Author details

Full Name

Xiaole Shirley Liu

Affiliation

ORCID

Career Start Year

2002

Papers

224

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37169596	Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data.		2023
36264143	A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin-MLL Inhibition.	Cancer Discov	2023
37570771	Advances in the Structure of GGGGCC Repeat RNA Sequence and Its Interaction with Small Molecules and Protein Partners.		2023
37149682	MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment.		2023
37391666	Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA.		2023
36811466	Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-Secreted Cytokines.	Cancer Discov	2023
37258680	Transfer learning enables predictions in network biology.	Nature	2023
36745048	Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.	Cancer Discov	2023
35262677	Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer.	Clin Cancer Res	2022
36240281	Machine learning on syngeneic mouse tumor profiles to model clinical immunotherapy response.	Science advances	2022
36219700	Hippo Signaling Pathway Regulates Cancer Cell-Intrinsic MHC-II Expression.	Cancer Immunology Research	2022
35561684	Topical therapy for regression and melanoma prevention of congenital giant nevi.	Cell	2022
36068320	MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells.	Nature Methods	2022
35605261	Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies.	Cancer Immunology Research	2022
35534777	IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia.	Nat Cancer	2022
36494034	Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation.		2022
35031563	Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress.	Proc Natl Acad Sci U S A	2022
34534350	TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.	Nucleic Acids Res	2022
35263565	A high-resolution view of intra-tumoral B cell immunity.	Immunity	2022
34772935	Fast alignment and preprocessing of chromatin profiles with Chromap.	Nature Communications	2021
33707234	CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor Cells and T Cells.	Cancer Discov	2021
33592174	Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis.	Cell	2021
33589424	Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade.	Cancer Discov	2021
33567269	Systematic characterization of mutations altering protein degradation in human cancers.	Mol Cell	2021
33986545	TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.	Nature Methods	2021
33720354	Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation.	Blood	2021
33419780	Network for Biomarker Immunoprofiling for Cancer Immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC).	Clin Cancer Res	2021
33323402	Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network.	Clin Cancer Res	2021
33158814	Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer.	Cancer Research	2021
34737445	FGFR-inhibitor-mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces adaptive therapeutic resistance.	Nat Cell Biol	2021
34493872	A single-cell and spatially resolved atlas of human breast cancers.	Nat Genet	2021
33051080	Computational Approaches to Modeling Transcription Factor Activity and Gene Regulation.	Trends in Biochemical Sciences	2020
32424124	Determinants of transcription factor regulatory range.	Nature Communications	2020
32413516	CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma.	Genomics Proteomics Bioinformatics	2020
32124325	Computational Deconvolution of Tumor-Infiltrating Immune Components with Bulk Tumor Gene Expression Data.	Methods in Molecular Biology	2020
32442275	TIMER2.0 for analysis of tumor-infiltrating immune cells.	Nucleic Acids Research	2020
32767996	Integrative analyses of single-cell transcriptome and regulome using MAESTRO.		2020
32728046	An integrative ENCODE resource for cancer genomics.	Nat Commun	2020
33059736	Clonal tracing reveals diverse patterns of response to immune checkpoint blockade.	Genome Biol	2020
32839551	Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy.	Nature Cell Biology	2020
32723834	Inhibition of MAN2A1 Enhances the Immune Response to Anti-PD-L1 in Human Tumors.	Clin Cancer Res	2020
31101897	Publisher Correction: Landscape of B cell immunity and related immune evasion in human cancers.	Nat Genet	2019
31727847	Deciphering essential cistromes using genome-wide CRISPR screens.	Proc Natl Acad Sci U S A	2019
30224544	Targeting the MIF/CXCR7/AKT Signaling Pathway in Castration-Resistant Prostate Cancer.	Molecular Cancer Research	2019
30358813	A Bayesian model for single cell transcript expression analysis on MERFISH data.		2019
30462313	Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.	Nucleic Acids Research	2019
30875429	A Bayesian model for single cell transcript expression analysis on MERFISH data.		2019
30742113	Landscape of B cell immunity and related immune evasion in human cancers.	Nat Genet	2019
31053864	Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks.	Nucleic Acids Research	2019
31342013	Big Data Approaches for Modeling Response and Resistance to Cancer Drugs.	Annu Rev Biomed Data Sci	2018