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| 1 | A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas显示文摘Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature. | Antti Ylipaa Olli Yli-Harja Wei Zhang Matti Nykter | 2011 | Chinese Journal of Cancer2011，30，1： | 3 |
| 2 | Twist predicts poor outcome of patients with astrocytic glioma显示文摘 | Nordfors Kristiina Haapasalo Joonas Makela Katri Granberg Kirsi J Nykter Matti Korja Miikka Paavonen Timo Haapasalo Hannu Soini Ylermi | 2015 | Journal of Clinical Pathology2015，，11： | 1 |
| 3 | Gene Expression Dynamics in the Macrophage Exhibit Criticality 显示文摘 | Nykter M Price N D Shmulevieh I | 2008 | Proceedings of the National Academy of Sciences of the USA2008，105，： | 1 |
| 4 | Critical networks exhibit maximal information diversity in structure-dynamics relationships显示文摘 | Nykter M Price N D Shmulevich I | 2008 | Physical Review Letters2008，100，05： | 1 |
| 5 | Quality characteristics of edible linseed oil 显示文摘 | NYKTER M KYMALAINEN H R | 2006 | Agricultural and Food Science2006，15，4： | 1 |
| 6 | Quality characteristics of edible linseed oil显示文摘 | Nykter M Kymalainen H R Gates F | 2006 | Agricultural and Food Science2006，15，4： | 1 |
| 7 | Cancer systems biology:signal processing for cancer research显示文摘In this editorial we introduce the research paradigms of signal processing in the era of systems biology.Signal processing is a field of science traditionally focused on modeling electronic and communications systems,but recently it has turned to biological applications with astounding results.The essence of signal processing is to describe the natural world by mathematical models and then,based on these models,develop efficient computational tools for solving engineering problems.Here,we underline,with examples,the endless possibilities which arise when the battle-hardened tools of engineering are applied to solve the problems that have tormented cancer researchers.Based on this approach,a new field has emerged,called cancer systems biology.Despite its short history,cancer systems biology has already produced several success stories tackling previously impracticable problems.Perhaps most importantly,it has been accepted as an integral part of the major endeavors of cancer research,such as analyzing the genomic and epigenomic data produced by The Cancer Genome Atlas(TCGA) project.Finally,we show that signal processing and cancer research,two fields that are seemingly distant from each other,have merged into a field that is indeed more than the sum of its parts. | Olli Yli-Harja Antti Ylipaeae Matti Nykter Wei Zhang | 2011 | Chinese Journal of Cancer2011，30，4： | 1 |
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