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

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
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: 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: CANCER MEDICINE. 2023;12(8):10156-10168

Comprehensive transcriptomic analysis to identify biological and clinical differences in cholangiocarcinoma.

Silvestri M; Nghia Vu T; 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):32

Prediction model for drug response of acute myeloid leukemia patients.

Trac QT; Pawitan Y; Mou T; 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; 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; Kläppe 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.

Trac QT; Zhou T; Pawitan Y; Vu TN
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; Vu TN
Article: BMC GENOMICS. 2022;23(1):106

Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data.

Nguyen MH; Nguyen H-N; Vu TN
Article: BIOINFORMATICS. 2022;38(5):1287-1294

Isoform-level quantification for single-cell RNA sequencing.

Pan L; Dinh HQ; Pawitan Y; Vu TN
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; Österroos A; Siavelis L; Bäckvall H; Erkers T; Kiviluoto S; Seashore-Ludlow B; Östling P; Orre LM; Kallioniemi O; Lehmann S; Lehtiö J; Vu TN
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; Vu TN
Article: BIOINFORMATICS. 2019;35(22):4679-4687

Cell-level somatic mutation detection from single-cell RNA sequencing.

Vu TN; Nguyen H-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; Vu TN
Article: BMC GENOMICS. 2018;19(1):786

A fast detection of fusion genes from paired-end RNA-seq data.

Vu TN; Deng W; Trac QT; 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; Vu TN; Li M; Shi L; Pawitan Y
Article: BIOINFORMATICS. 2018;34(14):2392-2400

Isoform-level gene expression patterns in single-cell RNA-sequencing data.

Vu TN; 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 1D NMR spectra processing and quantification.

Beirnaert C; Meysman P; Vu TN; 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; Vu TN; 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.

Vu TN; 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; Vu TN; 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.

Vu TN; Bittremieux W; Valkenborg D; Goethals B; Lemière 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; Vu TN; Laukens K; Meijnders P; Van Gestel D; Williams KJ; Van den Weyngaert D; Vermorken JB; Pauwels P; Peeters M; Lardon F
Article: PROTEOME SCIENCE. 2014;12(1):54

Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques.

Vu TN; Mrzic A; Valkenborg D; Maes E; Lemière F; Goethals B; Laukens K
Article: IMMUNOBIOLOGY. 2014;219(1):37-44

The role of monocytes in the development of Tuberculosis-associated Immune Reconstitution Inflammatory Syndrome.

Tran HTT; Van den Bergh R; Vu TN; Laukens K; Worodria W; Loembé MM; Colebunders R; Kestens L; De Baetselier P; Raes G; TB-IRIS Study Group
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

(1)H 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; Lemière 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

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. 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. 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
Predicting drug responses of tumours by deep learning technologies with application in Acute Myeloid Leukemia

Swedish Research Council

1 January 2020 - 31 December 2023

Om mig

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Forskningsbidrag

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