Search Results - "Välimäki, Niko"

Indexing Graphs for Path Queries with Applications in Genome Research by Siren, Jouni, Valimaki, Niko, Makinen, Veli

“…We propose a generic approach to replace the canonical sequence representation of genomes with graph representations, and study several applications of such…”
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Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease–Associated Colorectal Cancer by Rajamäki, Kristiina, Taira, Aurora, Katainen, Riku, Välimäki, Niko, Kuosmanen, Anna, Plaketti, Roosa-Maria, Seppälä, Toni T., Ahtiainen, Maarit, Wirta, Erkki-Ville, Vartiainen, Emilia, Sulo, Päivi, Ravantti, Janne, Lehtipuro, Suvi, Granberg, Kirsi J., Nykter, Matti, Tanskanen, Tomas, Ristimäki, Ari, Koskensalo, Selja, Renkonen-Sinisalo, Laura, Lepistö, Anna, Böhm, Jan, Taipale, Jussi, Mecklin, Jukka-Pekka, Aavikko, Mervi, Palin, Kimmo, Aaltonen, Lauri A.

“…Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC…”
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Towards pan-genome read alignment to improve variation calling by Valenzuela, Daniel, Norri, Tuukka, Välimäki, Niko, Pitkänen, Esa, Mäkinen, Veli

“…Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD,…”
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Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes by Lees, John A., Vehkala, Minna, Välimäki, Niko, Harris, Simon R., Chewapreecha, Claire, Croucher, Nicholas J., Marttinen, Pekka, Davies, Mark R., Steer, Andrew C., Tong, Steven Y. C., Honkela, Antti, Parkhill, Julian, Bentley, Stephen D., Corander, Jukka

“…Bacterial genomes vary extensively in terms of both gene content and gene sequence. This plasticity hampers the use of traditional SNP-based methods for…”
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Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations by McNally, Alan, Oren, Yaara, Kelly, Darren, Pascoe, Ben, Dunn, Steven, Sreecharan, Tristan, Vehkala, Minna, Välimäki, Niko, Prentice, Michael B, Ashour, Amgad, Avram, Oren, Pupko, Tal, Dobrindt, Ulrich, Literak, Ivan, Guenther, Sebastian, Schaufler, Katharina, Wieler, Lothar H, Zhiyong, Zong, Sheppard, Samuel K, McInerney, James O, Corander, Jukka

“…The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the…”
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Genetic predisposition to uterine leiomyoma is determined by loci for genitourinary development and genome stability by Välimäki, Niko, Kuisma, Heli, Pasanen, Annukka, Heikinheimo, Oskari, Sjöberg, Jari, Bützow, Ralf, Sarvilinna, Nanna, Heinonen, Hanna-Riikka, Tolvanen, Jaana, Bramante, Simona, Tanskanen, Tomas, Auvinen, Juha, Uimari, Outi, Alkodsi, Amjad, Lehtonen, Rainer, Kaasinen, Eevi, Palin, Kimmo, Aaltonen, Lauri A

“…Uterine leiomyomas (ULs) are benign tumors that are a major burden to women's health. A genome-wide association study on 15,453 UL cases and 392,628 controls…”
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Storage and retrieval of highly repetitive sequence collections by Mäkinen, Veli, Navarro, Gonzalo, Sirén, Jouni, Välimäki, Niko

“…A repetitive sequence collection is a set of sequences which are small variations of each other. A prominent example are genome sequences of individuals of the…”
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Exome-wide somatic mutation characterization of small bowel adenocarcinoma by Hänninen, Ulrika A, Katainen, Riku, Tanskanen, Tomas, Plaketti, Roosa-Maria, Laine, Riku, Hamberg, Jiri, Ristimäki, Ari, Pukkala, Eero, Taipale, Minna, Mecklin, Jukka-Pekka, Forsström, Linda M, Pitkänen, Esa, Palin, Kimmo, Välimäki, Niko, Mäkinen, Netta, Aaltonen, Lauri A

“…Small bowel adenocarcinoma (SBA) is an aggressive disease with limited treatment options. Despite previous studies, its molecular genetic background has…”
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Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival by Cajuso, Tatiana, Sulo, Päivi, Tanskanen, Tomas, Katainen, Riku, Taira, Aurora, Hänninen, Ulrika A., Kondelin, Johanna, Forsström, Linda, Välimäki, Niko, Aavikko, Mervi, Kaasinen, Eevi, Ristimäki, Ari, Koskensalo, Selja, Lepistö, Anna, Renkonen-Sinisalo, Laura, Seppälä, Toni, Kuopio, Teijo, Böhm, Jan, Mecklin, Jukka-Pekka, Kilpivaara, Outi, Pitkänen, Esa, Palin, Kimmo, Aaltonen, Lauri A.

“…Genomic instability pathways in colorectal cancer (CRC) have been extensively studied, but the role of retrotransposition in colorectal carcinogenesis remains…”
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Exploration and retrieval of whole-metagenome sequencing samples by Seth, Sohan, Välimäki, Niko, Kaski, Samuel, Honkela, Antti

“…Over the recent years, the field of whole-metagenome shotgun sequencing has witnessed significant growth owing to the high-throughput sequencing technologies…”
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Histopathologic and Molecular Characterization of Uterine Leiomyoma–like Inflammatory Myofibroblastic Tumor: Comparison to Molecular Subtypes of Uterine Leiomyoma by Kuisma, Heli, Jokinen, Vilja, Pasanen, Annukka, Heikinheimo, Oskari, Karhu, Auli, Välimäki, Niko, Aaltonen, Lauri, Bützow, Ralf

“…Uterine leiomyoma (UL) is a common benign neoplasm which can sometimes be difficult to differentiate from the uterine inflammatory myofibroblastic tumor (IMT)…”
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GNAS mutation inhibits growth and induces phosphodiesterase 4D expression in colorectal cancer cell lines by Nummela, Pirjo, Zafar, Sadia, Veikkolainen, Erika, Ukkola, Iiris, Cinella, Vincenzo, Ayo, Abiodun, Asghar, Muhammad Yasir, Välimäki, Niko, Törnquist, Kid, Karhu, Auli, Laakkonen, Pirjo, Aaltonen, Lauri A., Ristimäki, Ari

“…Approximately 5% of colorectal cancers (CRCs) have a gain‐of‐function mutation in the GNAS gene, which leads to the activation of cAMP‐dependent signaling…”
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Parity associates with chromosomal damage in uterine leiomyomas by Kuisma, Heli, Bramante, Simona, Rajamäki, Kristiina, Sipilä, Lauri J., Kaasinen, Eevi, Kaukomaa, Jaana, Palin, Kimmo, Mäkinen, Netta, Sjöberg, Jari, Sarvilinna, Nanna, Taipale, Jussi, Kauppi, Liisa, Tumiati, Manuela, Hassinen, Antti, Pitkäniemi, Janne, Jalkanen, Jyrki, Heikkinen, Sanna, Pasanen, Annukka, Heikinheimo, Oskari, Bützow, Ralf, Välimäki, Niko, Aaltonen, Lauri A.

“…Mechanical forces in a constrained cellular environment were recently established as a facilitator of chromosomal damage. Whether this could contribute to…”
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Inherited mutations affecting the SRCAP complex are central in moderate-penetrance predisposition to uterine leiomyomas by Välimäki, Niko, Jokinen, Vilja, Cajuso, Tatiana, Kuisma, Heli, Taira, Aurora, Dagnaud, Olivia, Ilves, Sini, Kaukomaa, Jaana, Pasanen, Annukka, Palin, Kimmo, Heikinheimo, Oskari, Bützow, Ralf, Aaltonen, Lauri A., Karhu, Auli

“…Uterine leiomyomas (ULs) are benign smooth muscle tumors that are common in premenopausal women. Somatic alterations in MED12, HMGA2, FH, genes encoding…”
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Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis by Weinert, Lucy A., Chaudhuri, Roy R., Wang, Jinhong, Peters, Sarah E., Corander, Jukka, Jombart, Thibaut, Baig, Abiyad, Howell, Kate J., Vehkala, Minna, Välimäki, Niko, Harris, David, Chieu, Tran Thi Bich, Van Vinh Chau, Nguyen, Campbell, James, Schultsz, Constance, Parkhill, Julian, Bentley, Stephen D., Langford, Paul R., Rycroft, Andrew N., Wren, Brendan W., Farrar, Jeremy, Baker, Stephen, Hoa, Ngo Thi, Holden, Matthew T.G., Tucker, Alexander W., Maskell, Duncan J.

“…Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic…”
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Whole-Genome Sequencing of Growth Hormone (GH)-Secreting Pituitary Adenomas by Välimäki, Niko, Demir, Hande, Pitkänen, Esa, Kaasinen, Eevi, Karppinen, Atte, Kivipelto, Leena, Schalin-Jäntti, Camilla, Aaltonen, Lauri A, Karhu, Auli

“…Context: The somatic landscape of pituitary adenomas is largely unknown. Identification of somatic alterations aims at better understanding of tumor pathology…”
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Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma by Berta, Davide G., Kuisma, Heli, Välimäki, Niko, Räisänen, Maritta, Jäntti, Maija, Pasanen, Annukka, Karhu, Auli, Kaukomaa, Jaana, Taira, Aurora, Cajuso, Tatiana, Nieminen, Sanna, Penttinen, Rosa-Maria, Ahonen, Saija, Lehtonen, Rainer, Mehine, Miika, Vahteristo, Pia, Jalkanen, Jyrki, Sahu, Biswajyoti, Ravantti, Janne, Mäkinen, Netta, Rajamäki, Kristiina, Palin, Kimmo, Taipale, Jussi, Heikinheimo, Oskari, Bützow, Ralf, Kaasinen, Eevi, Aaltonen, Lauri A.

“…One in four women suffers from uterine leiomyomas (ULs)—benign tumours of the uterine wall, also known as uterine fibroids—at some point in premenopausal life…”
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Previously reported CCDC26 risk variant and novel germline variants in GALNT13, AR, and MYO10 associated with familial glioma in Finland by Nurminen, Riikka, Afyounian, Ebrahim, Paunu, Niina, Katainen, Riku, Isomäki, Mari, Nurminen, Anssi, Scaravilli, Mauro, Tolppanen, Jenni, Fey, Vidal, Kivinen, Anni, Helén, Pauli, Välimäki, Niko, Kesseli, Juha, Aaltonen, Lauri A., Haapasalo, Hannu, Nykter, Matti, Rautajoki, Kirsi J.

“…Predisposing factors underlying familial aggregation of non-syndromic gliomas are still to be uncovered. Whole-exome sequencing was performed in four Finnish…”
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Genetic and Epigenetic Characterization of Growth Hormone-Secreting Pituitary Tumors by Välimäki, Niko, Schalin-Jäntti, Camilla, Karppinen, Atte, Paetau, Anders, Kivipelto, Leena, Aaltonen, Lauri A, Karhu, Auli

“…Somatic driver mechanisms of pituitary adenoma pathogenesis have remained incompletely characterized; apart from mutations in the stimulatory Gα protein (Gα…”
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Lynch syndrome-associated and sporadic microsatellite unstable colorectal cancers: different patterns of clonal evolution yield highly similar tumours by Martin, Samantha, Katainen, Riku, Taira, Aurora, Välimäki, Niko, Ristimäki, Ari, Seppälä, Toni, Renkonen-Sinisalo, Laura, Lepistö, Anna, Tahkola, Kyösti, Mattila, Anne, Koskensalo, Selja, Mecklin, Jukka-Pekka, Rajamäki, Kristiina, Palin, Kimmo, Aaltonen, Lauri A

“…Microsatellite unstable colorectal cancer (MSI-CRC) can arise through germline mutations in mismatch repair (MMR) genes in individuals with Lynch syndrome…”
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