| Year |
Title |
Altmetric |
| 2022
|
WINNER: A network biology tool for biomolecular characterization and prioritization.
Frontiers in Big Data.
5.
2022
|
|
| 2022
|
An in vivo model of glioblastoma radiation resistance identifies long noncoding RNAs and targetable kinases.
JCI Insight.
7.
2022
|
|
| 2022
|
DEMA: A distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.
Bioinformatics.
38:I359-I368.
2022
|
|
| 2022
|
The Periodontal Pathogen Fusobacterium nucleatum Exacerbates Alzheimer’s Pathogenesis via Specific Pathways.
Frontiers in Aging Neuroscience.
14.
2022
|
|
| 2022
|
Single Nucleus Transcriptomics: Apical Resection in Newborn Pigs Extends the Time Window of Cardiomyocyte Proliferation and Myocardial Regeneration.
Circulation.
145:1744-1747.
2022
|
|
| 2022
|
Identification and Characterization of a Novel Long Noncoding RNA that Regulates Osteogenesis in Diet-Induced Obesity Mice.
Frontiers in Cell and Developmental Biology.
10.
2022
|
|
| 2022
|
PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics.
Frontiers in Genetics.
13.
2022
|
|
| 2022
|
A novel adiponectin receptor agonist (AdipoAI) ameliorates type 2 diabetes-associated periodontitis by enhancing autophagy in osteoclasts..
Journal of Periodontal Research.
57:381-391.
2022
|
|
| 2022
|
A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts.
Immunity.
55:494-511.e11.
2022
|
|
| 2022
|
Editorial: Artificial Intelligence for Precision Medicine.
Frontiers in Artificial Intelligence.
4.
2022
|
|
| 2022
|
A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis.
JAMA Network Open.
5.
2022
|
|
| 2021
|
Metabolic alterations mediated by STAT3 promotes drug persistence in CML.
Leukemia.
35:3371-3382.
2021
|
|
| 2021
|
Vitamin D and lumisterol derivatives can act on liver X receptors (LXRs).
Scientific Reports.
11.
2021
|
|
| 2021
|
Editorial: AI-Enabled Data Science for COVID-19.
Frontiers in Big Data.
4.
2021
|
|
| 2021
|
Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples (Front. Big Data (2021), 4, (725276), 10.3389/fdata.2021.725276).
Frontiers in Big Data.
4.
2021
|
|
| 2021
|
Roles and Mechanisms of Irisin in Attenuating Pathological Features of Osteoarthritis.
Frontiers in Cell and Developmental Biology.
9.
2021
|
|
| 2021
|
Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.
Frontiers in Big Data.
4.
2021
|
|
| 2021
|
Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data
2021
|
|
| 2021
|
Guest Editorial for Selected Papers from BIOKDD 2019.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
18:809-810.
2021
|
|
| 2021
|
Scalable de Novo Genome Assembly Using a Pregel-Like Graph-Parallel System.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
18:731-744.
2021
|
|
| 2021
|
Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.
BMC Medical Informatics and Decision Making.
21.
2021
|
|
| 2021
|
PAGER-CoV: A comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.
Nucleic Acids Research.
49:D589-D599.
2021
|
|
| 2021
|
Biological Network Mining.
Methods in Molecular Biology.
2328:139-151.
2021
|
|
| 2020
|
Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
17:1832-1834.
2020
|
|
| 2020
|
Decoding sars-cov-2 hijacking of host mitochondria in covid-19 pathogenesis
2020
|
|
| 2020
|
IL-23 promotes a coordinated B cell germinal center program for class-switch recombination to IgG2b in BXD2 mice.
Journal of Immunology.
205:346-358.
2020
|
|
| 2020
|
Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury.
PLoS One.
15.
2020
|
|
| 2020
|
Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information
2020
|
|
| 2020
|
Erratum: Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection (BMC Infectious Diseases (2019) 19 (1046) DOI: 10.1186/s12879-019-4681-0).
BMC Infectious Diseases.
20.
2020
|
|
| 2019
|
Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection.
BMC Infectious Diseases.
19.
2019
|
|
| 2019
|
WIPER: Weighted in-Path Edge Ranking for biomolecular association networks.
Quantitative biology (Beijing, China).
7:313-326.
2019
|
|
| 2019
|
BEERE: a web server for biomedical entity expansion, ranking and explorations.
Nucleic Acids Research.
47:W578-W586.
2019
|
|
| 2019
|
Gsslasso Cox: A Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.
BMC Bioinformatics.
20.
2019
|
|
| 2019
|
A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia
2019
|
|
| 2018
|
Multiscale and Multimodal Analysis for Computational Biology.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15:1951-1952.
2018
|
|
| 2018
|
Super Gene Set Causal Relationship Discovery from Functional Genomics Data.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15:1991-1998.
2018
|
|
| 2018
|
Simulation study of cDNA dataset to investigate possible association of differentially expressed genes of human THP1-monocytic cells in cancer progression affected by bacterial shiga toxins.
Frontiers in Microbiology.
9.
2018
|
|
| 2018
|
Development and Therapeutic Potential of Small-Molecule Modulators of Circadian Systems.
Annual Review of Pharmacology and Toxicology.
58:231-252.
2018
|
|
| 2018
|
PAGER 2.0: An update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.
Nucleic Acids Research.
46:D668-D676.
2018
|
|
| 2018
|
Regenerative potential of neonatal porcine hearts.
Circulation.
138:2809-2816.
2018
|
|
| 2017
|
Repositioning drugs by targeting network modules: A Parkinson's disease case study.
BMC Bioinformatics.
18.
2017
|
|
| 2017
|
Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases.
Rheumatic Disease Clinics of North America.
43:449-466.
2017
|
|
| 2017
|
HAPPI-2: A Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions.
BMC Genomics.
18.
2017
|
|
| 2017
|
Cellular signaling pathways in insulin resistance-systems biology analyses of microarray dataset reveals new drug target gene signatures of type 2 diabetes mellitus.
Frontiers in Physiology.
8.
2017
|
|
| 2017
|
Repositioning drugs by targeting network modules: a Parkinson's disease case study.
2017
|
|
| 2016
|
A method for identifying discriminative isoform-specific peptides for clinical proteomics application.
BMC Genomics.
17.
2016
|
|
| 2016
|
Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation.
American Journal of Transplantation.
16:2342-2351.
2016
|
|
| 2015
|
A method for developing regulatory gene set networks to characterize complex biological systems.
BMC Genomics.
16.
2015
|
|
| 2015
|
DMAP: A connectivity map database to enable identification of novel drug repositioning candidates.
BMC Bioinformatics.
16.
2015
|
|
| 2015
|
MicroRNA expression profiling of human respiratory epithelium affected by invasive candida infection.
PLoS One.
10.
2015
|
|
| 2015
|
Knowledge Discovery Using Big Data in Biomedical Systems.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
12:726-728.
2015
|
|
| 2015
|
PAGER: Constructing PAGs and new PAG-PAG relationships for network biology.
Bioinformatics.
31:i250-i257.
2015
|
|
| 2014
|
Pathway and network analysis in proteomics.
Journal of Theoretical Biology.
362:44-52.
2014
|
|
| 2014
|
SLDR: A computational technique to identify novel genetic regulatory relationships.
BMC Bioinformatics.
15.
2014
|
|
| 2014
|
MicroRNA expression signature for Satb2-induced osteogenic differentiation in bone marrow stromal cells
2014
|
|
| 2014
|
Prioritizing drug targets in Clostridium botulinum with a computational systems biology approach.
Genomics.
104:24-35.
2014
|
|
| 2014
|
Seed-weighted random walk ranking for cancer biomarker prioritisation: A case study in leukaemia.
International Journal of Data Mining and Bioinformatics.
9:135-148.
2014
|
|
| 2013
|
Network medicine: Finding the links to personalized therapy.
Clinical Pharmacology and Therapeutics.
94:613-616.
2013
|
|
| 2013
|
Transcriptome network analysis of potential candidate genes for heart failure
2013
|
|
| 2013
|
Small molecule modifiers of circadian clocks.
Cellular and Molecular Life Sciences.
70:2985-2998.
2013
|
|
| 2013
|
Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structures.
Proteomics.
13:313-324.
2013
|
|
| 2012
|
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes.
BMC Systems Biology.
6.
2012
|
|
| 2012
|
Towards a metadata model for mass-spectrometry based clinical proteomics.
Current Bioinformatics.
7:246-254.
2012
|
|
| 2012
|
PAGED: A pathway and gene-set enrichment database to enable molecular phenotype discoveries.
BMC Bioinformatics.
13.
2012
|
|
| 2012
|
Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays..
Journal of Integrative Bioinformatics.
9:113-125.
2012
|
|
| 2012
|
Biological knowledge discovery and data mining
2012
|
|
| 2012
|
C²Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships..
BMC Genomics.
13 Suppl 6:S17.
2012
|
|
| 2012
|
Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays..
Journal of Integrative Bioinformatics.
9:213.
2012
|
|
| 2012
|
Reordering based integrative expression profiling for microarray classification..
BMC Bioinformatics.
13 Suppl 2.
2012
|
|
| 2011
|
An integrated proteomics analysis of bone tissues in response to mechanical stimulation.
BMC Systems Biology.
5.
2011
|
|
| 2011
|
Predicting adverse side effects of drugs.
BMC Genomics.
12.
2011
|
|
| 2011
|
Enhanced osseointegration of titanium implant through the local delivery of transcription factor SATB2.
Clinical materials.
32:8676-8683.
2011
|
|
| 2011
|
HOMER: A human organ-specific molecular electronic repository.
BMC Bioinformatics.
12.
2011
|
|
| 2011
|
Erratum: Tumor necrosis factor-α- and interleukin-1-induced cellular responses: Coupling proteomic and genomic information (Journal of Proteome Research (2007) 6 (2176-2185) DOI: 10.1021/pr060665l).
Journal of Proteome Research.
10:4886.
2011
|
|
| 2011
|
Critical-size calvarial bone defects healing in a mouse model with silk scaffolds and SATB2-modified iPSCs.
Clinical materials.
32:5065-5076.
2011
|
|
| 2011
|
Effects of miR-335-5p in modulating osteogenic differentiation by specifically downregulating Wnt antagonist DKK1.
Journal of Bone and Mineral Research.
26:1953-1963.
2011
|
|
| 2011
|
Roles of SATB2 in osteogenic differentiation and bone regeneration
2011
|
|
| 2011
|
Adiponectin inhibits osteoclastogenesis and bone resorption via APPL1-mediated suppression of Akt1.
Journal of Biological Chemistry.
286:12542-12553.
2011
|
|
| 2011
|
Disease phenotypes and gender association of FCRL3 single-nucleotide polymorphism -169T/C in Taiwanese patients with systemic lupus erythematosus and rheumatoid arthritis.
Journal of Rheumatology.
38:264-270.
2011
|
|
| 2011
|
Application of induced pluripotent stem (iPS) cells in periodontal tissue regeneration.
Journal of Cellular Physiology.
226:150-157.
2011
|
|
| 2011
|
Data Mining Methods in Omics-Based Biomarker Discovery.
Methods in Molecular Biology.
719:511-526.
2011
|
|
| 2011
|
New threats to health data privacy..
BMC Bioinformatics.
12 Suppl 12.
2011
|
|
| 2010
|
A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT.
BMC Genomics.
11.
2010
|
|
| 2010
|
Impact of sildenafil therapy on pulmonary arterial hypertension in adults with congenital heart disease.
Cardiovascular Therapeutics.
28:350-355.
2010
|
|
| 2010
|
Discovery of pathway biomarkers from coupled proteomics and systems biology methods.
BMC Genomics.
11.
2010
|
|
| 2010
|
PEPPI: A peptidomic database of human protein isoforms for proteomics experiments.
BMC Bioinformatics.
11.
2010
|
|
| 2010
|
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments..
BMC Bioinformatics.
11 Suppl 6:S7.
2010
|
|
| 2010
|
Data mining in bioinformatics: Selected papers from BIOKDD.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
7:195-196.
2010
|
|
| 2010
|
[The use of kidney-shaped pressure bandage to prevent postoperative salivary fistula]..
Shanghai kou qiang yi xue = Shanghai journal of stomatology.
19:144-146.
2010
|
|
| 2010
|
GeneTerrain: Visual exploration of differential gene expression profiles organized in native biomolecular interaction networks.
Information Visualization.
9:1-12.
2010
|
|
| 2010
|
A GMM-IG framework for selecting genes as expression panel biomarkers.
Artificial Intelligence in Medicine.
48:75-82.
2010
|
|
| 2010
|
MG-132 Inhibits Carcinoid Growth and Alters the Neuroendocrine Phenotype.
Journal of Surgical Research.
158:15-19.
2010
|
|
| 2009
|
Osterix enhances BMSC-associated osseointegration of implants
2009
|
|
| 2009
|
HPD: An online integrated human pathway database enabling systems biology studies.
BMC Bioinformatics.
10.
2009
|
|
| 2009
|
HPD: an online integrated human pathway database enabling systems biology studies..
BMC Bioinformatics.
10 Suppl 11:S5.
2009
|
|
| 2009
|
Mandibular repair in rats with premineralized silk scaffolds and BMP-2-modified bMSCs.
Clinical materials.
30:4522-4532.
2009
|
|
| 2009
|
Design of an online physician-mediated personal health record system.
Studies in Computational Intelligence.
224:265-279.
2009
|
|
| 2009
|
HAPPI: An online database of comprehensive human annotated and predicted protein interactions.
BMC Genomics.
10.
2009
|
|
| 2009
|
Pattern discovery in breast cancer specific protein interaction network..
AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science.
2009:1-5.
2009
|
|
| 2009
|
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.
PLoS Computational Biology.
5.
2009
|
|
| 2009
|
Connecting protein interaction data, mutations, and disease using bioinformatics..
Methods in Molecular Biology.
541:449-461.
2009
|
|
| 2009
|
Disease gene-fishing in molecular interaction networks: A case study in colorectal cancer.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference.
6416-6419.
2009
|
|
| 2009
|
Dissecting the human plasma proteome and inflammatory response biomarkers.
Proteomics.
9:470-484.
2009
|
|
| 2009
|
Finding fractal patterns in molecular interaction networks: A case study in Alzheimer's disease.
International Journal of Computational Biology and Drug Design.
2:340-352.
2009
|
|
| 2009
|
Network topological reordering revealing systemic patterns in yeast protein interaction networks.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference.
6954-6957.
2009
|
|
| 2008
|
ProteoLens: A visual analytic tool for multi-scale database-driven biological network data mining.
BMC Bioinformatics.
9.
2008
|
|
| 2008
|
HIP2: an online database of human plasma proteins from healthy individuals..
BMC Medical Genomics.
1:12.
2008
|
|
| 2008
|
Introduction.
Journal of Bioinformatics and Computational Biology.
6.
2008
|
|
| 2007
|
A systems biology approach to the study of cisplatin drug resistance in ovarian cancers..
Journal of Bioinformatics and Computational Biology.
5:383-405.
2007
|
|
| 2007
|
A case study of integrating protein interaction data using semantic web technology.
International Journal of Bioinformatics Research and Applications.
3:286-302.
2007
|
|
| 2007
|
DisProt: The database of disordered proteins.
Nucleic Acids Research.
35.
2007
|
|
| 2007
|
International Journal of Bioinformatics Research and Applications: Editorial.
International Journal of Bioinformatics Research and Applications.
3:261-267.
2007
|
|
| 2007
|
Tumor necrosis factor-α- and interleukin-1-induced cellular responses: Coupling proteomic and genomic information.
Journal of Proteome Research.
6:2176-2185.
2007
|
|
| 2006
|
Disorder and sequence repeats in hub proteins and their implications for network evolution.
Journal of Proteome Research.
5:2985-2995.
2006
|
|
| 2006
|
A statistical framework to discover true associations from multiprotein complex pull-down proteomics data sets
2006
|
|
| 2006
|
Porous silk fibroin 3-D scaffolds for delivery of bone morphogenetic protein-2 in vitro and in vivo.
Journal of Biomedical Materials Research Part A.
78:324-334.
2006
|
|
| 2006
|
A systems biology case study of ovarian cancer drug resistance..
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference.
389-398.
2006
|
|
| 2005
|
Tissue- and bone cell-specific expression of bone sialoprotein is directed by a 9.0 kb promoter in transgenic mice.
Matrix Biology.
24:341-352.
2005
|
|
| 2005
|
Data mining in protein interactomics.
IEEE Pulse.
24:95-102.
2005
|
|
| 2005
|
Silk implants for the healing of critical size bone defects.
Bone.
37:688-698.
2005
|
|
