Beräkningsmedicin och bioinformatik – Trung Nghia Vus forskargrupp

Publikationer

Alla gruppmedlemmars 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
• 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
• 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
• 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
• 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: 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
• 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

  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
• 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

  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
• 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 (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
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Medarbetare och kontakt

Gruppledare

• 

  Trung Nghia Vu

  Senior Forskare

  Telefon +46852482268

  E-postadress trungnghia.vu@ki.se

Alla medarbetare i gruppen

• 

  Gulser Caliskan

  Postdoktor

  Telefon +46852482267

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

  Anknuten till Forskning

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

  Trung Nghia Vu

  Senior Forskare

  Telefon +46852482268

  E-postadress trungnghia.vu@ki.se
• 

  Qingyue Wang

  E-postadress qingyue.wang@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