BioNumbers

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More detailed information about this field from each metasource.

BioNumbers
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:20.192607

bionumbers
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:20.192607

Other names: bionumbers

Useful biological numbers

Webpage:

http://www.bionumbers.hms.harvard.edu

Publications:

Publications
More detailed information about this field from each metasource.

BioNumbers--the database of key numbers in molecular and cell biology
PMID: 19854939
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:20.192607

http://nar.oxfordjournals.org/content/38/suppl_1/D750
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

BioNumbers--the database of key numbers in molecular and cell biology PubMed citations: 334.

334 articles citing: BioNumbers--the database of key numbers in molecular and cell biology

Mitochondria transplantation between living cells. PMID:35320264
Self-assembled nanoparticle-enzyme aggregates enhance functional protein production in pure transcription-translation systems. PMID:35298538
Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. PMID:35269555
Kinetic model of GPCR-G protein interactions reveals allokairic modulation of signaling. PMID:35260563
Optimizing the Substrate Uptake Rate of Solute Carriers. PMID:35185619
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. PMID:35104290
Actomyosin-Assisted Pulling of Lipid Nanotubes from Lipid Vesicles and Cells. PMID:35089720
Counting protein molecules for single-cell proteomics. PMID:35063071
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws. PMID:34983366
Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin. PMID:34963660
DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. PMID:34951454
Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. PMID:34922010
A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. PMID:34858137
Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources. PMID:34833085
Application of Metabolomics in the Study of Starvation-Induced Autophagy in Saccharomyces cerevisiae: A Scoping Review. PMID:34829274
A primer on harnessing non-enzymatic post-translational modifications for drug design. PMID:34825181
An Agent-Based Model of Combination Oncolytic Viral Therapy and Anti-PD-1 Immunotherapy Reveals the Importance of Spatial Location When Treating Glioblastoma. PMID:34771476
RBS and Promoter Strengths Determine the Cell-Growth-Dependent Protein Mass Fractions and Their Optimal Synthesis Rates. PMID:34767708
Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates. PMID:34759911
Using continuous directed evolution to improve enzymes for plant applications. PMID:34718794
Multiplexed single-cell proteomics using SCoPE2. PMID:34716448
Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. PMID:34580310
Molecular competition can shape enhancer activity in the Drosophila embryo. PMID:34568782
Exploring the influence of cytosolic and membrane FAK activation on YAP/TAZ nuclear translocation. PMID:34509508
Data-driven network models for genetic circuits from time-series data with incomplete measurements. PMID:34493091
A topological look into the evolution of developmental programs. PMID:34480926
Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli. PMID:34389727
Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution. PMID:34385369
Evolution of diversity in metabolic strategies. PMID:34350825
Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies. PMID:34337948
A quantitative systems pharmacology modeling platform for evaluating triglyceride profiles in patients with high triglycerides receiving evinacumab. PMID:34327869
Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations. PMID:34297714
Multiple functions of flagellar motility and chemotaxis in bacterial physiology. PMID:34227665
Targeting Immunometabolism in Glioblastoma. PMID:34222022
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. PMID:34214468
Nanoscape, a data-driven 3D real-time interactive virtual cell environment. PMID:34191720
Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction. PMID:34150750
Scaling relation between genome length and particle size of viruses provides insights into viral life history. PMID:34113814
The folate antagonist methotrexate diminishes replication of the coronavirus SARS-CoV-2 and enhances the antiviral efficacy of remdesivir in cell culture models. PMID:34090962
PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling. PMID:34066057
A comprehensive survey of developmental programs reveals a dearth of tree-like lineage graphs and ubiquitous regeneration. PMID:34020630
The oncological relevance of fragile sites in cancer. PMID:33980983
Tracking adoptive T cell immunotherapy using magnetic particle imaging. PMID:33972919
Parental genome unification is highly error-prone in mammalian embryos. PMID:33964210
Resource Uptake and the Evolution of Moderately Efficient Enzymes. PMID:33964160
Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. PMID:33950392
Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model. PMID:33912585
Elevated expression of the adhesion GPCR ADGRL4/ELTD1 promotes endothelial sprouting angiogenesis without activating canonical GPCR signalling. PMID:33893326
Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures. PMID:33847263
Revising Berg-Purcell for finite receptor kinetics. PMID:33794148
Bacterial cyclic diguanylate signaling networks sense temperature. PMID:33790266
Succinate Mediates Tumorigenic Effects via Succinate Receptor 1: Potential for New Targeted Treatment Strategies in Succinate Dehydrogenase Deficient Paragangliomas. PMID:33776908
RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes. PMID:33771877
Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback. PMID:33740397
Automated methods for cell type annotation on scRNA-seq data. PMID:33613863
Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface. PMID:33595282
A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors. PMID:33566821
Potential Effects of Nonadherent on Adherent Human Umbilical Venous Endothelial Cells in Cell Culture. PMID:33540846
Toward long-lasting artificial cells that better mimic natural living cells. PMID:33523164
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. PMID:33504367
Diffusion of kinesin motors on cargo can enhance binding and run lengths during intracellular transport. PMID:33439674
Spatial correlations constrain cellular lifespan and pattern formation in corneal epithelium homeostasis. PMID:33433326
Identification of a Potential Membrane-Targeting Sequence in the C-Terminus of the F Plasmid Segregation Protein SopA. PMID:33427942
Signaling Microdomains in the Spotlight: Visualizing Compartmentalized Signaling Using Genetically Encoded Fluorescent Biosensors. PMID:33411579
Using Models to (Re-)Design Synthetic Circuits. PMID:33405217
Hybrid E/M Phenotype(s) and Stemness: A Mechanistic Connection Embedded in Network Topology. PMID:33375334
Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling. PMID:33352054
Selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells. PMID:33349694
Dynamics of TRF1 organizing a single human telomere. PMID:33347580
Rampant False Detection of Adaptive Phenotypic Optimization by ParTI-Based Pareto Front Inference. PMID:33346805
Micro- and Nano-Devices for Studying Subcellular Biology. PMID:33345457
Effective Biophysical Modeling of Cell Free Transcription and Translation Processes. PMID:33324619
Fundamental Cell Morphologies Examined With Cryo-TEM of the Species in the Novel Five Genera Robustly Correlate With New Classification in Family Mycobacteriaceae. PMID:33304323
A Multi-Scale Approach to Modeling E. coli Chemotaxis. PMID:33286869
Binary Expression Enhances Reliability of Messaging in Gene Networks. PMID:33286254
RNA, Genome Output and Input. PMID:33193726
Characterization of the Bacteriophage vB_VorS-PVo5 Infection on Vibrio ordalii: A Model for Phage-Bacteria Adsorption in Aquatic Environments. PMID:33193133
High photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy. PMID:33191951
Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR. PMID:33179918
Bacteriophages presence in nature and their role in the natural selection of bacterial populations. PMID:33170167
Targeting Hypoxia-A2A Adenosinergic Immunosuppression of Antitumor T Cells During Cancer Immunotherapy. PMID:33117358
Endogenous zinc nanoparticles in the rat olfactory epithelium are functionally significant. PMID:33116197
Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments. PMID:33104710
Anaplerotic Pathways in Halomonas elongata: The Role of the Sodium Gradient. PMID:33101236
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions. PMID:32976714
Multiplex in situ hybridization within a single transcript: RNAscope reveals dystrophin mRNA dynamics. PMID:32970731
On-chip protein separation with single-molecule resolution. PMID:32943759
Defining the nutritional input for genome-scale metabolic models: A roadmap. PMID:32797084
Primate lentiviruses require Inositol hexakisphosphate (IP6) or inositol pentakisphosphate (IP5) for the production of viral particles. PMID:32776974
Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts. PMID:32753656
A polycyclic aromatic hydrocarbon-enriched environmental chemical mixture enhances AhR, antiapoptotic signaling and a proliferative phenotype in breast cancer cells. PMID:32747956
Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. PMID:32732991
Unstructured kinetic models to simulate an arabinose switch that decouples cell growth from metabolite production. PMID:32695893
Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT. PMID:32676163
Single-cell protein analysis by mass spectrometry. PMID:32599342
A comparison of epigenetic mitotic-like clocks for cancer risk prediction. PMID:32580750
The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts. PMID:32568073
The Scaffold Protein Axin Promotes Signaling Specificity within the Wnt Pathway by Suppressing Competing Kinase Reactions. PMID:32553184
Branch point control at malonyl-CoA node: A computational framework to uncover the design principles of an ideal genetic-metabolic switch. PMID:32455112
β-Oxidation and autophagy are critical energy providers during acute glucose depletion in Saccharomyces cerevisiae. PMID:32430326
Identifying inhibitors of epithelial-mesenchymal plasticity using a network topology-based approach. PMID:32424264
Quantitative Imaging of Changes in Astrocytic and Neuronal Adenosine Triphosphate Using Two Different Variants of ATeam. PMID:32372916
Selective carbon sources influence the end products of microbial nitrate respiration. PMID:32372050
Toward a genome scale sequence specific dynamic model of cell-free protein synthesis in Escherichia coli. PMID:32280586
Insights from Microbial Transition State Theory on Monod's Affinity Constant. PMID:32210303
Antithetic population response to antibiotics in a polybacterial community. PMID:32181369
Formation of phage lysis patterns and implications on co-propagation of phages and motile host bacteria. PMID:32168336
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies. PMID:32140178
Control of Akt activity and substrate phosphorylation in cells. PMID:32125765
Ordered patterning of the sensory system is susceptible to stochastic features of gene expression. PMID:32101167
Are There 1031 Virus Particles on Earth, or More, or Fewer? PMID:32071093
Where does the cargo go?: Solutions to provide experimental support for the "extracellular vesicle cargo transfer hypothesis". PMID:32060725
In Vivo Rate of Formaldehyde Condensation with Tetrahydrofolate. PMID:32059429
Contribution of increasing plasma membrane to the energetic cost of early zebrafish embryogenesis. PMID:32049586
A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. PMID:32040502
Eukaryotic transcription factors can track and control their target genes using DNA antennas. PMID:31992709
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. PMID:31937763
Increasing growth rate slows adaptation when genotypes compete for diffusing resources. PMID:31910213
Growth-rate dependent resource investment in bacterial motile behavior quantitatively follows potential benefit of chemotaxis. PMID:31871173
Thickness of Polyelectrolyte Layers of Separately Confined Bacteria Alters Key Physiological Parameters on a Single Cell Level. PMID:31867314
An ultrasensitive fiveplex activity assay for cellular kinases. PMID:31857650
Identification and characterization of Schizophyllum commune type I metacaspases. PMID:31844687
Impact of consumer-resource dynamics on C. elegans-E. coli system exposed to nano zero-valent iron (nZVI). PMID:31823272
Dynamic Crowding Regulates Transcription. PMID:31818468
An Engineered Cas-Transposon System for Programmable and Site-Directed DNA Transpositions. PMID:31742433
Determination of the number of RAD51 molecules in different human cell lines. PMID:31731884
Multisite phosphorylation drives phenotypic variation in (p)ppGpp synthetase-dependent antibiotic tolerance. PMID:31723135
Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. PMID:31712697
Cytoplasmic convection currents and intracellular temperature gradients. PMID:31682599
Key challenges facing data-driven multicellular systems biology. PMID:31648301
Estimating numbers of intracellular molecules through analysing fluctuations in photobleaching. PMID:31645577
MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. PMID:31633026
An innovative non-invasive technique for subcutaneous tumour measurements. PMID:31609977
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Distinctive mutational spectrum and karyotype disruption in long-term cisplatin-treated urothelial carcinoma cell lines. PMID:31597922
Computational analysis of viable parameter regions in models of synthetic biological systems. PMID:31548864
Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. PMID:31525198
High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform. PMID:31509397
Supramolecular Fuzziness of Intracellular Liquid Droplets: Liquid-Liquid Phase Transitions, Membrane-Less Organelles, and Intrinsic Disorder. PMID:31500307
Homeostasis in the Central Dogma of molecular biology: the importance of mRNA instability. PMID:31418631
Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD. PMID:31251043
Targeting Adenosine in Cancer Immunotherapy to Enhance T-Cell Function. PMID:31244820
Stochastic protein multimerization, activity, and fitness. PMID:31214661
Head-mounted eye gaze tracking devices: An overview of modern devices and recent advances. PMID:31191938
The Cell and the Sum of Its Parts: Patterns of Complexity in Biosignatures as Revealed by Deep UV Raman Spectroscopy. PMID:31156562
Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PMID:31145734
Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes. PMID:31114898
Computational Analysis of Altering Cell Fate. PMID:31062319
Dissecting the Components of Sindbis Virus from Arthropod and Vertebrate Hosts: Implications for Infectivity Differences. PMID:30986033
Meta-Analytic Methodology for Basic Research: A Practical Guide. PMID:30971933
Marine RNA Virus Quasispecies Are Distributed throughout the Oceans. PMID:30944212
INDIANA: An in-cell diffusion method to characterize the size, abundance and permeability of cells. PMID:30904779
A Mathematical Framework for Modelling the Metastatic Spread of Cancer. PMID:30903592
Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells. PMID:30903027
The Inescapable Effects of Ribosomes on In-Cell NMR Spectroscopy and the Implications for Regulation of Biological Activity. PMID:30875837
Evaluation of dose point kernel rescaling methods for nanoscale dose estimation around gold nanoparticles using Geant4 Monte Carlo simulations. PMID:30837578
Folding Landscape of a Parallel G-Quadruplex. PMID:30802054
Pareto Optimality Explanation of the Glycolytic Alternatives in Nature. PMID:30796263
Modeling the interplay between DNA-PK, Artemis, and ATM in non-homologous end-joining repair in G1 phase of the cell cycle. PMID:30707386
Phosphoglycolate has profound metabolic effects but most likely no role in a metabolic DNA response in cancer cell lines. PMID:30670572
Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance. PMID:30638812
Central dogma rates and the trade-off between precision and economy in gene expression. PMID:30622246
Synchronization of speed, sound and iridescent color in a hummingbird aerial courtship dive. PMID:30563977
Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells. PMID:30557009
Centrifugation affects the purity of liquid biopsy-based tumor biomarkers. PMID:30551256
Numerical Simulation of Biomass Growth in OKTOP®9000 Reactor at Industrial Scale. PMID:30416255
Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria. PMID:30397005
Predicting bacterial growth conditions from mRNA and protein abundances. PMID:30388153
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. PMID:30343672
mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction. PMID:30322972
A Dimerization Function in the Intrinsically Disordered N-Terminal Region of Src. PMID:30304684
The bacterial Mre11-Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions. PMID:30277537
Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells. PMID:30271983
Connecting the Dots between Mechanosensitive Channel Abundance, Osmotic Shock, and Survival at Single-Cell Resolution. PMID:30201782
X-ray Fluorescence Nanotomography of Single Bacteria with a Sub-15 nm Beam. PMID:30194316
The role of solute carrier (SLC) transporters in actinomycin D pharmacokinetics in paediatric cancer patients. PMID:30167756
An estimate is worth about a thousand experiments: using order-of-magnitude estimates to identify cellular engineering targets. PMID:30165868
Identifying feasible operating regimes for early T-cell recognition: The speed, energy, accuracy trade-off in kinetic proofreading and adaptive sorting. PMID:30114236
Poor codon optimality as a signal to degrade transcripts with frameshifts. PMID:30105929
Single cell protein analysis for systems biology. PMID:30072488
An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PMID:30040834
Design principles of the paradoxical feedback between pancreatic alpha and beta cells. PMID:30013127
A thiol-reactive Ru(II) ion, not CO release, underlies the potent antimicrobial and cytotoxic properties of CO-releasing molecule-3. PMID:30007887
Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. PMID:29950558
Transformative Opportunities for Single-Cell Proteomics. PMID:29945450
The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation. PMID:29849027
A physical model of cell metabolism. PMID:29844352
Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. PMID:29844191
How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes. PMID:29813054
Data-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation. PMID:29720454
Computer simulations of the signalling network in FLT3 +-acute myeloid leukaemia - indications for an optimal dosage of inhibitors against FLT3 and CDK6. PMID:29699481
Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis. PMID:29679008
Stochastic system identification without an a priori chosen kinetic model-exploring feasible cell regulation with piecewise linear functions. PMID:29675268
In-vivo turnover frequency of the cyanobacterial NiFe-hydrogenase during photohydrogen production outperforms in-vitro systems. PMID:29666458
On the role of extrinsic noise in microRNA-mediated bimodal gene expression. PMID:29664903
A comprehensive and quantitative exploration of thousands of viral genomes. PMID:29624169
A network modeling approach to elucidate drug resistance mechanisms and predict combinatorial drug treatments in breast cancer. PMID:29623959
Kinetic Modeling of Virus Growth in Cells. PMID:29592895
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. PMID:29579036
Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures. PMID:29483636
Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies. PMID:29476010
Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins. PMID:29382730
Modeling the multi-scale mechanisms of macromolecular resource allocation. PMID:29367175
XIAP Regulation by MNK Links MAPK and NFκB Signaling to Determine an Aggressive Breast Cancer Phenotype. PMID:29351901
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PMID:29324779
Eight Kinetically Stable but Thermodynamically Activated Molecules that Power Cell Metabolism. PMID:29272116
Ribosome surface properties may impose limits on the nature of the cytoplasmic proteome. PMID:29154755
Assessing species biomass contributions in microbial communities via metaproteomics. PMID:29146960
Characterizing steady states of genome-scale metabolic networks in continuous cell cultures. PMID:29131817
An Effective Model of the Retinoic Acid Induced HL-60 Differentiation Program. PMID:29085021
Genome-wide analysis of wheat calcium ATPases and potential role of selected ACAs and ECAs in calcium stress. PMID:29078753
ScaPD: a database for human scaffold proteins. PMID:28984188
Centrifugation-Free Magnetic Isolation of Functional Mitochondria Using Paramagnetic Iron Oxide Nanoparticles. PMID:28862341
Principles of cellular resource allocation revealed by condition-dependent proteome profiling. PMID:28857745
Lissencephaly-1 dependent axonal retrograde transport of L1-type CAM Neuroglian in the adult drosophila central nervous system. PMID:28837701
Transcriptional control of motility enables directional movement of Escherichia coli in a signal gradient. PMID:28827562
Quantifying enzyme activity in living cells. PMID:28784664
Ribosomes are optimized for autocatalytic production. PMID:28726822
Expanding discriminative dimensions for analysis and imaging. PMID:28706678
Physiologically based pharmacokinetic modeling of human exposure to perfluorooctanoic acid suggests historical non drinking-water exposures are important for predicting current serum concentrations. PMID:28684146
The Physiology of Phagocytosis in the Context of Mitochondrial Origin. PMID:28615286
Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch. PMID:28591615
Epithelial/mesenchymal plasticity: how have quantitative mathematical models helped improve our understanding? PMID:28548388
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities. PMID:28531184
Energetic cost of building a virus. PMID:28512219
SteadyCom: Predicting microbial abundances while ensuring community stability. PMID:28505184
Convergent ERK1/2, p38 and JNK mitogen activated protein kinases (MAPKs) signalling mediate catecholoestradiol-induced proliferation of ovine uterine artery endothelial cells. PMID:28437005
Interrogating the topological robustness of gene regulatory circuits by randomization. PMID:28362798
Scaling single-cell genomics from phenomenology to mechanism. PMID:28102262
The Origin of Floral Organ Identity Quartets. PMID:28100708
A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate. PMID:28065574
Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity. PMID:28060865
Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1. PMID:28027307
HIC1 and miR-23~27~24 clusters form a double-negative feedback loop in breast cancer. PMID:28009350
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. PMID:27930676
NAD+ Is a Food Component That Promotes Exit from Dauer Diapause in Caenorhabditis elegans. PMID:27907064
Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein. PMID:27824148
Bacterial Inner-membrane Display for Screening a Library of Antibody Fragments. PMID:27805609
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution. PMID:27591251
An Aryl Hydrocarbon Receptor-Mediated Amplification Loop That Enforces Cell Migration in ER-/PR-/Her2- Human Breast Cancer Cells. PMID:27573671
Adaptive Benefits of Storage Strategy and Dual AMPK/TOR Signaling in Metabolic Stress Response. PMID:27505075
Total Cellular RNA Modulates Protein Activity. PMID:27456029
Noise processing by microRNA-mediated circuits: The Incoherent Feed-Forward Loop, revisited. PMID:27441269
The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA. PMID:27365049
A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. PMID:27289091
Investigating the Role of TNF-α and IFN-γ Activation on the Dynamics of iNOS Gene Expression in LPS Stimulated Macrophages. PMID:27276061
An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations. PMID:27047384
The Structure Inventory of the Nuclear Pore Complex. PMID:27016207
Stability of the hybrid epithelial/mesenchymal phenotype. PMID:27008704
Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues. PMID:26989612
α-Tubulin Tyrosination and CLIP-170 Phosphorylation Regulate the Initiation of Dynein-Driven Transport in Neurons. PMID:26972003
The 3D Genome as Moderator of Chromosomal Communication. PMID:26967279
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. PMID:26951675
Microfluidic gradient device for studying mesothelial cell migration and the effect of chronic carbon nanotube exposure. PMID:26937070
The Competitive Interplay between Allosteric HIV-1 Integrase Inhibitor BI/D and LEDGF/p75 during the Early Stage of HIV-1 Replication Adversely Affects Inhibitor Potency. PMID:26910179
Identification of Unintuitive Features of Sumoylation through Mathematical Modeling. PMID:26861881
Biocompatible 3D Matrix with Antimicrobial Properties. PMID:26805790
Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria. PMID:26802122
Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii. PMID:26633994
Practical guidelines for B-cell receptor repertoire sequencing analysis. PMID:26589402
Application of physiologically-based pharmacokinetic modeling to explore the role of kidney transporters in renal reabsorption of perfluorooctanoic acid in the rat. PMID:26522833
Molecular architecture of the DED chains at the DISC: regulation of procaspase-8 activation by short DED proteins c-FLIP and procaspase-8 prodomain. PMID:26494467
Real-time metabolome profiling of the metabolic switch between starvation and growth. PMID:26366986
Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa. PMID:26305928
Life as a moving fluid: fate of cytoplasmic macromolecules in dynamic fungal syncytia. PMID:26226449
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. PMID:26201343
Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. PMID:26201334
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. PMID:26056000
Decoy receptors block TRAIL sensitivity at a supracellular level: the role of stromal cells in controlling tumour TRAIL sensitivity. PMID:26050621
Metabolism at evolutionary optimal States. PMID:26042723
Mathematical modelling of metabolic regulation in aging. PMID:25923415
Streamline based design guideline for deterministic microfluidic hydrodynamic single cell traps. PMID:25825618
High-throughput fluorescence correlation spectroscopy enables analysis of proteome dynamics in living cells. PMID:25774713
Beyond iron: non-classical biological functions of bacterial siderophores. PMID:25764171
Spatial and temporal dynamics of the cardiac mitochondrial proteome. PMID:25752359
Computationally Modeling Lipid Metabolism and Aging: A Mini-review. PMID:25750699
Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. PMID:25584625
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
Quantitative imaging of glutathione in live cells using a reversible reaction-based ratiometric fluorescent probe. PMID:25531746
Targeted intracellular delivery of proteins with spatial and temporal control. PMID:25490248
Explicit tracking of uncertainty increases the power of quantitative rule-of-thumb reasoning in cell biology. PMID:25468340
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. PMID:25378328
The quantified cell. PMID:25368429
Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans. PMID:25262602
Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures. PMID:25243355
Stochastic cellular fate decision making by multiple infecting lambda phage. PMID:25105971
Biosensor architectures for high-fidelity reporting of cellular signaling. PMID:25099816
Effect of chromosome tethering on nuclear organization in yeast. PMID:25020108
How to control proteins with light in living systems. PMID:24937071
Stoichiometry of site-specific lysine acetylation in an entire proteome. PMID:24917678
System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PMID:24688849
Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. PMID:24640988
Weighting schemes in metabolic graphs for identifying biochemical routes. PMID:24592291
A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes. PMID:24586138
MOPED enables discoveries through consistently processed proteomics data. PMID:24350770
A systems' biology approach to study microRNA-mediated gene regulatory networks. PMID:24350286
Cell wall-related bionumbers and bioestimates of Saccharomyces cerevisiae and Candida albicans. PMID:24243791
Multi-input regulation and logic with T7 promoters in cells and cell-free systems. PMID:24194933
Photosynthesis-related quantities for education and modeling. PMID:24162971
What is the total number of protein molecules per cell volume? A call to rethink some published values. PMID:24114984
Transimulation - protein biosynthesis web service. PMID:24040122
The receptor AXL diversifies EGFR signaling and limits the response to EGFR-targeted inhibitors in triple-negative breast cancer cells. PMID:23921085
RACK1 to the future--a historical perspective. PMID:23915285
Vascular injury involves the overoxidation of peroxiredoxin type II and is recovered by the peroxiredoxin activity mimetic that induces reendothelialization. PMID:23820076
Quasi-cellular systems: stochastic simulation analysis at nanoscale range. PMID:23815522
Computational modelling of the regulation of Insulin signalling by oxidative stress. PMID:23705851
Modelling the regulation of telomere length: the effects of telomerase and G-quadruplex stabilising drugs. PMID:23620229
Regulating the many to benefit the few: role of weak small RNA targets. PMID:23601324
Indirect and suboptimal control of gene expression is widespread in bacteria. PMID:23591776
Attractor metabolic networks. PMID:23554883
Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts. PMID:23442824
Preparing synthetic biology for the world. PMID:23355834
Microfluidic Western blotting. PMID:23223527
Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. PMID:23178124
Metabolic shifts: a fitness perspective for microbial cell factories. PMID:22936303
Reaction networks as systems for resource allocation: a variational principle for their non-equilibrium steady states. PMID:22815715
Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. PMID:22748295
A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. PMID:22737065
Stochastic simulations of a synthetic bacteria-yeast ecosystem. PMID:22672814
A sensitive switch for visualizing natural gene silencing in single cells. PMID:22530199
Prediction of antibacterial activity from physicochemical properties of antimicrobial peptides. PMID:22194847
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. PMID:22034591
Identification of widespread ultra-edited human RNAs. PMID:22028664
Robust control of PEP formation rate in the carbon fixation pathway of C(4) plants by a bi-functional enzyme. PMID:22024416
The ten grand challenges of synthetic life. PMID:21949672
One-step preservation of phosphoproteins and tissue morphology at room temperature for diagnostic and research specimens. PMID:21858221
Efficient gene targeting mediated by a lentiviral vector-associated meganuclease. PMID:21715375
Scaffold proteins: hubs for controlling the flow of cellular information. PMID:21551057
Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. PMID:20967426
Transcription by the numbers redux: experiments and calculations that surprise. PMID:20801657
A comprehensive, quantitative, and genome-wide model of translation. PMID:20686685
A feeling for the numbers in biology. PMID:20018695
http://nar.oxfordjournals.org/content/38/suppl_1/D750

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