Principles of Systems Biology, No. 18.

Abstract:

:This month: imaging the organelle interactome (Lippincott-Schwartz), big data immunology (Pulendran, Ginhoux), protein interactomes expand (Barna, Harper, Marcotte), and computation/engineering insights (Milinkovitch, Silver, and Sastry).

journal_name

Cell Syst

journal_title

Cell systems

authors

doi

10.1016/j.cels.2017.06.010

subject

Has Abstract

pub_date

2017-06-28 00:00:00

pages

576-578

issue

6

eissn

2405-4712

issn

2405-4720

pii

S2405-4712(17)30238-7

journal_volume

4

pub_type

杂志文章
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    abstract::It is known that the calcium-dependent transcription factor NFAT initiates transcription in response to pulsatile loads of calcium signal. However, the relative contributions of calcium oscillation frequency, amplitude, and duty cycle to transcriptional activity remain unclear. Here, we engineer HeLa cells to permit o...

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  • Genotype-Fitness Maps of EGFR-Mutant Lung Adenocarcinoma Chart the Evolutionary Landscape of Resistance for Combination Therapy Optimization.

    abstract::Cancer evolution poses a central obstacle to cure, as resistant clones expand under therapeutic selection pressures. Genome sequencing of relapsed disease can nominate genomic alterations conferring resistance but sample collection lags behind, limiting therapeutic innovation. Genome-wide screens offer a complementary...

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    doi:10.1016/j.cels.2019.10.002

    authors: Bolan PO,Zviran A,Brenan L,Schiffman JS,Dusaj N,Goodale A,Piccioni F,Johannessen CM,Landau DA

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  • The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

    abstract::The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data,...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2017.11.001

    authors: Keenan AB,Jenkins SL,Jagodnik KM,Koplev S,He E,Torre D,Wang Z,Dohlman AB,Silverstein MC,Lachmann A,Kuleshov MV,Ma'ayan A,Stathias V,Terryn R,Cooper D,Forlin M,Koleti A,Vidovic D,Chung C,Schürer SC,Vasiliauskas J,

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  • Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.

    abstract::Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth migh...

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    authors: Durand NC,Robinson JT,Shamim MS,Machol I,Mesirov JP,Lander ES,Aiden EL

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  • Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity.

    abstract::Recent advances in synthetic biology and biological system engineering have allowed the design and construction of engineered live biotherapeutics targeting a range of human clinical applications. In this review, we outline how systems approaches have been used to move from simple constitutive systems, where a single ...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2018.06.008

    authors: Ozdemir T,Fedorec AJH,Danino T,Barnes CP

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  • Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling.

    abstract::Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2018.06.002

    authors: Rukhlenko OS,Khorsand F,Krstic A,Rozanc J,Alexopoulos LG,Rauch N,Erickson KE,Hlavacek WS,Posner RG,Gómez-Coca S,Rosta E,Fitzgibbon C,Matallanas D,Rauch J,Kolch W,Kholodenko BN

    更新日期:2018-08-22 00:00:00

  • How Can Systems Biology Test Principles and Tools Using Immune Cells as a Model?

    abstract::The field of systems immunology has grown extensively over the last few years, spurred by the generation of large datasets, new analytical tools, and modeling approaches. In this piece and its counterpart in Trends in Immunology [http://www.cell.com/trends/immunology/fulltext/S1471-4906(18)30013-9], eight authors disc...

    journal_title:Cell systems

    pub_type: 社论,面试

    doi:10.1016/j.cels.2018.02.005

    authors:

    更新日期:2018-02-28 00:00:00

  • Proteomics Moves into the Fast Lane.

    abstract::Three studies demonstrate the potential of state-of-the-art mass spectrometry-based proteomics for rapid, deep characterization of proteomes. ...

    journal_title:Cell systems

    pub_type: 评论,杂志文章

    doi:10.1016/j.cels.2016.03.002

    authors: Riley NM,Hebert AS,Coon JJ

    更新日期:2016-03-23 00:00:00

  • Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.

    abstract::Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.10.004

    authors: Lukačišin M,Bollenbach T

    更新日期:2019-11-27 00:00:00

  • Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning.

    abstract::Mechanistic models explicitly represent hypothesized biological knowledge. As such, they offer more generalizability than data-driven models. However, identifying model curation efforts that improve performance for mechanistic models is nontrivial. Here, we develop a solution to this problem for genome-scale metabolic...

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    doi:10.1016/j.cels.2019.11.006

    authors: Medlock GL,Papin JA

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  • The Hidden Memory of Differentiating Cells.

    abstract::An integrated approach unifies experimental observations and mathematical modeling to represent differentiation dynamics as discrete transition events underpinned by stochastic transitions between hidden states. ...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2017.09.009

    authors: Moris N,Arias AM

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  • How Do Chaperones Protect a Cell's Proteins from Oxidative Damage?

    abstract::The accumulation of protein damage in aging organisms is thought to contribute to many aging-related diseases. Yet the properties determining which proteins are most susceptible remain poorly understood. Are certain conformations more vulnerable? Which chaperones are the main guardians? We address these questions with...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2018.05.001

    authors: Santra M,Dill KA,de Graff AMR

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  • Omics Meets Metabolic Pathway Engineering.

    abstract::A principled approach to integrating metabolomics, proteomics, and genome-scale metabolic modeling facilitaties rational pathway engineering of E. coli. ...

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    doi:10.1016/j.cels.2016.05.005

    authors: Chen GQ

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  • Protein Networks in Alzheimer's Disease.

    abstract::Overlap of RNA and protein networks reveals glia cells as key players for the development of symptomatic Alzheimer's disease in humans. ...

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    doi:10.1016/j.cels.2017.02.006

    authors: Carlsen EM,Rasmussen R

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  • Master regulators of infiltrate recruitment in autoimmune disease identified through network-based molecular deconvolution.

    abstract::Network-based molecular modeling of physiological behaviors has proven invaluable in the study of complex diseases such as cancer, but these approaches remain largely untested in contexts involving interacting tissues such as autoimmunity. Here, using Alopecia Areata (AA) as a model, we have adapted regulatory network...

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    authors: Chen JC,Cerise JE,Jabbari A,Clynes R,Christiano AM

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  • Orientation of Turing-like Patterns by Morphogen Gradients and Tissue Anisotropies.

    abstract::Patterning of periodic stripes during development requires mechanisms to control both stripe spacing and orientation. A number of models can explain how stripe spacing is controlled, including molecular mechanisms, such as Turing's reaction-diffusion model, as well as cell-based and mechanical mechanisms. However, how...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2015.12.001

    authors: Hiscock TW,Megason SG

    更新日期:2015-12-23 00:00:00

  • Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network.

    abstract::Cell-to-cell variation in gene expression and the propagation of such variation (PoV or "noise propagation") from one gene to another in the gene network, as reflected by gene-gene correlation across single cells, are commonly observed in single-cell transcriptomic studies and can shape the phenotypic diversity of cel...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.03.002

    authors: Martins AJ,Narayanan M,Prüstel T,Fixsen B,Park K,Gottschalk RA,Lu Y,Andrews-Pfannkoch C,Lau WW,Wendelsdorf KV,Tsang JS

    更新日期:2017-04-26 00:00:00

  • Entraining Oscillations in the NF-κB Signaling System: With a Little Help from Noise.

    abstract::Two studies show that noise is a key ingredient of new mechanisms for entraining the NF-κB system. ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2016.12.008

    authors: Lefranc M

    更新日期:2016-12-21 00:00:00

  • Breaking New Ground in the Landscape of Single-Cell Analysis.

    abstract::Here, we outline p-Creode, a new algorithm to construct multi-branching cell lineage trajectories from single-cell data. Application of this platform to diverse sources of single-cell data demonstrates its robustness and scalability, while the discovery of a new origin for rare gut tuft cells showcases the utility of ...

    journal_title:Cell systems

    pub_type: 评论,杂志文章

    doi:10.1016/j.cels.2017.12.015

    authors: Kamimoto K,Morris SA

    更新日期:2018-01-24 00:00:00

  • Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy.

    abstract::Cell classifiers are genetic logic circuits that transduce endogenous molecular inputs into cell-type-specific responses. Designing classifiers that achieve optimal differential response between specific cell types is a hard computational problem because it involves selection of endogenous inputs and optimization of b...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.01.003

    authors: Mohammadi P,Beerenwinkel N,Benenson Y

    更新日期:2017-02-22 00:00:00

  • Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

    abstract::Accurately translating genotype to phenotype requires accounting for the functional impact of genetic variation at many biological scales. Here we present a strategy for genotype-phenotype reasoning based on existing knowledge of cellular subsystems. These subsystems and their hierarchical organization are defined by ...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2016.02.003

    authors: Yu MK,Kramer M,Dutkowski J,Srivas R,Licon K,Kreisberg J,Ng CT,Krogan N,Sharan R,Ideker T

    更新日期:2016-02-24 00:00:00

  • Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.

    abstract::Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disp...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.03.010

    authors: Lane K,Van Valen D,DeFelice MM,Macklin DN,Kudo T,Jaimovich A,Carr A,Meyer T,Pe'er D,Boutet SC,Covert MW

    更新日期:2017-04-26 00:00:00

  • Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics.

    abstract::Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multi...

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    doi:10.1016/j.cels.2017.05.001

    authors: Liu TY,Huang HH,Wheeler D,Xu Y,Wells JA,Song YS,Wiita AP

    更新日期:2017-06-28 00:00:00

  • All for One, and One for All.

    abstract::Hemizygous deletion of a gene in tumor cells frequently causes reduced expression of its encoded mRNA and protein, as well as reduced protein-but not mRNA-expression of other members in the same protein complex. ...

    journal_title:Cell systems

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    doi:10.1016/j.cels.2017.10.005

    authors: Kim E,Hart T

    更新日期:2017-10-25 00:00:00

  • A Pandemic on a Pandemic: Racism and COVID-19 in Blacks.

    abstract::Racism and COVID-19 represent a pandemic on a pandemic for Blacks. The pandemics find themselves synergized to the detriment of Blacks and their health. The complexity of the combination of these pandemics are evident when examining the interplay between racist policing practices and health. ...

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    doi:10.1016/j.cels.2020.07.002

    authors: Laurencin CT,Walker JM

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  • Reduced Repertoire of Cortical Microstates and Neuronal Ensembles in Medically Induced Loss of Consciousness.

    abstract::Medically induced loss of consciousness (mLOC) during anesthesia is associated with a macroscale breakdown of brain connectivity, yet the neural microcircuit correlates of mLOC remain unknown. To explore this, we applied different analytical approaches (t-SNE/watershed segmentation, affinity propagation clustering, PC...

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    doi:10.1016/j.cels.2019.03.007

    authors: Wenzel M,Han S,Smith EH,Hoel E,Greger B,House PA,Yuste R

    更新日期:2019-05-22 00:00:00

  • Entropy-scaling search of massive biological data.

    abstract::Many data sets exhibit well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here we introduce a framework for similarity search based on characterizing a data set's entropy and fractal dimension. We prove that searching scales in tim...

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    doi:10.1016/j.cels.2015.08.004

    authors: Yu YW,Daniels NM,Danko DC,Berger B

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  • Synthetic 5' UTRs Can Either Up- or Downregulate Expression upon RNA-Binding Protein Binding.

    abstract::The construction of complex gene-regulatory networks requires both inhibitory and upregulatory modules. However, the vast majority of RNA-based regulatory "parts" are inhibitory. Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.04.007

    authors: Katz N,Cohen R,Solomon O,Kaufmann B,Atar O,Yakhini Z,Goldberg S,Amit R

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  • Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.

    abstract::Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.10.014

    authors: Yu KH,Berry GJ,Rubin DL,Ré C,Altman RB,Snyder M

    更新日期:2017-12-27 00:00:00

  • Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate.

    abstract::Systematic assessment of tyrosine kinase-substrate relationships is fundamental to a better understanding of cellular signaling and its profound alterations in human diseases such as cancer. In human cells, such assessments are confounded by complex signaling networks, feedback loops, conditional activity, and intra-k...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.08.001

    authors: Corwin T,Woodsmith J,Apelt F,Fontaine JF,Meierhofer D,Helmuth J,Grossmann A,Andrade-Navarro MA,Ballif BA,Stelzl U

    更新日期:2017-08-23 00:00:00