Bioinformatics and Computational Biology articles for Stanford University, United States of America (USA)

Time frame: 1 June 2025 - 30 May 2026

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Count: 125

Article ‘Count’ for Bioinformatics and Computational Biology.

Journal Count Share
7 3.19
Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies 0.03
Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants 1.00
Local ancestry-informed GWAS of warfarin dose requirement in African Americans identifies a CYP2C19 splicing QTL 0.18
Unveiling tissue heterogeneity through genomic interaction-encoded image representation of RNA-sequencing data 1.00
Estimation of demography and mutation rates from one million haploid genomes 0.33
A calcium-sensing receptor allelic series and underdiagnosis of genetically driven hypocalcemia 0.11
Haplotype analysis reveals pleiotropic disease associations in the HLA region 0.53
2 0.44
Mapping Cell Metabolic States by Image-Enabled Gating Metabolomic Cytometry 0.16
Exploration of Semiconductor Chip-Based Single-Molecule Protein Sequencing for Identification of Hemoglobin Variants 0.29
1 0.01
Gain of function NOTCH4 variants disrupt angiogenesis in systemic sclerosis 0.01
1 0.05
Correlates and consequences of clonal hematopoiesis expansion rate: a 16-year longitudinal study of 6976 women 0.05
2 0.96
Deep learning-based cell type profiles reveal signatures of Alzheimer’s disease resilience and resistance 0.93
Novel modelling approaches to elucidate the genetic architecture of resilience to Alzheimer’s disease 0.03
1 0.04
IGSF11-VISTA is a critical and targetable immune checkpoint axis in diffuse midline glioma 0.04
6 0.98
D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response 0.03
Multi-cohort proteogenomic analyses reveal genetic effects across the proteome and diseasome 0.03
Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles 0.01
Large-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis 0.03
Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells 0.80
Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue 0.09
3 1.16
Adaptive genomic divergence parallels migratory behavior in Atlantic bluefin tuna 0.50
Rapid and repeated evolution of myosin copy number in threespine stickleback 0.58
A new Cambrian stem-group echinoderm reveals the evolution of the anteroposterior axis 0.08
1 0.08
Clonal haematopoiesis of indeterminate potential and mortality in coronary artery disease 0.08
2 1.76
A cell type-specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage 0.89
A genome-wide, CRISPR-based screen reveals new requirements for translation initiation and ubiquitination in driving adipogenic fate change 0.88
5 2.52
Autoencoders for genomic variation analysis 0.50
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway 0.45
CGC1, a new reference genome for Caenorhabditis elegans 0.27
Contiguous and complete assemblies ofiBlastocystis/igut microbiome–associated protists reveal evolutionary diversification to host ecology 0.30
Analytical validation of germline small variant detection using long-read HiFi genome sequencing 1.00
1 0.03
The hematopoietic stem cell MYB enhancer is essential and recurrently amplified during T-cell leukemogenesis 0.03
1 0.20
Root cause discovery via permutations and Cholesky decomposition 0.20
3 1.17
Chromatin architectures underlying plasmid-based assays for regulatory variant effects 0.09
Large-scale mapping of environmental-genetic interactions illustrates the dynamic nature of cell-cycle and DNA repair regulation 0.08
Structure of the transcriptional co-activator SAGA complex, including the histone acetyltransferase module 1.00
1 0.00
Leveraging transdiagnostic genetic liability to psychiatric disorders to dissect clinical outcomes of anorexia nervosa 0.00
17 5.07
Accelerating scientific discovery with Co-Scientist 0.06
Non-invasive profiling of the tumour microenvironment with spatial ecotypes 0.27
Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup 0.02
Transposable elements are driving rapid adaptation of Enterococcus faecium 0.92
Saturation editing of reveals distinct dominant and recessive disorders 0.02
Multiomics and deep learning dissect regulatory syntax in human development 0.71
A sorghum pangenome reference improves global crop trait discovery 0.00
Genome modelling and design across all domains of life with Evo 2 0.21
An expanded registry of candidate -regulatory elements 0.12
Mapping the genetic landscape across 14 psychiatric disorders 0.00
Causal modelling of gene effects from regulators to programs to traits 0.60
Specificity, length and luck drive gene rankings in association studies 0.61
Thymic epithelial cells amplify epigenetic noise to promote immune tolerance 0.16
A molecular cell atlas of mouse lemur, an emerging model primate 0.57
Mouse lemur cell atlas informs primate genes, physiology and disease 0.58
Complex genetic variation in nearly complete human genomes 0.02
In vivo mapping of mutagenesis sensitivity of human enhancers 0.20
7 2.85
Scoring gene importance by interpreting single-cell foundation models 0.03
Reference-free discovery with barcoded single-cell sequencing 0.64
Scalable single-cell total RNA sequencing unifies coding and noncoding transcriptomics 0.74
Single-molecule peptide sequencing through reverse translation of peptides into DNA 1.00
Revealing a coherent cell-state landscape across single-cell datasets with CONCORD 0.01
Single-cell polygenic risk scores dissect cellular and molecular heterogeneity of complex human diseases 0.26
Improving gene isoform quantification with miniQuant 0.17
26 6.91
Multi-ancestry transcriptome-wide association studies uncover insights into breast cancer genetics and biology 0.01
Heterogeneous endocrine cell composition defines human islet functional phenotypes 0.17
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC 0.19
Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion 0.01
Genetic architecture of lumbar spinal stenosis 0.00
Genetic modifiers of -ε4-associated cognitive decline 0.02
Cross-ancestry comparison of aptamer and antibody protein measures 0.02
Preventing premature deaths through polygenic risk scores 0.17
Cysteine-enabled cleavability to advance cross-linking mass spectrometry for global analysis of endogenous protein-protein interactions 0.14
Patient-derived colon epithelial organoids reveal lipid-related metabolic dysfunction in pediatric ulcerative colitis 0.76
Human plasma proteomic profile of clonal hematopoiesis 0.03
Data navigation on the ENCODE portal 1.00
Genetic determinants and genomic consequences of non-leukemogenic somatic point mutations 0.02
A deep single cell mass cytometry approach to capture canonical and noncanonical cell cycle states 1.00
Polygenic risk score for type 2 diabetes shows context-dependent effects across populations 0.02
: a web-based application for in-depth exploration of multi-omics data with brightfield histology 0.04
Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis 0.96
Mechanically activated snai1b coordinates the initiation of myocardial delamination for trabeculation 0.14
: AI generation of multiplex immunofluorescence staining from histopathology images 0.19
Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions 0.40
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing 0.53
Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets 0.01
Automated cell annotation and classification on histopathology for spatial biomarker discovery 0.85
Scaling laws of bacterial and archaeal plasmids 0.13
Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome 0.11
Shared genetic architecture of posttraumatic stress disorder with cardiovascular imaging, risk, and diagnoses 0.00
8 0.61
Exome-wide association study of blood lipids in 1,158,017 individuals from diverse populations 0.07
Genome-wide association analyses of autoimmune hypothyroidism reveal autoimmune and thyroid-specific contributions and an inverse relationship with cancer risk 0.04
Spatiotemporal gene expression and cellular dynamics of the developing human heart 0.04
DNA methylation influences human centromere positioning and function 0.11
Improved multiancestry fine-mapping identifies -regulatory variants underlying molecular traits and disease risk 0.09
Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs 0.25
Disruption of TAD hierarchy promotes LTR co-option in cancer 0.00
Transferability of European-derived Alzheimer’s disease polygenic risk scores across multiancestry populations 0.00
1 0.06
Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis 0.06
5 1.60
An atlas of exposome–phenome associations in health and disease risk 0.33
Clinical genetic variation across Hispanic populations in the Mexican Biobank 0.01
AI-enabled virtual spatial proteomics from histopathology for interpretable biomarker discovery in lung cancer 1.00
A consensus immune dysregulation framework for sepsis and critical illnesses 0.25
Polygenic prediction of body mass index and obesity through the life course and across ancestries 0.00
7 2.59
CellVoyager: AI CompBio agent generates new insights by autonomously analyzing biological data 1.00
cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions 0.07
Squidiff: predicting cellular development and responses to perturbations using a diffusion model 0.17
Improved reconstruction of single-cell developmental potential with CytoTRACE 2 0.77
Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data 0.44
Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing 0.10
Morphological map of under- and overexpression of genes in human cells 0.04
3 1.40
Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments 0.67
Comparative gene annotation and orthology assignments across 301 species of Drosophilidae 0.13
Simple scaling laws control the genetic architectures of human complex traits 0.61
5 2.09
HLA-DQB1*03:01 strongly affects age of onset of type 1 narcolepsy independently of DQA1 and ethnicity 0.15
Physical models reveal indirect reader protein interactions that facilitate epigenetic crosstalk 0.75
Disrupted developmental signaling induces novel transcriptional states 0.08
Exceedingly low genetic diversity in snow leopards due to persistently small population size 0.11
Improving polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features 1.00
1 0.50
A unifying theoretical framework for tick-borne disease risk to explain conflicting results of exclosure experiments across scales 0.50
4 1.48
TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution 0.06
The functional landscape of coding variation in the familial hypercholesterolemia gene LDLR 0.09
A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness 0.33
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging 1.00
4 0.47
Discovery of White Sea assemblage fossils from Laurentia 0.25
Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer 0.03
Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction 0.08
A narrow range of transcript-error rates across the Tree of Life 0.11

Numerical information only (in the tables above) is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International.