Unsupervised Learning and Multipartite Network Models: A Promising Approach for Understanding Traditional Medicine

UNaProd: A Universal Natural Product Database for Materia Medica of Iranian Traditional Medicine

(2020) Ayeh Naghizadeh et al.   Evidence-based Complementary and Alternative Medicine

Why geneticists stole cancer research even though cancer is primarily a signaling disease

(2019) Michael B. Yaffe   Science Signaling

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

(2019) Ruth Nussinov et al.   PLoS Computational Biology

Predicting Meridian in Chinese traditional medicine using machine learning approaches

(2019) Yinyin Wang et al.   PLoS Computational Biology

BNPMDA: Bipartite Network Projection for MiRNA–Disease Association prediction

(2018) Xing Chen et al.   BIOINFORMATICS

Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer

(2018) Farnaz Barneh et al.   BRIEFINGS IN BIOINFORMATICS

Valproic acid inhibits the protective effects of stromal cells against chemotherapy in breast cancer: Insights from proteomics and systems biology

(2018) Farnaz Barneh et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Patient Similarity Networks for Precision Medicine

(2018) Shraddha Pai et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting drug-disease associations and their therapeutic function based on the drug-disease association bipartite network

(2018) Wen Zhang et al.   METHODS

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

(2018) Alexandra B. Keenan et al.   Cell Systems

Clinically applicable deep learning for diagnosis and referral in retinal disease

(2018) Jeffrey De Fauw et al.   NATURE MEDICINE

PMLPR: A novel method for predicting subcellular localization based on recommender systems

(2018) Elnaz Mirzaei Mehrabad et al.   Scientific Reports

A systematic literature review and classification of knowledge discovery in traditional medicine

(2018) Goli Arji et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

UK Biobank debuts as a powerful resource for genomic research

(2018) Teri A. Manolio   NATURE MEDICINE

SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping

(2018) Yang Wu et al.   NUCLEIC ACIDS RESEARCH

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

In vitro study of antioxidant and antibacterial activities of Lactobacillus probiotic spp.

(2017) Z. Pourramezan et al.   FOLIA MICROBIOLOGICA

A comparative quality study of saffron constituents through HPLC and HPTLC methods followed by isolation of crocins and picrocrocin

(2017) Maryam Kabiri et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

TCMID 2.0: a comprehensive resource for TCM

(2017) Lin Huang et al.   NUCLEIC ACIDS RESEARCH

A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology

(2017) Mohieddin Jafari et al.   PLoS One

Community detection in networks: A user guide

(2016) Santo Fortunato et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Proteomics of hot-wet and cold-dry temperaments proposed in Iranian traditional medicine: a Network-based Study

(2016) Hassan Rezadoost et al.   Scientific Reports

Polarity-based fractionation in proteomics: hydrophilic interaction vs reversed-phase liquid chromatography

(2015) M. Jafari et al.   BIOMEDICAL CHROMATOGRAPHY

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms

(2015) Mohieddin Jafari et al.   BMC BIOINFORMATICS

Updates on drug–target network; facilitating polypharmacology and data integration by growth of DrugBank database

(2015) Farnaz Barneh et al.   BRIEFINGS IN BIOINFORMATICS

Publisher's Note: Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction

(2015)   COMPUTATIONAL BIOLOGY AND CHEMISTRY

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Think locally, act locally: Detection of small, medium-sized, and large communities in large networks

(2015) Lucas G. S. Jeub et al.   PHYSICAL REVIEW E

Impact of upfront cellular enrichment by laser capture microdissection on protein and phosphoprotein drug target signaling activation measurements in human lung cancer: Implications for personalized medicine

(2015) Elisa Baldelli et al.   Proteomics Clinical Applications

Cluster-Based Analysis for Personalized Stress Evaluation Using Physiological Signals

(2015) Qianli Xu et al.   IEEE Journal of Biomedical and Health Informatics

Personalized- and One- Medicine: Bioinformatics Foundation in Health and its Economic Feasibility

(2015) Richard M. Kream   MEDICAL SCIENCE MONITOR

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets

(2014) Qiaonan Duan et al.   BIOINFORMATICS

Individualized Medicine from Prewomb to Tomb

(2014) Eric J. Topol   CELL

Network Pharmacology Strategies Toward Multi-Target Anticancer Therapies: From Computational Models to Experimental Design Principles

(2014) Jing Tang et al.   CURRENT PHARMACEUTICAL DESIGN

International classification of diseases, 10th edition, clinical modification and procedure coding system: descriptive overview of the next generation HIPAA code sets

(2014) Steven J Steindel   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Clinical phenotype network: the underlying mechanism for personalized diagnosis and treatment of traditional Chinese medicine

(2014) Xuezhong Zhou et al.   Frontiers of Medicine

Transcriptional profiling of Chinese medicinal formula Si-Wu-Tang on breast cancer cells reveals phytoestrogenic activity

(2013) Mandy Liu et al.   BMC Complementary and Alternative Medicine

Systems pharmacology in drug discovery and therapeutic insight for herbal medicines

(2013) Chao Huang et al.   BRIEFINGS IN BIOINFORMATICS

Atopic dermatitis-associated protein interaction network lead to new insights in chronic sulfur mustard skin lesion mechanisms

(2013) Mojtaba Amiri et al.   Expert Review of Proteomics

Biomedical imaging informatics in the era of precision medicine: progress, challenges, and opportunities

(2013) William Hsu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Defining and evaluating network communities based on ground-truth

(2013) Jaewon Yang et al.   KNOWLEDGE AND INFORMATION SYSTEMS

Evolutionarily conserved motifs and modules in mitochondrial protein–protein interaction networks

(2013) Mohieddin Jafari et al.   MITOCHONDRION

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction

(2012) Hang T. T. Phan et al.   BIOINFORMATICS

Exploring the human diseasome: the human disease network

(2012) K.-I. Goh et al.   Briefings in Functional Genomics

Network-Based Gene Expression Biomarkers for Cold and Heat Patterns of Rheumatoid Arthritis in Traditional Chinese Medicine

(2012) Cheng Lu et al.   Evidence-based Complementary and Alternative Medicine

TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis

(2012) Ruichao Xue et al.   NUCLEIC ACIDS RESEARCH

Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome

(2012) Bai Jiang et al.   Scientific Reports

Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae

(2011) Shao Li et al.   BMC BIOINFORMATICS

Reference-free particle selection enhanced with semi-supervised machine learning for cryo-electron microscopy

(2011) Robert Langlois et al.   JOURNAL OF STRUCTURAL BIOLOGY

Modernization: One step at a time

(2011) Zhiguo Xu   NATURE

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases

(2011) Anna Bauer-Mehren et al.   PLoS One

Systems biology and the future of medicine

(2011) Joseph Loscalzo et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs

(2010) Mara L Hartsperger et al.   BMC BIOINFORMATICS

The Nested Structure of Cancer Symptoms

(2010) S. K. Bhavnani et al.   METHODS OF INFORMATION IN MEDICINE

Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network

(2010) Tao Ma et al.   Molecular BioSystems

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Cold and heat pattern of rheumatoid arthritis in traditional Chinese medicine: distinct molecular signatures indentified by microarray expression profiles in CD4-positive T cell

(2010) Cheng Lu et al.   RHEUMATOLOGY INTERNATIONAL

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

(2008) M. T. Dittrich et al.   BIOINFORMATICS

Latent tree models and diagnosis in traditional Chinese medicine

(2007) Nevin L. Zhang et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE