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Author Details

Jake Y. Chen (CM4AI)
University of Alabama at Birmingham
0000-0001-8829-7504
2003
180
34
Teaming, bioinformatics
PMIDPaper TitleJournal TitlePublished Year
36803800How cancer hijacks the body's homeostasis through the neuroendocrine system.Trends Neurosci2023
37100826Analysis of cardiac single-cell RNA-sequencing data can be improved by the use of artificial-intelligence-based tools.Sci Rep2023
35263568A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts.Immunity2022
35666813Single Nucleus Transcriptomics: Apical Resection in Newborn Pigs Extends the Time Window of Cardiomyocyte Proliferation and Myocardial Regeneration.Circulation2022
35495152PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics.Front Genet2022
35758816DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.Bioinformatics2022
35852875An in vivo model of glioblastoma radiation resistance identifies long noncoding RNAs and targetable kinases.JCI Insight2022
36407327WINNER: A network biology tool for biomolecular characterization and prioritization.Front Big Data2022
36317800Neuroendocrine signaling in the skin with a special focus on the epidermal neuropeptides.Am J Physiol Cell Physiol2022
35128393Editorial: Artificial Intelligence for Precision Medicine.Front Artif Intell2022
31180898Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System.IEEE/ACM Trans Comput Biol Bioinform2021
33627109Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.BMC Med Inform Decis Mak2021
33850196Vitamin D and lumisterol derivatives can act on liver X receptors (LXRs).Sci Rep2021
34901846Editorial: AI-Enabled Data Science for COVID-19.Front Big Data2021
34870191Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.Front Big Data2021
34958962Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data.Genomics Proteomics Bioinformatics2021
34604741Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.Front Big Data2021
34251623Biological Network Mining.Methods Mol Biol2021
34120146Metabolic alterations mediated by STAT3 promotes drug persistence in CML.Leukemia2021
33245774PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.Nucleic Acids Res2021
32510973Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis.Am J Physiol Cell Physiol2020
32039707Correction to: Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection.BMC Infect Dis2020
32730272Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury.PLoS One2020
32703184Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors.BMC Mol Cell Biol2020
32554431IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice.J Immunol2020
30993080A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia.J Biol Res (Thessalon)2019
31822287Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection.BMC Infect Dis2019
31406955Graft-Versus-Host Disease-Free Antitumoral Signature After Allogeneic Donor Lymphocyte Injection Identified by Proteomics and Systems Biology.JCO Precis Oncol2019
30813883Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.BMC Bioinformatics2019
31114876BEERE: a web server for biomedical entity expansion, ranking and explorations.Nucleic Acids Res2019
29126216PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.Nucleic Acids Res2018
30040650"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data.IEEE/ACM Trans Comput Biol Bioinform2018
30030418Regenerative Potential of Neonatal Porcine Hearts.Circulation2018
29593668Simulation 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.Front Microbiol2018
28711145Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases.Rheum Dis Clin North Am2017
28212602HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions.BMC Genomics2017
28179884Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus.Front Physiol2017
29297292Repositioning drugs by targeting network modules: a Parkinson's disease case study.BMC Bioinformatics2017
28640894Characterization and analysis of long non-coding rna (lncRNA) in In Vitro- and Ex Vivo-derived cardiac progenitor cells.PLoS One2017
27557076A method for identifying discriminative isoform-specific peptides for clinical proteomics application.BMC Genomics2016
26072489PAGER: constructing PAGs and new PAG-PAG relationships for network biology.Bioinformatics2015
26423722DMAP: a connectivity map database to enable identification of novel drug repositioning candidates.BMC Bioinformatics2015
26313489MicroRNA Expression Profiling of Human Respiratory Epithelium Affected by Invasive Candida Infection.PLoS One2015
26605379Knowledge Discovery Using Big Data in Biomedical Systems.IEEE/ACM Trans Comput Biol Bioinform2015
26576648A method for developing regulatory gene set networks to characterize complex biological systems.BMC Genomics2015
24911777Pathway and network analysis in proteomics.J Theor Biol2014
25350940SLDR: a computational technique to identify novel genetic regulatory relationships.BMC Bioinformatics2014
24837790Prioritizing drug targets in Clostridium botulinum with a computational systems biology approach.Genomics2014
24864375Seed-weighted random walk ranking for cancer biomarker prioritisation: a case study in leukaemia.Int J Data Min Bioinform2014
22492191Semantic Web meets Integrative Biology: a survey.Brief Bioinform2013
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Collaborators

Jake Y Chen
Co-authored papers 97
Zongliang Yue
University of Alabama at Birmingham, USA Informatics Institute
Co-authored papers 18
Xiaogang Wu
The University of Texas MD Anderson Cancer Center
Co-authored papers 18
Thanh Nguyen
University of Alabama at Birmingham
Co-authored papers 14
Fan Zhang
College of Life Sciences, ShanDong Normal University
Co-authored papers 10
Ragini Pandey
Bristol Royal Hospital for Children, University Hospital Bristol NHS Trust
Co-authored papers 8
Hui Huang
Shanghai Jiao Tong University
Co-authored papers 8
Syed Aun Muhammad
Mid and South Essex NHS Foundation Trust
Co-authored papers 6
Changyu Shen
College of Materials Science and Engineering, Zhengzhou University
Co-authored papers 6
Tianxiao Huan
and Blood Institute, National Institutes of Health
Co-authored papers 5
Radomir M Slominski
University of Alabama at Birmingham
Co-authored papers 5
Eric Zhang
University of Alabama at Birmingham.
Co-authored papers 4
Christopher D Willey
University of Alabama at Birmingham
Co-authored papers 4
Gregory P Walcott
University of Alabama at Birmingham
Co-authored papers 4
Scott H Harrison
North Carolina Agricultural and Technical State University
Co-authored papers 4
Andrey Sivachenko
Cystic Fibrosis Foundation
Co-authored papers 4
X Frank Yang
Indiana University School of Medicine
Co-authored papers 3
Meng Zhao
National Engineering Research Center of Cell Products, AmCellGene Engineering Co.
Co-authored papers 3
Jiao Li
The First Affiliated Hospital of Hunan University of Chinese Medicine
Co-authored papers 3
Andrzej T Slominski
University of Alabama at Birmingham
Co-authored papers 3
Ping Wan
College of Plant Science and Technology, Beijing University of Agriculture
Co-authored papers 3
Vincent A Laufer
University of Alabama at Birmingham
Co-authored papers 3
Mu Wang
Academy of Pharmacy, Xi'an Jiaotong-Liverpool University
Co-authored papers 3
Michael T Neylon
Co-authored papers 3
Jianyi Zhang
University of Alabama at Birmingham, 1670 University Boulevard
Co-authored papers 3
Karen B Fowler
Heersink School of Medicine, University of Alabama at Birmingham
Co-authored papers 2
Sudipto Saha
Bose Institute
Co-authored papers 2
William J Britt
Heersink School of Medicine, University of Alabama at Birmingham
Co-authored papers 2
Madhankumar Sonachalam
Indiana University Indianapolis
Co-authored papers 2
Timothy L Ratliff
Purdue University
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Release 1.2