OOIR: Observatory of International Research

Papers

(The H4-Index of Cell Systems is 43. 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 2020-11-01 to 2024-11-01.)

Article	Citations
Large-Scale Multi-omic Analysis of COVID-19 Severity	420
Learning the protein language: Evolution, structure, and function	252
Artificial intelligence for proteomics and biomarker discovery	149
A time-resolved proteomic and prognostic map of COVID-19	136
A platform for experimental precision medicine: The extended BXD mouse family	123
Informed training set design enables efficient machine learning-assisted directed protein evolution	120
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data	117
ProGen2: Exploring the boundaries of protein language models	115
Biophysics of Temporal Interference Stimulation	99
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design	99
Hotspot identifies informative gene modules across modalities of single-cell genomics	99
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis	93
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions	83
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells	80
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	79
Perfect adaptation in biology	76
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy	74
Functional attractors in microbial community assembly	72
The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis	71
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	71
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids	70
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins	68
Machine learning for perturbational single-cell omics	67
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism	67
NAD+ flux is maintained in aged mice despite lower tissue concentrations	65

Consciousness depends on integration between parietal cortex, striatum, and thalamus	65
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer	61
The sound of silence: Transgene silencing in mammalian cell engineering	58
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	58
Morphology and gene expression profiling provide complementary information for mapping cell state	57
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering	57
Diversity of the Gβγ complexes defines spatial and temporal bias of GPCR signaling	55
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	55
Noise distorts the epigenetic landscape and shapes cell-fate decisions	53
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution	50
The context-dependent, combinatorial logic of BMP signaling	48
Biological feedback control—Respect the loops	46
Database-independent de novo metaproteomics of complex microbial communities	45
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	45
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies	44
Ligand-receptor promiscuity enables cellular addressing	44
Human plasma IgG1 repertoires are simple, unique, and dynamic	44
Context-aware synthetic biology by controller design: Engineering the mammalian cell	43
Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus	43