OOIR: Observatory of International Research

Papers

(The TQCC of Cell Systems is 17. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-04-01 to 2025-04-01.)

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
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
Deep computational analysis details dysregulation of eukaryotic translation initiation complex eIF4F in human cancers	54
A tale of two rhythms: Locked clocks and chaos in biology	52
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	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
Data-driven batch detection enhances single-cell omics data analysis	28
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	28
Human plasma IgG1 repertoires are simple, unique, and dynamic	27
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
The trans-regulatory landscape of gene networks in plants	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
Advances in ligand-specific biosensing for structurally similar molecules	22
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
More is different with a vengeance	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
The in silico lab: Improving academic code using lessons from biology	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
Localized electrical stimulation triggers cell-type-specific proliferation in biofilms	21
Mapping the dynamic transfer functions of eukaryotic gene regulation	20
The need for speed: Migratory cells in tight spaces boost their molecular clock	20
Tumor architecture and emergence of strong genetic alterations are bottlenecks for clonal evolution in primary prostate cancer	19
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
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	18
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
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
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