المؤلفون: Pihlajamaa, Päivi, Kauko, Otto, Sahu, Biswajyoti, Kivioja, Teemu, Taipale, Jussi

المساهمون: ATG - Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Medicum, Faculty of Medicine, Department of Computer Science, Department of Pathology, Jussi Taipale / Principal Investigator

مصطلحات موضوعية: C-MYC, PHOSPHORYLATION SITES, READ ALIGNMENT, DNA-BINDING, GENE, CELLS, ACTIVATION, KINASE, SENESCENCE, REPRESSION, Medical biotechnology, 11832 Microbiology and virology

وصف الملف: application/pdf

العلاقة: We thank A. M. Luoto, K. Jussila and K. Sarin for technical assistance. We also thank HiLIFE research infrastructures, including the Biomedicum Functional Genomics Unit (FuGU), the Sequencing Laboratory of the Institute for Molecular Medicine Finland FIMM Technology Centre and the Flow Cytometry Unit, University of Helsinki. J.T. was supported by grants from the Academy of Finland (Finnish Center of Excellence program: 2012-2017, 250345 and 2018-2025, 312042), the Finnish Cancer Foundation, the United Kingdom Research and Innovation Medical Research Council (grant MR/V000500/1) and Cancer Research UK (grant C55958/A28801/RG99643). P.P. was supported by the Academy of Finland (288836). B.S. was supported by the Academy of Finland (274555 and 317807), the Finnish Cancer Foundation and the Sigrid Juselius and Jane and Aatos Erkko Foundations.; Pihlajamaa , P , Kauko , O , Sahu , B , Kivioja , T & Taipale , J 2022 , ' A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites ' , Nature Biotechnology , vol. 41 , pp. 197–203 . https://doi.org/10.1038/s41587-022-01444-6Test; ORCID: /0000-0001-6576-5440/work/130598100; ORCID: /0000-0001-9725-6907/work/137860637; http://hdl.handle.net/10138/355607Test; c81ced36-7594-4b3f-a47c-f67cde768883; 000859845900002

الإتاحة: http://hdl.handle.net/10138/355607Test

المؤلفون: Sahu, Biswajyoti, Pihlajamaa, Päivi, Zhang, Kaiyang, Palin, Kimmo, Ahonen, Saija, Cervera, Alejandra, Ristimäki, Ari, Aaltonen, Lauri A, Hautaniemi, Sampsa, Taipale, Jussi

العلاقة: info:eu-repo/grantAgreement/AKA//312041/; info:eu-repo/grantAgreement/AKA//335823/; info:eu-repo/grantAgreement/AKA//274555/; info:eu-repo/grantAgreement/EC/H2020/667403/; info:eu-repo/grantAgreement/AKA//319083/; info:eu-repo/grantAgreement/AKA//250345/; info:eu-repo/grantAgreement/AKA//320185/; info:eu-repo/grantAgreement/AKA//317807/; info:eu-repo/grantAgreement/AKA//320149/; https://zenodo.org/record/4973023Test; https://doi.org/10.5281/zenodo.4973023Test; oai:zenodo.org:4973023

الإتاحة: https://doi.org/10.5281/zenodo.4973023Test
https://doi.org/10.1101/525600Test
https://doi.org/10.5281/zenodo.4973022Test
https://zenodo.org/record/4973023Test

المؤلفون: Sahu, Biswajyoti, Hartonen, Tuomo, Pihlajamaa, Päivi, Wei, Bei, Dave, Kashyap, Zhu, Fangjie, Kaasinen, Eevi, Lidschreiber, Katja, Lidschreiber, Michael, Daub, Carsten O., Cramer, Patrick, Kivioja, Teemu, Taipale, Jussi

المساهمون: Research Programs Unit, Medicum, Department of Biochemistry and Developmental Biology, ATG - Applied Tumor Genomics, Faculty of Medicine, Institute for Molecular Medicine Finland, Jussi Taipale / Principal Investigator, HUSLAB, Department of Pathology

مصطلحات موضوعية: TRANSCRIPTION-FACTOR-BINDING, DEVELOPMENTAL ENHANCERS, ACTIVE ENHANCERS, DNA, CHROMATIN, PROTEINS, MAPS, SITE, SPECIFICITIES, EXPRESSION, 3111 Biomedicine, 1184 Genetics, developmental biology, physiology

وصف الملف: application/pdf

العلاقة: We thank M. Taipale, S. Wickstrom and M. Vartiainen for critical reading of the manuscript; A. M. Luoto, K. Jussila and A. Kolterud for technical assistance; and L. Fei, J. Xia and N. Poddar for their help during the revision. We also thank HiLIFE research infrastructures, including Biomedium Functional Genomics, FIMM technology center and sequencing core facilities of Karolinska Institute and SciLifeLab. We wish to acknowledge CSC -IT Center for Science, Finland for computational resources. J.T. was supported by the Academy of Finland (Finnish Center of Excellence program grants 2012-2017, 250345 and 2018-2025, 312042), United Kingdom Research and Innovation Medical Research Council (grant MR/V000500/1) and Cancer Research UK (grant C55958/A28801/RG99643). B.S. was supported by the Academy of Finland (grants 274555 and 317807), the Finnish Cancer Foundation and the Sigrid Juselius and Jane and Aatos Erkko foundations. T.H. was supported by a personal grant from Emil Aaltonen Foundation, and P.P. was supported by the Academy of Finland (grant 288836). K.L., M.L. and P.C. were funded by The Center for Medical Innovation (CIMED) and SciLifeLab.; Sahu , B , Hartonen , T , Pihlajamaa , P , Wei , B , Dave , K , Zhu , F , Kaasinen , E , Lidschreiber , K , Lidschreiber , M , Daub , C O , Cramer , P , Kivioja , T & Taipale , J 2022 , ' Sequence determinants of human gene regulatory elements ' , Nature Genetics , vol. 54 , no. 3 , pp. 283-+ . https://doi.org/10.1038/s41588-021-01009-4Test; ORCID: /0000-0001-6576-5440/work/111914855; ORCID: /0000-0002-1333-8049/work/111917992; ORCID: /0000-0001-9725-6907/work/137860639; 85b88be6-7ee2-4fee-a838-7e05979d4837; http://hdl.handle.net/10138/342898Test; 000758968100001

الإتاحة: http://hdl.handle.net/10138/342898Test

المؤلفون: Pihlajamaa, Päivi, Kauko, Otto, Sahu, Biswajyoti, Kivioja, Teemu, Taipale, Jussi

المساهمون: Academy of Finland, Syöpäjärjestöt, Jane ja Aatos Erkon Säätiö, Sigrid Juséliuksen Säätiö, RCUK | Medical Research Council, Cancer Research UK

المصدر: Nature Biotechnology ; volume 41, issue 2, page 197-203 ; ISSN 1087-0156 1546-1696

مصطلحات موضوعية: Biomedical Engineering, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biotechnology

الإتاحة: https://doi.org/10.1038/s41587-022-01444-6Test
https://www.nature.com/articles/s41587-022-01444-6.pdfTest
https://www.nature.com/articles/s41587-022-01444-6Test

المؤلفون: Aavikko, Mervi, Kaasinen, Eevi, Andersson, Noora, Pentinmikko, Nalle, Sulo, Päivi, Donner, Iikki, Pihlajamaa, Päivi, Kuosmanen, Anna, Bramante, Simona, Katainen, Riku, Sipilä, Lauri J, Martin, Samantha, Arola, Johanna, Carpén, Olli, Heiskanen, Ilkka, Mecklin, Jukka-Pekka, Taipale, Jussi, Ristimäki, Ari, Lehti, Kaisa, Gucciardo, Erika, Katajisto, Pekka, Schalin-Jäntti, Camilla, Vahteristo, Pia, Aaltonen, Lauri A.

المساهمون: Medicum, Institute for Molecular Medicine Finland, Department of Medical and Clinical Genetics, ATG - Applied Tumor Genomics, Helsinki Institute of Life Science HiLIFE, HUSLAB, Department of Pathology, Centre of Excellence in Stem Cell Metabolism, Institute of Biotechnology, Organismal and Evolutionary Biology Research Programme, Lauri Antti Aaltonen / Principal Investigator, Doctoral Programme in Biomedicine, HUS Diagnostic Center, Precision Cancer Pathology, Olli Mikael Carpen / Principal Investigator, Research Program in Systems Oncology, HUS Abdominal Center, II kirurgian klinikka, Biosciences, Jussi Taipale / Principal Investigator, Kaisa Irene Lehti / Principal Investigator, Faculty Common Matters (Faculty of Biology and Environmental Sciences), INDIVIDRUG - Individualized Drug Therapy, Faculty of Biological and Environmental Sciences, Clinicum, Endokrinologian yksikkö

مصطلحات موضوعية: 3111 Biomedicine, 3121 General medicine, internal medicine and other clinical medicine, CARCINOID-TUMORS, CYSTIC-FIBROSIS, CANCER-RISK, GENOME, NATIONWIDE, MUTATION, DOMAINS, MAP

وصف الملف: application/pdf

العلاقة: Aavikko , M , Kaasinen , E , Andersson , N , Pentinmikko , N , Sulo , P , Donner , I , Pihlajamaa , P , Kuosmanen , A , Bramante , S , Katainen , R , Sipilä , L J , Martin , S , Arola , J , Carpén , O , Heiskanen , I , Mecklin , J-P , Taipale , J , Ristimäki , A , Lehti , K , Gucciardo , E , Katajisto , P , Schalin-Jäntti , C , Vahteristo , P & Aaltonen , L A 2021 , ' WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas ' , Human Molecular Genetics , vol. 30 , no. 24 , pp. 2429-2440 . https://doi.org/10.1093/hmg/ddab206Test; Bibtex: 10.1093/hmg/ddab206; ORCID: /0000-0001-6839-4286/work/105558059; ORCID: /0000-0002-1333-8049/work/105558536; ORCID: /0000-0003-4481-8798/work/105558642; ORCID: /0000-0002-7002-0803/work/105558650; ORCID: /0000-0001-9725-6907/work/137860630; 324c71d5-4885-46cf-97a5-aa8a371c2205; http://hdl.handle.net/10138/338076Test; 000733807400006

الإتاحة: http://hdl.handle.net/10138/338076Test

المؤلفون: Sahu, Biswajyoti, Pihlajamaa, Päivi, Zhang, Kaiyang, Palin, Kimmo, Ahonen, Saija, Cervera, Alejandra, Ristimäki, Ari, Aaltonen, Lauri A., Hautaniemi, Sampsa, Taipale, Jussi

المساهمون: Department of Biochemistry and Developmental Biology, Digital Precision Cancer Medicine (iCAN), ATG - Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Research Program in Systems Oncology, Sampsa Hautaniemi / Principal Investigator, Lauri Antti Aaltonen / Principal Investigator, Department of Medical and Clinical Genetics, Research Programs Unit, Department of Pathology, HUSLAB, Medicum, HUS Diagnostic Center, Helsinki University Hospital Area, Faculty Common Matters (Faculty of Medicine), Bioinformatics, Jussi Taipale / Principal Investigator

مصطلحات موضوعية: HEPATOCELLULAR-CARCINOMA, HUMAN FIBROBLASTS, RAS ONCOGENES, CANCER, TUMOR, GENES, MYC, METHYLATION, INDUCTION, TUMORIGENESIS, 3122 Cancers

وصف الملف: application/pdf

العلاقة: JT was supported by grants from Academy of Finland (Finnish Center of Excellence in Tumor Genetics Research 2018-2025, grant number 312042 and 2012-2017; 250345), Finnish Cancer Foundation, and Cancer Research UK (grant number RG99643). BS was supported by the Academy of Finland (post-doctoral fellowship, 274555; research fellowship, 317807), Finnish Cancer Foundation, Sigrid Juselius Foundation, Jane and Aatos Erkko Foundation and iCAN Digital Precision Cancer Medicine Flagship. PP was supported by the post-doctoral fellowship 288836 from Academy of Finland. AR was supported by Finska Lakaresallskapet, Helsinki University Central Hospital Research Funds, and Sigrid Juselius Foundation. LA was supported by Academy of Finland (grant numbers 312041, 335823, 250345, 319083, 320149), iCAN Digital Precision Cancer Medicine Flagship (grant number 320185), Finnish Cancer Foundation, Sigrid Juselius Foundation and Jane and Aatos Erkko Foundation. SH was supported by the European Union's Horizon 2020 research and innovDation program under Grant Agreement No. 667403 for HERCULES. Open access funding provided by University of Helsinki including Helsinki University Central Hospital.; Sahu , B , Pihlajamaa , P , Zhang , K , Palin , K , Ahonen , S , Cervera , A , Ristimäki , A , Aaltonen , L A , Hautaniemi , S & Taipale , J 2021 , ' Human cell transformation by combined lineage conversion and oncogene expression ' , Oncogene , vol. 40 , pp. 5533-5547 . https://doi.org/10.1038/s41388-021-01940-0Test; ORCID: /0000-0001-6576-5440/work/100080565; ORCID: /0000-0002-7749-2694/work/100082556; ORCID: /0000-0003-3313-784X/work/100083280; ORCID: /0000-0001-6839-4286/work/101502619; ORCID: /0000-0001-9725-6907/work/137860634; d94dafde-bb3b-4084-aa00-83bb4a6383a4; http://hdl.handle.net/10138/334405Test; 000676064800002

الإتاحة: http://hdl.handle.net/10138/334405Test

المؤلفون: Palin, Kimmo, Pitkänen, Esa, Turunen, Mikko, Sahu, Biswajyoti, Pihlajamaa, Päivi, Kivioja, Teemu, Kaasinen, Eevi, Välimäki, Niko, Hänninen, Ulrika A., Cajuso, Tatiana, Aavikko, Mervi, Tuupanen, Sari, Kilpivaara, Outi, van den Berg, Linda, Kondelin, Johanna, Tanskanen, Tomas, Katainen, Riku, Grau, Marta, Rauanheimo, Heli, Plaketti, Roosa-Maria, Taira, Aurora, Sulo, Päivi, Hartonen, Tuomo, Dave, Kashyap, Schmierer, Bernhard, Botla, Sandeep, Sokolova, Maria, Vähärautio, Anna, Gladysz, Kornelia, Ongen, Halit, Dermitzakis, Emmanouil, Bramsen, Jesper Bertram, Orntoft, Torben Falck, Andersen, Claus Lindbjerg, Ristimäki, Ari, Lepistö, Anna, Renkonen-Sinisalo, Laura, Mecklin, Jukka-Pekka, Taipale, Jussi, Aaltonen, Lauri A.

المساهمون: Research Programs Unit, Lauri Antti Aaltonen / Principal Investigator, Genome-Scale Biology (GSB) Research Program, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Doctoral Programme in Integrative Life Science, Centre of Excellence in Stem Cell Metabolism, Nutrient sensing laboratory, Jussi Taipale / Principal Investigator, Institute of Biotechnology, Department of Pathology, HUSLAB, Gastrointestinal tumorigenesis, Clinicum, Doctoral Programme in Clinical Research, Department of Surgery, II kirurgian klinikka, HUS Abdominal Center

مصطلحات موضوعية: HUMAN-COLON, GENOME, CELLS, ENHANCERS, GENES, 3111 Biomedicine

وصف الملف: application/pdf

العلاقة: We thank Heikki Metsola, Sini Marttinen, Kirsi Pylvanainen, Tuula Lehtinen, Jiri Hamberg, Alison Ollikainen, Marjo Rajalaakso, Sirpa Soisalo, Inga-Lill Aberg, Iina Vuoristo, Lijuan Hu, Asal Fotouhi, Tomi Leung, and Anu Luoto for technical assistance and Alison Ollikainen and Samantha Martin for proofreading the manuscript. This work was supported by grants from the Jane and Aatos Erkko Foundation, Academy of Finland (Finnish Center of Excellence Program 2012-2017, 250345 and 2018-2025, 312041 and Post-doctoral Fellowships 274555, 287665, and 288836), the Finnish Cancer Society, the Finnish Cancer Foundation, the Paulo Foundation, K. Albin Johanssons stiftelse, Paivikki and Sakari Sohlberg Foundation, Cancer Society of Finland, the State Research Funding, Integrated Life Science Doctoral Program (ILS), University of Helsinki, the Sigrid Juselius Foundation and SYSCOL (an EU FP7 Collaborative Project, 258236), the Novo Nordic Foundation (NNF14OC0012747), the Danish Cancer Society (R107-A7035 and R133-A8520), the Danish Council for Independent Research broken vertical bar Medical Science (DFF-4183-00619), the Nordic Information for Action eScience Center (NIASC); a Nordic Center of Excellence financed by NordForsk (Project number 62721) and Nordic biobank-based study of causes and biomarkers of cancer: Pilot study financed by NordForsk 07 BM 11/424. We acknowledge the computational resources provided by the ELIXIR node hosted at CSC-IT Center for Science funded by the Academy of Finland (grants 271642, 263164) and the Ministry of Education and Culture, Finland. The Danish Cancer Biobank is acknowledged for biological material. We also acknowledge the support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure.; Palin , K , Pitkänen , E , Turunen , M , Sahu , B , Pihlajamaa , P , Kivioja , T , Kaasinen , E , Välimäki , N , Hänninen , U A , Cajuso , T , Aavikko , M , Tuupanen , S , Kilpivaara , O , van den Berg , L , Kondelin , J , Tanskanen , T , Katainen , R , Grau , M , Rauanheimo , H , Plaketti , R-M , Taira , A , Sulo , P , Hartonen , T , Dave , K , Schmierer , B , Botla , S , Sokolova , M , Vähärautio , A , Gladysz , K , Ongen , H , Dermitzakis , E , Bramsen , J B , Orntoft , T F , Andersen , C L , Ristimäki , A , Lepistö , A , Renkonen-Sinisalo , L , Mecklin , J-P , Taipale , J & Aaltonen , L A 2018 , ' Contribution of allelic imbalance to colorectal cancer ' , Nature Communications , vol. 9 , 3664 . https://doi.org/10.1038/s41467-018-06132-1Test; ORCID: /0000-0001-6576-5440/work/49156899; ORCID: /0000-0003-4721-3954/work/49158607; ORCID: /0000-0002-5866-4059/work/49162394; ORCID: /0000-0001-5965-8518/work/49162696; ORCID: /0000-0002-1333-8049/work/91815955; ORCID: /0000-0001-6839-4286/work/101502577; ORCID: /0000-0001-9725-6907/work/137860629; ORCID: /0000-0002-1179-8500/work/156152270; ORCID: /0000-0001-8467-2100/work/156157832; http://hdl.handle.net/10138/247091Test; d71e2d42-6fcd-41ae-bc47-0bbf3d35b633; 85053197758; 000444078300007

الإتاحة: http://hdl.handle.net/10138/247091Test

المؤلفون: Heinonen, Henna, Lepikhova, Tatiana, Sahu, Biswajyoti, Pehkonen, Henna Maria, Pihlajamaa, Päivi, Louhimo, Riku, Gao, Ping, Wei, Gong-Hong, Hautaniemi, Sampsa, Jänne, Olli A., Monni, Outi Maria

المساهمون: Research Programs Unit, Outi Monni / Principal Investigator, Genome-Scale Biology (GSB) Research Program, Department of Biochemistry and Developmental Biology, Medicum, Department of Physiology, Jussi Taipale / Principal Investigator, Sampsa Hautaniemi / Principal Investigator, Bioinformatics

مصطلحات موضوعية: 3122 Cancers, 3111 Biomedicine, 3123 Gynaecology and paediatrics

وصف الملف: application/pdf

العلاقة: Heinonen , H , Lepikhova , T , Sahu , B , Pehkonen , H M , Pihlajamaa , P , Louhimo , R , Gao , P , Wei , G-H , Hautaniemi , S , Jänne , O A & Monni , O M 2015 , ' Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer ' , International Journal of Cancer , vol. 137 , no. 10 , pp. 2374-2383 . https://doi.org/10.1002/ijc.29616Test; ORCID: /0000-0001-6576-5440/work/30364414; ORCID: /0000-0002-7749-2694/work/29942489; ORCID: /0000-0001-9725-6907/work/137860638; 84941908588; e76f84bb-47a3-431b-8f9c-c4b3ff055168; http://hdl.handle.net/10138/208081Test; 000362842600010

الإتاحة: http://hdl.handle.net/10138/208081Test

المؤلفون: Silander, Kristian M., Pihlajamaa, Päivi, Sahu, Biswajyoti, Jänne, Olli A., Andersson, Leif C.

المصدر: Bioscience Reports ; volume 37, issue 4 ; ISSN 0144-8463 1573-4935

مصطلحات موضوعية: Cell Biology, Molecular Biology, Biochemistry, Biophysics

الإتاحة: https://doi.org/10.1042/bsr20170163Test

المؤلفون: Heinonen, Henna, Lepikhova, Tatiana, Sahu, Biswajyoti, Pehkonen, Henna, Pihlajamaa, Päivi, Louhimo, Riku, Gao, Ping, Wei, Gong‐Hong, Hautaniemi, Sampsa, Jänne, Olli A., Monni, Outi

المساهمون: Academy of Finland, Finnish Cancer Organizations and Sigrid Jusélius Foundation

المصدر: International Journal of Cancer ; volume 137, issue 10, page 2374-2383 ; ISSN 0020-7136 1097-0215

الإتاحة: https://doi.org/10.1002/ijc.29616Test