Cell Systems

Article	Citations
Approaching deconvolution with Fermi’s mindset	332
Modeling non-genetic adaptation in tumor cells	212
Spatial transcriptomics-aided localization for single-cell transcriptomics with STALocator	164
DeST-OT: Alignment of spatiotemporal transcriptomics data	155
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom	153
Highly parallel production of designer organoids by mosaic patterning of progenitors	146
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	103
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors	94
Observations and implication of thermal tolerance in the Arabidopsis proteome	92
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	91
Self-organization of plasticity and specialization in a primitively social insect	91
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	90
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	88
How has the AI boom impacted algorithmic biology?	79
Periodic spatial patterning with a single morphogen	78
Pitfalls of genotyping microbial communities with rapidly growing genome collections	78
Unraveling phenotypic plasticity and evolution in small cell lung cancer	76
Minding the gaps: The importance of navigating holes in protein fitness landscapes	75
Reproducibility metrics for context-specific CRISPR screens	69
Systems analysis of de novo mutations in congenital heart diseases identified a protein network in the hypoplastic left heart syndrome	67
Seeds of their own destruction: Dominant-negative peptide screening yields functional insight and therapeutic leads	65
ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data	63
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	61
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	60
Advancing remote homology detection: A step toward understanding and accurately predicting protein function	60

What are the keys to succeeding as a computational biologist in today’s research climate?	60
Evaluation of Peterson et al.: MAPK cascades don’t work in silos: MAP3K cross-activation of MAPKs and the effect of crosstalk on cellular responses	57
Group dynamics goes awry: PolyQ-expanded huntingtin gains unwanted partners	56
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	55
Context matters: DNA virus infection reshapes DNA damage response pathways	55
Deep computational analysis details dysregulation of eukaryotic translation initiation complex eIF4F in human cancers	54
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	54
What cannot be seen correctly in 2D visualizations of single-cell ‘omics data?	54
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	52
A tale of two rhythms: Locked clocks and chaos in biology	52
The resilience of Ukrainian scientists	51
Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing	51
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	50
Evaluation of De Vries et al.: Quantifying cellular shapes and how they correlate to cellular responses	50
What is the key challenge in engineering microbiomes?	50
Decoupled degradation and translation enables noise modulation by poly(A) tails	50
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	47
Alignment of single-cell trajectories by tuMap enables high-resolution quantitative comparison of cancer samples	45
Engineering highly active nuclease enzymes with machine learning and high-throughput screening	44
Becoming fluent in proteins	44
Sustainable protein regeneration in encapsulated materials	43
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	42
Cross-evaluation of E. coli’s operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons	41
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	40
A synthetic gene circuit for imaging-free detection of signaling pulses	37
Engineering functional materials through bacteria-assisted living grafting	37
A framework for ultra-low-input spatial tissue proteomics	37
Biological feedback control—Respect the loops	35
Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity	34
Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines	34
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	33
Systematically quantifying morphological features reveals constraints on organoid phenotypes	32
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery	31
Convolutions are competitive with transformers for protein sequence pretraining	31
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	31
NAD+ flux is maintained in aged mice despite lower tissue concentrations	30
Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection	29
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	28
Data-driven batch detection enhances single-cell omics data analysis	28
Human plasma IgG1 repertoires are simple, unique, and dynamic	27
The trans-regulatory landscape of gene networks in plants	26
ProGen2: Exploring the boundaries of protein language models	26
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	26
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	26
High-throughput discovery and characterization of viral transcriptional effectors in human cells	26
Which image-based phenotypes are most promising for using AI to understand cellular functions and why?	25
Making sense of BMP signaling complexity	25
SEMPER: Stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes for compact, ratio-tunable multi-gene expression	25
Multilevel relations among plankton stitched together with an eco-evolutionary needle	25
Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient	25

Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	25
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	25
Controlling the human microbiome	25
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	24
How do you anticipate computational protein design will change biotechnology and therapeutic development?	24
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	24
Sparse dictionary learning recovers pleiotropy from human cell fitness screens	23
The unreasonable effectiveness of equilibrium gene regulation through the cell cycle	22
RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer	22
The in silico lab: Improving academic code using lessons from biology	22
pH and buffering capacity: Fundamental yet underappreciated drivers of algal-bacterial interactions	22
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease	22
Advances in ligand-specific biosensing for structurally similar molecules	22
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	22
Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells	22
More is different with a vengeance	22
Localized electrical stimulation triggers cell-type-specific proliferation in biofilms	21
The need for speed: Migratory cells in tight spaces boost their molecular clock	20
Mapping the dynamic transfer functions of eukaryotic gene regulation	20
Versatile system cores as a conceptual basis for generality in cell and developmental biology	19
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression	19
Tumor architecture and emergence of strong genetic alterations are bottlenecks for clonal evolution in primary prostate cancer	19
Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer	18
A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia	18
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	18
BayesTME: An end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment	17
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	17
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	17
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	17
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer	17
Should biology put complexity first?	16
High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing	16
Accurate top protein variant discovery via low-N pick-and-validate machine learning	16
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones	15
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution	15
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods	15
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	15
Fundamentals to function: Quantitative and scalable approaches for measuring protein stability	15
A new age in protein design empowered by deep learning	14
Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations	14
Meta learning addresses noisy and under-labeled data in machine learning-guided antibody engineering	14
Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding	13
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	13
Perfect adaptation in biology	13
The context-dependent, combinatorial logic of BMP signaling	13
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset	13
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions	13
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	13
Context-aware synthetic biology by controller design: Engineering the mammalian cell	13
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	13
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	13
Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges	13
Cold and hot fibrosis define clinically distinct cardiac pathologies	13
Ligand-receptor promiscuity enables cellular addressing	13
Virtual screening for small-molecule pathway regulators by image-profile matching	12
Parallel engineering and activity profiling of a base editor system	12
What are the current bottlenecks in developing and applying CRISPR technologies?	12
A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens	12
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain	12
Synthetic symmetry breaking and programmable multicellular structure formation	12
Assembly of stool-derived bacterial communities follows “early-bird” resource utilization dynamics	12
Rationally reprogramming single-cell aging trajectories and lifespan through dynamic modulation of environmental inputs	11
Homeostasis	11
A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids	11
What differentiates a stress response from responsiveness in general?	11
Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data	11
Informed training set design enables efficient machine learning-assisted directed protein evolution	11
Tissue Schematics: A framework to decipher tissue architecture and assembly	11
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	11
The community-function landscape of microbial consortia	11
Evo-velocity: Protein language modeling accelerates the study of evolution	10
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	10
Synthetically programmed antioxidant delivery by a domesticated skin commensal	10
Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model	10
What are the current driving questions in immune repertoire research?	10
What do you most hope spatial molecular profiling will help us understand? Part 1	10
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	10
What is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling?	10
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	9
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	9

What do you most want to understand about how collective features emerge in microbial communities?	9
SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays	9
What do you most hope spatial molecular profiling will help us understand? Part 2	9
Contrastive learning of T cell receptor representations	9
Engineering allosteric transcription factors guided by the LacI topology	8
HOGVAX: Exploiting epitope overlaps to maximize population coverage in vaccine design with application to SARS-CoV-2	8
Unveiling the hidden network of STING’s subcellular regulation	8
Widespread alteration of protein autoinhibition in human cancers	8
High immigration rates critical for establishing emigration-driven diversity in microbial communities	8
How can concepts from ecology enable insights about cellular communities?	8
Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models	8
The structure of the human cell cycle	8
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	8
CDK2 activity crosstalk on the ERK kinase translocation reporter can be resolved computationally	7
DNA-PK and ATM drive phosphorylation signatures that antagonistically regulate cytokine responses to herpesvirus infection or DNA damage	7
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	7
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	7
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	7
Microengineered in vitro CAR T cell screens and assays	7
Stimulus-response signaling dynamics characterize macrophage polarization states	7
Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity	7
A forecast for large-scale, predictive biology: Lessons from meteorology	6
Metabolic immunoengineering approaches to enhance CD8+ T cell-based cancer immunotherapy	6
The time-resolved genomic impact of Wnt/β-catenin signaling	6
Transcriptome data are insufficient to control false discoveries in regulatory network inference	6
Integrated, data-driven health management: A step closer to personalized and predictive healthcare	6
Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote	6
Analysis of scientific society honors reveals disparities	6
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	6
Optimized reporters for multiplexed detection of transcription factor activity	6
Quantifying stimulus-response specificity to probe the functional state of macrophages	6
Inferring metabolic objectives and trade-offs in single cells during embryogenesis	6
The geometry of cell fate	6
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	6
Democratizing long-read genome assembly	6
Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity	6
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	5
Macrophage memory emerges from coordinated transcription factor and chromatin dynamics	5
Studying stochastic systems biology of the cell with single-cell genomics data	5
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer	5
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	5
A time-resolved proteomic and prognostic map of COVID-19	5
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	5
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders	5
Proliferation history and transcription factor levels drive direct conversion to motor neurons	5
Morphology and gene expression profiling provide complementary information for mapping cell state	5
Truncated protein isoforms generate diversity of protein localization and function in yeast	5
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	5
Single-cell colocalization analysis using a deep generative model	5
Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback	5
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	5
Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces	5
Acute response to pathogens in the early human placenta at single-cell resolution	5
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	5
Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast	5