abstract：:While decades of research have elucidated many steps of the alphavirus lifecycle, the earliest replication dynamics have remained unclear. This missing time window has obscured early replicase strand-synthesis behavior and prevented elucidation of how the first events of infection might influence subsequent viral comp...

journal_title：Cell systems

authors： Singer ZS,Ambrose PM,Danino T,Rice CM

更新日期：2021-01-21 00:00:00

abstract：:Temporal interference (TI) is a non-invasive neurostimulation technique that utilizes high-frequency external electric fields to stimulate deep neuronal structures without affecting superficial, off-target structures. TI represents a potential breakthrough for treating conditions, such as Parkinson's disease and chron...

journal_title：Cell systems

authors： Mirzakhalili E,Barra B,Capogrosso M,Lempka SF

更新日期：2020-12-16 00:00:00

abstract：:The recent increase of immunopeptidomics data, obtained by mass spectrometry or binding assays, opens up possibilities for investigating endogenous antigen presentation by the highly polymorphic human leukocyte antigen class I (HLA-I) protein. State-of-the-art methods predict with high accuracy presentation by HLA all...

journal_title：Cell systems

authors： Bravi B,Tubiana J,Cocco S,Monasson R,Mora T,Walczak AM

更新日期：2020-12-11 00:00:00

abstract：:All mammals progress through similar physiological stages throughout life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects underlying genomic events is unclear. Here, we map the common methylation changes experienced by mammalian genomes as they age, foc...

journal_title：Cell systems

authors： Wang T,Ma J,Hogan AN,Fong S,Licon K,Tsui B,Kreisberg JF,Adams PD,Carvunis AR,Bannasch DL,Ostrander EA,Ideker T

更新日期：2020-08-26 00:00:00

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. ...

journal_title：Cell systems

authors： Laurencin CT,Walker JM

更新日期：2020-07-22 00:00:00

abstract：:Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA and identify the key parameters that govern the overall rate of protein synthesis,...

journal_title：Cell systems

authors： Erdmann-Pham DD,Dao Duc K,Song YS

更新日期：2020-02-26 00:00:00

abstract：:Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes that affects their activity and/or function a...

journal_title：Cell systems

authors： Heusel M,Frank M,Köhler M,Amon S,Frommelt F,Rosenberger G,Bludau I,Aulakh S,Linder MI,Liu Y,Collins BC,Gstaiger M,Kutay U,Aebersold R

更新日期：2020-02-26 00:00:00

abstract：:One snapshot of the peer review process for "Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast" (Kuroda et al., 2019). ...

journal_title：Cell systems

authors： Hittinger CT

更新日期：2020-02-26 00:00:00

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...

journal_title：Cell systems

authors： Medlock GL,Papin JA

更新日期：2020-01-22 00:00:00

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...

journal_title：Cell systems

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

更新日期：2020-01-22 00:00:00

abstract：:The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a comput...

journal_title：Cell systems

authors： Mohammadi S,Davila-Velderrain J,Kellis M

更新日期：2019-12-18 00:00:00

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

authors： Lukačišin M,Bollenbach T

更新日期：2019-11-27 00:00:00

abstract：:Despite improved methods for MHC affinity prediction, the vast majority of computationally predicted tumor neoantigens are not immunogenic experimentally, indicating that high-quality neoantigens are beyond current algorithms to discern. To enrich for neoantigens with the greatest likelihood of immunogenicity, we deve...

journal_title：Cell systems

authors： Richman LP,Vonderheide RH,Rech AJ

更新日期：2019-10-23 00:00:00

abstract：:Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by...

journal_title：Cell systems

authors： Tan Y,Cahan P

更新日期：2019-08-28 00:00:00

abstract：:One snapshot of the peer review process for "Death Rate of E. coli during Starvation Is Set by Maintenance Cost and Biomass Recycling" (Schink et al., 2019). ...

journal_title：Cell systems

authors： Laman Trip DS,Maire T,Youk H

更新日期：2019-07-24 00:00:00

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

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

更新日期：2019-07-24 00:00:00

abstract：:Large-scale single-cell RNA sequencing (scRNA-seq) studies that profile hundreds of thousands of cells are becoming increasingly common, overwhelming existing analysis pipelines. Here, we describe how to enhance and accelerate single-cell data analysis by summarizing the transcriptomic heterogeneity within a dataset u...

journal_title：Cell systems

authors： Hie B,Cho H,DeMeo B,Bryson B,Berger B

更新日期：2019-06-26 00:00:00

abstract：:Longitudinal DNA sequencing of cancer patients yields insight into how tumors evolve over time or in response to treatment. However, sequencing data from bulk tumor samples often have considerable ambiguity in clonal composition, complicating the inference of ancestral relationships between clones. We introduce Cancer...

journal_title：Cell systems

authors： Myers MA,Satas G,Raphael BJ

更新日期：2019-06-26 00:00:00

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...

journal_title：Cell systems

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

abstract：:Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occa...

journal_title：Cell systems

authors： Rozowsky J,Kitchen RR,Park JJ,Galeev TR,Diao J,Warrell J,Thistlethwaite W,Subramanian SL,Milosavljevic A,Gerstein M

更新日期：2019-04-24 00:00:00

abstract：:Gram-negative bacteria are intrinsically resistant to drugs because of their double-membrane envelope structure that acts as a permeability barrier and as an anchor for efflux pumps. Antibiotics are blocked and expelled from cells and cannot reach high-enough intracellular concentrations to exert a therapeutic effect....

journal_title：Cell systems

authors： Masuda I,Matsubara R,Christian T,Rojas ER,Yadavalli SS,Zhang L,Goulian M,Foster LJ,Huang KC,Hou YM

更新日期：2019-04-24 00:00:00

abstract：:Although genetic mutations that alter organisms' average lifespans have been identified in aging research, our understanding of the dynamic changes during aging remains limited. Here, we integrate single-cell imaging, microfluidics, and computational modeling to investigate phenotypic divergence and cellular heterogen...

journal_title：Cell systems

authors： Jin M,Li Y,O'Laughlin R,Bittihn P,Pillus L,Tsimring LS,Hasty J,Hao N

更新日期：2019-03-27 00:00:00

abstract：:DNA shape adds specificity to sequence motifs but has not been explored systematically outside this context. We hypothesized that DNA-binding proteins (DBPs) preferentially occupy DNA with specific structures ("shape motifs") regardless of whether or not these correspond to high information content sequence motifs. We...

journal_title：Cell systems

authors： Samee MAH,Bruneau BG,Pollard KS

更新日期：2019-01-23 00:00:00

abstract：:Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with s...

journal_title：Cell systems

authors： Parekh U,Wu Y,Zhao D,Worlikar A,Shah N,Zhang K,Mali P

更新日期：2018-11-28 00:00:00

abstract：:One snapshot of the peer review process for "Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability" (Hansen et al., 2018). ...

journal_title：Cell systems

authors： Olsman N,Xiao F,Doyle J

更新日期：2018-10-24 00:00:00

abstract：:Cell-to-cell transcriptional variability in otherwise homogeneous cell populations plays an important role in tissue function and development. Single-cell RNA sequencing can characterize this variability in a transcriptome-wide manner. However, technical variation and the confounding between variability and mean expre...

journal_title：Cell systems

authors： Eling N,Richard AC,Richardson S,Marioni JC,Vallejos CA

更新日期：2018-09-26 00:00:00

abstract：:This month: selected work from the 2018 RECOMB meeting, organized by Ecole Polytechnique and held last April in Paris. ...

journal_title：Cell systems

authors： Cho H,Berger B,Peng J,Galitzine C,Vitek O,Beltran PMJ,Cristea IM,Görtler F,Solbrig S,Wettig T,Oefner PJ,Spang R,Altenbuchinger M,Basso RS,Hochbaum D,Vandin F,Silverbush D,Cristea S,Yanovich G,Geiger T,Beerenwinkel

更新日期：2018-08-22 00:00:00

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

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

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

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

更新日期：2018-07-25 00:00:00

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

authors： Santra M,Dill KA,de Graff AMR

更新日期：2018-06-27 00:00:00

abstract：:Alterations of circadian clock genes are associated with patient survival, tumor stage, and clinical subtype across various cancer types, highlighting the importance of timing in cancer treatment. ...

journal_title：Cell systems

authors： El-Athman R,Relógio A

更新日期：2018-03-28 00:00:00

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

authors：

更新日期：2018-02-28 00:00:00

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

authors： Kamimoto K,Morris SA

更新日期：2018-01-24 00:00:00

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

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,

更新日期：2018-01-24 00:00:00

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

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

更新日期：2017-12-27 00:00:00

abstract：:Isogenic cells in a common environment show substantial cell-to-cell variation in gene expression, often referred to as "expression noise." Here, we use multiple single-cell RNA-sequencing datasets to identify features associated with high or low expression noise in mouse embryonic stem cells. These include the core p...

journal_title：Cell systems

authors： Faure AJ,Schmiedel JM,Lehner B

更新日期：2017-11-22 00:00:00

abstract：:Although molecular mechanisms that prompt cell-cycle arrest in response to DNA damage have been elucidated, the systems-level properties of DNA damage checkpoints are not understood. Here, using time-lapse microscopy and simulations that model the cell cycle as a series of Poisson processes, we characterize DNA damage...

journal_title：Cell systems

authors： Chao HX,Poovey CE,Privette AA,Grant GD,Chao HY,Cook JG,Purvis JE

更新日期：2017-11-22 00:00:00

abstract：:Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally observed correlations between mother-daughter generation times that...

journal_title：Cell systems

authors： Lin J,Amir A

更新日期：2017-10-25 00:00:00

abstract：:Escherichia coli gene expression knockdown using synthetic small RNA (sRNA) can be fine-tuned by altering sRNA sequences to modulate target mRNA-binding ability, but this requires thorough checking for off-target effects. Here, we present an sRNA gene expression knockdown system fine-tuned by using different promoters...

journal_title：Cell systems

authors： Noh M,Yoo SM,Kim WJ,Lee SY

更新日期：2017-10-25 00:00:00

abstract：:The tumor-suppressing transcription factor p53 is highly conserved at the protein level and plays a key role in the DNA damage response. One important aspect of p53 regulation is its dynamics in response to DNA damage, which include oscillations. Here, we observe that, while the qualitative oscillatory nature of p53 d...

journal_title：Cell systems

authors： Stewart-Ornstein J,Cheng HWJ,Lahav G

更新日期：2017-10-25 00:00:00