CellEnBoost: A Boosting-Based Ligand-Receptor Interaction Identification Model for Cell-to-Cell Communication Inference

DeepCF-PPI: improved prediction of protein-protein interactions by combining learned and handcrafted features based on attention mechanisms

(2023) Hoai-Nhan Tran et al.   APPLIED INTELLIGENCE

MM-StackEns: A new deep multimodal stacked generalization approach for protein–protein interaction prediction

(2023) Alexandra-Ioana Albu et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

(2023) Zixuan Cang et al.   NATURE METHODS

An improved hierarchical variational autoencoder for cell–cell communication estimation using single-cell RNA-seq data

(2023) Shuhui Liu et al.   Briefings in Functional Genomics

High Risk-Human Papillomavirus in HNSCC: Present and Future Challenges for Epigenetic Therapies

(2022) Lavinia Ghiani et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

InterCellDB: A User‐Defined Database for Inferring Intercellular Networks

(2022) Ziyang Jin et al.   Advanced Science

Cell–cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies

(2022) Lihong Peng et al.   BRIEFINGS IN BIOINFORMATICS

Prognostic biomarker IL17A correlated with immune infiltrates in head and neck cancer

(2022) Meng Yu et al.   World Journal of Surgical Oncology

Context-aware deconvolution of cell–cell communication with Tensor-cell2cell

(2022) Erick Armingol et al.   Nature Communications

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

(2022) Daniel Dimitrov et al.   Nature Communications

Modeling intercellular communication in tissues using spatial graphs of cells

(2022) David S. Fischer et al.   NATURE BIOTECHNOLOGY

spaCI: deciphering spatial cellular communications through adaptive graph model

(2022) Ziyang Tang et al.   BRIEFINGS IN BIOINFORMATICS

MARPPI: boosting prediction of protein–protein interactions with multi-scale architecture residual network

(2022) Xue Li et al.   BRIEFINGS IN BIOINFORMATICS

Investigating cardiotoxicity related with hERG channel blockers using molecular fingerprints and graph attention mechanism

(2022) Tianyi Wang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Prediction of protein-protein interactions based on ensemble residual convolutional neural network

(2022) Hongli Gao et al.   COMPUTERS IN BIOLOGY AND MEDICINE

iBLP: An XGBoost-Based Predictor for Identifying Bioluminescent Proteins

(2021) Dan Zhang et al.   Computational and Mathematical Methods in Medicine

Understanding cell‐cell communication and signaling in the colorectal cancer microenvironment

(2021) Shaikha AlMusawi et al.   Clinical and Translational Medicine

Prediction of protein-protein interaction sites through eXtreme gradient boosting with kernel principal component analysis

(2021) Xue Wang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification

(2021) Liqian Zhou et al.   BMC BIOINFORMATICS

VDA-RWLRLS: An anti-SARS-CoV-2 drug prioritizing framework combining an unbalanced bi-random walk and Laplacian regularized least squares

(2021) Ling Shen et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Deep Neural Network and Extreme Gradient Boosting Based Hybrid Classifier for Improved Prediction of Protein-Protein Interaction

(2021) Satyajit Mahapatra et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

DLEU1 promotes oral squamous cell carcinoma progression by activating interferon-stimulated genes

(2021) Yui Hatanaka et al.   Scientific Reports

Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer

(2020) Anthony R. Cillo et al.   IMMUNITY

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

(2020) Zixuan Cang et al.   Nature Communications

Deep-belief network for predicting potential miRNA-disease associations

(2020) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

AdaBoost-CNN: An adaptive boosting algorithm for convolutional neural networks to classify multi-class imbalanced datasets using transfer learning

(2020) Aboozar Taherkhani et al.   NEUROCOMPUTING

Predicting cell-to-cell communication networks using NATMI

(2020) Rui Hou et al.   Nature Communications

Head and neck squamous cell carcinoma

(2020) Daniel E. Johnson et al.   Nature Reviews Disease Primers

PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq

(2019) Scott R. Tyler et al.   Cell Reports

PyFeat: A Python-based Effective Feature Generation Tool for DNA, RNA, and Protein Sequences

(2019) Rafsanjani Muhammod et al.   BIOINFORMATICS

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

Single-cell transcriptomic profiling of the aging mouse brain

(2019) Methodios Ximerakis et al.   NATURE NEUROSCIENCE

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Prediction of bacteriophage proteins located in the host cell using hybrid features

(2018) Jing-Hui Cheng et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart

(2018) Daniel A. Skelly et al.   Cell Reports

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

(2017) Joseph X. Zhou et al.   Scientific Reports

Transcriptome Analysis of Individual Stromal Cell Populations Identifies Stroma-Tumor Crosstalk in Mouse Lung Cancer Model

(2015) Hyejin Choi et al.   Cell Reports

Multi-class AdaBoost

(2013) Trevor Hastie et al.   Statistics and Its Interface

Correction: A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications

(2011) Mo Deng et al.   PLoS One

Large-Scale Prediction of Human Protein−Protein Interactions from Amino Acid Sequence Based on Latent Topic Features

(2010) Xiao-Yong Pan et al.   JOURNAL OF PROTEOME RESEARCH