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Author Details

Yang Xie
Quantitative Biomedical Research Center
2007
221
58
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
38043788Deep Learning-Based H-Score Quantification of Immunohistochemistry-Stained Images.Mod Pathol2024
36454649Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm.J Clin Invest2023
37662289Progressive plasticity during colorectal cancer metastasis.bioRxiv2023
37619429Unsupervised domain adaptation for nuclei segmentation: Adapting from hematoxylin & eosin stained slides to immunohistochemistry stained slides using a curriculum approach.Comput Methods Programs Biomed2023
37580069T-cell tolerant fraction as a predictor of immune-related adverse events.J Immunother Cancer2023
37600329Silencing of <i>GRHL2</i> induces epithelialâ¿¿toâ¿¿mesenchymal transition in lung cancer cell lines with different effects on proliferation and clonogenic growth.Oncol Lett2023
37255415A Comparative Study of Neuroendocrine Heterogeneity in Small Cell Lung Cancer and Neuroblastoma.Mol Cancer Res2023
37285748Systemic immune parameters after prior radiation therapy in patients receiving immune checkpoint inhibitors.Transl Oncol2023
36945650Spatial Transcriptomics Arena (STAr): an Integrated Platform for Spatial Transcriptomics Methodology Research.bioRxiv2023
37208378Novel start codons introduce novel coding sequences in the human genomes.Sci Rep2023
37107679Deep-Learning-Based Hepatic Ploidy Quantification Using H&amp;E Histopathology Images.Genes (Basel)2023
37378310Dissecting molecular, pathological, and clinical features associated with tumor neural/neuroendocrine heterogeneity.iScience2023
37171983A comparative study of neuroendocrine heterogeneity in small cell lung cancer and neuroblastoma.Mol Cancer Res2023
37100227A Deep Learning Approach for Histology-Based Nucleus Segmentation and Tumor Microenvironment Characterization.Mod Pathol2023
37461694Deep Learning of Cell Spatial Organizations Identifies Clinically Relevant Insights in Tissue Images.Res Sq2023
36890029Deep learning in digital pathology for personalized treatment plans of cancer patients.Semin Diagn Pathol2023
36647832Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer.J Clin Invest2023
36669682Enhanced Pathology Image Quality with Restore-Generative Adversarial Network.Am J Pathol2023
34773277RCRdiff: A fully integrated Bayesian method for differential expression analysis using raw NanoString nCounter data.Stat Med2022
35803262TK216 targets microtubules in Ewing sarcoma cells.Cell Chem Biol2022
35635448Isolation of Group 2 Innate Lymphoid Cells from Mouse Nasal Mucosa to Detect the Expression of CD226.J Vis Exp2022
35596002Correction to: Divergent prognostic effects of pre-existing and treatment-emergent thyroid dysfunction in patients treated with immune checkpoint inhibitors.Cancer Immunol Immunother2022
35390316Deep Learning of Rhabdomyosarcoma Pathology Images for Classification and Survival Outcome Prediction.Am J Pathol2022
35927477Sprod for de-noising spatially resolved transcriptomics data based on position and image information.Nat Methods2022
36077736A Pan-Cancer Assessment of <i>RB1</i>/<i>TP53</i> Co-Mutations.Cancers (Basel)2022
35072744Divergent prognostic effects of pre-existing and treatment-emergent thyroid dysfunction in patients treated with immune checkpoint inhibitors.Cancer Immunol Immunother2022
35003896Association between immune-related adverse event timing and treatment outcomes.Oncoimmunology2022
35267634Association between Antibiotic Exposure and Systemic Immune Parameters in Cancer Patients Receiving Checkpoint Inhibitor Therapy.Cancers (Basel)2022
34751162Lung Cancer Computational Biology and Resources.Cold Spring Harb Perspect Med2022
32770205Spatial molecular profiling: platforms, applications and analysis tools.Brief Bioinform2021
33495338Tumor-suppressor function of Beclin 1 in breast cancer cells requires E-cadherin.Proc Natl Acad Sci U S A2021
33543271MB-GAN: Microbiome Simulation via Generative Adversarial Network.Gigascience2021
33713107MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data.G3 (Bethesda)2021
33841507SMIXnorm: Fast and Accurate RNA-Seq Data Normalization for Formalin-Fixed Paraffin-Embedded Samples.Front Genet2021
33750914Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer.Commun Biol2021
33500426A deep learning-based model for screening and staging pneumoconiosis.Sci Rep2021
33604654Evaluating short-term forecasting of COVID-19 cases among different epidemiological models under a Bayesian framework.Gigascience2021
34617573Silencing of MBD2 and EZH2 inhibits the proliferation of colorectal carcinoma cells by rescuing the expression of SFRP.Oncol Rep2021
34730508Association of Healthcare Access With Intensive Care Unit Utilization and Mortality in Patients of Hispanic Ethnicity Hospitalized With COVID-19.J Hosp Med2021
34722619Upfront Brain Treatments Followed by Lung Surgery Improves Survival for Stage IV Non-small Cell Lung Cancer Patients With Brain Metastases: A Large Cohort Analysis.Front Surg2021
34127546Association between body mass index, dosing strategy, and efficacy of immune checkpoint inhibitors.J Immunother Cancer2021
34146105Bayesian modeling of spatial molecular profiling data via Gaussian process.Bioinformatics2021
34081116Assessing consistency across functional screening datasets in cancer cells.Bioinformatics2021
33328639Sorting nexin 5 mediates virus-induced autophagy and immunity.Nature2021
31501522Correction: LCE: an open web portal to explore gene expression and clinical associations in lung cancer.Oncogene2020
31929521VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning.PLoS Comput Biol2020
32042080Biomarkers for RBM39 degradation in acute myeloid leukemia.Leukemia2020
31947823Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets.Genes (Basel)2020
31915129Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer.Cancer Res2020
33027755Experience, Perceptions, and Recommendations Concerning COVID-19-Related Clinical Research Adjustments.J Natl Compr Canc Netw2020
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Collaborators

Guanghua Xiao
The University of Texas Southwestern Medical Center
Co-authored papers 92
John D Minna
University of Texas Southwestern Medical Center at Dallas
Co-authored papers 52
Xiaowei Zhan
Southwestern Medical Center, University of Texas
Co-authored papers 27
Tao Wang
University of Texas Southwestern Medical Center
Co-authored papers 26
Hao Tang
Guizhou Medical University
Co-authored papers 20
Yunyun Zhou
Children's Hospital of Philadelphia
Co-authored papers 15
Beibei Chen
University of Texas Southwestern Medical Center
Co-authored papers 10
Michael Peyton
Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center
Co-authored papers 9
Gustavo Stolovitzky
IBM T.J. Watson Research Center
Co-authored papers 6
Simon J Craddock Lee
Co-authored papers 5
He Zhang
Co-authored papers 5
Quan-Zhen Li
Co-authored papers 5
Michael A White
University of Georgia
Co-authored papers 5
Thea Norman
Bill & Melinda Gates Foundation
Co-authored papers 5
Stephen H Friend
University of Oxford
Co-authored papers 4
Jennifer Cai
University of Texas Southwestern Medical Center
Co-authored papers 3
Rahul K Kollipara
McDermott Center for Human Growth and Development.
Co-authored papers 3
Peddinti Gopalacharyulu
Technical Research Centre of Finland
Co-authored papers 3
Julio Saez-Rodriguez
Institute of Computational Biomedicine, Heidelberg University
Co-authored papers 3
Tero Aittokallio
Institute for Molecular Medicine Finland (FIMM), University of Helsinki
Co-authored papers 3
Suleiman A Khan
Helsinki Institute for Information Technology (HIIT), Aalto University
Co-authored papers 3
Lewis C Cantley
Co-authored papers 3
Lara M Mangravite
Children's Hospital Oakland Research Institute
Co-authored papers 3
James Christopher Bare
Institute for Systems Biology
Co-authored papers 3
Yunguan Wang
Co-authored papers 3
Wei Zhang
Montefiore Medical Center
Co-authored papers 2
Allen Dearry
National Institute of Environmental Health Sciences
Co-authored papers 2
Ralf Kittler
McDermott Center for Human Growth and Development.
Co-authored papers 2
Gina M DeNicola
H. Lee. Moffitt Cancer Center
Co-authored papers 2
Benjamin D Greenberg
Warren Alpert School of Medicine, Brown University, Butler Hospital
Co-authored papers 2
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