Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey

Graph contextualized attention network for predicting synthetic lethality in human cancers

(2021) Yahui Long et al.   BIOINFORMATICS

KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers

(2021) Shike Wang et al.   BIOINFORMATICS

Identifying driver genes for individual patients through inductive matrix completion

(2021) Tong Zhang et al.   BIOINFORMATICS

CMF-Impute: An accurate imputation tool for single cell RNA-seq data

(2020) Junlin Xu et al.   BIOINFORMATICS

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation

(2020) Ke Jin et al.   BIOINFORMATICS

DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion

(2020) Wenjuan Zhang et al.   BIOINFORMATICS

Biomedical data and computational models for drug repositioning: a comprehensive review

(2020) Huimin Luo et al.   BRIEFINGS IN BIOINFORMATICS

Dual-Dropout Graph Convolutional Network for Predicting Synthetic Lethality in Human Cancers

(2020) Ruichu Cai et al.   BIOINFORMATICS

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks

(2020) Zi-Chao Zhang et al.   BIOINFORMATICS

Predicting Human Microbe-Drug Associations via Graph Convolutional Network with Conditional Random Field

(2020) Yahui Long et al.   BIOINFORMATICS

Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing

(2020) Zichen Wang et al.   BIOINFORMATICS

Predicting human microbe–disease associations via graph attention networks with inductive matrix completion

(2020) Yahui Long et al.   BRIEFINGS IN BIOINFORMATICS

MCCMF: collaborative matrix factorization based on matrix completion for predicting miRNA-disease associations

(2020) Tian-Ru Wu et al.   BMC BIOINFORMATICS

Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information

(2020) Jason Fan et al.   BIOINFORMATICS

Combining sequence and network information to enhance protein–protein interaction prediction

(2020) Leilei Liu et al.   BMC BIOINFORMATICS

Recent advances in network-based methods for disease gene prediction

(2020) Sezin Kircali Ata et al.   BRIEFINGS IN BIOINFORMATICS

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data

(2019) Aanchal Mongia et al.   Frontiers in Genetics

To Embed or Not: Network Embedding as a Paradigm in Computational Biology

(2019) Walter Nelson et al.   Frontiers in Genetics

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

(2019) Geng Chen et al.   Frontiers in Genetics

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization

(2019) Lihua Zhang et al.   NUCLEIC ACIDS RESEARCH

Modeling of Flocculation and Sedimentation Using Population Balance Equation

(2019) Zhipeng Shi et al.   Journal of Chemistry

Predicting synthetic lethal interactions using heterogeneous data sources

(2019) Herty Liany et al.   BIOINFORMATICS

Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction

(2019) Jin Li et al.   BIOINFORMATICS

Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization

(2019) Jiang Huang et al.   BMC BIOINFORMATICS

NCMCMDA: miRNA–disease association prediction through neighborhood constraint matrix completion

(2019) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

SL2MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization

(2019) Yong Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prediction of lncRNA–disease associations based on inductive matrix completion

(2018) Chengqian Lu et al.   BIOINFORMATICS

DrImpute: imputing dropout events in single cell RNA sequencing data

(2018) Wuming Gong et al.   BMC BIOINFORMATICS

Computational prediction of drug–target interactions using chemogenomic approaches: an empirical survey

(2018) Ali Ezzat et al.   BRIEFINGS IN BIOINFORMATICS

Drug knowledge bases and their applications in biomedical informatics research

(2018) Yongjun Zhu et al.   BRIEFINGS IN BIOINFORMATICS

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

TCM visualizes trajectories and cell populations from single cell data

(2018) Wuming Gong et al.   Nature Communications

Manifold regularized matrix factorization for drug-drug interaction prediction

(2018) Wen Zhang et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Majorization-Minimization Algorithms in Signal Processing, Communications, and Machine Learning

(2017) Ying Sun et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization

(2017) Ali Ezzat et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Synthetic lethality and cancer

(2017) Nigel J. O'Neil et al.   NATURE REVIEWS GENETICS

Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data

(2017) Cheng Jia et al.   NUCLEIC ACIDS RESEARCH

Nonnegative matrix factorization algorithms for link prediction in temporal networks using graph communicability

(2017) Xiaoke Ma et al.   PATTERN RECOGNITION

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction

(2017) Zhu-Hong You et al.   PLoS Computational Biology

Robust classification of single-cell transcriptome data by nonnegative matrix factorization

(2016) Chunxuan Shao et al.   BIOINFORMATICS

Protein complex detection based on partially shared multi-view clustering

(2016) Le Ou-Yang et al.   BMC BIOINFORMATICS

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types

(2016) Kyle M. Loh et al.   CELL

Computational methods for trajectory inference from single-cell transcriptomics

(2016) Robrecht Cannoodt et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction

(2016) Yong Liu et al.   PLoS Computational Biology

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets

(2015) Jing Guo et al.   NUCLEIC ACIDS RESEARCH

Inductive matrix completion for predicting gene-disease associations

(2014) N. Natarajan et al.   BIOINFORMATICS

Detecting temporal protein complexes from dynamic protein-protein interaction networks

(2014) Le Ou-Yang et al.   BMC BIOINFORMATICS

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

(2013) Murat Can Cobanoglu et al.   Journal of Chemical Information and Modeling

Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization

(2013) Hua Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

HMDD v2.0: a database for experimentally supported human microRNA and disease associations

(2013) Yang Li et al.   NUCLEIC ACIDS RESEARCH

Protein Complex Detection via Weighted Ensemble Clustering Based on Bayesian Nonnegative Matrix Factorization

(2013) Le Ou-Yang et al.   PLoS One

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

(2012) M. Gonen   BIOINFORMATICS

Drug–target interaction prediction by learning from local information and neighbors

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

Single-cell genomics

(2011) Tomer Kalisky et al.   NATURE METHODS

Synthetic lethality: General principles, utility and detection using genetic screens in human cells

(2010) Sebastian M.B. Nijman   FEBS LETTERS

Matrix Completion With Noise

(2010) Emmanuel J Candes et al.   PROCEEDINGS OF THE IEEE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Semantic web for integrated network analysis in biomedicine

(2009) H. Chen et al.   BRIEFINGS IN BIOINFORMATICS

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS