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

Time frame: 1 June 2025 - 30 May 2026

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Count: 104

Article ‘Count’ for Bioinformatics and Computational Biology.

Journal Count Share
5 3.11
Integrative genomics and single-cell CRISPRi screening dissect Alzheimer GWAS non-coding variants regulating TSPAN14 0.88
Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies 0.01
Inclusion bias affects common variant discovery and replication in a health-system linked biobank 0.29
Expanded chromatin accessibility mapping explains genetic variation associated with complex traits in liver 1.00
A deep dive into statistical modeling of RNA splicing QTLs reveals variants that explain neurodegenerative disease 0.94
1 0.05
Genetic Associations with Placental and Pregnancy Proteins in Maternal Serum Identify Biomarkers for Hypertension in Pregnancy 0.05
1 0.02
Gain of function NOTCH4 variants disrupt angiogenesis in systemic sclerosis 0.02
1 0.03
Novel modelling approaches to elucidate the genetic architecture of resilience to Alzheimer’s disease 0.03
1 0.07
Path2Omics Enhances Transcriptomic and Methylation Prediction Accuracy from Tumor Histopathology. 0.07
4 0.18
D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response 0.00
AI-predicted spatial transcriptomics unlocks breast cancer biomarkers from pathology 0.06
Advancing precision health discovery in a genetically diverse health system 0.06
50,000 years of evolutionary history of India: Impact on health and disease variation 0.06
1 0.70
Cardiac sarcoidosis: new insights beyond the granuloma using spatial proteomics 0.70
1 0.01
Highly accurate assembly polishing with DeepPolisher 0.01
1 0.11
Metabolic remodeling and the modulatory role of vitamin D deficiency in African American children and adolescents with obesity 0.11
1 0.12
Drug-Gene Interactions and Clinical Outcomes After Vascular Surgery in the Million Veteran Program 0.12
1 0.09
Transcriptome and chromatin accessibility divergence during differentiation of a bipotential progenitor cell population to erythroblasts and megakaryocytes 0.09
1 0.06
Hypothalamic-pituitary deficiency after radiation in childhood cancer survivors is associated with rare variants in TNS2 0.06
1 0.21
The cell-type-specific genetic architecture of chronic pain in brain and dorsal root ganglia 0.21
1 0.92
Unnatural Cytosine Analogs Potentiate a Customizable, Enzymatic Method for Integrated Epigenetic and Four-Base Genetic Sequencing 0.92
2 0.85
Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich’s ataxia 0.72
Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex 0.13
2 0.13
Leveraging transdiagnostic genetic liability to psychiatric disorders to dissect clinical outcomes of anorexia nervosa 0.01
Genetically modeled GLP1R and GIPR agonism reduce binge drinking and alcohol-associated phenotypes: a multi-ancestry drug-target Mendelian randomization study 0.13
6 1.40
Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup 0.48
An integrated view of the structure and function of the human 4D nucleome 0.06
Causal modelling of gene effects from regulators to programs to traits 0.00
Mapping the genetic landscape across 14 psychiatric disorders 0.00
Spatial joint profiling of DNA methylome and transcriptome in tissues 0.83
Complex genetic variation in nearly complete human genomes 0.02
2 0.10
Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state 0.05
Improving gene isoform quantification with miniQuant 0.06
2 1.28
Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation 0.70
Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues 0.58
35 6.95
Multi-ancestry transcriptome-wide association studies uncover insights into breast cancer genetics and biology 0.01
N-Orbit: towards a universal model and metric for comparing tissue microenvironments 0.44
Multi-omics integration predicts the incidence of 17 diseases in the UK Biobank 0.04
SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing 0.29
Enhancer placement impacts transcriptional dynamics in Drosophila embryos 0.73
Rapid adaptive increase of amylase gene copy number in Indigenous Andeans 0.06
Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials 0.05
Dynamic partitioning of a critical elongation factor between LEC and SEC regulates cellular snRNA and proliferation-related mRNA transcription 0.05
Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion 0.00
Combining multiplexed assays of variant effect for enhanced BRCA2 variant classification 0.11
Collective behavior and memory states in flow networks with tunable bistability 0.50
A single cluster of RNA Polymerase II molecules is stably associated with active genes 0.39
Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics 0.20
Shared Genetic Liability across Systems of Psychiatric and Physical Illness 0.22
Genetic modifiers of -ε4-associated cognitive decline 0.10
KidneyGenAfrica multi-cohort Genome-wide association study and polygenic prediction of kidney function in 110,000 Africans 0.01
Epigenome-wide analysis identifies DNA methylation mediators of treatment-related cardiometabolic risk in survivors of childhood cancer 0.04
Cross-ancestry comparison of aptamer and antibody protein measures 0.02
PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells 0.08
Leveraging genomic and transcriptomic data of diverse ancestry to uncover mechanisms of psychiatric risk in the adult and developing brain 0.04
Mapping rare protein-coding variants on multi-organ imaging traits 0.35
Proteome-wide association study of prostate cancer risk across populations 0.05
Benchmarking DNA foundation models for genomic and genetic tasks 0.11
Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation 0.01
G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data 0.70
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells 0.20
The effect of type 2 diabetes genetic predisposition on non-cardiovascular comorbidities 0.07
Polygenic risk score for type 2 diabetes shows context-dependent effects across populations 0.00
TP53 variant clusters stratify phenotypic diversity in germline carriers and reveal an osteosarcoma-prone subgroup 0.08
Revealing the biophysics of lamina-associated domain formation by integrating theoretical modeling and high-resolution imaging 0.58
Epigenomic diagnosis and prognosis of Acute Myeloid Leukemia 0.02
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing 0.40
Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell 0.08
Shared genetic architecture of posttraumatic stress disorder with cardiovascular imaging, risk, and diagnoses 0.00
Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues 0.90
12 1.54
Exome-wide association study of blood lipids in 1,158,017 individuals from diverse populations 0.07
H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs 0.05
De novo formation of -regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion 0.17
Multi-trait and multi-ancestry genetic analysis of comorbid lung diseases and traits improves genetic discovery and polygenic risk prediction 0.06
Genomic and transcriptomic analyses of aortic stenosis enhance therapeutic target discovery and disease prediction 0.02
A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic interaction effects 0.08
Scalable and accurate rare variant meta-analysis with Meta-SAIGE 0.25
An African ancestry-specific nonsense variant in CD36 is associated with a higher risk of dilated cardiomyopathy 0.10
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks 0.06
Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas 0.67
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 0.01
4 1.03
Proteomic risk score for early prediction of kidney disease progression in individuals with high-risk genotypes 0.40
A consensus immune dysregulation framework for sepsis and critical illnesses 0.07
The proteogenomic landscape of the human kidney and implications for cardio-kidney-metabolic health 0.54
Polygenic prediction of body mass index and obesity through the life course and across ancestries 0.01
5 0.96
SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads 0.01
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus 0.11
cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions 0.01
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE 0.28
Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data 0.56
2 0.17
Structural insight into how RAD51 paralog exchange regulates RAD51 filament formation 0.06
Dynamics of microcompartment formation at the mitosis-to-G1 transition 0.11
1 0.13
Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments 0.13
4 3.19
ADNP regulates chromatin architecture and lineage fidelity during neural differentiation 0.53
Igf2 adult-specific skeletal muscle enhancer activity revealed in mice with intergenic CTCF boundary deletion 1.00
The length and strength of compartmental interactions are modulated by condensin II activity. 0.75
Titin-Truncating variants predispose to dilated cardiomyopathy in populations genetically similar to african and european reference populations. 0.92
4 2.43
Coalescence and translation: A language model for population genetics 0.10
Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes 1.00
The DELAYED ABAXIAL TRICHOMES Helitron has dual functions in vegetative and pollen development in Arabidopsis thaliana 1.00
Predicting the unseen: A diffusion-based debiasing framework for transcriptional response prediction at single-cell resolution 0.33
2 1.15
Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation 0.15
Basis for lineage-determining pioneer factors targeting distinct repressed chromatin states 1.00

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