular by components of the ubiquitin system, proximity labelling, affinity purification and RNAi screening approaches were performed. Our study provides an intricate time-resolved molecular map of different phases of NLRP3 inflammasome activation. Also, we show that ubiquitin C-terminal hydrolase 1 (UCH-L1) interacts with the NACHT domain of NLRP3. Downregulation of UCH-L1 decreases pro-IL-1{beta} levels. UCH-L1 chemical inhibition with small molecules interfered with NLRP3 puncta formation and ASC oligomerization, leading to altered IL-1{beta} cleavage and secretion, particularly in microglia cells, which exhibited elevated UCH-L1 expression as compared to monocytes/macrophages. Altogether, we profiled NLRP3 inflammasome activation dynamics and highlight UCH-L1 as an important modulator of NLRP3-mediated IL-1{beta} production, suggesting that a pharmacological inhibitor of UCH-L1 may decrease inflammation-associated pathologies.

biochemistry↗

Single-cell impedance cytometry of anticancer drug-treated tumor cells exhibiting mitotic arrest state to apoptosis using low-cost silver-PDMS microelectrodes

Chemotherapeutic drugs such as paclitaxel and vinblastine interact with the microtubules, and thus induce complex cell states of mitosis arrest at the G2/M phase followed by apoptosis dependent on drug exposure time and concentration. Microfluidic impedance cytometry (MIC) as a label-free and high-throughput technology for single-cell analysis, has been applied for viability assay of cancer cells post drug exposure at fixed time and dosage, yet verification of this technique for varied tumor cell states after anticancer drug treatment remains vacant. Here we present a novel MIC device and for the first time perform impedance cytometry on carcinoma cells exhibiting progressive states of G2/M arrest followed by apoptosis related to drug concentration and exposure time, after treatments by paclitaxel and vinblastine, respectively. Our results from impedance cytometry reveal increased amplitude and negative phase shift at low frequency, as well as higher opacity for the Hela cells under G2/M mitotic arrest compared to the untreated cells. The cells under apoptosis, on the other hand, exhibit opposite changes in these electrical parameters. Therefore, the impedance features differentiate the Hela cells under progressive states post anticancer drug treatment. We also demonstrate that vinblastine poses a more potent drug effect than paclitaxel especially at low concentrations. Our device is fabricated with a unique sacrificial layer-free soft lithography process as compared to the existing MIC device, which gives rise to readily aligned parallel microelectrodes made of silver-PDMS embedded in PDMS channel sidewalls with one molding step. Our results uncover the potential of the MIC device, with a fairly simple and low-cost fabrication process, for cellular state screening in anticancer drug therapy.

cell biology↗

Group A Streptococcus remains viable inside fibrin clots and gains access to human plasminogen for subsequent fibrinolysis and dissemination

Group A Streptococcus (GAS) is a Gram-positive bacterial pathogen that causes a wide spectrum of illnesses ranging from pharyngitis and rheumatic fever to more invasive and severe diseases such as necrotizing fasciitis and toxic shock syndrome. Invasive outcomes of GAS infections often result from entry of the bacteria via an open wound into tissue and blood systems. The coagulation cascade serves as an innate defense mechanism that initiates fibrin clots to sequester bacteria and restrict its growth and prevent dissemination into deeper tissues. GAS, especially skin-tropic bacterial strains, utilize the specific virulence factors Plasminogen binding M-protein (PAM) and streptokinase (SK) to manipulate hemostasis and ultimately activate human plasminogen to cause fibrinolysis and escape from the fibrin clot. A major unresolved question regarding this process is to understand the temporal dynamics of how GAS that is enmeshed in a fibrin clot accesses host plasminogen for dissolution of the clot and eventual dissemination. Using fluorescently labeled plasminogen and fibrinogen, we established conditions to observe the process of fibrin clot dissolution by GAS (an AP53 CovR+S-strain) that is sequestered in a fibrin clot using real-time imaging microscopy. We hypothesized that initiation of fibrinolysis by GAS inside a fibrin clot would be determined by the rate of hPg access into the fibrin clot where bacteria are trapped. Our live imaging studies show that GAS trapped inside a fibrin clot, has limited access to hPg; however, at 4.25 h post incubation, when sufficient hPg is accessible to the bacterium, fibrinolysis quickly occurs. If hPg is bound to the bacterial surface prior to being trapped inside a clot, dissolution and bacterial dissemination occurs at a much faster rate of 2.5 h post incubation. During the time which bacteria are trapped in the clot without access to hPg, we did not observe any growth of GAS; however, we demonstrate that the bacteria continue to remain viable inside the fibrin clot. We performed RNA-seq analysis of GAS and the isogenic GAS SK-deficient mutant to understand SK-dependent transcriptional changes during the lag-phase of the GAS bacteria inside the fibrin clot. We observed a dramatic change in the transcription profile of wt GAS inside the fibrin clot over time prior to escape from the fibrin clot (22 gene expression changes at 4h, to 802 gene expression changes at 8h). Furthermore, we also identified gene expression changes that were distinct between wt GAS and the GAS SK-deficient mutant. Our findings reveal for the first time that GAS can engage a latent, growth suspended phase whereby physical structures such as fibrin clots and Neutrophil extracellular traps that immobilize an invading pathogen allow bacteria to remain viable and transcriptionally active for an extended time during host infection. GAS that is trapped in a fibrin clot will therefore enter a state in which the bacteria suspend growth, but remain viable, until sufficient access to hPg allow it to initiate fibrinolysis and escape into surrounding tissues. The viability of GAS while trapped and its readiness to avoid immune defenses allow GAS to act quickly to disseminate when host conditions are more favorable for the bacteria.

microbiology↗

GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model

Deciphering the universal gene regulatory mechanisms in diverse organisms holds great potential to advance our knowledge of fundamental life process and facilitate research on clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms, resulting in limited collection and integration of complex features on various cell types across species. Recent breakthroughs in single-cell sequencing and advancements in deep learning techniques present an unprecedented opportunity to tackle this challenge. In this study, we developed GeneCompass, the first knowledge-informed, cross-species foundation model pre-trained on an extensive dataset of over 120 million single-cell transcriptomes from human and mouse. During pre-training, GeneCompass effectively integrates four types of biological prior knowledge to enhance the understanding of gene regulatory mechanisms in a self-supervised manner. Fine-tuning towards multiple downstream tasks, GeneCompass outperforms competing state-of-the-art models in multiple tasks on single species and unlocks new realms of cross-species biological investigation. Overall, GeneCompass marks a milestone in advancing knowledge of universal gene regulatory mechanisms and accelerating the discovery of key cell fate regulators and candidate targets for drug development.

bioinformatics↗

CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks

Cell fate changes are determined by gene regulatory network (GRN), a sophisticated system regulating gene expression in precise spatial and temporal patterns. However, existing methods for reconstructing GRNs suffer from inherent limitations, leading to compromised accuracy and application generalizability. In this study, we introduce CellPolaris, a computational system that leverages transfer learning algorithms to generate high-quality, cell-type-specific GRNs. Diverging from conventional GRN inference models, which heavily rely on integrating epigenomic data with transcriptomic information or adopt causal strategies through gene co-expression networks, CellPolaris employs high-confidence GRN sources for model training, relying exclusively on transcriptomic data to generate previously unknown cell-type-specific GRNs. Applications of CellPolaris demonstrate remarkable efficacy in predicting master regulatory factors and simulating in-silico perturbations of transcription factors during cell fate transition, attaining state-of-the-art performance in accurately predicting candidate key factors and outcomes in cell reprogramming and spermatogenesis with validated datasets. It is worth noting that, with a transfer learning framework, CellPolaris can perform GRN based predictions in all cell types even across species. Together, CellPolaris represents a significant advancement in deciphering the mechanisms of cell fate regulation, thereby enhancing the precision and efficiency of cell fate manipulation at high resolution.

bioinformatics↗

CD4+ T cell senescence is associated with reduced reactogenicity in severe/critical COVID-19

BackgroundAging is a critical risk factor for unfavorable clinical outcomes among COVID-19 patients and may affect vaccine efficacy. However, whether the senescence of T cells impact the progression to severe COVID-19 in the elderly individuals remains unclear. MethodsBy using flow cytometry, we analyzed the frequency of senescent T cells (Tsens) in the peripheral blood from 100 elderly patients hospitalized for COVID-19 and compared the difference between mild/moderate and severe/critical illness. We also assessed correlations between the percentage of Tsens and the quantity and quality of spike-specific antibodies by ELISA, neutralizing antibody test kit and Elispot assay respectively, cytokine production profile of COVID-19 reactive T cells as well as plasma soluble factors by cytometric bead array (CBA). ResultsWe found a significant elevated level of CD4+ Tsens in severe/critical disease compared to mild/moderate illness and patients with a higher level of CD4+ Tsens (>19.78%) showed a decreased survival rate as compared to those with a lower level (<19.78%), especially in the breakthrough infection. The percentage of CD4+ Tsens was negatively correlated with spike-specific antibody titers, neutralization ability and COVID-19 reactive IL-2+ CD4+ T cells. Additionally, IL-2 producing T cells and plasma levels of IL-2 were positively correlated with antibody levels. ConclusionOur data illustrated that the percentage of CD4+ Tsens in the peripheral blood could act as an efficient biomarker for the capacity of spike-specific antibody production and the prognosis of severe COVID-19, especially in the breakthrough infection. Therefore, restoration of the immune response of CD4+ Tsens is one of the key factors to prevent severe illness and improve vaccine efficacy in older adults.

immunology↗

Chromatin-associated RNA Dictates the ecDNA Interactome in the Nucleus

Extrachromosomal DNA (ecDNA) promotes cancer by driving copy number heterogeneity and amplifying oncogenes along with functional enhancers. More recent studies suggest two additional mechanisms for further enhancing their oncogenic potential, one via forming ecDNA hubs to augment oncogene expression 1 and the other through acting as portable enhancers to trans- activate target genes 2. However, it has remained entirely elusive about how ecDNA explores the three-dimensional space of the nucleus and whether different ecDNA have distinct interacting mechanisms. Here, by profiling the DNA-DNA and DNA-RNA interactomes in tumor cells harboring different types of ecDNAs in comparison with similarly amplified homogenously staining regions (HSRs) in the chromosome, we show that specific ecDNA interactome is dictated by ecDNA-borne nascent RNA. We demonstrate that the ecDNA co-amplifying PVT1 and MYC utilize nascent noncoding PVT1 transcripts to mediate specific trans-activation of both ecDNA and chromosomal genes. In contrast, the ecDNA amplifying EGFR is weak in this property because of more efficient splicing to remove chromatin-associated nascent RNA. These findings reveal a noncoding RNA-orchestrated program hijacked by cancer cells to enhance the functional impact of amplified oncogenes and associated regulatory elements.

genomics↗

Introducing PandaNovo for practical large-scale de novo peptide sequencing

De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing model{pi} -HelixNovo based on Transformer architecture.{pi} -HelixNovo outperforms other state-of-the-art models and enhances the taxonomic resolution of gut metaproteome, taking a significant step forward in de novo sequencing.

bioinformatics↗