Browsing by Subject "Computational methods"

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    Lighting up Nobel Prize-winning studies with protein intrinsic disorder
    (Springer, 2022-07-26) Piersimoni, Lolita; Abd el Malek, Marina; Bhatia, Twinkle; Bender, Julian; Brankatschk, Christin; Sánchez, Jaime Calvo; Dayhoff, Guy W.; Di Ianni, Alessio; Parra, Jhonny Oscar Figueroa; Garcia-Martinez, Dailen; Hesselbarth, Julia; Köppen, Janett; Lauth, Luca M.; Lippik, Laurin; Machner, Lisa; Sachan, Shubhra; Schmidt, Lisa; Selle, Robin; Skalidis, Ioannis; Sorokin, Oleksandr; Ubbiali, Daniele; Voigt, Bruno; Wedler, Alice; Wei, Alan An Jung; Zorn, Peter; Dunker, Alan Keith; Köhn, Marcel; Sinz, Andrea; Uversky, Vladimir N.; Biochemistry and Molecular Biology, School of Medicine
    Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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    Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data
    (Oxford University Press, 2018-11-27) Yan, Jingwen; Risacher, Shannon L.; Shen, Li; Saykin, Andrew J.; BioHealth Informatics, School of Informatics and Computing
    In the past decade, significant progress has been made in complex disease research across multiple omics layers from genome, transcriptome and proteome to metabolome. There is an increasing awareness of the importance of biological interconnections, and much success has been achieved using systems biology approaches. However, because of the typical focus on one single omics layer at a time, existing systems biology findings explain only a modest portion of complex disease. Recent advances in multi-omics data collection and sharing present us new opportunities for studying complex diseases in a more comprehensive fashion, and yet simultaneously create new challenges considering the unprecedented data dimensionality and diversity. Here, our goal is to review extant and emerging network approaches that can be applied across multiple biological layers to facilitate a more comprehensive and integrative multilayered omics analysis of complex diseases.