IT services and software design manuscripts

Spjuth O, Heikkinen J, Litton J-E, Palmgren J, Krestyaninova M. Data integration between Swedish national clinical health registries and biobanks using an availability system. Springer, Proceedings for 10th International Conference on Data Integration in the Life Sciences, July 17-18 2014, Lisbon, Portugal.  Lecture Notes in Computer Science Volume 8574, 2014, pp 32-40.

Heikkinen J. Activity White paper. SIMBioMS, 2014.

S. Guha Neogi et al. MoDa – A Data Warehouse for Multi-“Omics” Data. 2013;J Data Mining Genomics Proteomics 4:145.

Krestyaninova M, Tammisto Yu. Services design in a collaborative network for multidisciplinary research projects. Springer, Proceedings for13th IFIP Working Conference on VIRTUAL ENTERPRISES, Oct 2012, Bournemouth, UK.

Andrade AQ, Kreuzthaler M, Hastings J, Krestyaninova M, Schulz S. Requirements for semantic biobanks. Stud Health Technol Inform. 2012;180:569-73. PMID: 22874255

Krestyaninova M, Spjuth O, Hastings J, Dietrich J, Rebholz-Schuhmann D. Biobank metaportal to enhance collaborative research: Journal of Systemics, Cybernetics and Informatics. 2012 (vol 10, N 4), pp 5-10.

Kanterakis S and Krestyaninova M. Assembling an IT Infrastructure in Data Intensive Collaborative Projects in the Life Sciences. ICTA-DeMset 2011. Proceedings.

Gostev M, Fernandez-Banet J, Rung J, Dietrich J, Prokopenko I, Ripatti S, McCarthy MI, Brazma A, Krestyaninova M. SAIL–a software system for sample and phenotype availability across biobanks and cohorts. Bioinformatics. 2011 Feb 15;27(4):589-91. Epub 2010 Dec 17.

Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A.A System for Information Management in BioMedical Studies–SIMBioMS. Bioinformatics. 2009 Oct 15;25(20):2768-9. Epub 2009 Jul 24.

Viksna J, Celms E, Opmanis M, Podnieks K, Rucevskis P, Zarins A, Barrett A, Neogi SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U. PASSIM – an open source software system for managing information in biomedical studies. BMC Bioinformatics. 2007 Feb 9;8:52.

Brazma A, Krestyaninova M, Sarkans U.Standards for systems biology. Nat Rev Genet. 2006 Aug; 7(8):593-605. Review.


Data analysis manuscripts

Differential methylation of the TRPA1 promoter in pain sensitivity. Bell JT, et al. (2014)

A common biological basis of obesity and nicotine addiction. Thorgeisson TE, et al. (2013)

Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Grunberg E, et al. (2013)

Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India. Saxena R, et al. (2013)

New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism. Horikoshi M, et al (2012)

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. Manning AK, et al (2012)

Mapping cis- and trans-regulatory effects across multiple tissues in twins. Grundberg E, et al (2012)

Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. Bell JT, et al. (2012)

Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. Cho YS, et al. (2011)

Common variants at 12q15 and 12q24 are associated with infant head circumference. Taal HR, et al. (2012)

A Genome-Wide Metabolic QTL Analysis in Europeans Implicates Two Loci Shaped by Recent Positive Selection. Nicholson G, et al. (2011)

Human metabolic profiles are stably controlled by genetic and environmental variation. Nicholson G, et al. (2011)

Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. Thorgeirsson TE, et al. (2010)

Variants in MTNR1B influence fasting glucose levels. Prokopenko I, et al. (2009)


Statistical methods manuscripts

PPISURV: a novel bioinformatics tool for uncovering the hidden role of specific genes in cancer survival outcome. Antonov AV, Krestyaninova M, Knight RA, Rodchenkov I, Melino G, Barlev NA. (2014)

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. (2010)



Presentation at PRO-VE Conference (2012)

Presentation at 2nd Annual Biobank China (2012)

Presentation at DeMSET (2011)

SIMBioMS Abstract forDeMSET (2011)

SAIL/Kite Abstract for DeMSET (2011)

Presentation at the Data Integration Meeting at Karolinska (Mar 2011)

Abstract for Bio-IT (2010)

Abstract for ISMB (2010)

Presentation at the ENGAGE workshop on “Data analysis and data management” (Feb 2010)

Presentation at the Industry Meeting at EBI (Jun 2009)

Presentation at I3-CRB. Biobanks: Interoperability, Database and Ontology (2010)

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