Trung Nghia Vu
Principal Researcher
E-mail: trungnghia.vu@ki.se
Telephone: +46852482268
Visiting address: Nobels v盲g 12A, 17165 Solna
Postal address: C8 Medicinsk epidemiologi och biostatistik, C8 MEB I Vu Trung, 171 77 Stockholm
About me
Personal webpage:
- 2009 - 2014: PhD, Department of Mathematics and Computer Science,
University of Antwerp, Belgium.
- 2006 - 2008: MSc, Department of Computer Engineering, Korea Aerospace
University, South Korea.
- 2000 - 2004: BSC, Faculty of Technology, Vietnam National University
in Hanoi, Viet Nam.
Research
My research focuses on developing and applying statistical and bioinformatics methods for molecular biology and medicine. I am interested in methodologies to analyze single cell data, discover fusion genes, circular RNAs, and driver genes from cancer, quantify isoform and gene expression from transcriptomics and metagenomics, predict drug responses and drug repurposing using pharmacogenomics data.
Further details can be read at the webpage of my research group: /en/research/research-areas-centres-and-networks/research-groups/trung-nghia-vus-research-group
Our group has developed 20 statistical and bioinformatics/statistical tools which are mostly published in a peer-reviewed scientific articles and publicly available for academic use. Most of tools are implemented using R, Rshiny, C/C++ and available at the Biostat Wiki webpage ()
Our research is supported by the Swedish Research Council, CancerFonden, and 探花精选
Teaching
SUPERVISION
To defense
- Quang Thinh Trac (PhD student, KI, main supervisor, completed Oct 2024)
- Lu Pan (PhD student, KI, main supervisor, completed Mar 2023)
- Wenjiang Deng (PhD student, KI, co-supervisor, completed Sep 2021)
- Thanh Dat Nguyen (master student, Tel-Aviv University, thesis supervisor, completed 2020)
Ongoing
- Gulser Caliskan (postdoc, KI, main supervisor, since 2023)
- Meghana Alugunoolla (master student, Upsala University, main supervisor, since 2024)
- Yuying Li (PhD student, KI, co-supervisor, since 2021)
- Aron Arzoomand (PhD student, KI, co-supervisor, since 2021)
TEACHING
- Master course 鈥淏iostatistics鈥 in the Master of Molecular Techniques, KI, Sweden (2023 & 2024)
- Doctoral course 鈥淚ntroduction to R for data analysis鈥, KI, Sweden (2025)
Articles
- Article: NUCLEIC ACIDS RESEARCH. 2025;53(14):gkaf714Wang Q; Khatri P; Dinh HQ; Huang J; Pawitan Y; Vu TN
- Journal article: ELIFE. 2025;13Trac QT; Huang Y; Erkers T; 脰stling P; Bohlin A; Osterroos A; Vesterlund M; Jafari R; Siavelis I; Backvall H; Kiviluoto S; Orre L; Rantalainen M; Lehti枚 J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
- Article: CONSERVATION PHYSIOLOGY. 2024;12(1):coae054De Boeck G; Lardon I; Eyckmans M; Vu TN; Laukens K; Dommisse R; Wood CM
- Article: EJHAEM. 2024;5(4):721-727Caliskan G; Pawitan Y; Vu TN
- Article: BMC BIOINFORMATICS. 2024;25(1):31Nguyen T-H; Nguyen H-N; Vu TN
- Journal article: PHENOMICS. 2023;:1Pan L; Zheng C; Yang Z; Pawitan Y; Vu TN; Shen X
- Article: PHENOMICS. 2023;3(3):217-227Pan L; Zheng C; Yang Z; Pawitan Y; Vu TN; Shen X
- Article: DATA IN BRIEF. 2023;47:108932Nguyen TT; Le HV; Xuan DP; Vu TN; Nguyen MH; Tran HTT
- Journal article: CANCER RESEARCH. 2023;83(7):6612Erkers T; Struyf N; James T; Marabita F; Vesterlund M; Vu N; Arnroth C; Osterroos A; Bohlin A; Bengtzen S; Stahl M; Jafari R; Orre L; Pawitan Y; Seashore-Ludlow B; Lehtio J; Lehmann S; Ostling P; Kallioniemi O
- Article: CANCER MEDICINE. 2023;12(8):10156-10168Silvestri M; Vu TN; Nichetti F; Niger M; Di Cosimo S; De Braud F; Pruneri G; Pawitan Y; Calza S; Cappelletti V
- Article: NPJ PRECISION ONCOLOGY. 2023;7(1):32Trac QT; Pawitan Y; Mou T; Erkers T; Ostling P; Bohlin A; Osterroos A; Vesterlund M; Jafari R; Siavelis I; Backvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehtio J; Lehmann S; Kallioniemi O; Vu TN
- Article: SENSORS. 2023;23(3):1432Mou T; Liang J; Vu TN; Tian M; Gao Y
- Article: NATURE COMMUNICATIONS. 2022;13(1):6733Yazdani S; Seitz C; Cui C; Lovik A; Pan L; Piehl F; Pawitan Y; Klappe U; Press R; Samuelsson K; Yin L; Vu TN; Joly A-L; Westerberg LS; Evertsson B; Ingre C; Andersson J; Fang F
- Article: GIGASCIENCE. 2022;11:giac091Quang TT; Zhou T; Pawitan Y; Trung NV
- Article: NAR GENOMICS AND BIOINFORMATICS. 2022;4(3):lqac052Deng W; Mou T; Pawitan Y; Trung NV
- Article: FRONTIERS IN GENETICS. 2022;13:820493Deng W; Murugan S; Lindberg J; Chellappa V; Shen X; Pawitan Y; Vu TN
- Article: BMC GENOMICS. 2022;23(1):106Manh HN; Ha-Nam N; Trung NV
- Article: BIOINFORMATICS. 2022;38(5):1287-1294Pan L; Dinh HQ; Pawitan Y; Trung NV
- Article: BMC BIOINFORMATICS. 2021;22(1):495Nguyen DT; Trac QT; Nguyen T-H; Nguyen H-N; Ohad N; Pawitan Y; Vu TN
- Article: AMERICAN JOURNAL OF HEMATOLOGY. 2021;96(5):580-588Mou T; Pawitan Y; Stahl M; Vesterlund M; Deng W; Jafari R; Bohlin A; Osterroos A; Siavelis L; Backvall H; Erkers T; Kiviluoto S; Seashore-Ludlow B; Ostling P; Orre LM; Kallioniemi O; Lehmann S; Lehtio J; Trung NV
- Article: BIOINFORMATICS. 2020;36(3):805-812Deng W; Mou T; Kalari KR; Niu N; Wang L; Pawitan Y; Trung NV
- Article: FRONTIERS IN GENETICS. 2020;10:1331Mou T; Deng W; Gu F; Pawitan Y; Trung NV
- Article: BIOINFORMATICS. 2019;35(22):4679-4687Trung NV; Ha-Nam N; Calza S; Kalari KR; Wang L; Pawitan Y
- Article: BMC GENOMICS. 2018;19(1):786Trung NV; Deng W; Quang TT; Calza S; Hwang W; Pawitan Y
- Article: BIOLOGY DIRECT. 2018;13(1):14Suo C; Deng W; Trung NV; Li M; Shi L; Pawitan Y
- Article: BIOINFORMATICS. 2018;34(14):2392-2400Trung NV; Wills QF; Kalari KR; Niu N; Wang L; Pawitan Y; Rantalainen M
- Article: PLOS COMPUTATIONAL BIOLOGY. 2018;14(3):e1006018Beirnaert C; Meysman P; Trung NV; Hermans N; Apers S; Pieters L; Covaci A; Laukens K
- Article: RAPID COMMUNICATIONS IN MASS SPECTROMETRY. 2017;31(17):1396-1404Mrzic A; Lermyte F; Trung NV; Valkenborg D; Laukens K
- Article: ONCOTARGET. 2016;7(42):68851-68863Vu TN; Pramana S; Calza S; Suo C; Lee D; Pawitan Y
- Article: BIOINFORMATICS. 2016;32(14):2128-2135Trung NV; Wills QF; Kalari KR; Niu N; Wang L; Rantalainen M; Pawitan Y
- Article: BRIEFINGS IN BIOINFORMATICS. 2015;16(2):216-231Naulaerts S; Meysman P; Bittremieux W; Trung NV; Vanden Berghe W; Goethals B; Laukens K
- Article: PROTEOME SCIENCE. 2014;12(1):54Trung NV; Mrzic A; Valkenborg D; Maes E; Lemiere F; Goethals B; Laukens K
- Article: JOURNAL OF PROTEOME RESEARCH. 2014;13(9):4175-4183Trung NV; Bittremieux W; Valkenborg D; Goethals B; Lemiere F; Laukens K
- Article: EUPA OPEN PROTEOMICS. 2014;4:87-100Dittwald P; Nghia VT; Harris GA; Caprioli RM; Van de Plas R; Laukens K; Gambin A; Valkenborg D
- Article: BMC CANCER. 2014;14:594Wouters A; Pauwels B; Burrows N; Baay M; Deschoolmeester V; Trung NV; Laukens K; Meijnders P; Van Gestel D; Williams KJ; Van den Weyngaert D; Vermorken JB; Pauwels P; Peeters M; Lardon F
- Article: IMMUNOBIOLOGY. 2014;219(1):37-44Huyen TTT; Van den Bergh R; Trung NV; Laukens K; Worodria W; Loembe MM; Colebunders R; Kestens L; De Baetselier P; Raes G
- Article: METABOLOMICS. 2013;9(6):1216-1227Lardon I; Eyckmans M; Trung NV; Laukens K; De Boeck G; Dommisse R
- Article: METABOLITES. 2013;3(2):259-276Trung NV; Laukens K
- Article: METABOLOMICS. 2013;9(2):311-323Lardon I; Nilsson GE; Stecyk JAW; Trung NV; Laukens K; Dommisse R; De Boeck G
- Article: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2011;1812(11):1371-1379Verwaest KA; Vu TN; Laukens K; Clemens LE; Nguyen HP; Van Gasse B; Martins JC; Van der Linden A; Dommisse R
- Article: BMC BIOINFORMATICS. 2011;12:405Vu TN; Valkenborg D; Smets K; Verwaest KA; Dommisse R; Lemiere F; Verschoren A; Goethals B; Laukens K
- Article: IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS. 2009;E92D(2):346-348Vu T-N; Ohn S-Y
- Show more
All other publications
- Preprint: ELIFE. 2025Trac QT; Huang Y; Erkers T; Ostling P; Bohlin A; Osterroos A; Vesterlund M; Jafari R; Siavelis I; Backvall H; Kiviluoto S; Orre L; Rantalainen M; Lehtio J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
- Preprint: ELIFE SCIENCES PUBLICATIONS, LTD. 2025Trac QT; Huang Y; Erkers T; 脰stling P; Bohlin A; 脰sterroos A; Vesterlund M; Jafari R; Siavelis I; B盲ckvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehti枚 J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
- Preprint: ELIFE SCIENCES PUBLICATIONS, LTD. 2025Trac QT; Huang Y; Erkers T; 脰stling P; Bohlin A; 脰sterroos A; Vesterlund M; Jafari R; Siavelis I; B盲ckvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehti枚 J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
- Preprint: ELIFE SCIENCES PUBLICATIONS, LTD. 2024Trac QT; Huang Y; Erkers T; 脰stling P; Bohlin A; 脰sterroos A; Vesterlund M; Jafari R; Siavelis I; B盲ckvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehti枚 J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
- Preprint: BIORXIV. 2024Trac QT; Huang Y; Erkers T; 脰stling P; Bohlin A; 脰sterroos A; Vesterlund M; Jafari R; Siavelis I; B盲ckvall H; Kiviluoto S; Orre L; Rantalainen M; Lehti枚 J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
- Conference publication: 2023;00:1-4Hoang VP; Trac QT; Nguyen H-N; Vu TN
- Conference publication: HUMAN HEREDITY. 2017;83(1):4-5Vu N; Calza S; Pawitan Y
- Conference publication: 2012;1:1-4Do Duc D; Le T-T; Vu T-N; Dinh HQ; Huan HX
- Conference publication: 2009;:130-136Le T-T; Vu T-N; Trang NTT; Nguyen H-N
- Book chapter: MEDICAL BIOMETRICS: LECTURE NOTES IN COMPUTER SCIENCE. 2007;p. 17-24Vu T-N; Ohn S-Y; Kim C-W
- Book chapter: MICAI 2006: ADVANCES IN ARTIFICIAL INTELLIGENCE: LECTURE NOTES IN COMPUTER SCIENCE. 2006;p. 532-542Nguyen H-N; Vu T-N; Ohn S-Y; Park Y-M; Han MY; Kim CW
Grants
- Swedish Research Council1 January 2024 - 31 December 2026The overall aim is to utilize multi-omics approach to identify novel etiopathogenesis and early detection biomarkers for stomach cancer and its precursor lesions. To achieve this aim, first we will use stored serum samples to perform metabolomics profiling among 12,599 twin subjects, among whom 1034 were deemed to have chronic atrophic gastritis based on measured pepsinogen I and II levels. Logistic regression will be used to search for metabolites related to the risk of chronic atrophic gastritis. Second, we will further measure serum proteome by using two quantitatively precise proteomics assays, among the above-mentioned twin subjects. Identified protein biomarkers will be combined with metabolomics biomarkers to create a prediction model for chronic atrophic gastritis. Last, we have created a cohort of subjects who were histopathologically diagnosed with chronic atrophic gastritis or more severe precursor lesions. They were followed for stomach cancer occurrence, and a nested case-control study will be performed. Baseline formalin-fixed paraffin-embedded tissue blocks will be retrieved for both stomach cancer cases and their matched controls, and patterns of tissue proteome and transcriptome will be compared, to identify driving factors associated with progression of precursor lesions to malignancy. The results will hopefully improve our understanding of the etiological factors and provide promising early detection biomarkers for stomach cancer and its precursor lesions.
- Swedish Cancer Society1 January 2023Acute myeloid leukemia (AML) is an aggressive blood cancer that is highly genetically complex and cell diversified. The heterogeneity of both tumor genetic changes and cellular subtypes means that response to treatment is very difficult to predict. The response is a crucial part of individualized cancer treatment. While the relationship between drug sensitivity and genetic changes has been largely investigated at the tissue level, studies at the single-cell level, such as cellular heterogeneity, are still limited. We will investigate how response to cancer treatment is affected by the heterogeneity of cells in AML patients. We will evaluate how drug sensitivity is associated with cell heterogeneity in AML tumors detected from single-cell data. We will investigate the diversity of changes by integrating multiple biological features including mutations, immune cell type, RNA expression and alternative splicing patterns. We will use the expanded information, other biologically meaningful features from tissue-level omics data, and advanced machine learning methods to improve prediction of response to individual cancer drugs and drug combinations for patients with AML, and to explore carcinogenic mechanisms of cancer drugs. To develop knowledge about the relationship between drug sensitivity and cell heterogeneity in AML tumors. To develop improved prediction models of drug response for patients with AML.
- Swedish Research Council1 January 2020 - 31 December 2023