Cell Systems

A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs.

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.

Continuum of Gene-Expression Profiles Provides Spatial Division of Labor within a Differentiated Cell Type.

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.

Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design.

Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules.

Neoantigen Dissimilarity to the Self-Proteome Predicts Immunogenicity and Response to Immune Checkpoint Blockade.

Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance

Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community.

Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa.

A Comprehensive Network Atlas Reveals That Turing Patterns Are Common but Not Robust.

tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance.

Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.

A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing.

Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data.

Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming.

Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development.

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks.

Decoupling of Rates of Protein Synthesis from Cell Expansion Leads to Supergrowth.

Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells.

Automated Design of Pluripotent Stem Cell Self-Organization.

Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data.

Building Containerized Workflows Using the BioDepot-Workflow-Builder.

High-Throughput Assessment of Kinome-wide Activation States

Mechanical Force Induces Phosphorylation-Mediated Signaling that Underlies Tissue Response and Robustness in Xenopus Embryos.

Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network

A Simple and Flexible Computational Framework for Inferring Sources of Heterogeneity from Single-Cell Dynamics.

Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation.

Untangling Aging Using Dynamic, Organism-Level Phenotypic Networks.

Subpopulation Detection and Their Comparative Analysis across Single-Cell Experiments with scPopCorn.

Compression Generated by a 3D Supracellular Actomyosin Cortex Promotes Embryonic Stem Cell Colony Growth and Expression of Nanog and Oct4.

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

Defining Higher-Order Interactions in Synthetic Ecology: Lessons from Physics and Quantitative Genetics.

Protein Structure from Experimental Evolution.

The Limited Information Capacity of Cross-Reactive Sensors Drives the Evolutionary Expansion of Signaling.

iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast.

Design and Analysis of a Proportional-Integral-Derivative Controller with Biological Molecules.

Proteomics-Based Monitoring of Pathway Activity Reveals that Blocking Diacylglycerol Biosynthesis Rescues from Alpha-Synuclein Toxicity

Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development.

Of Gene Expression and Cell Division Time: A Mathematical Framework for Advanced Differential Gene Expression and Data Analysis.

Inferring Leading Interactions in the p53/Mdm2/Mdmx Circuit through Live-Cell Imaging and Modeling.

Mango: Exploratory Data Analysis for Large-Scale Sequencing Datasets.

mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.

Computing the Statistical Significance of Overlap between Genome Annotations with iStat.

Reporting p Values.