Junbai Wang

Image of Junbai Wang
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Visiting address Sykehusveien 25 1474 Nordbyhagen
Postal address Akershus universitetssykehus 1478 Lørenskog

Dr. Wang was trained as a theoretical and computational physicist at Bergen University.

His first post-doc position was at the Cancer Research Institute of Norwegian Radium Hospital. The main goal was to develop data-mining software for biologists for analyzing microarray experiments.

His second post-doc training was at the Biology Department of Columbia University in New York City. The objective was to expand the knowledge in molecular biology and to be able to solve biology problems with computer simulation.

From year 2007 to 2021, he was a scientist at the Oslo University Hospital - Norwegian Radium Hospital, and frequently collaborates with biologists in research projects.

Currently, he is a researcher in University of Oslo. His main research interest is to design/develop advanced mathematical methods and computational tools for solving problems in cancer biology.

Current PhD students and co-supervised with Professor Magnar Bjørås:

  •     Amna Farooq (UiO PhD student in Computational biology)
  •     Omer Ali (UiO PhD student in Bioinformatics)
  •     Marco Pannone (NTNU PhD student in Computational biology)

Past students and postdoc:

 

  •     Dr. Kirill Batmanov (former postdoc in bioinformatics, now at University of Pennsylvania)
  •     MSc. Sindre Gronmyr (UiO master student in bioinformatics)
  •     MSc. Alireza Sahaf Naeini (former PhD student, left academia to take an industry job)
Tags: biostatistics, cancer, bioinformatics, Computational Biology, Life science

Publications

  • li, jingwei; fang, kun; Choppavarapu, Lavanya; Yang, Ke; Yang, Yini & Wang, Junbai [Show all 9 contributors for this article] (2021). Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance. Clinical Epigenetics. ISSN 1868-7075. 13(175). doi: 10.1186/s13148-021-01167-6.
  • Gatti, Francesca; Mia, Sobuj; Hammarström, Clara; Frerker, Nadine; Fosby, Bjarte & Wang, Junbai [Show all 11 contributors for this article] (2021). Nuclear IL-33 restrains the early conversion of fibroblasts to an extracellular matrix-secreting phenotype. Scientific Reports. ISSN 2045-2322. 11(1), p. 1–13. doi: 10.1038/s41598-020-80509-5. Full text in Research Archive
  • Zhou, Yufan; Cheng, Xiaolong; Yang, Yini; Li, Tian; Li, Jingwei & Huang, Tim H.-M. [Show all 9 contributors for this article] (2020). Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. Genome Medicine. ISSN 1756-994X. 12(12). doi: 10.1186/s13073-020-00769-8.
  • Naeini, Alireza Sahaf; Farooq, Amna; Bjørås, Magnar & Wang, Junbai (2020). IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity. Computational and Structural Biotechnology Journal. ISSN 2001-0370. 18, p. 1270–1286. doi: 10.1016/j.csbj.2020.05.024.
  • Farooq, Amna; Grønmyr, Sindre; Omer, Ali Avan; Rognes, Torbjørn; Scheffler, Katja & Bjørås, Magnar [Show all 7 contributors for this article] (2020). HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data. Computational and Structural Biotechnology Journal. ISSN 2001-0370. 18, p. 2877–2889. doi: 10.1016/j.csbj.2020.09.038. Full text in Research Archive
  • Pihlstrøm, Hege; Ueland, Thor; Michelsen, Annika; Aukrust, Pål; Gatti, Francesca & Hammarström, Clara Louise [Show all 15 contributors for this article] (2020). Exploring the potential effect of paricalcitol on markers of inflammation in de novo renal transplant recipients. PLOS ONE. ISSN 1932-6203. 15:e0243759(12), p. 1–14. doi: 10.1371/journal.pone.0243759. Full text in Research Archive
  • Yang, Yini; Choppavarapu, Lavanya; Fang, Kun; Naeini, Alireza Sahaf; Nosirov, Bakhtiyor & Li, Jingwei [Show all 14 contributors for this article] (2020). The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. ISSN 1874-9399. 1863(11). doi: 10.1016/j.bbagrm.2020.194631.
  • Batmanov, Kirill; Delabie, Jan & Wang, Junbai (2019). BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts. Frontiers in Genetics. ISSN 1664-8021. 10, p. 1–8. doi: 10.3389/fgene.2019.00282.
  • Zhou, Yufan; Gerrard, Diana L; Wang, Junbai; li, tian; Yang, Yini & Fritz, Andrew J [Show all 12 contributors for this article] (2019). Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. Nature Communications. ISSN 2041-1723. 10(1). doi: 10.1038/s41467-019-09320-9.
  • La Cour Poulsen, Lars; Edelmann, Reidunn Jetne; Krüger, Stig; Diéguez-Hurtado, Rodrigo; Shah, Akshay & Stav-Noraas, Tor Espen [Show all 22 contributors for this article] (2018). Inhibition of endothelial NOTCH1 signaling attenuates inflammation by reducing cytokine-mediated histone acetylation at inflammatory enhancers . Arteriosclerosis, Thrombosis and Vascular Biology. ISSN 1079-5642. 38(4), p. 854–869. doi: 10.1161/ATVBAHA.117.310388. Full text in Research Archive
  • Gerrard, DL; Wang, Y; Gaddis, M; Zhou, Y; Wang, Junbai & witt, H [Show all 10 contributors for this article] (2018). Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. Journal of Cellular Biochemistry. ISSN 0730-2312. 120(3), p. 3056–3070. doi: 10.1002/jcb.27449.
  • Olsen, Maria Belland; Hildrestrand, Gunn Annette; Scheffler, Katja; Vinge, Leif Erik; Alfsnes, Katrine & Palibrk, Vuk [Show all 29 contributors for this article] (2017). NEIL3-Dependent Regulation of Cardiac Fibroblast Proliferation Prevents Myocardial Rupture. Cell reports. ISSN 2211-1247. 18, p. 82–92. doi: 10.1016/j.celrep.2016.12.009. Full text in Research Archive
  • Pihlstrøm, Hege; Gatti, Francesca; Hammarström, Clara Louise; Eide, Ivar Anders; Kasprzycka, Monika & Wang, Junbai [Show all 13 contributors for this article] (2017). Early introduction of oral paricalcitol in renal transplant recipients. An open-label randomized study. Transplant International. ISSN 0934-0874. 30(8), p. 827–840. doi: 10.1111/tri.12973.
  • Li, Xiaoran; Lu, Jie; Kan, Quancheng; Li, Xiaoli; Fan, Qiong & Li, Yaqing [Show all 17 contributors for this article] (2017). Metabolic reprogramming is associated with flavopiridol resistance in prostate cancer DU145 cells. Scientific Reports. ISSN 2045-2322. 7:5081, p. 1–20. doi: 10.1038/s41598-017-05086-6.
  • Batmanov, Kirill; Wang, Wei; Bjørås, Magnar; Delabie, Jan & Wang, Junbai (2017). Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma. Scientific Reports. ISSN 2045-2322. 7(1). doi: 10.1038/s41598-017-07226-4. Full text in Research Archive
  • Batmanov, Kirill & Wang, Junbai (2017). Predicting Variation of DNA Shape Preferences in Protein-DNA Interaction in Cancer Cells with a New Biophysical Model. Genes. ISSN 2073-4425. 8(9). doi: 10.3390/genes8090233.
  • Malecka, Agnieszka Maria; Trøen, Gunhild; Tierens, Anne; Østlie, Ingunn; Malecki, Jedrzej Mieczyslaw & Randen, Ulla [Show all 10 contributors for this article] (2017). Frequent somatic mutations of KMT2D (MLL2) and CARD11 genes in primary cold agglutinin disease. British Journal of Haematology. ISSN 0007-1048. 183(5), p. 838–842. doi: 10.1111/bjh.15063.
  • Wang, Junbai; Wu, Qianqian; Hu, Xiaohua Tony & Tian, Tianhai (2016). An integrated approach to infer dynamic protein-gene interactions – A case study of the human P53 protein. Methods. ISSN 1046-2023. 110, p. 3–13. doi: 10.1016/j.ymeth.2016.08.001.
  • Li, Xiaoran; Zhong, Yali; Lu, Jie; Axcrona, Karol; Eide, Lars & Syljuåsen, Randi G. [Show all 13 contributors for this article] (2016). MtDNA depleted PC3 cells exhibit Warburg effect and cancer stem cell features. OncoTarget. ISSN 1949-2553. 7(26), p. 40297–40313. doi: 10.18632/oncotarget.9610. Full text in Research Archive
  • Tangen, Jon-Magnus; Tierens, Anne; Caers, Jo; Binsfeld, Marilene; Olstad, Ole Kristoffer & Siebke, Anne-Marie [Show all 9 contributors for this article] (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 Research International. ISSN 2314-6133. doi: 10.1155/2015/718539.
  • Wang, Junbai & Batmanov, Kirill (2015). BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations. Nucleic Acids Research (NAR). ISSN 0305-1048. 43:e147(21), p. 1–13. doi: 10.1093/nar/gkv733.
  • Wang, Junbai; Malecka, Agnieszka Maria; Trøen, Gunhild & Delabie, Jan (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. ISSN 1471-2164. 16(Suppl7:S12), p. 1–15. doi: 10.1186/1471-2164-16-S7-S12.
  • Huang, Ruixia; Wang, Junbai; Zhong, Yali; Liu, Yishan; Stokke, Trond & Tropé, Claes Gøran [Show all 8 contributors for this article] (2015). Mitochondrial DNA deficiency in ovarian cancer cells and cancer stem cell-like properties. Anticancer Research. ISSN 0250-7005. 35(7), p. 3743–3754.
  • Wang, Junbai (2014). Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence. BMC Bioinformatics. ISSN 1471-2105. 15(289). doi: 10.1186/1471-2105-15-289.
  • Ward, Lucas D.; Wang, Junbai & Bussemaker, Harmen J. (2014). Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. BMC Genomics. ISSN 1471-2164. 15(1). doi: 10.1186/1471-2164-15-494.
  • Pollheimer, Jürgen; Bodin, Johanna; Sundnes, Olav; Bekkeheien, Reidunn C; Skånland, Sigrid Strand & Sponheim, Jon [Show all 16 contributors for this article] (2013). Interleukin-33 drives a proinflammatory endothelial activation that selectively targets nonquiescent cells. Arteriosclerosis, Thrombosis and Vascular Biology. ISSN 1079-5642. 33(2), p. e47–e55. doi: 10.1161/ATVBAHA.112.253427.
  • Wang, Junbai; Lan, Xun; Hsu, Pei-Yin; Hsu, Hang-Kai; Huang, Kun & Parvin, Jeffrey [Show all 8 contributors for this article] (2013). Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. BMC Genomics. ISSN 1471-2164. 14. doi: 10.1186/1471-2164-14-70.
  • Wang, Junbai & Tian, Tianhai (2012). Effective Non-linear Methods for Inferring Genetic Regulation from Time-Series Microarray Gene Expression Data. Methods in molecular biology. ISSN 1064-3745. 802, p. 235–246. doi: 10.1007/978-1-61779-400-1_15.
  • Kim, Geoffrey; Davidson, Ben; Henning, Ryan; Wang, Junbai; Yu, Minshu & Annunziata, Christina [Show all 8 contributors for this article] (2012). Adhesion molecule protein signature in ovarian cancer effusions is prognostic of patient outcome. Cancer. ISSN 0008-543X. 118(6), p. 1543–1553. doi: 10.1002/cncr.26449.
  • Warsam, Abdirashid Ali; Delabie, Jan; Malecka, Agnieszka Maria; Wang, Junbai; Trøen, Gunhild & Tierens, Anne (2012). Monocytoid B cells: An Enigmatic B cell Subset Showing Evidence of Extrafollicular Immunoglobulin gene Somatic Hypermutation. Scandinavian Journal of Immunology. ISSN 0300-9475. 75(5), p. 500–509. doi: 10.1111/j.1365-3083.2012.02688.x.
  • Wang, Junbai (2011). Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. BMC Genomics. ISSN 1471-2164. 12. doi: 10.1186/1471-2164-12-172.
  • Lan, Xun; Adams, Christopher J.; Landers, Mark; Dudas, Miroslav; Krissinger, Daniel & Marnellos, George [Show all 12 contributors for this article] (2011). High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology. PLOS ONE. ISSN 1932-6203. 6(7). doi: 10.1371/journal.pone.0022226.
  • Gillet, Jean-Pierre; Wang, Junbai; Calcagno, Anna Maria; Green, Lisa J.; Varma, Sudhir & Elstrand, Mari Bunkholt [Show all 10 contributors for this article] (2011). Clinical relevance of multidrug resistance gene expression in ovarian serous carcinoma effusions. Molecular Pharmaceutics. ISSN 1543-8384. 8(6), p. 2080–2088. doi: 10.1021/mp200240a.
  • Wang, Junbai & Tian, Tianhai (2010). Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53. BMC Bioinformatics. ISSN 1471-2105. 11. doi: 10.1186/1471-2105-11-36.
  • Tierens, Anne; Holte, Harald; Warsam, Abdirashid Ali; Ikonomou, Ida Merete Münster; Wang, Junbai & Chan, Wing C [Show all 7 contributors for this article] (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. ISSN 0390-6078. 95(8), p. 1334–1341. doi: 10.3324/haematol.2009.014100.
  • Wang, Junbai (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. ISSN 1471-2105. 11. doi: 10.1186/1471-2105-11-412.
  • Elgaaen, Bente Vilming; Foss, Kari Bente; Wang, Junbai; Olstad, Ole Kristoffer; Fortunati, Dario & Onsrud, Mathias [Show all 9 contributors for this article] (2010). POLD2 and KSP37 (FGFBP2) Correlate Strongly with Histology, Stage and Outcome in Ovarian Carcinomas. PLOS ONE. ISSN 1932-6203. 5(11). doi: 10.1371/journal.pone.0013837.
  • Wang, Qing; He, Wei; Lu, CD; Wang, Zhihui; Wang, Junbai & Giercksky, Karl-Erik [Show all 8 contributors for this article] (2009). Oct3/4 and Sox2 Are Significantly Associated with an Unfavorable Clinical Outcome in Human Esophageal Squamous Cell Carcinoma. Anticancer Research. ISSN 0250-7005. 29(4), p. 1233–1241.
  • Wang, Junbai & Morigen, M. (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. ISSN 1471-2105. 10. doi: 10.1186/1471-2105-10-345.
  • Wang, Junbai (2008). Computational biology of genome expression and regulation - A review of microarray bioinformatics. Journal of Environmental Pathology And Toxicology. ISSN 0731-8898. 27(3), p. 157–179.
  • Wang, Junbai (2007). A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle. Journal of Biomedical Informatics. ISSN 1532-0464. doi: 10.1016/j.jbi.2007.02.003.
  • Berner, Jeanne-Marie; Muller, Christoph Rainer; Holden, Marit; Wang, Junbai; Hovig, Eivind & Myklebost, Ola (2006). Sampling effects on gene expression data from a human tumour xenograft. Scandinavian Journal of Laboratory Animal Science. ISSN 0901-3393. 33, p. 17–34.
  • Moorman, C; Sun, LV; Wang, Junbai; de wit, E; Ward, LD & Lu, XJ [Show all 9 contributors for this article] (2006). Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. doi: 10.1073/pnas.0605003103.
  • Meza-Zepeda, L. A.; Kresse, Stine Henrichson; Barragan-Polania, AH; Bjerkehagen, Bodil; Ohnstad, Hege Oma & Namløs, Heidi Maria [Show all 9 contributors for this article] (2006). Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas. Cancer Research. ISSN 0008-5472. doi: 10.1158/0008-5472.CAN-06-1972.
  • Wang, Junbai; Cheung, Leo Wang-Kit & Delabie, Jan (2005). New probabilistic graphical models for genetic regulatory networks studies. Journal of Biomedical Informatics. ISSN 1532-0464. doi: 10.1016/j.jbi.2005.04.003.
  • Hjortland, Geir Olav; Lillehammer, Trine; Somme, Stig; Wang, Junbai; Halvorsen, Thomas & Juell, Siri [Show all 9 contributors for this article] (2004). Plasminogen activator inhibitor-1 increases the expression of VEGF in human glioma cells. Experimental Cell Research. ISSN 0014-4827. 294, p. 130–139. doi: 10.1016/j.yexcr.10.013.
  • Wang, Junbai; Meza-Zepeda, LA; Kresse, Stine Henrichson & Myklebost, Ola (2004). M-CGH: analysing microarray-based CGH experiments. BMC Bioinformatics. ISSN 1471-2105. doi: 10.1186/1471-2105-5-74.
  • Wang, Junbai; Myklebost, Ola & Hovig, Eivind (2003). MGraph: graphical models for microarray data analysis. Bioinformatics. ISSN 1367-4803. 19, p. 2210–2211.
  • Wang, Junbai; Myklebost, Ola; Hovig, Eivind; Henriksen, Jørn; Mælandsmo, Gunhild Mari & Lothe, Ragnhild A [Show all 14 contributors for this article] (2003). Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics. ISSN 1471-2105. 4.
  • Tierens, Anne; Delabie, Jan; Malecka, Agnieszka Maria; Wang, Junbai; Gruszka-Westwood, A & Catovsky, D [Show all 7 contributors for this article] (2003). Splenic marginal zone lymphoma with villous lymphocytes shows on-going immunoglobulin gene mutations. American Journal of Pathology. ISSN 0002-9440. doi: 10.1016/S0002-9440%2810%2963862-X.
  • Wang, Junbai; Delabie, Jan; aasheim, Hans-Christian; Smeland, Erlend B & Myklebost, Ola (2002). Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics. ISSN 1471-2105.
  • Wang, Junbai; Delabie, Jan; Åsheim, Hans-Christian; Smeland, Erlend B. & Myklebost, Ola (2002). Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics. ISSN 1471-2105. doi: 10.1186/1471-2105-3-36.
  • Hansen, JP; Kocbach, Ladislav; Synnes, SA & Wang, Junbai (1998). Origin of the structures in the excitation cross sections in ion-atom collisions, Physical Review A. Atomic, Molecular, and Optical Physics (PRA). ISSN 1050-2947. doi: 10.1103/PhysRevA.57.R4086.

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  • Wang, Junbai; Tian, Tianhai & Tan, Aik Choon (2012). Next Generation Microarray Bioinformatics. Humana Press. ISBN 978-1-61779-399-8. 802(1). 401 p.

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  • Li, Xiaoran; Zhong, Yali; Lu, Jie; Axcrona, Karol; Eide, Lars & Syljuåsen, Randi G. [Show all 13 contributors for this article] (2017). Correction: MtDNA depleted PC3 cells exhibit Warburg effect and cancer stem cell features. OncoTarget. ISSN 1949-2553. 8(4), p. 7208–7213. doi: 10.18632/oncotarget.14800.
  • Shen, Bairong; Ma, Jian; Wang, Jiajun & Wang, Junbai (2014). Biomedical informatics and computational biology for high-throughput data analysis. Scientific World Journal. ISSN 1537-744X. 2014. doi: 10.1155/2014/398181.
  • Wang, Junbai; Nygaard, Vegard; Smith-Sørensen, Birgitte; Hovig, Eivind & Myklebost, M. (2002). MARRAY:analysing single, replicated or reversed microarray experiments. Bioinformatics. ISSN 1367-4803. 8, p. 1139–1140.

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Published Mar. 10, 2021 2:35 PM - Last modified Oct. 7, 2021 11:19 PM