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Recognising the need for strong expertise in the field of bioinformatics and big data analysis, Rīga Stradiņš University (RSU) has recently established a Bioinformatics Research Unit. The main focus of the unit is the analysis and integration of genome, transcriptome, microbiome and other omics data with epidemiological, clinical, as well as environmental and lifestyle information in the context of personalised medicine, which aims at tailoring the diagnostics and therapy to individuals' needs.

We provide support in the following areas:

  • Bioinformatics consulting: research design, data interpretation and hypothesis generation, answering particular questions related to bioinformatics, statistics or integrative multi-omics data mining;
  • Data analysis and visualisation: customised pipelines for particular research topics of interest and data sets at hand;
  • Scientific writing: writing or reviewing the bioinformatics part in grant application and scientific publications.

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Expertise

Genomic data: genotyping array and exome and whole genome sequencing (WES/WGS) data analysis, including quality control and data cleaning, genetic variant calling and functional annotation, adjustment for confounders, imputation, association analyses and visualisation.

Transcriptome data: RNA-seq, microarray and RT-qPCR data analysis, including quality control, data filtering, normalisation, differential expression analyses and visualisation. Both protein coding and non-coding RNA transcripts can be analyzed at gene or isoform-level.

Microbiome data: 16S rRNA amplicon sequencing data quality control, pre-processing, taxonomic classification and down-stream analyses, such as alpha and beta analyses, co-occurrence networks and predictive functional profiling of the microbial communities.

Exploratory analyses and visualisation to detect patterns and trends in the data, to extract meaningful information from the data and to prepare for further inferential analysis and prepare publication-ready figures.

Medical image analyses: Collaboration and advice for the design of research projects involving the use of medical images for medical diagnosis and prediction using artificial intelligence, from defining specifications, to deployment and scaling.

Data integration: integrating genetic variants with transcript co-expression patterns, protein and metabolite levels, phenotypic traits, experimental read-outs or clinical patient data.

Staff

Baiba Vilne, PhD, Principal Investigator, Bioinformatics Research Unit & Project Manager, Research Department. Vilne has more than 10 years of experience in bioinformatics and systems medicine, analysing genomic data (arrays, WES/WGS) transcriptome and microbiome data. Her major focus has been integrative multi-omics analysis for precision medicine, starting from pair-wise integrations (e.g., expression quantitative trait loci; eQTLs), followed by re-construction of gene co-expression networks/modules, linking those to the life-style and environment data.

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Baiba Alkšere, MSc, Scientific assistant, Bioinformatics Research Unit & PhD student, Scientific Laboratory of Molecular Genetics. Alkšere is a molecular geneticist, currently a PhD student. Her PhD thesis focuses on the genetic causes of sperm formation defects in infertile individuals. Currently, Baiba is also engaged into the bioinformatics analyses of SARS-Cov-2 sequencing data for the project 'Multidisciplinary approach to monitoring, control and control of COVID19 and other future epidemics in Latvia' (COV-MITIGATE) (No. VPP-COVID-2020 / 1-0008).

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Sergio Uribe, DDS, OMFR, PhD, is a Leading Researcher at the Bioinformatics Research Unit. Uribe's research focuses on how to improve people's oral health with better clinical or imaging diagnostic methods for dental caries, temporomandibular disorders or oral cancer, the identification of modifiable risk factors for these conditions, and the clinical and community evaluation of the effectiveness of oral health interventions and precision medicine. He is Associate Editor BMC Oral Health, Dental Traumatology

Keywords: epidemiological studies, systematic reviews and meta-analyses, clinical trials, diagnostic accuracy, tidyverse, data analysis, biostatistics, regression modelling

ORCID 0000-0003-0684-2025

Twitter: @sergiouribe

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Katrīna Daila Neiburga, BSc in Biology, is currently a bioinformatics Master's student working on a thesis identifying transcriptional biomarkers in bacterial vs viral infection in children with fever and identifying hypoxia associated biomarkers in HER2+ breast cancer cell lines.

Has previously worked on translational profiling of neuronal cells and mathematical modelling of plant metabolic pathways.

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Methods, Tools and Equipment

Genomic data: PLINK, SNPTEST, BWA-MEM, GATK4, DeepVariant, VarScan, Mutect2, BreakDancer, ANNOVAR

Transcriptome data: FastQC, Trimmomatic, STAR, featureCounts, edgeR, LIMMA, DESeq2, ToppFun

Microbiome data: FastQC, Trimmomatic, QIIME2, BMTagger, Kraken, PROKKA, MetaWRAP

Exploratory analyses and visualisation R, Tidyverse

Medical image analyses: oro.dicom, oro.nifti, spm12r, neurobase, oro.dti, Neuroconductor

Data integration: Correlation analyses (Pearson), co-expression networks (WGCNA), Machine Learning (caret)

For data analysis and storage, we have access to the high-performance computing (HPC) cluster at the Riga Technical University (RTU), which consists of 55 nodes and 1200 cores, providing 8 TB of total RAM (random access memory) and 0.5 PB of hard disk space.

Publications List

2020
  • Montalban, E., Giralt, A., Taing, L., Nakamura, Y., Martin, C., de Pins, B., Pelosi, A., Goutebroze, L., Castell, L., Wang, W., Neiburga, K. D., Vestito, L., Nairn, A. C., Valjent, E., Hervé, D., Heintz, N., Le Novère, N. G., Greengard, P., Roussarie, J.-P., Girault, J.-A., 2020. Translational profiling of mouse dopaminoceptive neurons reveals a role of PGE2 in dorsal striatum. [PREPRINT] doi:10.1101/2020.09.02.279240
  • Araujo, M. P., Uribe, S., Robertson, M. D., Mendes, F. M., Raggio, D. P., Innes, N. P. T., 2020. "The Hall Technique and exfoliation of primary teeth: a retrospective cohort study." Br. Dent. J. 228, 213–217.
  • Aguilera-Muñoz, F., Uribe, S., Sandoval-Valdés, F., 2020. "Diagnostic Agreement of Bone Measurements for Dental Implants by Cone-Beam Computed Tomography." Int. J. Odontostomat. 14, 89–94.
2019
  • Alksere, B., Berzina, D., Dudorova, A., Conka, U., Andersone, S., Pimane, E., Krasucka, S., Blumberga, A., Dzalbs, A., Grinfelde, I., Vedmedovska, N., Fodina, V., Erenpreiss, J., 2019. Case of Inherited Partial AZFa Deletion without Impact on Male Fertility. Case Rep. Genet. 2019, 3802613.
  • Fodina, V., Dudorova, A., Alksere, B., Dzalbs, A., Vedmedovska, N., Andersone, S., Una, C., Juris, E., Dace, B., 2019. The application of PGT-A for carriers of balanced structural chromosomal rearrangements. Gynecol. Endocrinol. 35, 18–23.
  • Innes, N. P. T., Chu, C. H., Fontana, M., Lo, E. C. M., Thomson, W. M., Uribe, S., Heiland, M., Jepsen, S., Schwendicke, F., 2019. "A Century of Change towards Prevention and Minimal Intervention in Cariology." J. Dent. Res. 98, 611–617.
  • Uribe, S., 2019. "The Routine Use of 3D Imaging May Not Reduce the Risk of Injuries to the Alveolar Inferior Nerve During Third Molar Extraction." J. Evid. Based. Dent. Pract. 19, 89–90.
  • Vilne, B., Meistere, I., Grantiņa-Ieviņa, L., Ķibilds, J., 2019. "Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks." Front. Microbiol. 10, 1722.
2018
  • Volozonoka, L., Perminov, D., Korņejeva, L., Alkšere, B., Novikova, N., Pīmane, E. J., Blumberga, A., Kempa, I., Miskova, A., Gailīte, L., Fodina, V., 2018. Performance comparison of two whole genome amplification techniques in frame of multifactor preimplantation genetic testing. J. Assist. Reprod. Genet. 35, 1457–1472.
  • Clement, J., Uribe, S., Mariño, R. J., 2018. "Non-clinical Oral Health Practice Specialities", en: Mariño, R. J., Morgan, M. V., Walmsley, A. D. (Eds.), Career Paths in Oral Health. Springer International Publishing, Cham, pp. 95–104.
  • Fejerskov, O., Uribe, S., Mariño, R. J., 2018. "Dentistry in a Historical Perspective and a Likely Future of the Profession", en: Mariño, R. J., Morgan, M. V., Walmsley, A. D. (Eds.), Career Paths in Oral Health. Springer International Publishing, Cham, pp. 3–19.
  • Lira-Oetiker, M., Seguel-Galdames, F., Quero-Vallejos, I., Uribe, S., 2018. "Randomised clinical trial of patient satisfaction with traditional and simplified complete dentures." J. Oral Rehabil. 45, 386–392.
  • Lempiäinen, H., Brænne, I., Michoel, T., Tragante, V., Vilne, B., Webb, T. R., Kyriakou, T., Eichner, J., Zeng, L., Willenborg, C., Franzen, O., Ruusalepp, A., Goel, A., van der Laan, S. W., Biegert, C., Hamby, S., Talukdar, H.A., Foroughi Asl, H., CVgenes@target consortium, Pasterkamp, G., Watkins, H., Samani, N. J., Wittenberger, T., Erdmann, J., Schunkert, H., Asselbergs, F. W., Björkegren, J. L. M., 2018. "Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets." Sci. Rep. 8, 3434.
  • Vilne, B., Schunkert, H., 2018. "Integrating Genes Affecting Coronary Artery Disease in Functional Networks by Multi-OMICs Approach." Front Cardiovasc Med 5, 89.
  • Schunkert, H., von Scheidt, M., Kessler, T., Stiller, B., Zeng, L., Vilne, B., 2018. "Genetics of coronary artery disease in the light of genome-wide association studies." Clin. Res. Cardiol. 107, 2–9.
2017
  • Uribe, S., 2017. "Radiographic prediction of inferior alveolar nerve injury in third molar surgery." Evid. Based. Dent. 18, 88–89.
  • Vilne, B., Skogsberg, J., Foroughi Asl, H., Talukdar, H.A., Kessler, T., Björkegren, J. L. M., Schunkert, H., 2017. "Network analysis reveals a causal role of mitochondrial gene activity in atherosclerotic lesion formation." Atherosclerosis 267, 39–48.
  • Kessler, T., Wobst, J., Wolf, B., Eckhold, J., Vilne, B., Hollstein, R., von Ameln, S., Dang, T. A., Sager, H. B., Moritz Rumpf, P., Aherrahrou, R., Kastrati, A., Björkegren, J. L. M., Erdmann, J., Lusis, A. J., Civelek, M., Kaiser, F. J., Schunkert, H., 2017. "Functional Characterization of the GUCY1A3 Coronary Artery Disease Risk Locus." Circulation 136, 476–489.
2016
  • Senakola E, Maldupa I, Uribe S, Niznamovs M, 2016. "MUTES VESELĪBAS PĒTĪJUMS SKOLĒNIEM LATVIJĀ." The Centre for Disease Prevention and Control of Latvia.
  • Mariño, R., Ramos-Gómez, F., Manton, D. J., Onetto, J. E., Hugo, F., Feldens, C. A., Bedi, R., Uribe, S., Zillmann, G., 2016. "The future of pediatric dentistry education and curricula: a Chilean perspective." BMC Oral Health 17, 20.
  • Kessler, T., Erdmann, J., Vilne, B., Bruse, P., Kurowski, V., Diemert, P., Schunkert, H., Sager, H. B., 2016. "Serum microRNA-1233 is a specific biomarker for diagnosing acute pulmonary embolism." J. Transl. Med. 14, 120.
  • Kessler, T., Vilne, B., Schunkert, H., 2016. "The impact of genome-wide association studies on the pathophysiology and therapy of cardiovascular disease." EMBO Mol. Med. 8, 688–701.
2015
  • López, N.J., Uribe, S., Martinez, B., 2015. "Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses." Periodontol. 2000 67, 87–130.
  • Franke, K., Vilne, B., Prazeres da Costa, O., Rudelius, M., Peschel, C., Oostendorp, R.A.J., Keller, U., 2015. "In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment." Oncotarget 6, 21827–21839.
  • Istvánffy, R., Vilne, B., Schreck, C., Ruf, F., Pagel, C., Grziwok, S., Henkel, L., Prazeres da Costa, O., Berndt, J., Stümpflen, V., Götze, K. S., Schiemann, M., Peschel, C., Mewes, H.-W., Oostendorp, R. A. J., 2015. "Stroma-Derived Connective Tissue Growth Factor Maintains Cell Cycle Progression and Repopulation Activity of Hematopoietic Stem Cells In Vitro." Stem Cell Reports 5, 702–715.
  • Brænne, I., Civelek, M., Vilne, B., Di Narzo, A., Johnson, A. D., Zhao, Y., Reiz, B., Codoni, V., Webb, T. R., Foroughi Asl, H., Hamby, S. E., Zeng, L., Trégouët, D.-A., Hao, K., Topol, E. J., Schadt, E. E., Yang, X., Samani, N. J., Björkegren, J. L. M., Erdmann, J., Schunkert, H., Lusis, A. J., Leducq Consortium CAD Genomics‡, 2015. "Prediction of Causal Candidate Genes in Coronary Artery Disease Loci." Arterioscler. Thromb. Vasc. Biol. 35, 2207–2217.

Seminars and Conferences

Upcoming
  • 2020, Fall Term. Mastering your Data - from Exploration to Visualization Sergio Uribe, Visiting Associate Professor at RSU, DDS, MSc in Maxillofacial Radiology, PhD in Medical Sciences
  • 2020, Nov 4th. Artificial Intelligence for Medical Imaging: A Brief Review of Clinical Evidence. Sergio Uribe, Visiting Associate Professor at RSU, DDS, MSc in Maxillofacial Radiology, PhD in Medical Sciences.
  • 2020, Nov 4th. Artificial Intelligence Workflow for Medical Imaging Diagnosis: 7 steps from acquisition to prediction. Sergio Uribe, Visiting Associate Professor at RSU, DDS, MSc in Maxillofacial Radiology, PhD in Medical Sciences
Past
  • 2020, June 3. The Role of Bioinformatics in Multi-OMICS-based Precision Medicine Baiba Vilne, Principal Investigator of the Bioinformatics Research Unit at RSU, PhD
  • 2020, The Challenges of Medical Imaging Data Analyses for Precision Medicine Sergio Uribe, Visiting Associate Professor at RSU, DDS (Oral Surgeon), MSc in Maxillofacial Radiology, PhD in Medical Sciences