Fragile Watermarking Scheme Exploiting Non-Deterministic Block-Wise Dependency. - Yinyin Yuan; Chang-Tsun Li (ICPR (4), 2004)

Partial Mixture Model for Tight Clustering in Exploratory Gene Expression Analysis. - Yinyin Yuan; Chang-Tsun Li (BIBE, 2007)

Probabilistic framework for gene expression clustering validation based on gene ontology and graph theory. - Yinyin Yuan; Chang-Tsun Li (ICASSP, 2008)

An unsupervised conditional random fields approach for clustering gene expression time series. - Chang-Tsun Li; Yinyin Yuan; Roland Wilson (Bioinform., 2008)

Partial mixture model for tight clustering of gene expression time-course. - Yinyin Yuan; Chang-Tsun Li; Roland Wilson (BMC Bioinform., 2008)

A Bayes Random Field Approach for Integrative Large-Scale Regulatory Network Analysis. - Yinyin Yuan; Chang-Tsun Li (J. Integr. Bioinform., 2008)

Inferring Causal Relations from Multivariate Time Series: A Fast Method for Large-Scale Gene Expression Data. - Yinyin Yuan; Chang-Tsun Li (BIBE, 2009)

Statistical inference from large-scale genomic data. - Yinyin Yuan (2009)

A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes. - Yinyin Yuan; Christina Curtis; Carlos Caldas; Florian Markowetz (BIBM, 2010)

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer. - Yinyin Yuan; Oscar M. Rueda; Christina Curtis; Florian Markowetz (Bioinform., 2011)

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes. - Yinyin Yuan; Richard S. Savage; Florian Markowetz (PLoS Comput. Biol., 2011)

A Sparse Regulatory Network of Copy-Number Driven Gene Expression Reveals Putative Breast Cancer Oncogenes. - Yinyin Yuan; Christina Curtis; Carlos Caldas; Florian Markowetz (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Capturing Global Spatial Context for Accurate Cell Classification in Skin Cancer Histology. - Konstantinos Zormpas-Petridis; Henrik Failmezger; Ioannis Roxanis; Matthew D. Blackledge; Yann Jamin; Yinyin Yuan (COMPAY/OMIA@MICCAI, 2018)

Deconvolving convolution neural network for cell detection. - Shan E Ahmed Raza; Khalid AbdulJabbar; Mariam Jamal-Hanjani; Selvaraju Veeriah; John Le Quesne; Charles Swanton; Yinyin Yuan (CoRR, 2018)

DeepSDCS: Dissecting cancer proliferation heterogeneity in Ki67 digital whole slide images. - Priya Lakshmi Narayanan; Shan E Ahmed Raza; Andrew Dodson; Barry Gusterson; Mitchell Dowsett; Yinyin Yuan (CoRR, 2018)

Deconvolving Convolutional Neural Network for Cell Detection. - Shan E Ahmed Raza; Khalid AbdulJabbar; Mariam Jamal-Hanjani; Selvaraju Veeriah; John Le Quesne; Charles Swanton; Yinyin Yuan (ISBI, 2019)

ConCORDe-Net: Cell Count Regularized Convolutional Neural Network for Cell Detection in Multiplex Immunohistochemistry Images. - Yeman Brhane Hagos; Priya Lakshmi Narayanan; Ayse U. Akarca; Teresa Marafioti; Yinyin Yuan (MICCAI (1), 2019)

Glioma Classification Using Multimodal Radiology and Histology Data. - Azam Hamidinekoo; Tomasz Pieciak; Maryam Afzali; Otar Akanyeti; Yinyin Yuan (BrainLes@MICCAI (2), 2020)

Automated Quantification Of Blood Microvessels In Hematoxylin And Eosin Whole Slide Images. - Azam Hamidinekoo; Anna Kelsey; Nicholas Trahearn; Joanna Selfe; Janet Shipley; Yinyin Yuan (COMPAY@MICCAI, 2021)

Symmetric Dense Inception Network for Simultaneous Cell Detection and Classification in Multiplex Immunohistochemistry Images. - Hanyun Zhang; Tami Grunewald; Ayse U. Akarca; Jonathan A. Ledermann; Teresa Marafioti; Yinyin Yuan (COMPAY@MICCAI, 2021)

Cell Abundance Aware Deep Learning For Cell Detection On Highly Imbalanced Pathological Data. - Yeman Brhane Hagos; Catherine S. Y. Lecat; Dominic Patel; Lydia Lee; Thien-An Tran; Manuel Rodriguez-Justo; Kwee Yong; Yinyin Yuan (ISBI, 2021)

Wisdom Of The Crowd For Early Detection In Barrett's Esophagus. - Justin Law; Thomas G. Paulson; Carissa A. Sanchez; Patricia C. Galipeau; Marnix Jansen; Matthew D. Stachler; Carlo C. Maley; Yinyin Yuan (ISBI, 2021)

MoNuSAC2020: A Multi-Organ Nuclei Segmentation and Classification Challenge. - Ruchika Verma; Neeraj Kumar 002; Abhijeet Patil; Nikhil Cherian Kurian; Swapnil Rane; Simon Graham; Quoc Dang Vu; Mieke Zwager; Shan-E-Ahmed Raza; Nasir M. Rajpoot; Xiyi Wu; Huai Chen; et al. (IEEE Trans. Medical Imaging, 2021)

Automated Dcis Identification From Multiplex Immunohistochemistry Using Generative Adversarial Networks. - Faranak Sobhani; Azam Hamidinekoo; Allison H. Hall; Lorraine M. King; Jeffrey R. Marks; Carlo C. Maley; Hugo M. Horlings; Eun-Sil Shelley Hwang; Yinyin Yuan (ISBI, 2022)

DeepMIF: Deep Learning Based Cell Profiling for Multispectral Immunofluorescence Images with Graphical User Interface. - Yeman Brhane Hagos; Ayse U. Akarca; Alan Ramsay; Riccardo L. Rossi; Sabine Pomplun; Alessia Moioli; Andrea Gianatti; Christopher Mcnamara; Alessandro Rambaldi; Sergio A. Quezada; David Linch; Giuseppe Gritti; et al. (MICCAI (4), 2022)

DCIS AI-TIL: Ductal Carcinoma In Situ Tumour Infiltrating Lymphocyte Scoring Using Artificial Intelligence. - Yeman Brhane Hagos; Faranak Sobhani; Simon P. Castillo; Allison H. Hall; Khalid AbdulJabbar; Roberto Salgado; Bryan Harmon; Kristalyn Gallagher; Mark Kilgore; Lorraine M. King; Jeffrey R. Marks; Carlo C. Maley; et al. (AIIIMA/MIABID@MICCAI, 2022)

Cross-Stream Interactions: Segmentation of Lung Adenocarcinoma Growth Patterns. - Xiaoxi Pan; Hanyun Zhang; Anca-Ioana Grapa; Khalid AbdulJabbar; Shan-E-Ahmed Raza; Ho Kwan Alvin Cheung; Takahiro Karasaki; John Le Quesne; David A. Moore; Charles Swanton; Yinyin Yuan (CMMCA@MICCAI, 2022)

Self-supervised Antigen Detection Artificial Intelligence (SANDI). - Hanyun Zhang; Khalid AbdulJabbar; Tami Grunewald; Ayse U. Akarca; Yeman Brhane Hagos; Catherine S. Y. Lecat; Dominic Patel; Lydia Lee; Manuel Rodriguez-Justo; Kwee Yong; Jonathan A. Ledermann; John Le Quesne; et al. (REMIA@MICCAI, 2022)

Exploring the value of qualitative and quantitative feedback in a mobile health edutainment system. - Manning Li; Yinyin Yuan; Jinyu Zhou; Haobo Zhang (PACIS, 2022)

A two-level multiphysics finite element method for a nonlinear poroelasticity model. - Zhihao Ge; Shuaichao Pei; Yinyin Yuan (Comput. Math. Appl., 2022)

Adaptive Self-Supervised Learning of Morphological Landscape for Leukocytes Classification in Peripheral Blood Smears. - Zhuohe Liu; Simon P. Castillo; Xin Han; Xiaoping Sun; Zhihong Hu; Yinyin Yuan (BHI, 2024)

Immune-Guided AI for Reproducible Regions of Interest Selection in Multiplex Immunofluorescence Pathology Imaging. - Tanishq Gautam; Karina P. Gonzalez; Maria E. Salvatierra; Alejandra Serrano; Pingjun Chen; Xiaoxi Pan; Yasin Shokrollahi; Sara Ranjbar; Leticia Rodriguez; Luisa Solis-Soto; Yinyin Yuan; Simon P. Castillo (MICCAI (4), 2024)

Predicting DNA Content Abnormalities in Barrett's Esophagus: A Weakly Supervised Learning Paradigm. - Caner Ercan; Xiaoxi Pan; Thomas G. Paulson; Matthew D. Stachler; Carlo C. Maley; William M. Grady; Yinyin Yuan (MIDL, 2024)

Advancing Multiplex Immunofluorescence Imaging Cell Detection using Semi-Supervised Learning with Pseudo-Labeling. - Yasin Shokrollahi; Karina Pinao Gonzales; Maria Esther Salvatierra; Simon P. Castillo; Tanishq Gautam; Pingjun Chen; Leticia Rodriguez; Sara Ranjbar; Patient Mosaic Team; Luisa Solis-Soto; Yinyin Yuan; Xiaoxi Pan (MIDL, 2024)

Optimizing Cell Recognition in Sarcoma Multiplex Immunohistochemistry Images via Pre-Training Strategies. - Pingjun Chen; Maria E. Salvatierra; Alejandra Serrano; Karina Pinao Gonzalez; Sara Ranjbar; Yasin Shokrollahi; Tanishq Gautam; Leticia Rodriguez; Patient Mosaic Team; Xiaoxi Pan; Luisa M. Solis Soto; Yinyin Yuan (ISBI, 2025)

CellSymphony: Deciphering the molecular and phenotypic orchestration of cells with single-cell pathomics. - Paul H. Acosta; Pingjun Chen; Simon P. Castillo; Maria Esther Salvatierra; Yinyin Yuan; Xiaoxi Pan (CoRR, 2025)