OOIR: Observatory of International Research

Papers

(The H4-Index of Cell Systems is 44. 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
Self-organization of plasticity and specialization in a primitively social insect	91
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	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
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

Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	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
Context matters: DNA virus infection reshapes DNA damage response pathways	55
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	55
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
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	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
Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing	51
The resilience of Ukrainian scientists	51
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
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	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