Trung Nghia Vu

Om mig
Publikationer
Forskningsbidrag
Populärvetenskap och samverkan

Om mig

Personal webpage: https://www.meb.ki.se/sites/truvu/

- 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.

Artiklar

Journal article: EJHAEM. 2024;5(4):721-727
Similarities and differences of bone marrow and peripheral blood samples from acute myeloid leukemia patients in terms of cellular heterogeneity and ex-vivo drug sensitivity
Caliskan G; Pawitan Y; Vu TN
Article: BMC BIOINFORMATICS. 2024;25(1):31
CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs
Nguyen T-H; Nguyen H-N; Vu TN
Journal article: CONSERVATION PHYSIOLOGY. 2024;12(1):coae054
Spiny dogfish, Squalus suckleyi, shows a good tolerance for hypoxia but need long recovery times
De Boeck G; Lardon I; Eyckmans M; Vu TN; Laukens K; Dommisse R; Wood CM
Article: PHENOMICS. 2023;3(3):217-227
Hidden Genetic Regulation of Human Complex Traits via Brain Isoforms
Pan L; Zheng C; Yang Z; Pawitan Y; Vu TN; Shen X
Journal article: CANCER RESEARCH. 2023;83(7):6612
Data-driven hallmarks of cancer as a new paradigm for precision medicine: multi-omics and functional profiling in acute myeloid leukemia
Erkers 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):10156-10168
Comprehensive transcriptomic analysis to identify biological and clinical differences in cholangiocarcinoma
Silvestri M; Vu TN; Nichetti F; Niger M; Di Cosimo S; De Braud F; Pruneri G; Pawitan Y; Calza S; Cappelletti V
Article: DATA IN BRIEF. 2023;47:108932
Whole-genome sequencing of antimicrobial-resistant Salmonella enterica isolates from a Cairina moschata carcass
Nguyen TT; Le HV; Xuan DP; Vu TN; Nguyen MH; Tran HTT
Article: NPJ PRECISION ONCOLOGY. 2023;7(1):32
Prediction model for drug response of acute myeloid leukemia patients
Trac 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):1432
A Comprehensive Landscape of Imaging Feature-Associated RNA Expression Profiles in Human Breast Tissue
Mou T; Liang J; Vu TN; Tian M; Gao Y
Journal article: PHENOMICS. 2023;:1
Hidden Genetic Regulation of Human Complex Traits via Brain Isoforms (vol 3, pg no 217-227, 2023)
Pan L; Zheng C; Yang Z; Pawitan Y; Vu TN; Shen X
Article: NATURE COMMUNICATIONS. 2022;13(1):6733
T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression
Yazdani 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:giac091
Discovery of druggable cancer-specific pathways with application in acute myeloid leukemia
Quang TT; Zhou T; Pawitan Y; Trung NV
Article: NAR GENOMICS AND BIOINFORMATICS. 2022;4(3):lqac052
Quantification of mutant-allele expression at isoform level in cancer from RNA-seq data
Deng W; Mou T; Pawitan Y; Trung NV
Article: BMC GENOMICS. 2022;23(1):106
Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data
Manh HN; Ha-Nam N; Trung NV
Article: BIOINFORMATICS. 2022;38(5):1287-1294
Isoform-level quantification for single-cell RNA sequencing
Pan L; Dinh HQ; Pawitan Y; Trung NV
Article: FRONTIERS IN GENETICS. 2022;13:820493
Fusion Gene Detection Using Whole-Exome Sequencing Data in Cancer Patients
Deng W; Murugan S; Lindberg J; Chellappa V; Shen X; Pawitan Y; Vu TN
Article: BMC BIOINFORMATICS. 2021;22(1):495
Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data
Nguyen DT; Trac QT; Nguyen T-H; Nguyen H-N; Ohad N; Pawitan Y; Vu TN
Article: AMERICAN JOURNAL OF HEMATOLOGY. 2021;96(5):580-588
The transcriptome-wide landscape of molecular subtype-specific mRNA expression profiles in acute myeloid leukemia
Mou 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):805-812
Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data
Deng W; Mou T; Kalari KR; Niu N; Wang L; Pawitan Y; Trung NV
Article: BIOINFORMATICS. 2019;35(22):4679-4687
Cell-level somatic mutation detection from single-cell RNA sequencing
Trung NV; Ha-Nam N; Calza S; Kalari KR; Wang L; Pawitan Y
Article: FRONTIERS IN GENETICS. 2019;10:1331
Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing
Mou T; Deng W; Gu F; Pawitan Y; Trung NV
Article: BMC GENOMICS. 2018;19(1):786
A fast detection of fusion genes from paired-end RNA-seq data
Trung NV; Deng W; Quang TT; Calza S; Hwang W; Pawitan Y
Article: BIOLOGY DIRECT. 2018;13(1):14
Accumulation of potential driver genes with genomic alterations predicts survival of high-risk neuroblastoma patients
Suo C; Deng W; Trung NV; Li M; Shi L; Pawitan Y
Article: BIOINFORMATICS. 2018;34(14):2392-2400
Isoform-level gene expression patterns in single-cell RNA-sequencing data
Trung NV; Wills QF; Kalari KR; Niu N; Wang L; Pawitan Y; Rantalainen M
Article: PLOS COMPUTATIONAL BIOLOGY. 2018;14(3):e1006018
speaq 2.0: A complete workflow for high-throughput 1 D NMR spectra processing and quantification
Beirnaert C; Meysman P; Trung NV; Hermans N; Apers S; Pieters L; Covaci A; Laukens K
Article: RAPID COMMUNICATIONS IN MASS SPECTROMETRY. 2017;31(17):1396-1404
InSourcerer: a high-throughput method to search for unknown metabolite modifications by mass spectrometry
Mrzic A; Lermyte F; Trung NV; Valkenborg D; Laukens K
Article: ONCOTARGET. 2016;7(42):68851-68863
Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer
Vu TN; Pramana S; Calza S; Suo C; Lee D; Pawitan Y
Article: BIOINFORMATICS. 2016;32(14):2128-2135
Beta-Poisson model for single-cell RNA-seq data analyses
Trung NV; Wills QF; Kalari KR; Niu N; Wang L; Rantalainen M; Pawitan Y
Article: BRIEFINGS IN BIOINFORMATICS. 2015;16(2):216-231
A primer to frequent itemset mining for bioinformatics
Naulaerts S; Meysman P; Bittremieux W; Trung NV; Vanden Berghe W; Goethals B; Laukens K
Article: JOURNAL OF PROTEOME RESEARCH. 2014;13(9):4175-4183
Efficient Reduction of Candidate Matches in Peptide Spectrum Library Searching Using the Top k Most Intense Peaks
Trung NV; Bittremieux W; Valkenborg D; Goethals B; Lemiere F; Laukens K
Article: EUPA OPEN PROTEOMICS. 2014;4:87-100
Towards automated discrimination of lipids versus peptides from full scan mass spectra.
Dittwald P; Nghia VT; Harris GA; Caprioli RM; Van de Plas R; Laukens K; Gambin A; Valkenborg D
Article: BMC CANCER. 2014;14:594
The radiosensitising effect of gemcitabine and its main metabolite dFdU under low oxygen conditions is in vitro not dependent on functional HIF-1 protein
Wouters 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):37-44
The role of monocytes in the development of Tuberculosis-associated Immune Reconstitution Inflammatory Syndrome
Huyen TTT; Van den Bergh R; Trung NV; Laukens K; Worodria W; Loembe MM; Colebunders R; Kestens L; De Baetselier P; Raes G
Article: PROTEOME SCIENCE. 2014;12(1):54
Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques
Trung NV; Mrzic A; Valkenborg D; Maes E; Lemiere F; Goethals B; Laukens K
Article: METABOLOMICS. 2013;9(6):1216-1227
¹H-NMR study of the metabolome of a moderately hypoxia-tolerant fish, the common carp (Cyprinus carpio)
Lardon I; Eyckmans M; Trung NV; Laukens K; De Boeck G; Dommisse R
Article: METABOLITES. 2013;3(2):259-276
Getting your peaks in line: a review of alignment methods for NMR spectral data.
Vu TN; Laukens K
Article: METABOLOMICS. 2013;9(2):311-323
¹H-NMR study of the metabolome of an exceptionally anoxia tolerant vertebrate, the crucian carp (Carassius carassius)
Lardon 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):1371-1379
¹H NMR based metabolomics of CSF and blood serum: A metabolic profile for a transgenic rat model of Huntington disease
Verwaest KA; Vu TN; Laukens K; Clemens LE; Nguyen HP; Van Gasse B; Martins JC; Van der Linden A; Dommisse R
Article: BMC BIOINFORMATICS. 2011;12:405
An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data
Vu 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):346-348
A Filter Method for Feature Selection for SELDI-TOF Mass Spectrum
Vu T-N; Ohn S-Y
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Alla övriga publikationer

Preprint: ELIFE SCIENCES PUBLICATIONS, LTD. 2024
Pathway activation model for personalized prediction of drug synergy
Trac QT; Huang Y; Erkers T; Östling P; Bohlin A; Österroos A; Vesterlund M; Jafari R; Siavelis I; Bäckvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehtiö J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
Preprint: BIORXIV. 2024
Pathway activation model for personalized prediction of drug synergy
Trac QT; Huang Y; Erkers T; Östling P; Bohlin A; Österroos A; Vesterlund M; Jafari R; Siavelis I; Bäckvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehtiö J; Lehmann S; Kallioniemi O; Pawitan Y; Vu TN
Conference publication: 2023;00:1-4
Analysis of Mutant-Allele Isoform Expression of TP53 in Breast Cancer
Hoang VP; Trac QT; Nguyen H-N; Vu TN
Conference publication: HUMAN HEREDITY. 2017;83(1):4-5
Cell-Specific Somatic Mutation Detection from Single-Cell RNA-Sequencing
Vu N; Calza S; Pawitan Y
Conference publication: 2012;1:1-4
GA_SVM: A genetic algorithm for improving gene regulatory activity prediction
Do Duc D; Le T-T; Vu T-N; Dinh HQ; Huan HX
Conference publication: 2009;:130-136
A New Filter Approach to Extract Relevant Features from Mass Spectrum Datasets
Le T-T; Vu T-N; Trang NTT; Nguyen H-N
Book chapter: MEDICAL BIOMETRICS: LECTURE NOTES IN COMPUTER SCIENCE (INCLUDING SUBSERIES LECTURE NOTES IN ARTIFICIAL INTELLIGENCE AND LECTURE NOTES IN BIOINFORMATICS). 2007;p. 17-24
RISC: A New Filter Approach for Feature Selection from Proteomic Data
Vu T-N; Ohn S-Y; Kim C-W
Book chapter: MICAI 2006: ADVANCES IN ARTIFICIAL INTELLIGENCE: LECTURE NOTES IN COMPUTER SCIENCE (INCLUDING SUBSERIES LECTURE NOTES IN ARTIFICIAL INTELLIGENCE AND LECTURE NOTES IN BIOINFORMATICS). 2006;p. 532-542
Feature Elimination Approach Based on Random Forest for Cancer Diagnosis
Nguyen H-N; Vu T-N; Ohn S-Y; Park Y-M; Han MY; Kim CW

Forskningsbidrag

Multi-omics approach for identification of etiopathogenesis and early detection biomarkers of stomach cancer and precursor lesions
Swedish Research Council
1 January 2024 - 31 December 2026
Vu, Trung Nghia – Clonal heterogeneity and drug sensitivity of Acute Myeloid Leukemia
Swedish Cancer Society
1 January 2023
Predicting drug responses of tumours by deep learning technologies with application in Acute Myeloid Leukemia
Swedish Research Council
1 January 2020 - 31 December 2023

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