Lindsey, Merry L Mayr, Manuel Gomes, Aldrin V Delles, Christian Arrell, D Kent Murphy, Anne M Lange, Richard A Costello, Catherine E Jin, Yu-Fang Laskowitz, Daniel T
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Published in
Circulation
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the c...
Lee, Soojin
Published in
Journal of pharmacopuncture
Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.
Fages, François Gay, Steven Soliman, Sylvain
In Mathematical Biology, many dynamical models of biochemical reaction systems are presented with Ordinary Differential Equations (ODE). Once kinetic parameter values are fixed, this simple mathematical formalism completely defines the dynamical behavior of a system of biochemical reactions and provides powerful tools for deterministic simulations,...
Costa, Rui Ponte Froemke, Robert C Sjöström, P Jesper van Rossum, Mark Cw
Published in
eLife
Although it is well known that long-term synaptic plasticity can be expressed both pre- and postsynaptically, the functional consequences of this arrangement have remained elusive. We show that spike-timing-dependent plasticity with both pre- and postsynaptic expression develops receptive fields with reduced variability and improved discriminabilit...
Mavor, David Roscoe, Benjamin P. Bolon, Daniel N. Fraser, James S.
Ubiquitination is an essential post-translational regulatory process that can control protein stability, localization, and activity. Ubiquitin is essential for eukaryotic life and is highly conserved, varying in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies in S. cerevisiae indicate that ubiquitin is ...
Tanenbaum, Marvin E Stern-Ginossar, Noam Weissman, Jonathan S Vale, Ronald D
Passage through mitosis is driven by precisely-timed changes in transcriptional regulation and protein degradation. However, the importance of translational regulation during mitosis remains poorly understood. Here, using ribosome profiling, we find both a global translational repression and identified ~200 mRNAs that undergo specific translational...
Korkut, Anil Wang, Weiqing Demir, Emek Aksoy, Bülent Arman Jing, Xiaohong Molinelli, Evan J Babur, Özgün Bemis, Debra L Onur Sumer, Selcuk Solit, David B
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Published in
eLife
Resistance to targeted cancer therapies is an important clinical problem. The discovery of anti-resistance drug combinations is challenging as resistance can arise by diverse escape mechanisms. To address this challenge, we improved and applied the experimental-computational perturbation biology method. Using statistical inference, we build network...
Kang, Jonghoon Park, Seyeon Venkat, Aarya Gopinath, Adarsh
New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. I...
Sasse, Sarah K Zuo, Zheng Kadiyala, Vineela Zhang, Liyang Pufall, Miles A Jain, Mukesh K Phang, Tzu L Stormo, Gary D Gerber, Anthony N
Published in
The Journal of biological chemistry
Combinatorial gene regulation through feed-forward loops (FFLs) can bestow specificity and temporal control to client gene expression; however, characteristics of binding sites that mediate these effects are not established. We previously showed that the glucocorticoid receptor (GR) and KLF15 form coherent FFLs that cooperatively induce targets suc...
Krumholz, Elias W Libourel, Igor G L
Published in
The Journal of biological chemistry
Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices in...
