Shaoheng Liang
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View article: Supplementary Table S10 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S10 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Differentially expressed genes of CD4 clusters
View article: Supplementary Table S18 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S18 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Differentially expressed genes of FCGR3A-positive vs FCGR3A-negative NK cells
View article: Supplementary Table S14 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S14 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Differentially expressed genes of CD8 clusters
View article: Supplementary Figures S1-S18 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Figures S1-S18 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Fig. S1. Patient disposition and characteristics. Fig. S2. Timing of OI biopsy collection did not correlate with response. Fig. S3. Major cell types identified in the tumor immune microenvironment. Fig. S4. CD4+ T cells identified in the t…
View article: Supplementary Table S19 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S19 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Statistical test for association of lymphocyte cluster proportion with progression
View article: Supplementary Table S7 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S7 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Single-cell RNA and TCR sequencing information and metrics
View article: Supplementary Table S9 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S9 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Sample-level cell counts of CD4 clusters
View article: Supplementary Table S20 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S20 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Clinical and single-cell features used in multivariable regression models
View article: Supplementary Table S15 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S15 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Statistical test for proportions of CD8+ T cell clusters in the tumor immune microenvironment stratified by histological response and timepoint
View article: Supplementary Table S16 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S16 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
CD8+ T-cell clonotypes with significant frequency changes in response to treatment
View article: Supplementary Table S12 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S12 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Differentially expressed genes of CD8+ T cells from MHRs vs non-MHRs at baseline
View article: Supplementary Table S8 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S8 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Statistical test for proportions of cell types in the tumor immune microenvironment stratified by histological response and timepoint
View article: Supplementary Table S13 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S13 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Sample-level cell counts of CD8 clusters
View article: Supplementary Tables S1-S6 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Tables S1-S6 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Table S1. Patient and tumor characteristics. Table S2. Representativeness of study participants. Table S3. Clinical and histopathologic characteristics of individual patients. Table S4. Treatment related adverse events that occurred after …
View article: Supplementary Table S11 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S11 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Statistical test for proportions of CD4+ T cell clusters in the tumor immune microenvironment stratified by histological response and timepoint
View article: Supplementary Table S17 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Supplementary Table S17 from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
Alpha- and beta-chain sequence data of validated anti-HPV16 TCRs
View article: Data from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Data from Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
In a phase II trial, patients with local-regionally advanced human papillomavirus–positive oropharyngeal carcinoma (n = 35) received ipilimumab (anti-CTLA4) and nivolumab (anti–PD-1) as induction immunotherapy and concurrently with …
View article: Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade
Depletion of Effector Regulatory T Cells Associates with Major Response to Induction Dual Immune Checkpoint Blockade Open
In a phase II trial, patients with local-regionally advanced human papillomavirus–positive oropharyngeal carcinoma (n = 35) received ipilimumab (anti-CTLA4) and nivolumab (anti–PD-1) as induction immunotherapy and concurrently with radioth…
View article: Steamboat: Attention-based multiscale delineation of cellular interactions in tissues
Steamboat: Attention-based multiscale delineation of cellular interactions in tissues Open
Spatial-omics technologies profile cells in their native spatial context within tissues, enabling more complete understanding of cellular properties. However, a key computational challenge remains: identifying cellular interactions that un…
View article: 553 Depletion of effector regulatory T cells drives major response to induction dual immune checkpoint blockade (ICB) in patients with oropharyngeal carcinoma (OPC)
553 Depletion of effector regulatory T cells drives major response to induction dual immune checkpoint blockade (ICB) in patients with oropharyngeal carcinoma (OPC) Open
View article: 1217 A novel transformer-based deep learning model for predicting binding interactions between HLA class I molecules and peptides
1217 A novel transformer-based deep learning model for predicting binding interactions between HLA class I molecules and peptides Open
View article: Label-aware distance mitigates temporal and spatial variability for clustering and visualization of single-cell gene expression data
Label-aware distance mitigates temporal and spatial variability for clustering and visualization of single-cell gene expression data Open
View article: Depletion of effector regulatory T cells drives major response to induction dual immune checkpoint blockade
Depletion of effector regulatory T cells drives major response to induction dual immune checkpoint blockade Open
In a phase 2 trial, local-regionally advanced HPV-positive oropharyngeal carcinoma (OPC) patients received ipilimumab (anti-CTLA-4) and nivolumab (anti-PD-1) as induction immunotherapy and concurrently with radiotherapy ( NCT03799445 ). Co…
View article: Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection
Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection Open
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 …
View article: Stromal-derived NRG1 enables oncogenic KRAS bypass in pancreas cancer
Stromal-derived NRG1 enables oncogenic KRAS bypass in pancreas cancer Open
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 and …
View article: Loss of metabolic fitness drives tumor resistance after CAR-NK cell therapy and can be overcome by cytokine engineering
Loss of metabolic fitness drives tumor resistance after CAR-NK cell therapy and can be overcome by cytokine engineering Open
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 the fate of CAR-NK cells after inf…
View article: Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data
Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data Open
View article: Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance
Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance Open
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of …
View article: An interpretable ML model to characterize patient-specific HLA-I antigen presentation
An interpretable ML model to characterize patient-specific HLA-I antigen presentation Open
Personalized immunotherapy holds the promise of revolutionizing cancer prevention and treatment. However, selecting HLA-bound peptide targets that are specific to patient tumors has been challenging due to a lack of patient-specific antige…
View article: novoRNABreak: local assembly for novel splice junction and fusion transcript detection from RNA-seq data
novoRNABreak: local assembly for novel splice junction and fusion transcript detection from RNA-seq data Open
We present novoRNABreak, a unified framework for cancer specific novel splice junction and fusion transcript detection in RNA-seq data obtained from human cancer samples. novoRNABreak is based on a local assembly model, which offers a trad…