Biology subjects

Truong, T.

Publications and source records attributed to Truong, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatial epigenomics reveals ancestry-associated regulatory states linked to aggressive prostate cancer biology

Prostate cancer (PCa) exhibits substantial biological heterogeneity, including population associated differences in tumor aggressiveness and clinical outcomes. Although socioeconomic and environmental factors contribute to these disparities, intrinsic tumor regulatory programs may also influence disease behavior. Here, we investigated whether differences in chromatin regulation contribute to distinct tumor states in Black and White men with localized PCa. We performed spatial chromatin accessibility profiling (ATAC-seq) of prostatectomy specimens from Black and White patients receiving equal healthcare access at the Center for Prostate Disease Research (USUHS) and Walter Reed National Military Medical Center. Tumors showed distinct chromatin accessibility landscapes between the two populations, with tumors from Black patients exhibiting reduced accessibility of motifs associated with the chromatin architectural regulator CTCF and enrichment of motifs linked to epithelial-mesenchymal transition and inflammatory programs. Reduced CTCF expression was independently validated by immunohistochemistry in 99 prostatectomy specimens. These findings identify population-associated differences in chromatin regulation in localized PCa and suggest that altered CTCF-associated regulation, inflammatory signaling, and epithelial plasticity may contribute to the biological heterogeneity underlying ancestry-dependent PCa disparities.

cancer biology↗

bioRxiv2026

Ultra-large targeted DNA integrations in primary human cells

Genetic engineering experiments and therapies are constrained by the size of DNA integrations into human cells genomes. Existing AAV, lentiviral, and non-viral methods rapidly decrease in integration efficiency beyond [~]5kb of sequence. Through systematic evaluation of non-viral DNA template formats, we identified circular ssDNA and dsDNA as capable of mediating >5kb integrations. Large circular DNA delivery efficiency and its impacts on cell viability and payload expression could be significantly improved with small DNA "helper" plasmids, mRNA-encoded nucleases, and sequence design optimizations. Collectively, these modifications enabled ultra-large--up to 10 kb DNA--integrations at >20% efficiency in primary human T cells at the TRAC locus and at >60% efficiency in human iPSCs at the AAVS1 locus. Finally, we demonstrate that GMP clinical-manufactured T cells with ultra-large integrations are functional in vitro and in vivo. Overall, we identified optimal template architectures, delivery modes, and sequence design rules for ultra-large DNA integrations in both research and clinical settings to accelerate basic genetic research and next-generation cellular therapies.

genetics↗

bioRxiv2026

Simultaneous broad protection against Ebola Sudan, Marburg and Lassa viruses conferred by a DNA primed MVA-vectored multivalent vaccine

Sub-Saharan Africa continues to experience recurrent outbreaks of zoonotic viral diseases that spill over unpredictably from animal reservoirs into human populations. In many regions, mpox co-circulates with viral hemorrhagic fevers (VHFs) caused by Ebola Sudan virus (SUDV), Marburg virus (MARV), and Lassa fever virus (LASV). Overlapping clinical syndromes that these VHF cause challenge surveillance, diagnostics and timely deployment of effective countermeasures. A single vaccine capable of protecting against these biologically and genetically distinct pathogens would markedly reduce the cost and complexity of outbreak response, lessen dependence on emergency international aid, and strengthen long-term health system resilience. Here, we report on the development of an MVA-based mpox vaccine engineered to express computationally designed, broad-coverage antigens targeting SUDV, MARV and LASV. In preclinical challenge studies, this multivalent vaccine elicited robust immune responses and conferred significant protection against lethal infection from all three pathogens in parallel challenge experiments. These findings establish preclinical proof-of-concept for a single, broadly protective VHF vaccine and support its clinical development for deployment across diverse settings in Sub-Saharan Africa. SignificanceOutbreak control in Sub-Saharan Africa is challenged by the co-circulation of different high consequence human infections such as mpox and diverse viral hemorrhagic fevers (VHF) such as SUDV, MARV, and LASV pathogens. These VHFs have overlapping early clinical syndromes, complicating triage and delaying effective targeted interventions. We developed a single MVA-based vaccine encoding computationally designed, conserved antigens from all three VHFs encoded within the MVA vector analogous to the licensed mpox vaccine. In simultaneous challenge models, this multivalent vaccine elicited robust humoral and cellular responses and conferred significant protection against lethal infection by each hemorrhagic fever pathogen. This work provides preclinical proof-of-concept for a unified, broadly protective countermeasure compatible with existing MVA-mpox vaccine manufacturing and deployment experience. By reducing dependence on rapid differential diagnostics and streamlining logistics relative to maintaining multiple pathogen-specific vaccine stockpiles, this approach can lower costs, accelerate response, and increase equity of access during syndromic outbreaks. The platforms engineered antigen breadth and human safety profile of MVA together support a pragmatic translational pathway toward clinical evaluation and regional readiness for zoonotic spillover events that are intensifying with human and environmental changes.

immunology↗

bioRxiv2026

Advanced models of lobular breast cancer metastasis capture clinical organ tropism, endocrine response, and bone remodeling

Patients with invasive lobular carcinoma of the breast (ILC) are at high risk of long-term recurrence and metastatic progression with poor prognoses due to delayed detection and treatment-refractory disease. Unfortunately, few models are available to investigate metastatic ILC (mILC) and understand the unique metastatic patterns and phenotypes, including abdominal metastases, leptomeningeal disease, and mixed osteosclerotic/lytic bone metastases. Therefore, we expanded upon the previously established mammary intraductal (MIND) cell line xenograft model by supplementing mice with low-dose estradiol to promote disease progression. We observed spontaneous multi-organ spread from the mammary gland to common and mILC-specific tissues, with micro-metastatic disease as early as 12 weeks post-engraftment and macro-metastatic disease in 24-30 weeks, without the need for primary tumor resection. Primary and metastatic tumors remain highly endocrine responsive, allowing for the evaluation of novel therapeutics in the setting of disseminated metastasis. Derivative cell lines were isolated from various metastatic lesions, a total of 13 derivates from 7 sites across three hosts, and were found to have shared gene expression changes related to metabolism and intercellular signaling. Focusing on bone-derived variant cells as bone is the most common site for mILC to present, we found that bone-derived variant lines maintain multi-organ metastatic potential upon rechallenge by MIND or intratibial injection, despite increased aggressiveness and maintained endocrine response. Notably, bone lesions from either challenge route showed mixed osteosclerotic/lytic features characteristic to clinical ILC. Accordingly, we found that conditioned medium from ILC cells and the mILC bone-derived variants induce osteoblast differentiation and suppressed osteoclast differentiation in vitro, consistent with their effect on bone remodeling in vivo and in clinical disease. Together, the models developed herein can be utilized to understand the unique metastatic processes of mILC, and to investigate new therapeutic combinations in the setting of endocrine-responsive primary and metastatic ILC.

cancer biology↗

bioRxiv2026

Springtail-inspired compliant hinge enables terrain-adaptable takeoff in insect-scale robots

Springtails execute millisecond-scale escape jumps with a single appendage, the furca, on soil, snow, leaf litter, and water. Across 15 taxonomic families (n=552 individuals), relative furca length is bimodal. High-speed video and confocal imaging show that in some long-furca springtails, the resilin-rich manubrium-dens joint behaves as a compliant hinge. It bends during push-off to prolong contact, suppress pitch, and bias takeoff forward, whereas rigid joints drive backward launches with rapid body rotation. We translate this mechanism to a 20-mm, 84-mg jumping robot with an elastic robo-furca hinge. This flexible hinge reduces body rotation by [~] 90% on flat ground compared to rigid-hinge designs, while maintaining takeoff speed on gravel, springboards, leaves, and pine needles, enabling passive, terrain-adaptable launches for power-limited insect-scale robots without onboard sensing or active control.

animal behavior and cognition↗

bioRxiv2026

Synthetic Hybrid Receptors for Safer and Programmable T Cell Therapy

Engineered T cell therapies have achieved significant clinical success in hematological malignancies but remain largely ineffective in solid tumors. Overcoming this limitation requires strategies that enhance T cell function while avoiding systemic immune toxicities and pathological T cell states. Existing approaches typically rely on constitutive gene overexpression or suppression to augment potency or remodel the tumor microenvironment, but these strategies frequently lead to dysregulated immune activation and dose-limiting toxicity. Here, we present Hybrid Receptors (Hybrid-Rs), a modular receptor platform that integrates features of chimeric antigen receptors (CARs) and SyNthetic Intramembrane Proteolysis Receptors (SNIPRs) to couple antigen-dependent T cell activation with programmable gene regulation. Hybrid-Rs enable precise, context-dependent control of T cell potency, differentiation states, and conditional expression of secreted immunotherapeutic payloads with otherwise prohibitive toxicity. Hybrid-Rs are readily humanized and compatible with precision genome editing in primary human T cells, providing a direct and practical path to clinical translation.

bioengineering↗

bioRxiv2025

A VSV-vector vaccine simultaneously targeting H5N1 hemagglutinin (HA) and matrix protein 2 (M2) induces robust neutralizing and ADCC antibody responses and provides full protection against lethal H5N1 infection in a mouse model

Human (avian) influenza A viruses, especially highly pathogenic avian influenza (HPAI) viruses, pose a significant public health threat, and a multivalent vaccine is the primary prophylactic measure to control these viruses. To establish such a vaccine, we generated two multivalent vesicular stomatitis virus (VSV)-based vaccine candidates (V-EtM2e/H505 and V-EtM2e/H522) and characterized their ability to induce protective immune responses. Our results revealed that vaccine immunization in mice induced high humoral immune responses against both the HPAI hemagglutinin (HA) protein and the ectodomain of M2 (M2e) protein. Intriguingly, vaccine-immunized mouse sera exhibited highly efficient neutralizing activity against the corresponding H5 pseudovirus and mediated potent and broad antibody-dependent cellular cytotoxicity (ADCC) activity against M2e derived from human and avian influenza H5, H1, H3, and H7 viruses. Furthermore, both intranasal and intramuscular immunization provided efficient protection against HPAI H5N1 virus challenge in mice, with a 100% survival rate and a nondetectable viral load in several tissues. Notably, noninvasive mucosal (IN) delivery of V-EtM2e/H522 achieved protection equal to that of IM delivery at a 100-fold lower immunizing dose. These findings provide strong evidence for the effectiveness of a multivalent VSV-based vaccine against human (avian) influenza A viruses.

microbiology↗

bioRxiv2025

Progesterone receptors drive advanced breast cancer phenotypes including circulating tumor- and stem-like cell expansion in the context of ESR1 mutation

Endocrine therapy resistance remains a major challenge in the treatment of advanced estrogen receptor positive (ER+) breast cancer. This can be driven by acquired mutations in the estrogen receptor gene (ESR1), such as Y537S or D538G, that primarily emerge in patients with prior aromatase inhibitor therapy and results in constitutive estrogen-independent ER activity. Progesterone receptors (PR) are important modifiers of ER activity, in part via direct binding. We previously showed that PR mediates expansion of cancer stem-like cell (CSC) populations and promotes tamoxifen resistance in nuclear ER/PR transcriptional complexes. In this study, we sought to define whether PR function changes in the context of ESR1 mutations. PR readily interacted with wild type (WT), but not Y537S or D538G ERs. RNA-seq and ChIP-seq studies demonstrated that ER+ breast cancer models expressing Y537S ER exhibited a distinct response to progesterone. CSC populations were enhanced in Y537S ER+ cells compared to WT ER+ cells. PR knockdown demonstrated that this property required PR expression but was unresponsive to antiprogestins. Moreover, we identified PR-dependent transcriptional programs such as the unfolded protein response (UPR) that can be leveraged to target CSC populations in Y537S ESR1-mutant breast cancer. The UPR activator ErSO, but not UPR inhibitors, blocked expansion of CSCs in WT as well as Y537S ER+ models. Together, our findings demonstrate a critical interplay between PR and mutant ER function and provide insight into PR-driven pathways including hyperactivation of the stress-sensing UPR that can be exploited as potential therapeutic avenues in advanced ER+ breast cancer.

cancer biology↗

bioRxiv2025

Evaluating Flavoprotein Fluorescence Imaging as a Biomarker of Early Retinal Ganglion Cell Mitochondrial Stress

PurposeRetinal neurodegeneration is difficult to monitor due to insensitive disease endpoints. Mitochondrial dysfunction and oxidative stress are promising early biomarkers of retinal ganglion cell (RGC) degeneration. This study investigates dynamics of flavoprotein fluorescence (FPF), a non-invasive mitochondrial oxidative stress measure, and sensitivity to early neurodegeneration and neuroprotection in vitro and in vivo. MethodsFPF activity in response to neurodegeneration and neuroprotection were characterized in vitro in wild-type (WT) and SARM1 knockout (SARMKO) human embryonic stem cell-derived RGCs with and without Vacor treatment over 24 hours and confirmed with mitochondrial reactive oxygen species (ROS) measures. Further FPF evaluation was explored in vivo using the optic nerve crush (ONC) model in WT and SARMKO mice to compare early RGC stress detection within rodent retinas. ResultsIn vitro FPF intensities in WT RGCs increased within 8 hours of degeneration induction, preceding significant mitochondrial ROS production. Neuroprotective SARMKO RGCs maintained comparable FPF and ROS levels following insult. In vivo FPF changes were not observed in WT and SARMKO mice over 4 days following ONC, while only early retinal thickening was observed from OCT. Early FPF and OCT changes were not reflective of late RGC survival observed from ex vivo RGC soma and axon counts. ConclusionsThese findings highlight differences in FPF sensitivity to mitochondrial stress between simplified in vitro systems and complex in vivo rodent retinas. This study demonstrates the potential of FPF as an early neurodegeneration and neuroprotection endpoint in vitro while identifying limitations and areas of development for its translatability to preclinical in vivo assessment.

bioengineering↗

bioRxiv2025

Perturbation Recovery Time Identifies Subtle Human Balance Impairments and Features

Falls are a leading cause of injury and growing healthcare costs, particularly in aging populations. However, early-stage balance impairments often remain undetected until severe problems arise. Quantitative assessment of human balance therefore remains a critical challenge. Here, we introduce Perturbation Recovery Time, a novel state-space-based balance metric inspired by nonlinear dynamic system theory that quantifies the duration required for gait dynamics to consistently return to a steady-state neighborhood following a perturbation. Unlike conventional approaches based on steady-state walking, this framework evaluates balance through externally induced perturbations that reveal control mechanisms not observable during unperturbed gait. Using healthy participants with experimentally induced impairments, we identified key balance-related features, including the anterior-posterior center-of-mass-center-of-pressure distance, whole-body angular momentum in the frontal and sagittal planes, and vertical center-of-mass position and acceleration. These features capture the core mechanisms of balance control, including foot placement, inverted pendulum dynamics, push-off control, and trunk regulation. Perturbation Recovery Time reliably detected within-subject changes in balance associated with controlled impairments in sensory input, motor coordination, and movement consistency. These findings demonstrate that Perturbation Recovery Time provides a quantitative and sensitive measure of balance, offering a framework for early detection of balance impairments.

bioengineering↗

bioRxiv2025

OmnibusX: A unified platform for accessible multi-omics analysis

OmnibusX is an integrated, privacy-centric platform that enables code-free multi-omics data analysis by bridging computational methodologies with user-friendly interfaces. Designed to overcome challenges posed by fragmented analytical tools and high computational barriers, OmnibusX consolidates workflows for diverse technologies - including bulk RNA-seq, single-cell RNA-seq, single-cell ATAC-seq, and spatial transcriptomics - into a single, cohesive application. The application integrates established open-source tools such as Scanpy, DESeq2, SciPy, and scikit-learn into transparent, reproducible pipelines, offering users control over analytical parameters. Additionally, OmnibusX features proprietary modules, including a highly accurate cell-type prediction engine and an interactive plotting editor for generating publication-quality visualizations. Available as a standalone desktop application and an enterprise edition for centralized server deployment, OmnibusX ensures all data processing is conducted locally, eliminating external data transfer and usage tracking. By lowering technical barriers and enhancing reproducibility, OmnibusX aims to accelerate biological discovery and foster robust, data-driven collaborations. A fully documented trial version is accessible at: https://omnibusx.com/apps.

bioinformatics↗

bioRxiv2024

Illumina Complete Long Read Assay yields contiguous bacterial genomes from human gut metagenomes

Metagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic elements. Long-read sequencing approaches have successfully yielded circular bacterial genomes directly from metagenomes, but these approaches are low throughput, have high DNA input requirements, and can have high error rates. Illumina has recently launched the Illumina Complete Long Read (ICLR) assay, a new approach for generating kilobase-scale reads with low DNA input requirements and high accuracy. Here, we evaluate the performance of ICLR sequencing for gut metagenomics. We sequenced a microbial mock community and ten human gut microbiome samples with standard, shotgun 2x150 paired-end sequencing, ICLR sequencing, and nanopore long-read sequencing and compared performance in read lengths, assembly contiguity, and bin quality. We find that ICLR human metagenomic assemblies have higher N50 (119.5 {+/-} 24.8 kilobases) than short read assemblies (9.9 {+/-} 4.5 kilobases; p = 0.002), and comparable N50 to nanopore assemblies (91.0 {+/-} 43.8 kilobases; p = 0.32). Additionally, we find that ICLR draft microbial genomes are more complete (94.0% {+/-} 20.6%) than nanopore draft genomes (85.9% {+/-} 23.0%; p[≤] 0.001), and that nanopore draft genomes have truncated gene lengths (924.6 {+/-} 114.7 base pairs) relative to ICLR genomes (954.6 {+/-} 71.5 base pairs; p[≤] 0.001). Overall, we find that ICLR sequencing is a promising method for high-throughput and accurate assembly of microbial genomes from gut metagenomes. ImportanceMetagenomic sequencing allows scientists to directly measure the genome content and structure of microbes residing in complex microbial communities. Traditional short-read metagenomic sequencing methods often yield fragmented genomes, whereas advanced long-read sequencing methods improve genome assembly quality but often suffer from high error rates and are logistically limited due to low throughput and high input requirements. A new method, the Illumina Complete Long Read Assay (ICLR), is capable of generating highly-accurate kilobase-scale sequencing reads with minimal input material. To evaluate the utility of ICLR in metagenomic contexts, we applied short-read, long-read, and ICLR methods to simple and complex microbial communities. We found that ICLR outperforms short-read methods, and yields comparable metagenomic assemblies to standard long-read approaches while requiring less input material. Overall, ICLR represents a high-throughput and efficient solution for assembling complete genomes from complex metagenomes.

genomics↗

bioRxiv2024

The balance between antiviral and antibacterial responses during M. Tuberculosis infection is regulated by the ubiquitin ligase CBL

As a first line of host defense, macrophages must be able to effectively sense and respond to diverse types of pathogens, and while a particular type of immune response may be beneficial in some circumstances, it can be detrimental in others. Upon infecting a macrophage, M. tuberculosis (Mtb) induces proinflammatory cytokines that activate antibacterial responses. Surprisingly, Mtb also triggers antiviral responses that actually hinder the ability of macrophages to control Mtb infection. The ubiquitin ligase CBL suppresses these antiviral responses and shifts macrophages toward a more antibacterial state during Mtb infection, however, the mechanisms by which CBL regulates immune signaling are unknown. We found that CBL controls responses to multiple stimuli and broadly suppresses the expression of antiviral effector genes. We then used mass-spectrometry to investigate potential CBL substrates and identified over 46,000 ubiquitylated peptides in Mtb-infected macrophages, as well as roughly 400 peptides with CBL-dependent ubiquitylation. We then performed genetic interaction analysis of CBL and its putative substrates, and identified the Fas associated factor 2 (FAF2) adapter protein as a key signaling molecule protein downstream of CBL. Together, these analyses identify thousands of new ubiquitin-mediated signaling events during the innate immune response and reveal an important new regulatory hub in this response.

immunology↗

bioRxiv2023

Benchmarking AlphaSC: A Leap in Single-Cell Data Processing

AO_SCPLOWBSTRACTC_SCPLOWWe benchmarked AlphaSC, BioTurings GPU-accelerated single-cell analytics package, against other popular tools including Scanpy, Seurat, and RAPIDS. The results demonstrate that AlphaSC operates thousands of times faster than Seurat and Scanpy. Additionally, it surpasses RAPIDS, another GPU-accelerated package from NVIDIA, by an order of magnitude in terms of speed while also consuming considerably less RAM and GPU memory. Importantly, this significant increase in AlphaSCs performance does not compromise its quality. 1

bioinformatics↗

bioRxiv2023

IC-VAE: A Novel Deep Learning Framework for Interpreting Multiplexed Tissue Imaging Data.

AO_SCPLOWBSTRACTC_SCPLOWInterpreting protein expression in multiplexed tissue imaging data presents a significant challenge due to the high dimensionality of the resulting images, the variety of intracellular structures, cell shapes resulting from 2-D tissue sectioning, and the presence of technological noise and imaging artifacts. Here, we introduce the Information-Controlled Variational Autoencoder (IC-VAE), a deep generative model designed to tackle this challenge. The contribution of IC-VAE to the VAE framework is the ability to control the shared information among latent subspaces. We use IC-VAE to factorize each cells image into its true protein expression, various cellular components, and background noise, while controlling the shared information among some of these components. Compared with other normalization methods, this approach leads to superior results in downstream analysis, such as analyzing the expression of biomarkers, classification for cell types, or visualizing cell clusters using t-SNE/UMAP techniques.

bioinformatics↗

bioRxiv2023

TDP-43-stratified single-cell proteomic profiling of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis

Unbiased proteomics has been employed to interrogate central nervous system (CNS) tissues (brain, spinal cord) and fluid matrices (CSF, plasma) from amyotrophic lateral sclerosis (ALS) patients; yet, a limitation of conventional bulk tissue studies is that motor neuron (MN) proteome signals may be confounded by admixed non-MN proteins. Recent advances in trace sample proteomics have enabled quantitative protein abundance datasets from single human MNs (Cong et al., 2020b). In this study, we leveraged laser capture microdissection (LCM) and nanoPOTS (Zhu et al., 2018c) single-cell mass spectrometry (MS)-based proteomics to query changes in protein expression in single MNs from postmortem ALS and control donor spinal cord tissues, leading to the identification of 2515 proteins across MNs samples (>900 per single MN) and quantitative comparison of 1870 proteins between disease groups. Furthermore, we studied the impact of enriching/stratifying MN proteome samples based on the presence and extent of immunoreactive, cytoplasmic TDP-43 inclusions, allowing identification of 3368 proteins across MNs samples and profiling of 2238 proteins across TDP-43 strata. We found extensive overlap in differential protein abundance profiles between MNs with or without obvious TDP-43 cytoplasmic inclusions that together point to early and sustained dysregulation of oxidative phosphorylation, mRNA splicing and translation, and retromer-mediated vesicular transport in ALS. Our data are the first unbiased quantification of single MN protein abundance changes associated with TDP-43 proteinopathy and begin to demonstrate the utility of pathology-stratified trace sample proteomics for understanding single-cell protein abundance changes in human neurologic diseases.

pathology↗

bioRxiv2022

Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics

The sensitivity of single-cell proteomics (SCP) has increased dramatically in recent years due to advances in experimental design, sample preparation, separations and mass spectrometry instrumentation. Further increasing the sensitivity of SCP methods and instrumentation will enable the study of proteins within single cells that are expressed at copy numbers too small to be measured by current methods. Here we combine efficient nanoPOTS sample preparation and ultra-low-flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in fast label-free analyses. WWA is based on data-dependent acquisition (DDA) but employs larger precursor isolation windows to intentionally co-isolate and co-fragment additional precursors along with the selected precursor. The resulting chimeric MS2 spectra are then resolved using the CHIMERYS search engine within Proteome Discoverer 3.0. Compared to standard DDA workflows, WWA employing isolation windows of 8-12 Th increases peptide and proteome coverage by ~28% and ~39%, respectively. For a 40-min LC gradient operated at ~15 nL/min, we identified an average of 2,150 proteins per single-cell-sized aliquots of protein digest directly from MS2 spectra, which increased to an average of 3,524 proteins including proteins identified with MS1-level feature matching. Reducing the active gradient to 20 min resulted in a modest 10% decrease in proteome coverage. We also compared the performance of WWA with DIA. DIA underperformed WWA in terms of proteome coverage, especially with faster separations. Average proteome coverage for single HeLa and K562 cells was respectively 1,758 and 1,642 based on MS2 identifications with 1% false discovery rate and 3042 and 2891 with MS1 feature matching. As such, WWA combined with efficient sample preparation and rapid separations extends the depths of the proteome that can be studied at the single-cell level.

cell biology↗

bioRxiv2022

An Entropy Approach for Choosing Gene Expression Cutoff

Annotating cell types using single-cell transcriptome data usually requires binarizing the expression data to distinguish between the background noise vs. real expression or low expression vs. high expression cases. A common approach is choosing a "reasonable" cutoff value, but it remains unclear how to choose it. In this work, we describe a simple yet effective approach for finding this threshold value.

bioinformatics↗