Guilt-by-association goes global

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

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Life with 6000 Genes

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Direct analysis of protein complexes using mass spectrometry

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Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels

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Systematic functional analysis of the yeast genome

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Characterization of the Yeast Transcriptome

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Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens

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Characterization of Sm‐like proteins in yeast and their association with U6 snRNA

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A protein–protein interaction map of yeast RNA polymerase III

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Oligomer-chip technology

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Pan-Cancer Analysis Reveals the Prognostic Potential of the THAP9/THAP9-AS1 Sense–Antisense Gene Pair in Human Cancers

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Redescription mining on data with background network information

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Supervised contrastive knowledge graph learning for ncRNA–disease association prediction

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Global insights into protein complexes through integrated analysis of the reliable interactome and knockout lethality

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NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis

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A Top-Down Systems Biology Approach for the Identification of Targets for Fungal Strain and Process Development

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An analysis of the validity and utility of the proximon proposition

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A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks

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Evaluation of drug efficacy based on the spatial position comparison of drug–target interaction centers

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A reliable and unbiased human protein network with the disparity filterPreprint

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A mini-atlas of gene expression for the domestic goat ( Capra hircus ) reveals transcriptional differences in immune signatures between sheep and goatsPreprint

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Multiparameter Screen Optimizes Immunoprecipitation

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Sulfate biology genes are associated with mineralization in mouse and human

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Engineering next‐generation crops through CRISPR ‐mediated horizontal gene transfer

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A two-stage geometric method for detecting unreliable links in protein-protein networks

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Applications of Network Analysis in Biomedicine

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Network-based methods with heterogeneous data to identify severe COVID immune-related genes

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Transcriptome organization of white blood cells through gene co-expression network analysis in a large RNA-seq dataset

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GPACDA – circRNA-Disease Association Prediction with Generating Polynomials

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Genome-wide association reveals novel insights into the molecular mechanisms regulating stem volume in Pinus taeda

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An Evolutionary Biology Approach to Understanding Neurological Disorders

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Learning functional linkage networks with a cost-sensitive approach

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Computational Analysis of the Chaperone Interaction Networks

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Evaluating the impact of topological protein features on the negative examples selection

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Network Pharmacology and Modern Drug R&D Cases

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FLOW MODEL OF THE PROTEIN-PROTEIN INTERACTION NETWORK FOR FINDING CREDIBLE INTERACTIONS

Okada, K., Asai, K., & Arita, M. (2007) · Asia-Pacific Bioinformatics Conference · doi:10.1142/9781860947995_0034 · Cited by 2

THE EXTENSION, APPLICATION, AND GENERALIZATION OF A PHAGE T7 INTRACELLULAR GROWTH MODEL

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Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chickenPreprint

Bush, S. J., Freem, L. J., MacCallum, A. J., O’Dell, J., Wu, C., Afrasiabi, C., Psifidi, A., Stevens, M. P., Smith, J., SUMMERS, K. M., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/295535 · Cited by 2

Gene expression in the cardiovascular system of the domestic sheep ( Ovis aries ); a new tool to advance our understanding of cardiovascular diseasePreprint

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猪链球菌全基因组序列比较分析

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Modular gene interactions drive modular pan-genome evolution in bacteriaPreprint

Castro, J., & Brown, S. (2023) · bioRxiv · doi:10.1101/2022.11.15.516554 · Cited by 2

Gene Function Discovery for Kinetoplastid Pathogens

Salavati, R., & Gazestani, V. (2018) · Trends in Parasitology · doi:10.1016/j.pt.2018.09.003 · Cited by 1

DapBCH: a disease association prediction model Based on Cross-species and Heterogeneous graph embedding

Shi, W., Feng, H., Li, J., Liu, T., & Liu, Z. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1222346 · Cited by 1

Exploring Teachers' Perspectives on Attitude Change Instruction in Social Studies Education

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Protein structural domain-disease association prediction based on heterogeneous networks

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The role of protein embeddings for protein–protein interaction prediction with graph neural networks

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Mining new protein-protein interactions

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Predictive model for yeast protein functions using modular neural approach

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Data Wisdom in Computational Genomics Research

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CBDCEM: An effective centrality based differential co-expression method for critical gene finding

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On functional annotation with gene co-expression networks

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Identifying function modules from protein–protein interaction networks based on Szemerédi’s Regularity Lemma

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Consecutive postural adjustments in a single step

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A Random Forest proximity matrix as a new measure for gene annotation

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Constructing Reliable Protein-Protein Interaction (PPI) Networks

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064653 · Cited by 2

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Yeast Systems Biology: The Continuing Challenge of Eukaryotic Complexity

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Identification of key genes for type 1 diabetes mellitus by network-based guilt by association

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Special Protein Molecules Computational Identification

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Pan-Cancer Analysis Reveals Functional Similarity of Three lncRNAs across Multiple Tumors

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The use of functional genomics to understand components of plant metabolism and the regulation occurring at molecular, cellular and whole plant levels

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Prediction of Protein Functions Using Protein Interaction Data

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Integrative analysis of heterogeneous genomic datasets to discover genetic etiology of autism spectrum disorders

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Annotation of Novel Proteins Utilizing A Functional Genome Shotgun Coupled with High-Throughput Protein Interaction MappingPreprint

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The Proximon: Representation, Evaluation, and Applications of Metagenomic Functional Interactions

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Topics in Nucleic Acids Structure: DNA Interactions and Folding

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First large-scale peach gene coexpression network: A new tool for predicting gene functionPreprint

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Protein-protein interaction is a major source of epistasis in genetic interaction networksPreprint

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Towards reconstruction of the human interactome from positive and negative experimental evidencePreprint

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Online Prediction of Interacting Proteins with a User-Specified Protein

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Can 1H NMR Derived Metabolic Profiles Contribute to Proteomic Analyses?

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Reverse enGENEering of regulatory networks from Big Data: a guide for a biologistPreprint

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Regularized Network-Based Algorithm for Predicting Gene Functions with High-Imbalanced Data

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Modular neural network in prediction of protein function

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Mining Protein Interactome Networks to Measure Interaction Reliability and Select Hub Proteins

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Graph-based modeling for protein function prediction

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An eYFP Reporter Gene for the Yeast Two-hybrid System

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Topological analysis of structural roles of proteins in interactome networks

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Predictive Model for Protein Function Using Modular Neural Approach

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Using network clustering to predict copy number variations associated with health disparities

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Estimating the Reliability of Protein-Protein Interactions

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Title: Reverse enGENEering of regulatory networks from Big Data: a guide for a biologist

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Characterizing a potential β-barrel assembly machinery (BAM) complex in Treponema pallidum

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COMBINED PROFILING IN ASPEN A SYSTEMS BIOLOGY APPROACH

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Proteomics, now evolving

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Protein expression profiling in adenoid cystic carcinoma of the salivary glands

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The Proteomics Market

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Understanding the behaviour of pathogenic cells: proteome and metabolome analyses

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Genetic analysis of cellulose crystallization in Gluconacetobacter xylinus

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Graphical Analysis and Visualization Tools for Protein Interaction Networks

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Using machine learning and systems-biology approaches to analyse next-generation sequence data in cancers

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Membrane-associated higher-ordered protein mega-complexes for denitrification and motility in Pseudomonas aeruginosa

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Identifying Evolutionarily Conserved Protein Complexes

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Protein Complex Prediction in the Era of Systems Biology

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Introduction to Protein Complex Prediction

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064652

Evaluating Protein Complex Prediction Methods

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064655

Computational Methods for Protein Complex Prediction from PPI Networks

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064654

Open Challenges in Protein Complex Prediction

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064656

Identifying Dynamic Protein Complexes

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064657

Molecular Model for CKD

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GRAPH-BASED APPROACHES FOR IMBALANCED DATA IN FUNCTIONAL GENOMICS

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Functional characterization of DUF642 genes in Arabidopsis thaliana

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A Genome-Scale Analysis of Alternative Splicing Regulation by Splicing Factors in C. elegans

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Positive and Unlabeled Learning through Negative Selection and Imbalance-aware ClassificationPreprint

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Cluster Switches in Gene Expression Data

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