Top 4 Biorxiv Papers Today in Systems Biology


2.968 Mikeys
#1. Proteome-wide inference of protein kinase regulatory circuits
Brandon M. Invergo, Borgthor Petursson, David Bradley, Girolamo Giudice, Evangelia Petsalaki, Pedro Beltrao
Complex networks of regulatory relationships between protein kinases comprise a major component of intracellular signaling. Although many kinase-kinase regulatory relationships have been described in detail, these are biased towards well-studied kinases while the majority of possible relationships remains unexplored. Here, we implement data-driven, unbiased methods to predict human kinase-kinase regulatory relationships and whether they have activating or inhibiting effects. We incorporate high-throughput data, kinase specificity profiles, and structural information to produce our predictions. The results successfully recapitulate previously annotated regulatory relationships and can reconstruct known signaling pathways from the ground up. The full network of predictions is relatively sparse, with the vast majority of relationships assigned low probabilities. However, it nevertheless suggests denser modes of inter-kinase regulation than normally considered in intracellular signaling research.
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biorxivpreprint: Proteome-wide inference of protein kinase regulatory circuits https://t.co/BMtgjiCDZ7 #bioRxiv
biorxiv_sysbio: Proteome-wide inference of protein kinase regulatory circuits https://t.co/jEA4KurOCn #biorxiv_sysbio
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Authors: 6
Total Words: 0
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2.014 Mikeys
#2. Community standards to facilitate development and address challenges in metabolic modeling
Maureen A Carey, Andreas Draeger, Jason A Papin, James T Yurkovich
Standardization of data and models facilitates effective communication, especially in computational systems biology. However, both the development and consistent use of standards and resources remains challenging. As a result, the amount, quality, and format of the information contained within systems biology models are not consistent and therefore present challenges for widespread use and communication. Here, we focused on these standards, resources, and challenges in the field of metabolic modeling by conducting a community-wide survey. We used this feedback to (1) outline the major challenges that our field faces and to propose solutions and (2) identify a set of features that defines what a "gold standard" metabolic network reconstruction looks like concerning content, annotation, and simulation capabilities. We anticipate that this community-driven outline will help the long-term development of community-inspired resources as well as produce high-quality, accessible models. More broadly, we hope that these efforts can serve...
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tako_poke: A roadmap for standardizing metabolic models. @MaureenACarey and co. gratz for taking on this important challenge! https://t.co/2FZpiSIRH3 #COBRA
papinsysbio: RT @biorxivpreprint: Community standards to facilitate development and address challenges in metabolic modeling https://t.co/8tY0TfIyBE #b…
MaureenACarey: RT @biorxivpreprint: Community standards to facilitate development and address challenges in metabolic modeling https://t.co/8tY0TfIyBE #b…
oveoyas: RT @biorxiv_sysbio: Community standards to facilitate development and address challenges in metabolic modeling https://t.co/mZuA5tiycm #bi…
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supplemental information for our community standards manuscript

Repository: community_standards_supplemental
User: maureencarey
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Sample Sizes : [89, 89, 130, 144]
Authors: 4
Total Words: 4619
Unqiue Words: 1665

2.01 Mikeys
#3. Critical role of rhythmic poly(A) tail regulation in circadian gene expression
Xiangyu Yao, Shihoko Kojima, Jing Chen
The circadian rhythmicity is deeply rooted in rhythmic regulation of gene expression. The core clock pathway that generates circadian oscillation has been well studied, but it remains unclear how this core rhythm controls rhythmic gene expression. Besides that several core clock components are transcriptional factors and mediate genome-wide rhythmic transcriptional control, mounting evidence has demonstrated the importance of rhythmic posttranscriptional controls. A recent study particularly highlighted rhythmic control of poly(A) tail lengths in hundreds of genes in mouse liver and a strong correlation of poly(A) rhythm with protein expression rhythm. In this work we constructed a simplistic model to study the effect of rhythmic poly(A) tail regulation on circadian mRNA expression. The model depicted rhythmic control imposed upon basic mRNA expression processes, including transcription, polyadenylation, deadenylation and degradation. The model results revealed rhythmicity in deadenylation as the strongest contributor to the...
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biorxivpreprint: Critical role of rhythmic poly(A) tail regulation in circadian gene expression https://t.co/OI8ZOWJMY9 #bioRxiv
biorxiv_sysbio: Critical role of rhythmic poly(A) tail regulation in circadian gene expression https://t.co/CKdyFob83T #biorxiv_sysbio
Bacillusdynami1: RT @biorxivpreprint: Critical role of rhythmic poly(A) tail regulation in circadian gene expression https://t.co/OI8ZOWJMY9 #bioRxiv
NZthRzXeiplAQA6: RT @biorxivpreprint: Critical role of rhythmic poly(A) tail regulation in circadian gene expression https://t.co/OI8ZOWJMY9 #bioRxiv
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Authors: 3
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1.997 Mikeys
#4. Viral rebound kinetics following single and combination immunotherapy for HIV/SIV
Melanie Prague, Jeff M Gerold, Irene Balelli, Chloe Pasin, Jonathan Z Li, Dan H Barouch, James B Whitney, Alison Lynn Hill
HIV infection can be treated but not cured with antiretroviral therapy, motivating the devel- opment of new therapies that instead target host immune responses. Three such immunotherapies were recently tested in non-human primates - a TLR7-agonist, therapeutic vaccine, and broadly-neutralizing antibody - and cured a subset of animals by preventing or controlling viral rebound after antiretrovirals were stopped. However, their mechanism of action remains unknown; for example, whether they reduced the pool of latently-infected cells versus boosted antiviral immunity, and whether they acted independently or synergistically. Here we conduct a detailed analysis of the kinetics of viral rebound after immunotherapy, and use mathematical models combined with rigorous statistical fitting to quantify the impact of these interventions on viral dynamics. We find that the vaccine reduced reactivation of latent virus by 4-fold, and boosted the avidity of antiviral immune responses by 17-fold when alone and 210-fold when combined with the...
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SimonettiFR: RT @biorxivpreprint: Viral rebound kinetics following single and combination immunotherapy for HIV/SIV https://t.co/Q9fRG5ge76 #bioRxiv
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Sample Sizes : [8, 13, 9, 8, 9, 8, 11, 11, 11, 11]
Authors: 8
Total Words: 33247
Unqiue Words: 5734

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