OOIR: Observatory of International Research

Papers

(The H4-Index of Cell Systems is 47. 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 2020-04-01 to 2024-04-01.)

Article	Citations
Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection	429
Large-Scale Multi-omic Analysis of COVID-19 Severity	395
Learning the protein language: Evolution, structure, and function	192
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing	165
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer	152
MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Affinities	129
A time-resolved proteomic and prognostic map of COVID-19	124
Fast and Flexible Protein Design Using Deep Graph Neural Networks	119
A platform for experimental precision medicine: The extended BXD mouse family	113
Artificial intelligence for proteomics and biomarker discovery	109
Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning	103
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data	99
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus	96
Informed training set design enables efficient machine learning-assisted directed protein evolution	96
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design	92
A Pandemic on a Pandemic: Racism and COVID-19 in Blacks	89
Hotspot identifies informative gene modules across modalities of single-cell genomics	81
Biophysics of Temporal Interference Stimulation	78
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis	74
Encoding Membrane-Potential-Based Memory within a Microbial Community	73
A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences	69
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells	69
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions	67
Perfect adaptation in biology	65
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	64

The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis	62
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy	62
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids	59
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome	59
SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks	58
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	58
Functional attractors in microbial community assembly	58
Codon Usage and Splicing Jointly Influence mRNA Localization	57
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program	57
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins	56
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism	56
SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses	56
The Genetic Makeup of the Electrocardiogram	54
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer	53
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies	52
Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer	52
NAD+ flux is maintained in aged mice despite lower tissue concentrations	52
Machine learning for perturbational single-cell omics	52
Consciousness depends on integration between parietal cortex, striatum, and thalamus	50
SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing	50
SCHEEPDOG: Programming Electric Cues to Dynamically Herd Large-Scale Cell Migration	48
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering	48
Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions	47