A5055060386- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Cell Image Analysis Techniques
- Advanced Biosensing Techniques and Applications
- Molecular Junctions and Nanostructures
- Cancer-related molecular mechanisms research
- Metallic Glasses and Amorphous Alloys
- Acute Myeloid Leukemia Research
- RNA Research and Splicing
- Quantum and electron transport phenomena
- interferon and immune responses
- Cancer Immunotherapy and Biomarkers
- Phase-change materials and chalcogenides
- Advanced Image and Video Retrieval Techniques
- Gene Regulatory Network Analysis
- Immune cells in cancer
- SARS-CoV-2 and COVID-19 Research
- CRISPR and Genetic Engineering
- Monoclonal and Polyclonal Antibodies Research
- Genomic variations and chromosomal abnormalities
- Immune Cell Function and Interaction
- Protein Degradation and Inhibitors
- Surface and Thin Film Phenomena
- Epigenetics and DNA Methylation
Rice University
2019-2024
Carnegie Mellon University
2023-2024
The University of Texas MD Anderson Cancer Center
2018-2024
Houston Methodist
2020
Tsinghua University
2005-2018
Institute of Physics
2011-2014
Chinese Academy of Sciences
2013-2014
University of Hong Kong
2014
State Nuclear Power Technology Company (China)
2013
State Key Laboratory of Magnetism
2013
Immunity that cross-reacts between influenza type A viruses of distinct subtypes is called hetero(sub)typic (Het-I). We have studied Het-I by challenging PR8-immune mice with the heterosubtypic virus X31. did not prevent infection X31 but, at its height, strongly aided in recovery. The nature effector mechanisms involved was investigated simultaneous challenge and an immunologically unrelated B depleting individual lymphocyte subsets before challenge. study showed following: 1) were...
Chimeric antigen receptor (CAR) engineering of natural killer (NK) cells is promising, with early-phase clinical studies showing encouraging responses. However, the transcriptional signatures that control fate CAR-NK after infusion and factors influence tumor remain poorly understood. We performed single-cell RNA sequencing mass cytometry to study heterogeneity their in vivo evolution adoptive transfer, from phase relapse. Using a preclinical model noncurative lymphoma samples responder...
Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge gap, we perform a genome-wide CRISPR dropout screen and integrate analyses multi-omics data screen, association studies, single-cell RNA-Seq, host-virus proteins or protein/RNA interactome. This study uncovers many that currently underappreciated, including components V-ATPases, ESCRT,...
Attention based automatic image cropping aims at preserving the most visually important region in an image. A common task this kind of method is to search for smallest rectangle inside which summed attention maximized. We demonstrate that under appropriate formulations, can be achieved using efficient algorithms with low computational complexity. In a practically useful scenario where aspect ratio given, problem solved complexity linear number pixels. also study possibility multiple and new...
Abstract Single-cell RNA-seq is a powerful tool in decoding the heterogeneity complex tissues by generating transcriptomic profiles of individual cell. Here, we report single-nuclei (snRNA-seq) study on human retinal tissue, which composed multiple cell types with distinct functions. Six samples from three healthy donors are profiled and high-quality data obtained for 5873 single nuclei. All major observed marker genes each type identified. The gene expression macular peripheral retina...
Integration of single-cell multiomics profiles generated by different technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provided approximate solutions. Here, we present a novel mathematical solution named bi-order canonical correlation analysis (bi-CCA), which extends widely used CCA approach to iteratively align rows and columns between data matrices. Bi-CCA generally applicable combinations any two modalities....
Single-cell RNA-sequencing data generated by a variety of technologies, such as Drop-seq and SMART-seq, can reveal simultaneously the mRNA transcript levels thousands genes in cells. It is often important to identify informative or cell-type-discriminative markers reduce dimensionality achieve cell typing results. We present an ab initio method that performs unsupervised marker selection identifying have subpopulation-discriminative expression are co- mutually-exclusively expressed with...
Abstract We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of cell population based on single-cell copy number (SCCN) profiles, and statistical routine named lineage speciation analysis (LSA), whichty facilitates discovery fitness-associated alterations genes from SCCN trees. MEDALT appears more accurate than phylogenetics approaches in reconstructing lineage. From data 20 triple-negative breast cancer patients, our effectively...
SARS-CoV-2 vaccines pose as the most effective approach for mitigating COVID-19 pandemic. High-degree efficacy of in clinical trials indicates that vaccination invariably induces an adaptive immune response. However, emergence breakthrough infections vaccinated individuals suggests breadth and magnitude vaccine-induced response may vary. We assessed T cell 21 found SARS-CoV-2-specific cells, which were mainly CD4+ detected all but was varied. then investigated differentiation states cytokine...
Heterogeneity is a hallmark of cancer. The advent single-cell technologies has helped uncover heterogeneity in high-throughput manner different cancers across varied contexts. Here we apply sequencing to reveal inherent assumptively monoclonal pancreatic cancer (PDAC) cell lines and patient-derived organoids (PDOs). Our findings high degree both genomic transcriptomic polyclonality monolayer PDAC lines, custodial variation induced by growing apparently identical laboratories, shifts...
The development of a phenotype in multicellular organism often involves multiple, simultaneously occurring biological processes. Advances single-cell RNA-sequencing make it possible to infer latent developmental processes from the transcriptomic profiles cells at various stages. Accurate characterization is challenging however, particularly for periodic such as cell cycle. To address this, we develop Cyclum, an autoencoder approach identifying circular trajectories gene expression space....
Activating KRAS mutations (KRAS*) in pancreatic ductal adenocarcinoma (PDAC) drive anabolic metabolism and support tumor maintenance. KRAS* inhibitors show initial antitumor activity followed by recurrence due to cancer cell-intrinsic immune-mediated paracrine mechanisms. Here, we explored the potential role of cancer-associated fibroblasts (CAFs) enabling bypass identified CAF-derived NRG1 activation cell ERBB2 ERBB3 receptor tyrosine kinases as a mechanism which KRAS*-independent growth is...
Abstract Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. batch effect, i.e., the variability among samples gathered from different times, tissues, patients, introduces large between-group obscures true identities cells. To solve this problem, we introduce Label-Aware Distance ( Lad ), a metric using temporal/spatial locality effect to control for such factors. We validate...
We present a theoretical study of the tunneling magnetoresistance (TMR) and spin-polarized transport in Fe3Si/MgO/Fe3Si(001) magnetic tunnel junction (MTJ). It is found that conductance bias-dependent TMR ratios are rather sensitive to structure Fe3Si electrode. From symmetry analysis band structures, we there no Δ1 bands crossing Fermi level for cubic Fe3Si. In contrast, tetragonal driven by in-plane strain reveals half-metal nature terms state. The giant predicted both MTJs with electrodes...
Abstract Acquiring accurate single-cell multiomics profiles often requires performing unbiased in silico integration of data matrices generated by different technologies from the same biological sample. However, both rows and columns can represent entities matrices, making such a computational challenge that has only been solved approximately existing approaches. Here, we present bindSC, tool realizes simultaneous alignment between without approximations. Using datasets produced as gold...
Abstract Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell origin can impact response to therapy, it crucial understand lineage composition AML cells at time Here we leverage single-cell chromatin accessibility profiling 22 bone marrow aspirates from eight patients resistance and following subsequent characterize their landscape. Our findings reveal complex architecture therapy-resistant that are primed for stem...
A four-parameter equation of state (EOS), expressed in terms the equilibrium volume V0, cohesion energy EC, isothermal bulk modulus B0, and its first pressure derivative B0′, is proposed successfully applied to 40 selected metals. From EOS, thermal expansions α, melting points TM, ultimate strengths PC, critical VC metals are calculated good agreement with experimental observations. Besides, a strong correlation between PC∕B0 (VC−V0)∕V0 found be (PC∕B0)∕[(VC−V0)∕V0]≈0.31.
Sample barcoding is essential in mass cytometry analysis, since it can eliminate potential procedural variations, enhance throughput, and allow simultaneous sample processing acquisition. pooling after prior surface staining termed live-cell more desirable than intracellular barcoding, where samples are pooled fixation permeabilization, does not depend on fixation-sensitive antigenic epitopes. In the general approach uses two tags per out of a pool antibodies paired with five palladium (Pd)...
Long-chain alkanoic acids usually form close-packed monolayer films with alkyl chains highly oriented on substrates. Previous studies have reported the adsorption of stearic acid gold, aluminum, copper, silver, and aluminum oxide. However, there are no reports magnetic metals. In this work, characterization adsorbed Ni(111) surface has been studied experimentally first-principles calculation. The results suggest that is chemically via a bidentate interaction distance about 1.8 Å. Besides...
Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge gap, we performed a genome-wide CRISPR dropout screen and integrated analyses multi-omics data screen, association studies, single-cell RNA-seq, host-virus proteins or protein/RNA interactome. This study has uncovered many that were missed by including components V-ATPases, ESCRT,...
We report a theoretical study of magnetoresistance and spin-polarized transport series paracyclophane-based molecular tunnel junctions. predict that the junction using [2.2]-paracyclophane barrier has desired low resistance area product in combination with high ratio. In addition, we find conductance decreases exponentially increasing length, indicating nonresonant tunneling mechanism. particular, characteristic decay constant can be theoretically evaluated from complex band structure...
We propose and theoretically investigate an interesting potentially very attractive magnetic tunnel junction FePt/NaCl/FePt(001) for spintronics. It is because the strain at FePt/NaCl interface relatively small and, as a result, spin injection from FePt metal to NaCl barrier significant thus large TMR ratio can be obtained. The electronic bands with symmetry of L10 cross Fermi level both majority-spin minority-spin channels, evanescent state dominates electron transmission through fcc...