Kari Lavikka
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Explore the profile of Kari Lavikka including associated specialties, affiliations and a list of published articles.
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9
Citations
78
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Recent Articles
1.
Lavikka K, Maarala A, Oikkonen J, Hautaniemi S
Bioinformatics
. 2025 Feb;
41(3).
PMID: 39999015
Summary: Spatial and temporal intra-tumor heterogeneity drives tumor evolution and therapy resistance. Existing visualization tools often fail to capture both dimensions simultaneously. To address this, we developed Jellyfish, a tool...
2.
Lavikka K, Oikkonen J, Li Y, Muranen T, Micoli G, Marchi G, et al.
Gigascience
. 2024 Aug;
13.
PMID: 39101783
Background: Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires...
3.
Jamalzadeh S, Dai J, Lavikka K, Li Y, Jiang J, Huhtinen K, et al.
BMC Cancer
. 2024 Feb;
24(1):173.
PMID: 38317080
Copy-number alterations (CNAs) are a hallmark of cancer and can regulate cancer cell states via altered gene expression values. Herein, we have developed a copy-number impact (CNI) analysis method that...
4.
Koskela H, Li Y, Joutsiniemi T, Muranen T, Isoviita V, Huhtinen K, et al.
Gynecol Oncol
. 2023 Dec;
180:91-98.
PMID: 38061276
Objectives: We evaluated usability of single base substitution signature 3 (Sig3) as a biomarker for homologous recombination deficiency (HRD) in tubo-ovarian high-grade serous carcinoma (HGSC). Materials And Methods: This prospective...
5.
Ariotta V, Lehtonen O, Salloum S, Micoli G, Lavikka K, Rantanen V, et al.
J Pathol Inform
. 2023 Nov;
14:100339.
PMID: 37915837
Detecting cell types from histopathological images is essential for various digital pathology applications. However, large number of cells in whole-slide images (WSIs) necessitates automated analysis pipelines for efficient cell type...
6.
Lahtinen A, Lavikka K, Virtanen A, Li Y, Jamalzadeh S, Skorda A, et al.
Cancer Cell
. 2023 May;
41(6):1103-1117.e12.
PMID: 37207655
Ovarian high-grade serous carcinoma (HGSC) is typically diagnosed at an advanced stage, with multiple genetically heterogeneous clones existing in the tumors long before therapeutic intervention. Herein we integrate clonal composition...
7.
Senkowski W, Gall-Mas L, Marin Falco M, Li Y, Lavikka K, Kriegbaum M, et al.
Dev Cell
. 2023 May;
58(12):1106-1121.e7.
PMID: 37148882
The broad research use of organoids from high-grade serous ovarian cancer (HGSC) has been hampered by low culture success rates and limited availability of fresh tumor material. Here, we describe...
8.
Perez-Villatoro F, Oikkonen J, Casado J, Chernenko A, Gulhan D, Tumiati M, et al.
NPJ Precis Oncol
. 2022 Dec;
6(1):96.
PMID: 36581696
Homologous recombination DNA-repair deficiency (HRD) is a common driver of genomic instability and confers a therapeutic vulnerability in cancer. The accurate detection of somatic allelic imbalances (AIs) has been limited...
9.
Oikkonen J, Zhang K, Salminen L, Schulman I, Lavikka K, Andersson N, et al.
JCO Precis Oncol
. 2020 Sep;
3.
PMID: 32914024
Purpose: Circulating tumor DNA (ctDNA) detection is a minimally invasive technique that offers dynamic molecular snapshots of genomic alterations in cancer. Although ctDNA markers can be used for early detection...
10.
Cervera A, Rantanen V, Ovaska K, Laakso M, Nunez-Fontarnau J, Alkodsi A, et al.
Bioinformatics
. 2019 Feb;
35(19):3815-3817.
PMID: 30793160
Summary: Anduril is an analysis and integration framework that facilitates the design, use, parallelization and reproducibility of bioinformatics workflows. Anduril has been upgraded to use Scala for pipeline construction, which...