
Junbai Wang
- Scientist; PhD
Publications 2023
Identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data
iScience, 26 (8), 107266
DOI 10.1016/j.isci.2023.107266, PubMed 37520692
Publications 2022
abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis
BMC Bioinformatics, 23 (1), 83
DOI 10.1186/s12859-022-04615-z, PubMed 35240993
Mapping nucleosome and chromatin architectures: A survey of computational methods
Comput Struct Biotechnol J, 20, 3955-3962
DOI 10.1016/j.csbj.2022.07.037, PubMed 35950186
Integrating whole genome sequencing, methylation, gene expression, topological associated domain information in regulatory mutation prediction: A study of follicular lymphoma
Comput Struct Biotechnol J, 20, 1726-1742
DOI 10.1016/j.csbj.2022.03.023, PubMed 35495111
Publications 2021
Nuclear IL-33 restrains the early conversion of fibroblasts to an extracellular matrix-secreting phenotype
Sci Rep, 11 (1), 108
DOI 10.1038/s41598-020-80509-5, PubMed 33420328
Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance
Clin Epigenetics, 13 (1), 175
DOI 10.1186/s13148-021-01167-6, PubMed 34535185
Publications 2020
HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data
Comput Struct Biotechnol J, 18, 2877-2889
DOI 10.1016/j.csbj.2020.09.038, PubMed 33163148
Exploring the potential effect of paricalcitol on markers of inflammation in de novo renal transplant recipients
PLoS One, 15 (12), e0243759
DOI 10.1371/journal.pone.0243759, PubMed 33326471
IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity
Comput Struct Biotechnol J, 18, 1270-1286
DOI 10.1016/j.csbj.2020.05.024, PubMed 32612751
The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells
Biochim Biophys Acta Gene Regul Mech, 1863 (11), 194631
DOI 10.1016/j.bbagrm.2020.194631, PubMed 32956836
Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops
Genome Med, 12 (1), 69
DOI 10.1186/s13073-020-00769-8, PubMed 32787954
Author Correction: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
Nat Commun, 11 (1), 1967
DOI 10.1038/s41467-020-15789-6, PubMed 32313124
Publications 2019
BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts
Front Genet, 10, 282
DOI 10.3389/fgene.2019.00282, PubMed 31001324
Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
Nat Commun, 10 (1), 1522
DOI 10.1038/s41467-019-09320-9, PubMed 30944316
Publications 2018
Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature
J Cell Biochem, 120 (3), 3056-3070
DOI 10.1002/jcb.27449, PubMed 30548288
Inhibition of Endothelial NOTCH1 Signaling Attenuates Inflammation by Reducing Cytokine-Mediated Histone Acetylation at Inflammatory Enhancers
Arterioscler Thromb Vasc Biol, 38 (4), 854-869
DOI 10.1161/ATVBAHA.117.310388, PubMed 29449332
Publications 2017
Predicting Variation of DNA Shape Preferences in Protein-DNA Interaction in Cancer Cells with a New Biophysical Model
Genes (Basel), 8 (9)
DOI 10.3390/genes8090233, PubMed 28927002
Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma
Sci Rep, 7 (1), 7040
DOI 10.1038/s41598-017-07226-4, PubMed 28765546
Metabolic reprogramming is associated with flavopiridol resistance in prostate cancer DU145 cells
Sci Rep, 7 (1), 5081
DOI 10.1038/s41598-017-05086-6, PubMed 28698547
Correction: MtDNA depleted PC3 cells exhibit Warburg effect and cancer stem cell features
Oncotarget, 8 (4), 7208-7213
DOI 10.18632/oncotarget.14800, PubMed 28179591
Frequent somatic mutations of KMT2D (MLL2) and CARD11 genes in primary cold agglutinin disease
Br J Haematol, 183 (5), 838-842
DOI 10.1111/bjh.15063, PubMed 29265349
NEIL3-Dependent Regulation of Cardiac Fibroblast Proliferation Prevents Myocardial Rupture
Cell Rep, 18 (1), 82-92
DOI 10.1016/j.celrep.2016.12.009, PubMed 28052262
Early introduction of oral paricalcitol in renal transplant recipients. An open-label randomized study
Transpl Int, 30 (8), 827-840
DOI 10.1111/tri.12973, PubMed 28436117
Publications 2016
MtDNA depleted PC3 cells exhibit Warburg effect and cancer stem cell features
Oncotarget, 7 (26), 40297-40313
DOI 10.18632/oncotarget.9610, PubMed 27248169
An integrated approach to infer dynamic protein-gene interactions - A case study of the human P53 protein
Methods, 110, 3-13
DOI 10.1016/j.ymeth.2016.08.001, PubMed 27514497
Publications 2015
Mitochondrial DNA Deficiency in Ovarian Cancer Cells and Cancer Stem Cell-like Properties
Anticancer Res, 35 (7), 3743-53
PubMed 26124317
Immunomodulatory effects of the Agaricus blazei Murrill-based mushroom extract AndoSan in patients with multiple myeloma undergoing high dose chemotherapy and autologous stem cell transplantation: a randomized, double blinded clinical study
Biomed Res Int, 2015, 718539
DOI 10.1155/2015/718539, PubMed 25664323
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations
Nucleic Acids Res, 43 (21), e147
DOI 10.1093/nar/gkv733, PubMed 26202972
Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation
BMC Genomics, 16 Suppl 7 (Suppl 7), S12
DOI 10.1186/1471-2164-16-S7-S12, PubMed 26099425
Integrated Study to Infer Dynamic Protein-gene Interactions in human P53 Regulatory Networks
IEEE INT C BIOINFORM, 273-276
Publications 2014
Biomedical informatics and computational biology for high-throughput data analysis
ScientificWorldJournal, 2014, 398181
DOI 10.1155/2014/398181, PubMed 24688384
Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence
BMC Bioinformatics, 15 (1), 289
DOI 10.1186/1471-2105-15-289, PubMed 25158938
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
BMC Genomics, 15 (1), 494
DOI 10.1186/1471-2164-15-494, PubMed 24947676
Publications 2013
Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation
BMC Genomics, 14, 70
DOI 10.1186/1471-2164-14-70, PubMed 23368971
Publications 2012
Interleukin-33 drives a proinflammatory endothelial activation that selectively targets nonquiescent cells
Arterioscler Thromb Vasc Biol, 33 (2), e47-55
DOI 10.1161/ATVBAHA.112.253427, PubMed 23162017
Effective non-linear methods for inferring genetic regulation from time-series microarray gene expression data
Methods Mol Biol, 802, 235-46
DOI 10.1007/978-1-61779-400-1_15, PubMed 22130884
Publications 2011
Clinical relevance of multidrug resistance gene expression in ovarian serous carcinoma effusions
Mol Pharm, 8 (6), 2080-8
DOI 10.1021/mp200240a, PubMed 21761824
Adhesion molecule protein signature in ovarian cancer effusions is prognostic of patient outcome
Cancer, 118 (6), 1543-53
DOI 10.1002/cncr.26449, PubMed 22009736
High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology
PLoS One, 6 (7), e22226
DOI 10.1371/journal.pone.0022226, PubMed 21779396
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information
BMC Genomics, 12, 172
DOI 10.1186/1471-2164-12-172, PubMed 21457549
Publications 2010
POLD2 and KSP37 (FGFBP2) correlate strongly with histology, stage and outcome in ovarian carcinomas
PLoS One, 5 (11), e13837
DOI 10.1371/journal.pone.0013837, PubMed 21079801
Genome-wide transcription profile of endothelial cells after cardiac transplantation in the rat
Am J Transplant, 10 (7), 1534-44
DOI 10.1111/j.1600-6143.2010.03157.x, PubMed 20642680
Low levels of monoclonal small B cells in the bone marrow of patients with diffuse large B-cell lymphoma of activated B-cell type but not of germinal center B-cell type
Haematologica, 95 (8), 1334-41
DOI 10.3324/haematol.2009.014100, PubMed 20145271
The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data
BMC Bioinformatics, 11, 412
DOI 10.1186/1471-2105-11-412, PubMed 20684785
Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53
BMC Bioinformatics, 11, 36
DOI 10.1186/1471-2105-11-36, PubMed 20085646
Publications 2009
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
BMC Bioinformatics, 10, 345
DOI 10.1186/1471-2105-10-345, PubMed 19857274
Publications 2008
Computational biology of genome expression and regulation--a review of microarray bioinformatics
J Environ Pathol Toxicol Oncol, 27 (3), 157-79
DOI 10.1615/jenvironpatholtoxicoloncol.v27.i3.10, PubMed 18652564
Publications 2007
A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle
J Biomed Inform, 40 (6), 707-25
DOI 10.1016/j.jbi.2007.02.003, PubMed 17418646
Publications 2006
Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas
Cancer Res, 66 (18), 8984-93
DOI 10.1158/0008-5472.CAN-06-1972, PubMed 16982739
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
Proc Natl Acad Sci U S A, 103 (32), 12027-32
DOI 10.1073/pnas.0605003103, PubMed 16880385
Publications 2005
New probabilistic graphical models for genetic regulatory networks studies
J Biomed Inform, 38 (6), 443-55
DOI 10.1016/j.jbi.2005.04.003, PubMed 15996532
Publications 2004
Plasminogen activator inhibitor-1 increases the expression of VEGF in human glioma cells
Exp Cell Res, 294 (1), 130-9
DOI 10.1016/j.yexcr.2003.10.013, PubMed 14980508
M-CGH: analysing microarray-based CGH experiments
BMC Bioinformatics, 5, 74
DOI 10.1186/1471-2105-5-74, PubMed 15189572
Publications 2003
Splenic marginal zone lymphoma with villous lymphocytes shows on-going immunoglobulin gene mutations
Am J Pathol, 162 (2), 681-9
DOI 10.1016/S0002-9440(10)63862-X, PubMed 12547726
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
BMC Bioinformatics, 4, 60
DOI 10.1186/1471-2105-4-60, PubMed 14651757
MGraph: graphical models for microarray data analysis
Bioinformatics, 19 (17), 2210-1
DOI 10.1093/bioinformatics/btg298, PubMed 14630649
Publications 2002
Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study
BMC Bioinformatics, 3, 36
DOI 10.1186/1471-2105-3-36, PubMed 12445336
MArray: analysing single, replicated or reversed microarray experiments
Bioinformatics, 18 (8), 1139-40
DOI 10.1093/bioinformatics/18.8.1139, PubMed 12176840