"Computational medicine" och bioinformatik – Trung Nghia Vus forskargrupp

Publikationer

All publications from group members

• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
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Medlemmar och kontakt

Gruppledare

• 

  Trung Nghia Vu

  Senior Forskare

  Telefon +46852482268

  E-postadress trungnghia.vu@ki.se

Alla medlemmar i gruppen

• 

  Gulser Caliskan

  Postdoktor

  E-postadress gulser.caliskan@ki.se
• Thi Trang Nguyen

  Anknuten till Forskning

  E-postadress thi.trang.nguyen@ki.se
• 

  Quang Thinh Trac

  Doktorand

  E-postadress quang.thinh.trac@ki.se
• 

  Trung Nghia Vu

  Senior Forskare

  Telefon +46852482268

  E-postadress trungnghia.vu@ki.se

Besöksadress

Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Nobels väg 12A, Stockholm, 171 77, Sweden

Postadress

Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, PO Box 281, Stockholm, 171 77, Sweden