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 2020-05-01 to 2024-05-01.)

Article	Citations
Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection	435
Large-Scale Multi-omic Analysis of COVID-19 Severity	400
Learning the protein language: Evolution, structure, and function	197
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing	169
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer	158
A time-resolved proteomic and prognostic map of COVID-19	124
Fast and Flexible Protein Design Using Deep Graph Neural Networks	124
A platform for experimental precision medicine: The extended BXD mouse family	118
Artificial intelligence for proteomics and biomarker discovery	111
Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning	108
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data	102
Informed training set design enables efficient machine learning-assisted directed protein evolution	99
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus	97
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design	93
A Pandemic on a Pandemic: Racism and COVID-19 in Blacks	90
Hotspot identifies informative gene modules across modalities of single-cell genomics	86
Biophysics of Temporal Interference Stimulation	80
Encoding Membrane-Potential-Based Memory within a Microbial Community	75
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis	75
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	72
A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences	71
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells	70
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions	69
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome	66
Perfect adaptation in biology	65

CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy	64
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids	62
The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis	62
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism	61
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins	60
Functional attractors in microbial community assembly	60
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	59
SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks	59
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program	57
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer	57
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies	55
The Genetic Makeup of the Electrocardiogram	55
Consciousness depends on integration between parietal cortex, striatum, and thalamus	55
Machine learning for perturbational single-cell omics	53
NAD+ flux is maintained in aged mice despite lower tissue concentrations	52
SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing	51
ProGen2: Exploring the boundaries of protein language models	51
SCHEEPDOG: Programming Electric Cues to Dynamically Herd Large-Scale Cell Migration	50
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
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	46
Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast	45
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	44
Noise distorts the epigenetic landscape and shapes cell-fate decisions	43
Diversity of the Gβγ complexes defines spatial and temporal bias of GPCR signaling	43
Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus	41
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution	41
Morphology and gene expression profiling provide complementary information for mapping cell state	40
The context-dependent, combinatorial logic of BMP signaling	40
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies	40
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors	39
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	39
Database-independent de novo metaproteomics of complex microbial communities	38
Human plasma IgG1 repertoires are simple, unique, and dynamic	38
Context-aware synthetic biology by controller design: Engineering the mammalian cell	37
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing	37
Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics	37
Biological feedback control—Respect the loops	36
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees	36
Ligand-receptor promiscuity enables cellular addressing	36
Ultrasensitive molecular controllers for quasi-integral feedback	36
CELLector: Genomics-Guided Selection of Cancer In Vitro Models	35
Degradation of host translational machinery drives tRNA acquisition in viruses	35
The sound of silence: Transgene silencing in mammalian cell engineering	35
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning	33
Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity	32
Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines	32
Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets	32
Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer’s Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals	32
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	31

A tale of two rhythms: Locked clocks and chaos in biology	31
Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis	31
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity	31
Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging	31
Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures	31
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes	30
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation	30
Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays	30
Best Practices for Making Reproducible Biochemical Models	29
Systems-Level Properties of EGFR-RAS-ERK Signaling Amplify Local Signals to Generate Dynamic Gene Expression Heterogeneity	29
The community-function landscape of microbial consortia	27
Diploid hepatocytes drive physiological liver renewal in adult humans	27
Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons	26
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles	26
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	26
Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks	26
Deciphering the signaling network of breast cancer improves drug sensitivity prediction	25
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	25
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles	25
Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma	25
Multiomic profiling of the liver across diets and age in a diverse mouse population	25
Quantifying the Central Dogma in the p53 Pathway in Live Single Cells	25
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression	24
Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens	24
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease	24
High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants	24
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods	23
Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-adjuvant Combinations	23