Publication list - Publika - Scientific publications from Oslo University Hospital

Publications by Junbai Wang

59 publications found

Original articles

Yao Z, Jin S, Zhou F, Wang J, Wang K, Zou X (2024)
A novel multiscale framework for delineating cancer evolution from subclonal compositions
J Theor Biol, 582, 111743
DOI 10.1016/j.jtbi.2024.111743, PubMed 38307450

Yang M, Ali O, Bjørås M, Wang J (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

Farooq A, Trøen G, Delabie J, Wang J (2022)
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

Ali O, Farooq A, Yang M, Jin VX, Bjørås M, Wang J (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

Li J, Fang K, Choppavarapu L, Yang K, Yang Y, Wang J, Cao R, Jatoi I, Jin VX (2021)
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

Gatti F, Mia S, Hammarström C, Frerker N, Fosby B, Wang J, Pietka W, Sundnes O, Hol J, Kasprzycka M, Haraldsen G (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

Pihlstrøm HK, Ueland T, Michelsen AE, Aukrust P, Gatti F, Hammarström C, Kasprzycka M, Wang J, Haraldsen G, Mjøen G, Dahle DO, Midtvedt K, Eide IA, Hartmann A, Holdaas H (2020)
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

Farooq A, Grønmyr S, Ali O, Rognes T, Scheffler K, Bjørås M, Wang J (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

Yang Y, Choppavarapu L, Fang K, Naeini AS, Nosirov B, Li J, Yang K, He Z, Zhou Y, Schiff R, Li R, Hu Y, Wang J, Jin VX (2020)
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

Zhou Y, Cheng X, Yang Y, Li T, Li J, Huang TH, Wang J, Lin S, Jin VX (2020)
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

Sahaf Naeini A, Farooq A, Bjørås M, Wang J (2020)
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

Zhou Y, Gerrard DL, Wang J, Li T, Yang Y, Fritz AJ, Rajendran M, Fu X, Stein G, Schiff R, Lin S, Frietze S, Jin VX (2020)
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

Zhou Y, Gerrard DL, Wang J, Li T, Yang Y, Fritz AJ, Rajendran M, Fu X, Stein G, Schiff R, Lin S, Frietze S, Jin VX (2019)
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

Batmanov K, Delabie J, Wang J (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

Gerrard DL, Wang Y, Gaddis M, Zhou Y, Wang J, Witt H, Lin S, Farnham PJ, Jin VX, Frietze SE (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

Poulsen LC, Edelmann RJ, Krüger S, Diéguez-Hurtado R, Shah A, Stav-Noraas TE, Renzi A, Szymanska M, Wang J, Ehling M, Benedito R, Kasprzycka M, Bækkevold E, Sundnes O, Midwood KS, Scott H, Collas P, Siebel CW, Adams RH, Haraldsen G, Sundlisæter E, Hol J (2018)
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

Batmanov K, Wang J (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

Batmanov K, Wang W, Bjørås M, Delabie J, Wang J (2017)
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

Li X, Lu J, Kan Q, Li X, Fan Q, Li Y, Huang R, Slipicevic A, Dong HP, Eide L, Wang J, Zhang H, Berge V, Goscinski MA, Kvalheim G, Nesland JM, Suo Z (2017)
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

Pihlstrøm HK, Gatti F, Hammarström C, Eide IA, Kasprzycka M, Wang J, Haraldsen G, Svensson MHS, Midtvedt K, Mjøen G, Dahle DO, Hartmann A, Holdaas H (2017)
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

Li X, Zhong Y, Lu J, Axcrona K, Eide L, Syljuåsen RG, Peng Q, Wang J, Zhang H, Goscinski MA, Kvalheim G, Nesland JM, Suo Z (2017)
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

Olsen MB, Hildrestrand GA, Scheffler K, Vinge LE, Alfsnes K, Palibrk V, Wang J, Neurauter CG, Luna L, Johansen J, Øgaard JDS, Ohm IK, Slupphaug G, Kuśnierczyk A, Fiane AE, Brorson SH, Zhang L, Gullestad L, Louch WE, Iversen PO, Østlie I, Klungland A, Christensen G, Sjaastad I, Sætrom P et al. (2017)
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

Wang J, Wu Q, Hu XT, Tian T (2016)
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

Li X, Zhong Y, Lu J, Axcrona K, Eide L, Syljuåsen RG, Peng Q, Wang J, Zhang H, Goscinski MA, Kvalheim G, Nesland JM, Suo Z (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

Wang J, Batmanov K (2015)
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

Huang R, Wang J, Zhong Y, Liu Y, Stokke T, Trope CG, Nesland JM, Suo Z (2015)
Mitochondrial DNA Deficiency in Ovarian Cancer Cells and Cancer Stem Cell-like Properties
Anticancer Res, 35 (7), 3743-53
PubMed 26124317

Tangen JM, Tierens A, Caers J, Binsfeld M, Olstad OK, Trøseid AM, Wang J, Tjønnfjord GE, Hetland G (2015)
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

Wang J, Malecka A, Trøen G, Delabie J (2015)
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

Wang JB, Wu QQ, Tian TH (2015)
Integrated Study to Infer Dynamic Protein-gene Interactions in human P53 Regulatory Networks
IEEE INT C BIOINFORM, 273-276

Wang J (2014)
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

Ward LD, Wang J, Bussemaker HJ (2014)
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

Wang J, Lan X, Hsu PY, Hsu HK, Huang K, Parvin J, Huang TH, Jin VX (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

Pollheimer J, Bodin J, Sundnes O, Edelmann RJ, Skånland SS, Sponheim J, Brox MJ, Sundlisaeter E, Loos T, Vatn M, Kasprzycka M, Wang J, Küchler AM, Taskén K, Haraldsen G, Hol J (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

Wang J, Tian T (2012)
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

Kim G, Davidson B, Henning R, Wang J, Yu M, Annunziata C, Hetland T, Kohn EC (2011)
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

Gillet JP, Wang J, Calcagno AM, Green LJ, Varma S, Bunkholt Elstrand M, Trope CG, Ambudkar SV, Davidson B, Gottesman MM (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

Wang J (2011)
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

Lan X, Adams C, Landers M, Dudas M, Krissinger D, Marnellos G, Bonneville R, Xu M, Wang J, Huang TH, Meredith G, Jin VX (2011)
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

Elgaaen BV, Haug KB, Wang J, Olstad OK, Fortunati D, Onsrud M, Staff AC, Sauer T, Gautvik KM (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

Wang J (2010)
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

Mikalsen B, Fosby B, Wang J, Hammarström C, Bjaerke H, Lundström M, Kasprzycka M, Scott H, Line PD, Haraldsen G (2010)
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

Tierens AM, Holte H, Warsame A, Ikonomou IM, Wang J, Chan WC, Delabie J (2010)
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

Wang J, Tian T (2010)
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

Wang J, Morigen (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

Wang J (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

Meza-Zepeda LA, Kresse SH, Barragan-Polania AH, Bjerkehagen B, Ohnstad HO, Namløs HM, Wang J, Kristiansen BE, Myklebost O (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

Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B (2006)
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

Wang J, Cheung LW, Delabie J (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

Wang J, Meza-Zepeda LA, Kresse SH, Myklebost O (2004)
M-CGH: analysing microarray-based CGH experiments
BMC Bioinformatics, 5, 74
DOI 10.1186/1471-2105-5-74, PubMed 15189572

Hjortland GO, Lillehammer T, Somme S, Wang J, Halvorsen T, Juell S, Hirschberg H, Fodstad Ø, Engebraaten O (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

Wang J, Bø TH, Jonassen I, Myklebost O, Hovig E (2003)
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

Wang J, Myklebost O, Hovig E (2003)
MGraph: graphical models for microarray data analysis
Bioinformatics, 19 (17), 2210-1
DOI 10.1093/bioinformatics/btg298, PubMed 14630649

Tierens A, Delabie J, Malecka A, Wang J, Gruszka-Westwood A, Catovsky D, Matutes E (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

Wang J, Delabie J, Aasheim H, Smeland E, Myklebost O (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

Wang J, Nygaard V, Smith-Sørensen B, Hovig E, Myklebost O (2002)
MArray: analysing single, replicated or reversed microarray experiments
Bioinformatics, 18 (8), 1139-40
DOI 10.1093/bioinformatics/18.8.1139, PubMed 12176840

Review articles

Fang K, Wang J, Liu L, Jin VX (2022)
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

Wang J (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