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你正在浏览Cell Systems期刊下所有文献
  • 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

    pub_type： 评论,杂志文章

    doi：10.1016/j.cels.2017.10.005

    authors： Kim E,Hart T

    更新日期：2017-10-25 00:00:00

  • 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

    pub_type： 评论,杂志文章

    doi：10.1016/j.cels.2017.09.009

    authors： Moris N,Arias AM

    更新日期：2017-09-27 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

  • Incoherent Inputs Enhance the Robustness of Biological Oscillators.

    abstract：:Robust biological oscillators retain the critical ability to function in the presence of environmental perturbations. Although central architectures that support robust oscillations have been extensively studied, networks containing the same core vary drastically in their potential to oscillate, and it remains elusive...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2017.06.013

    authors： Li Z,Liu S,Yang Q

    更新日期：2017-07-26 00:00:00

  • Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

    abstract：:Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-paramet...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2017.06.003

    authors： Tan J,Doing G,Lewis KA,Price CE,Chen KM,Cady KC,Perchuk B,Laub MT,Hogan DA,Greene CS

    更新日期：2017-07-26 00:00:00

  • Stochastic Modeling Yields a Mechanistic Framework for Spindle Attachment Error Correction in Budding Yeast Mitosis.

    abstract：:Proper segregation of the replicated genome requires that kinetochores form and maintain bioriented, amphitelic attachments to microtubules from opposite spindle poles and eliminate erroneous, syntelic attachments to microtubules from the same spindle pole. Phosphorylation of kinetochore proteins destabilizes low-tens...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2017.05.003

    authors： Tubman ES,Biggins S,Odde DJ

    更新日期：2017-06-28 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...

    journal_title：Cell systems

    pub_type： 杂志文章

    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

  • 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_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2017.06.010

    authors：

    更新日期：2017-06-28 00:00:00

  • Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development.

    abstract：:Recent mass spectrometry maps of the human interactome independently support the existence of a large multiprotein complex, dubbed "Commander." Broadly conserved across animals and ubiquitously expressed in nearly every human cell type examined thus far, Commander likely plays a fundamental cellular function, akin to ...

    journal_title：Cell systems

    pub_type： 杂志文章,评审

    doi：10.1016/j.cels.2017.04.006

    authors： Mallam AL,Marcotte EM

    更新日期：2017-05-24 00:00:00

  • PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.

    abstract：:A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share meth...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2017.04.007

    authors： Li B,Tambe A,Aviran S,Pachter L

    更新日期：2017-05-24 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

  • 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

  • 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. ...

    journal_title：Cell systems

    pub_type： 评论,杂志文章

    doi：10.1016/j.cels.2017.02.006

    authors： Carlsen EM,Rasmussen R

    更新日期：2017-02-22 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

  • Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer.

    abstract：:It is unclear how standing genetic variation affects the prognosis of prostate cancer patients. To provide one controlled answer to this problem, we crossed a dominant, penetrant mouse model of prostate cancer to Diversity Outbred mice, a collection of animals that carries over 40 million SNPs. Integration of disease ...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2016.10.018

    authors： Winter JM,Gildea DE,Andreas JP,Gatti DM,Williams KA,Lee M,Hu Y,Zhang S,NISC Comparative Sequencing Program.,Mullikin JC,Wolfsberg TG,McDonnell SK,Fogarty ZC,Larson MC,French AJ,Schaid DJ,Thibodeau SN,Churchill GA,Craw

    更新日期：2017-01-25 00:00:00

  • Metabolism-Centric Trans-Omics.

    abstract：:Two recent studies in Cell and Science demonstrate the reconstruction of global mechanistic networks and identification of regulatory principles from multi-omics data. ...

    journal_title：Cell systems

    pub_type： 评论,杂志文章

    doi：10.1016/j.cels.2017.01.007

    authors： Yugi K,Kuroda S

    更新日期：2017-01-25 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

  • A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

    abstract：:Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2016.10.020

    authors： Hefzi H,Ang KS,Hanscho M,Bordbar A,Ruckerbauer D,Lakshmanan M,Orellana CA,Baycin-Hizal D,Huang Y,Ley D,Martinez VS,Kyriakopoulos S,Jiménez NE,Zielinski DC,Quek LE,Wulff T,Arnsdorf J,Li S,Lee JS,Paglia G,Loira N,

    更新日期：2016-11-23 00:00:00

  • Principles of Systems Biology, No. 8.

    abstract：:Advances in biological engineering headline this month's Cell Systems call (Cell Systems 1, 307), alongside intriguing applications of modeling from the Elf, Goentoro, and Wolf groups. Check out our recent blogpost: http://crosstalk.cell.com/blog/a-call-for-papers-on-biological-engineering-and-synthetic-biology. ...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2016.08.006

    authors：

    更新日期：2016-08-01 00:00:00

  • 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...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.07.012

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

    更新日期：2016-07-01 00:00:00

  • 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. ...

    journal_title：Cell systems

    pub_type： 评论,杂志文章

    doi：10.1016/j.cels.2016.05.005

    authors： Chen GQ

    更新日期：2016-06-22 00:00:00

  • Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

    abstract：:Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2016.04.004

    authors： Brunk E,George KW,Alonso-Gutierrez J,Thompson M,Baidoo E,Wang G,Petzold CJ,McCloskey D,Monk J,Yang L,O'Brien EJ,Batth TS,Martin HG,Feist A,Adams PD,Keasling JD,Palsson BO,Lee TS

    更新日期：2016-05-25 00:00:00

  • Optogenetic Control of Calcium Oscillation Waveform Defines NFAT as an Integrator of Calcium Load.

    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...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2016.03.010

    authors： Hannanta-Anan P,Chow BY

    更新日期：2016-04-27 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

  • 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

    pub_type： 杂志文章

    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

  • Hunting for Cis-Regulatory Elements in Proteins.

    abstract：:A new bioinformatics tool predicts natively disordered protein control elements that function in cis, opening the door to more systematic studies of this biomedically important class of protein modules. ...

    journal_title：Cell systems

    pub_type： 评论,杂志文章

    doi：10.1016/j.cels.2016.02.011

    authors： Gibson TJ,Kumar M

    更新日期：2016-02-24 00:00:00

  • 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

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.12.001

    authors： Hiscock TW,Megason SG

    更新日期：2015-12-23 00:00:00

  • Shedding Light on Synergistic Chemical Genetic Connections with Machine Learning.

    abstract：:Machine learning can be used to predict compounds acting synergistically, and this could greatly expand the universe of available potential treatments for diseases that are currently hidden in the dark chemical matter. ...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.12.005

    authors： Ekins S,Siqueira-Neto JL

    更新日期：2015-12-23 00:00:00

  • 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...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.11.001

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

    更新日期：2015-11-25 00:00:00

  • Studying Autism in Context.

    abstract：:Studying autism genes in the context of the protein complexes to which they belong illustrates the potential of network-centric approaches for understanding complex genetic disease. ...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.11.004

    authors： Das J,Meyer MJ,Yu H

    更新日期：2015-11-25 00:00:00

  • Computational Recipes in Enzymology.

    abstract：:How do rich biological behaviors arise from bi-molecular collisions? ...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.09.006

    authors： Rust MJ

    更新日期：2015-09-23 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...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.08.004

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

    更新日期：2015-08-26 00:00:00

  • Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells.

    abstract：:We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression of Oct4, a key regulato...

    journal_title：Cell systems

    pub_type： 杂志文章

    doi：10.1016/j.cels.2015.08.002

    authors： Ding L,Paszkowski-Rogacz M,Winzi M,Chakraborty D,Theis M,Singh S,Ciotta G,Poser I,Roguev A,Chu WK,Choudhary C,Mann M,Stewart AF,Krogan N,Buchholz F

    更新日期：2015-08-26 00:00:00

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