OOIR: Observatory of International Research

Papers

(The TQCC of Cell Systems is 23. 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 2020-07-01 to 2024-07-01.)

Article	Citations
Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection	452
Large-Scale Multi-omic Analysis of COVID-19 Severity	411
Learning the protein language: Evolution, structure, and function	216
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing	180
A time-resolved proteomic and prognostic map of COVID-19	130
Fast and Flexible Protein Design Using Deep Graph Neural Networks	130
Artificial intelligence for proteomics and biomarker discovery	128
A platform for experimental precision medicine: The extended BXD mouse family	120
Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning	114
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data	109
Informed training set design enables efficient machine learning-assisted directed protein evolution	106
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus	100
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design	96
A Pandemic on a Pandemic: Racism and COVID-19 in Blacks	91
Hotspot identifies informative gene modules across modalities of single-cell genomics	90
Biophysics of Temporal Interference Stimulation	84
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis	82
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells	75
A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences	74
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions	74
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	73
ProGen2: Exploring the boundaries of protein language models	72
Perfect adaptation in biology	71
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy	70
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome	68

Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids	66
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins	65
SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks	64
Functional attractors in microbial community assembly	64
The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis	64
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	63
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism	61
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program	60
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer	59
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies	59
Consciousness depends on integration between parietal cortex, striatum, and thalamus	59
Machine learning for perturbational single-cell omics	58
NAD+ flux is maintained in aged mice despite lower tissue concentrations	58
The Genetic Makeup of the Electrocardiogram	58
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	52
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering	50
Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions	49
Diversity of the Gβγ complexes defines spatial and temporal bias of GPCR signaling	49
Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast	48
Noise distorts the epigenetic landscape and shapes cell-fate decisions	48
Morphology and gene expression profiling provide complementary information for mapping cell state	45
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution	45
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	44
The context-dependent, combinatorial logic of BMP signaling	43
Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus	42
The sound of silence: Transgene silencing in mammalian cell engineering	42
Human plasma IgG1 repertoires are simple, unique, and dynamic	42
Database-independent de novo metaproteomics of complex microbial communities	41
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies	40
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	40
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing	39
Biological feedback control—Respect the loops	39
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors	39
Context-aware synthetic biology by controller design: Engineering the mammalian cell	39
Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics	38
Ligand-receptor promiscuity enables cellular addressing	38
Degradation of host translational machinery drives tRNA acquisition in viruses	37
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes	36
Ultrasensitive molecular controllers for quasi-integral feedback	36
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	36
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees	36
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning	35
Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis	34
Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer’s Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals	34
Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines	34
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation	33
Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity	33
Systems-Level Properties of EGFR-RAS-ERK Signaling Amplify Local Signals to Generate Dynamic Gene Expression Heterogeneity	32
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity	32
Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging	32

Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets	32
Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures	32
Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays	31
A tale of two rhythms: Locked clocks and chaos in biology	31
The community-function landscape of microbial consortia	31
Diploid hepatocytes drive physiological liver renewal in adult humans	29
Deciphering the signaling network of breast cancer improves drug sensitivity prediction	29
Best Practices for Making Reproducible Biochemical Models	29
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles	28
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	27
Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens	26
Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks	26
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression	26
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	26
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles	26
Multiomic profiling of the liver across diets and age in a diverse mouse population	25
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods	25
Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges	25
Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma	25
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease	25
High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants	24
Mapping the multiscale structure of biological systems	24
A convergent molecular network underlying autism and congenital heart disease	24
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	24
A Sweep of Earth’s Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease	23
Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations	23
Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-adjuvant Combinations	23