| Ernst |
2022 |
Universal annotation of the human genome through integration of over a thousand epigenomic datasets |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Garrison |
2022 |
The Human Pangenome Project: a global resource to map genomic diversity |
Nature |
Link |
Comp Genetics & Genomics |
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| Savage |
2022 |
Sublinear scaling of the cellular proteome with ploidy |
Nature Communications |
Link |
Mathematical Biology |
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| Hoffmann |
2022 |
Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling |
Cell Reports |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2022 |
Statistics or biology: the zero-inflation controversy about scRNA-seq data |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Zaitlen |
2022 |
Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus |
Science |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2022 |
Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Xiao |
2022 |
Single-cell analysis in lung adenocarcinoma implicates RNA editing in cancer innate immunity and patient prognosis |
Cancer Research |
Link |
Comp Genetics & Genomics |
|
| Li, JJ |
2022 |
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Xiao |
2022 |
scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq |
Science Advances |
Link |
Comp Genetics & Genomics |
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| Qu |
2022 |
R-on-T and the initiation of reentry revisited: Integrating old and new concepts |
Heart Rhythm |
Link |
Mathematical Biology |
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| Wollman |
2022 |
Quantifying the phenotypic information in mRNA abundance |
Molecular systems biology |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2022 |
PCA outperforms popular hidden variable inference methods for molecular QTL mapping |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Xiao |
2022 |
Multifaceted role of RNA editing in promoting loss-of-function of PODXL in cancer |
iScience |
Link |
Comp Genetics & Genomics |
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| Bell |
2022 |
Medical conditions of primary care patients with documented cannabis use and cannabis use disorder in electronic health records: a case control study from an academic health system in a medical marijuana state |
Substance abuse treatment, prevention, and policy |
Link |
Medical Informatics |
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| Qu |
2022 |
Kramers Rate Theory of Pacemaker Dynamics in Noisy Excitable Media |
Physical Review Letters |
Link |
Mathematical Biology |
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| Alber |
2022 |
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations |
Nature Methods |
Link |
Systems & Synthetic Biology |
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| Savage |
2022 |
Improving landscape-scale productivity estimates by integrating trait-based models and remotely-sensed foliar-trait and canopy-structural data |
Ecography |
Link |
Mathematical Biology |
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| Savage |
2022 |
How axon and dendrite branching are guided by time, energy, and spatial constraints |
Nature |
Link |
Mathematical Biology |
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| Pinter-Wollman |
2022 |
Harvester ant nest architecture is more strongly affected by intrinsic than extrinsic factors |
Behavioral Biology |
Link |
Mathematical Biology |
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| Garrison |
2022 |
Getting genetic ancestry right for science and society |
Science |
Link |
Comp Genetics & Genomics |
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| Geschwind |
2022 |
Functional regulatory variants implicate distinct transcriptional networks in dementia |
Science |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2022 |
Functional Hallmarks of Healthy Macrophage Responses: Their Regulatory Basis and Disease Relevance |
Annual review of immunology |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2022 |
Exaggerated false positives by popular differential expression methods when analyzing human population samples |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Savage |
2022 |
Evolution of antibiotic resistance impacts optimal temperature and growth rate in Escherichia coli and Staphylococcus epidermidis |
Journal of Applied Microbiology |
Link |
Mathematical Biology |
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| Garrison |
2022 |
Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives |
Annual review of genomics and human genetics |
Link |
Comp Genetics & Genomics |
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| Meyer |
2022 |
Dual data and motif clustering improves the modeling and interpretation of phosphoproteomic data |
Cell Reports Methods |
Link |
Systems & Synthetic Biology |
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| Jamshidi |
2022 |
Drug transporters OAT1 and OAT3 have specific effects on multiple organs and gut microbiome as revealed by contextualized metabolic network reconstructions |
Scientific Reports |
Link |
Systems & Synthetic Biology |
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| Bell |
2022 |
Distinct components of alert fatigue in physicians’ responses to a noninterruptive clinical decision support alert |
Journal of the American Medical Informatics Association |
Link |
Medical Informatics |
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| Bell |
2022 |
Displaying Cost and Completion Time for Reference Laboratory Test Orders-A Randomized Controlled Trial |
Applied clinical informatics |
Link |
Medical Informatics |
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| Zaitlen |
2022 |
Cross-trait assortative mating is widespread and inflates genetic correlation estimates |
Science |
Link |
Comp Genetics & Genomics |
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| Zhou |
2022 |
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Zhou |
2022 |
cfTrack: A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution |
Clinical Cancer Research |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2022 |
Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students |
PLoS One |
Link |
Comp Genetics & Genomics |
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| Geschwind |
2022 |
Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD |
Nature |
Link |
Comp Genetics & Genomics |
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| Qu |
2022 |
Bistable nerve conduction |
Biophysical Journal |
Link |
Mathematical Biology |
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| Boutros |
2022 |
Age influences on the molecular presentation of tumours |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Garrison |
2022 |
Addressing underrepresentation in genomics research through community engagement |
American journal of human genetics |
Link |
Comp Genetics & Genomics |
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| Jamshidi |
2022 |
A pipeline for automated deep learning liver segmentation (PADLLS) from contrast enhanced CT exams |
Scientific Reports |
Link |
Systems & Synthetic Biology |
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| Wilson |
2022 |
A network paradigm predicts drug synergistic effects using downstream protein–protein interactions |
CPT Pharmacometrics Syst Pharmacol. |
Link |
Systems & Synthetic Biology |
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| Ernst |
2022 |
A mammalian methylation array for profiling methylation levels at conserved sequences |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Meyer |
2022 |
A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity |
Communications Biology |
Link |
Systems & Synthetic Biology |
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| Ernst |
2022 |
A framework for group-wise summarization and comparison of chromatin state annotations |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Kruglyak |
2021 |
Whole-organism eQTL mapping at cellular resolution with single-cell sequencing |
eLife |
Link |
Comp Genetics & Genomics |
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| Bell |
2021 |
Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data |
Journal of the American Medical Informatics Association |
Link |
Medical Informatics |
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| Chou |
2021 |
Using excess deaths and testing statistics to determine COVID-19 mortalities |
European Journal of Epidemiology |
Link |
Mathematical Biology |
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| Hsu |
2021 |
Using deep neural networks and interpretability methods to identify gene expression patterns that predict radiomic features and histology in non-small cell lung cancer |
Journal of Medical Imaging |
Link |
Medical Informatics |
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| Suchard |
2021 |
Untangling introductions and persistence in COVID-19 resurgence in Europe |
Nature |
Link |
Mathematical Biology |
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| Franco |
2021 |
Ultrasensitive molecular controllers for quasi-integral feedback |
Cell Systems |
Link |
Systems & Synthetic Biology |
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| Zaitlen |
2021 |
Toward a fine-scale population health monitoring system |
Cell Press |
Link |
Medical Informatics |
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| Wollman |
2021 |
TNF controls a speed-accuracy tradeoff in the cell death decision to restrict viral spread |
Nature Communications |
Link |
Systems & Synthetic Biology |
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| Jamshidi |
2021 |
Tissue clearing techniques for three-dimensional optical imaging of intact human prostate and correlations with multi-parametric MRI |
Prostate |
Link |
Medical Informatics |
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| Qu |
2021 |
The transient outward potassium current plays a key role in spiral wave breakup in ventricular tissue |
American Journal of Physiology |
Link |
Mathematical Biology |
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| Boutros |
2021 |
The telomere length landscape of prostate cancer |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Pellegrini |
2021 |
The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data |
Gigascience |
Link |
Comp Genetics & Genomics |
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| Pinter-Wollman |
2021 |
The effect of individual learning on collective foraging in honey bees in complex environments |
Animal Bevahiour |
Link |
Mathematical Biology |
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| Pellegrini |
2021 |
The cellular architecture of the antimicrobial response network in human leprosy granulomas |
Nature Immunology |
Link |
Comp Genetics & Genomics |
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| Meyer |
2021 |
Tensor-structured decomposition improves systems serology analysis |
Molecular Systems Biology |
Link |
Systems & Synthetic Biology |
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| Pellegrini |
2021 |
Targeted bisulfite sequencing for biomarker discovery |
Methods |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2021 |
Stimulus-specific responses in innate immunity: Multilayered regulatory circuits |
Immunity |
Link |
Systems & Synthetic Biology |
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| Hoffmann |
2021 |
Stimulus-specific responses in innate immunity: Multilayered regulatory circuits |
Immunity |
Link |
Systems & Synthetic Biology |
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| Pellegrini |
2021 |
Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells |
Stem Cell Reports |
Link |
Comp Genetics & Genomics |
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| Boutros |
2021 |
Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2021 |
Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses |
Immunity |
Link |
Systems & Synthetic Biology |
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| Ernst |
2021 |
Single-nucleotide conservation state annotation of the SARS-CoV-2 genome |
Communications Biology |
Link |
Comp Genetics & Genomics |
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| Pellegrini |
2021 |
Single-cell sequencing of human white adipose tissue identifies new cell states in health and obesity |
Nature Immunology |
Link |
Comp Genetics & Genomics |
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| Pellegrini |
2021 |
Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase |
Plant Cell |
Link |
Comp Genetics & Genomics |
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| Qu |
2021 |
Simultaneous activation of the small conductance calcium-activated potassium current by acetylcholine and inhibition of sodium current by ajmaline cause J-wave syndrome in Langendorff-perfused rabbit ventricles |
Heart Rhythm |
Link |
Mathematical Biology |
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| Qu |
2021 |
Sex-specific I KAS activation in rabbit ventricles with drug-induced QT prolongation |
Heart Rhythm |
Link |
Mathematical Biology |
Download PDF |
| Li, JJ |
2021 |
scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2021 |
scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Deeds |
2021 |
Robustness and the evolution of length control strategies in the T3SS and flagellar hook |
Biophysical Journal |
Link |
Mathematical Biology |
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| Wang, S |
2021 |
Roadmap on biology in time varying environments |
Physical Biology |
Link |
Mathematical Biology |
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| Pasaniuc |
2021 |
Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Bell |
2021 |
Reducing Emergency Department Visits Among Patients With Diabetes by Embedding Clinical Pharmacists in the Primary Care Teams |
Medical Care |
Link |
Medical Informatics |
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| Pasaniuc |
2021 |
Quantifying the contribution of dominance deviation effects to complex trait variation in biobank-scale data |
American Journal of Human Genetics |
Link |
Comp Genetics & Genomics |
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| Sankararaman |
2021 |
Quantifying the contribution of dominance deviation effects to complex trait variation in biobank-scale data |
American Journal of Human Genetics |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2021 |
Quantifying information accumulation encoded in the dynamics of biochemical signaling |
Nature Communications |
Link |
Mathematical Biology |
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| Li, JJ |
2021 |
PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Bell |
2021 |
Privacy-protecting, reliable response data discovery using COVID-19 patient observations |
Journal of the American Medical Informatics Association |
Link |
Medical Informatics |
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| Bell |
2021 |
Primary nonadherence to statin medications: Survey of patient perspectives |
Preventive Medicine Reports |
Link |
Medical Informatics |
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| Garfinkel |
2021 |
Predicting wet age-related macular degeneration (AMD) using DARC (detecting apoptosing retinal cells) AI (artificial intelligence) technology |
Expert Review of Molecular Diagnostics |
Link |
Systems & Synthetic Biology |
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| Pasaniuc |
2021 |
Pre-existing conditions in Hispanics/Latinxs that are COVID-19 risk factors |
iScience |
Link |
Comp Genetics & Genomics |
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| Pasaniuc |
2021 |
Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data |
Journal of Computational Biology |
Link |
Comp Genetics & Genomics |
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| Arnold |
2021 |
Optimizing Spatial Biopsy Sampling for the Detection of Prostate Cancer |
The Journal of Urology |
Link |
Medical Informatics |
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| Arboleda |
2021 |
Novel variants in KAT6B spectrum of disorders expand our knowledge of clinical manifestations and molecular mechanisms |
Molecular Genetics & Genomics Medicine |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2021 |
NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages |
Science |
Link |
Systems & Synthetic Biology |
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| Hoffmann |
2021 |
NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages |
Science |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2021 |
Network Modeling in Biology: Statistical Methods for Gene and Brain Networks |
Statistical Science |
Link |
Comp Genetics & Genomics |
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| Wang, S |
2021 |
Naturally evolvable antibody affinity may be physically limited |
Editorial |
Link |
Mathematical Biology |
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| Pasaniuc |
2021 |
Multitrait transcriptome-wide association study (TWAS) tests |
Genetic Epidemiology |
Link |
Comp Genetics & Genomics |
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| Pinter-Wollman |
2021 |
Modularity and connectivity of nest structure scale with colony size |
International Journal of Organic Evolution |
Link |
Mathematical Biology |
Download PDF |
| Meyer |
2021 |
Modeling cell-specific dynamics and regulation of the common gamma chain cytokines |
Cell Reports |
Link |
Systems & Synthetic Biology |
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| Qu |
2021 |
Mitochondrial depolarization promotes calcium alternans: Mechanistic insights from a ventricular myocyte model |
PLoS Computational Biology |
Link |
Mathematical Biology |
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| Graeber |
2021 |
Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2-induced systemic toxicity |
JCI Insight |
Link |
Systems & Synthetic Biology |
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| Qu |
2021 |
Mechanisms of Premature Ventricular Complexes Caused by QT Prolongation |
Biophysical Journal |
Link |
Mathematical Biology |
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| Zaitlen |
2021 |
Mechanisms of phase-3 early afterdepolarizations and triggered activities in ventricular myocyte models |
Physiology Reports |
Link |
Mathematical Biology |
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| Li, JJ |
2021 |
mbImpute: an accurate and robust imputation method for microbiome data |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Chou |
2021 |
Mathematical Models of Blood-Brain Barrier Transport of Monoclonal Antibodies Targeting the Transferrin Receptor and the Insulin Receptor |
Pharmaceuticals |
Link |
Mathematical Biology |
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| Arboleda |
2021 |
Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples |
Nature Biomedical Engineering |
Link |
Comp Genetics & Genomics |
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| Kruglyak |
2021 |
Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples |
Nature Biomedical Engineering |
Link |
Comp Genetics & Genomics |
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| Pasaniuc |
2021 |
Mapping the human genetic architecture of COVID-19 |
Nature |
Link |
Comp Genetics & Genomics |
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| Zaitlen |
2021 |
Life and death saddles in the heart |
Physical Review E. |
Link |
Mathematical Biology |
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| Pasaniuc |
2021 |
Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies |
PLoS Genetics |
Link |
Comp Genetics & Genomics |
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| Pasaniuc |
2021 |
Leveraging eQTLs to identify individual-level tissue of interest for a complex trait |
PLoS Computational Biology |
Link |
Comp Genetics & Genomics |
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| Ernst |
2021 |
Learning a genome-wide score of human-mouse conservation at the functional genomics level |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Pasaniuc |
2021 |
Large-scale cross-cancer fine-mapping of the 5p15.33 region reveals multiple independent signals |
HGG Advances |
Link |
Comp Genetics & Genomics |
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| Chou |
2021 |
Kinetic theory for structured populations: application to stochastic sizer-timer models of cell proliferation |
Journal of Physics |
Link |
Mathematical Biology |
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| Wollman |
2021 |
Joint cell segmentation and cell type annotation for spatial transcriptomics |
Molecular Systems Biology |
Link |
Systems & Synthetic Biology |
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| Pasaniuc |
2021 |
Integrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Jamshidi |
2021 |
Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration |
Scientific Reports |
Link |
Systems & Synthetic Biology |
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| Halperin |
2021 |
Imputation of the continuous arterial line blood pressure waveform from non-invasive measurements using deep learning |
Scientific Reports |
Link |
Comp Genetics & Genomics |
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| Bigham |
2021 |
Identifying adaptive alleles in the human genome: from selection mapping to functional validation |
Human Genetics |
Link |
Comp Genetics & Genomics |
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| Savage |
2021 |
How Axon and Dendrite Branching Are Governed by Time, Energy, and Spatial Constraints |
|
Link |
Mathematical Biology |
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| Bigham |
2021 |
High-altitude deer mouse hypoxia-inducible factor-2α shows defective interaction with CREB-binding protein |
Journal of Biological Chemistry |
Link |
Comp Genetics & Genomics |
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| Arnold |
2021 |
Hierarchical Graph Pathomic Network for Progression Free Survival Prediction |
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) |
Link |
Medical Informatics |
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| Bigham |
2021 |
Genome-Wide Epigenetic Signatures of Adaptive Developmental Plasticity in the Andes |
Genome Biology and Evolution |
Link |
Comp Genetics & Genomics |
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| Hsu |
2021 |
Generalizability and Transportability of the National Lung Screening Trial data: Extending trial results to different populations |
Cancer Epidemiology, Biomarkers & Prevention |
Link |
Medical Informatics |
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| Pasaniuc |
2021 |
Gene Expression Imputation Across Multiple Tissue Types Provides Insight Into the Genetic Architecture of Frontotemporal Dementia and Its Clinical Subtypes |
Biological Psychiatry |
Link |
Comp Genetics & Genomics |
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| Arboleda |
2021 |
From chemoproteomic-detected amino acids to genomic coordinates: insights into precise multi-omic data integration |
Molecular Systems Biology |
Link |
Comp Genetics & Genomics |
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| Arnold |
2021 |
Federated Learning Improves Site Performance in Multi-Center Deep Learning Without Data Sharing |
Journal of the American Medical Informatics Association |
Link |
Medical Informatics |
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| Pellegrini |
2021 |
Extracellular traps released by antimicrobial TH17 cells contribute to host defense |
The Journal of clinical investigation |
Link |
Comp Genetics & Genomics |
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| Hsu |
2021 |
Experiment Selection in Meta-Analytic Piecemeal Causal Discovery |
IEEE Access |
Link |
Medical Informatics |
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| Geschwind |
2021 |
Evolutionary conservation and divergence of the human brain transcriptome |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Venugopal |
2021 |
Engaging biological oscillators through second messenger pathways permits emergence of a robust gastric slow-wave during peristalsis |
PLoS Computational Biology |
Link |
Systems & Synthetic Biology |
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| Franco |
2021 |
Dynamic self-assembly of compartmentalized DNA nanotubes |
Nature Communications |
Link |
Systems & Synthetic Biology |
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| Zaitlen |
2021 |
Disentangling selection on genetically correlated polygenic traits via whole-genome genealogies |
American Journal of Human Genetics |
Link |
Comp Genetics & Genomics |
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| Zaitlen |
2021 |
Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Bell |
2021 |
Comparative Effectiveness of Aspirin Dosing in Cardiovascular Disease |
The New England Journal of Medicine |
Link |
Medical Informatics |
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| Geschwind |
2021 |
Coexpression network architecture reveals the brain-wide and multiregional basis of disease susceptibility |
Nature Neuroscience |
Link |
Comp Genetics & Genomics |
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| Wang, S |
2021 |
Coevolutionary transitions emerging from flexible molecular recognition and eco-evolutionary feedback |
iScience |
Link |
Mathematical Biology |
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| Pellegrini |
2021 |
Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes |
Epigenetics |
Link |
Comp Genetics & Genomics |
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| Pasaniuc |
2021 |
CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity |
Nature Cancer |
Link |
Comp Genetics & Genomics |
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| Savage |
2021 |
Cancer as a Model System for Testing Metabolic Scaling Theory |
Frontiers in Ecololy and Evolution |
Link |
Mathematical Biology |
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| Savage |
2021 |
Branching principles of animal and plant networks identified by combining extensive data, machine learning and modelling |
J R Soc Interface |
Link |
Mathematical Biology |
Download PDF |
| Pellegrini |
2021 |
BiSulfite Bolt: A bisulfite sequencing analysis platform |
Gigascience |
Link |
Comp Genetics & Genomics |
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| Arnold |
2021 |
Bidirectional Representation Learning from Transformers using Multimodal Electronic Health Record Data to Predict Depression |
IEEE Journal of Biomedical and Health Informatics |
Link |
Medical Informatics |
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| Halperin |
2021 |
Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging |
NPJ Digital Medicine |
Link |
Comp Genetics & Genomics |
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| Hsu |
2021 |
Automated identification and assignment of colonoscopy surveillance recommendations for individuals with colorectal polyps |
Gastrointestinal Endoscopy |
Link |
Medical Informatics |
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| Arnold |
2021 |
Attention-Guided Discriminative Region Localization and Label Distribution Learning for Bone Age Assessment |
IEEE Journal of Biomedical and Health Informatics |
Link |
Medical Informatics |
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| Hsu |
2021 |
Association of Inclusion of More Black Individuals in Lung Cancer Screening With Reduced Mortality |
Jama Network Open |
Link |
Medical Informatics |
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| Kruglyak |
2021 |
Ancient balancing selection maintains incompatible versions of the galactose pathway in yeast |
Science |
Link |
Comp Genetics & Genomics |
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| Xiao |
2021 |
Allele-specific alternative splicing and its functional genetic variants in human tissues |
Genome Researchh |
Link |
Comp Genetics & Genomics |
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| Wang, S |
2021 |
Aging-induced fragility of the immune system |
Journal of Theoretical Biology |
Link |
Mathematical Biology |
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| Sankararaman |
2021 |
Advancing admixture graph estimation via maximum likelihood network orientation |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Qu |
2021 |
Activation of TRPC (Transient Receptor Potential Canonical) Channel Currents in Iron Overloaded Cardiac Myocytes |
Circulation: Arrhythmia and Electrophysiology |
Link |
Mathematical Biology |
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| Pasaniuc |
2021 |
A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Pinter-Wollman |
2021 |
A reproductive heir has a central position in multilayer social networks of paper wasps |
Animal Behavior |
Link |
Mathematical Biology |
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| Boutros |
2021 |
A practical guide to cancer subclonal reconstruction from DNA sequencing |
Nature Methods |
Link |
Comp Genetics & Genomics |
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| Arnold |
2021 |
A Multi-resolution Model for Histopathology Image Classification and Localization with Multiple Instance Learning |
Computers in Biology and Medicine |
Link |
Medical Informatics |
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| Zaitlen |
2021 |
A model and test for coordinated polygenic epistasis in complex traits |
PNAS |
Link |
Comp Genetics & Genomics |
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| Pinter-Wollman |
2021 |
A guide to choosing and implementing reference models for social network analysis |
Biological Reviews |
Link |
Mathematical Biology |
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| Chou |
2021 |
A frequency-dependent p-adaptive technique for spectral methods |
Journal of Computational Physics |
Link |
Mathematical Biology |
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| Chou |
2020 |
Why case fatality ratios can be misleading: individual- and population-based mortality estimates and factors influencing them |
Physical Biology |
Link |
Mathematical Biology |
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| Savage |
2020 |
Unraveling why we sleep: Quantitative analysis reveals abrupt transition from neural reorganization to repair in early development |
Science Advances |
Link |
Mathematical Biology |
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| Wang, S |
2020 |
Tuning environmental timescales to evolve and maintain generalists |
PNAS |
Link |
Mathematical Biology |
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| Arnold |
2020 |
Towards Heterogeneous Information Fusion: Bipartite Graph Convolutional Networks for In Silico Drug Repurposing |
Intelligent Systems for Molecular Biology (ISMB) |
Link |
Medical Informatics |
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| Coller |
2020 |
Towards a Machine-Learning-Assisted Dielectric Sensing Platform for Point-of-Care Wound Monitoring |
IEEE |
Link |
Medical Informatics |
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| Bell |
2020 |
The Impact of Resident Holdover Admissions on Length of Hospital Stay and Risk of Transfer to an Intensive Care Unit |
Journal of patient safety |
Link |
Medical Informatics |
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| Pellegrini |
2020 |
The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Sehl |
2020 |
The Effects of Anti-retroviral Therapy on Epigenetic Age Acceleration Observed in HIV-1-infected Adults |
Pathogens & Immunity |
Link |
Mathematical Biology |
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| Sehl |
2020 |
The acute effects of adjuvant radiation and chemotherapy on peripheral blood epigenetic age in early stage breast cancer patients |
NPJ Breast Cancer |
Link |
Mathematical Biology |
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| Geschwind |
2020 |
Tau Pathology Drives Dementia Risk-Associated Gene Networks toward Chronic Inflammatory States and Immunosuppression |
Cell Reports |
Link |
Comp Genetics & Genomics |
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| Xiao |
2020 |
Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2020 |
Statistical Hypothesis Testing versus Machine Learning Binary Classification: Distinctions and Guidelines |
CellPress Patterns |
Link |
Comp Genetics & Genomics |
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| Yang |
2020 |
Single-cell Study of Two Rat Models of Pulmonary Arterial Hypertension Reveals Connections to Human Pathobiology and Drug Repositioning |
American Journal of Respiratory and Critical Care Medicine |
Link |
Comp Genetics & Genomics |
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| Venugopal |
2020 |
Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis |
Neurobiology of Disease |
Link |
Systems & Synthetic Biology |
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| Garfinkel |
2020 |
Shaping Waves of Bone Morphogenetic Protein Inhibition During Vascular Growth |
Circulation Research |
Link |
Systems & Synthetic Biology |
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| Wang, S |
2020 |
Shaping Polyclonal Responses via Antigen-Mediated Antibody Interference |
iScience |
Link |
Mathematical Biology |
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| Boutros |
2020 |
Sex differences in oncogenic mutational processes |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Wilson |
2020 |
Scientific considerations for global drug development |
Science Translational Medicine |
Link |
Systems & Synthetic Biology |
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| Sankararaman |
2020 |
Scalable probabilistic PCA for large-scale genetic variation data |
PLoS Genetics |
Link |
Comp Genetics & Genomics |
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| Xiao |
2020 |
RNA editing in cancer impacts mRNA abundance in immune response pathways |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Garfinkel |
2020 |
Redundancy and multifunctionality among spinal locomotor networks |
Journal of Neurophysiology |
Link |
Systems & Synthetic Biology |
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| Sankararaman |
2020 |
Recovering signals of ghost archaic introgression in African populations |
Science Advances |
Link |
Comp Genetics & Genomics |
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| Zhou |
2020 |
Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA |
Journal of Translational Medicine |
Link |
Medical Informatics |
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| Chou |
2020 |
PDE models of adder mechanisms in cellular proliferations |
Society for Industrial and Applied Mathematics |
Link |
Mathematical Biology |
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| Pinter-Wollman |
2020 |
Observing the unwatchable: Integrating automated sensing, naturalistic observations and animal social network analysis in the age of big data |
Journal of Animal Ecology |
Link |
Mathematical Biology |
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| Yang |
2020 |
Multi-tissue Multi-omics Systems Biology of Complex Diseases |
Trends in Molecular Medicine |
Link |
Comp Genetics & Genomics |
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| Zaitlen |
2020 |
Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for “polygenic epistasis” |
PLoS Genetics |
Link |
Comp Genetics & Genomics |
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| Jamshidi |
2020 |
Metabolome Changes during In Vivo Red Cell Aging Reveal Disruption of Key Metabolic Pathways |
iScience |
Link |
Systems & Synthetic Biology |
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| Coller |
2020 |
Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma |
NPJ Genomic Medicine |
Link |
Systems & Synthetic Biology |
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| Coller |
2020 |
Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma |
NPJ Genomic Medicine |
Link |
Systems & Synthetic Biology |
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| Pellegrini |
2020 |
Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues |
Epigenetics |
Link |
Comp Genetics & Genomics |
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| Askary |
2020 |
In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription |
Nature Biotechnology |
Link |
Systems & Synthetic Biology |
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| Bell |
2020 |
Impact of a “Chart Closure” Hard Stop Alert on Prescribing for Elevated Blood Pressures Among Patients With Diabetes: Quasi-Experimental Study |
JMIR medical informatics |
Link |
Medical Informatics |
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| Ernst |
2020 |
Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Pinter-Wollman |
2020 |
Heritable learning phenotypes drive collective cognition |
|
Link |
Mathematical Biology |
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| Zaitlen |
2020 |
Genetic Influences on Disease Subtypes |
Annual Review of Genomics and Human Genetics |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2020 |
Gene Regulatory Strategies that Decode the Duration of NFkB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression |
Cell Systems |
Link |
Systems & Synthetic Biology |
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| Plath |
2020 |
Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation |
Nature Cell Biology |
Link |
Systems & Synthetic Biology |
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| Xiao |
2020 |
Extracellular microRNA 3’ end modification across diverse body fluids |
Epigenetics |
Link |
Comp Genetics & Genomics |
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| Xiao |
2020 |
Expanded encyclopaedias of DNA elements in the human and mouse genomes |
Nature |
Link |
Comp Genetics & Genomics |
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| Lloyd-Smith |
2020 |
Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19 |
eLife |
Link |
Medical Informatics |
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| Sankararaman |
2020 |
Efficient variance components analysis across millions of genomes |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2020 |
DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features |
Science Advances |
Link |
Comp Genetics & Genomics |
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| Chou |
2020 |
Diversity in Biology: definitions, quantification and models |
Physical Biology |
Link |
Mathematical Biology |
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| Boutros |
2020 |
Divergent mutational processes distinguish hypoxic and normoxic tumours |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Hsu |
2020 |
Discovering and interpreting transcriptomic drivers of imaging traits using neural networks |
Oxford Academic |
Link |
Medical Informatics |
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| Plath |
2020 |
Direct Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair Response |
Cell Stem Cell |
Link |
Systems & Synthetic Biology |
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| Deeds |
2020 |
Crosstalk and ultrasensitivity in protein degradation pathways |
PLoS Computational Biology |
Link |
Mathematical Biology |
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| Deeds |
2020 |
Cooperativity in Proteasome Core Particle Maturation |
iScience |
Link |
Mathematical Biology |
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| Sul |
2020 |
Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates |
Translational Psychiatry |
Link |
Comp Genetics & Genomics |
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| Ernst |
2020 |
ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation |
NAR Genomics and Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Pellegrini |
2020 |
Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes |
Epigenetics |
Link |
Comp Genetics & Genomics |
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| Pellegrini |
2020 |
Cardiac fibroblast proliferation rates and collagen expression mature early and are unaltered with advancing age |
JCI Insight |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2020 |
Bipartite Tight Spectral Clustering (BiTSC) Algorithm for Identifying Conserved Gene Co-clusters in Two Species |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Bui |
2020 |
Biomedical Real-time Health Evaluation (BREATHE): Toward an mHealth informatics platform |
JAMIA Open |
Link |
Medical Informatics |
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| Li, JJ |
2020 |
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data |
Cell Systems |
Link |
Comp Genetics & Genomics |
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| Bell |
2020 |
Association of a Care Bundle for Early Sepsis Management With Mortality Among Patients With Hospital-Onset or Community-Onset Sepsis |
JAMA Internal Medicine |
Link |
Medical Informatics |
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| Ernst |
2020 |
An integrative approach for fine-mapping chromatin interactions |
Bioinformatics |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2020 |
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions |
Molecular Systems Biology |
Link |
Systems & Synthetic Biology |
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| Wilson |
2020 |
An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias |
PLoS Computational Biology |
Link |
Systems & Synthetic Biology |
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| Lloyd-Smith |
2020 |
Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1 |
New England Journal of Medicine |
Link |
Systems & Synthetic Biology |
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| Pellegrini |
2020 |
ACTINN: automated identification of cell types in single cell RNA sequencing |
Bioinformatics |
Link |
Medical Informatics |
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| Halperin |
2020 |
Accurate estimation of cell composition in bulk expression through robust integration of single-cell information |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Bell |
2020 |
Accuracy of an Electronic Health Record Patient Linkage Module Evaluated between Neighboring Academic Health Care Centers |
Applied clinical informatics |
Link |
Medical Informatics |
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| Suchard |
2020 |
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2 |
Nature Communications |
Link |
Mathematical Biology |
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| Sankararaman |
2020 |
A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies |
Journal of Computational Biology |
Link |
Comp Genetics & Genomics |
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| Plath |
2020 |
A protein assembly mediates Xist localization and gene silencing |
Nature |
Link |
Systems & Synthetic Biology |
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| Plath |
2020 |
A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells |
Cell Stem Cell |
Link |
Systems & Synthetic Biology |
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| Boutros |
2020 |
A community effort to create standards for evaluating tumor subclonal reconstruction |
Nature Biotechnology |
Link |
Medical Informatics |
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| Li, JJ |
2019 |
Word and sentence embedding tools to measure semantic similarity of Gene Ontology terms by their definitions |
Journal of Computational Biology |
Link |
Medical Informatics |
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| Xiao |
2019 |
Widespread RNA Editing Dysregulation in Brains From Autistic Individuals |
Nature Neuroscience |
Link |
Comp Genetics & Genomics |
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| Bui |
2019 |
Using sequential decision making to improve lung cancer screening performance |
IEEE Access |
Link |
Medical Informatics |
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| Zaitlen |
2019 |
Ultra-rare variants drive substantial cis-heritability of human gene expression |
Nature Genetics |
Link |
Comp Genetics & Genomics |
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| Wang, S |
2019 |
Trait-space patterning and the role of feedback in antigen-immunity coevolution coevolution |
Physical Review Research |
Link |
Mathematical Biology |
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| Pinter-Wollman |
2019 |
The use of multilayer network analysis in animal behaviour |
Animal Behavior |
Link |
Mathematical Biology |
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| Boutros |
2019 |
The Proteogenomic Landscape of Curable Prostate Cancer |
Cancel Cell |
Link |
Comp Genetics & Genomics |
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| Ernst |
2019 |
Systematic discovery of conservation states for single-nucleotide annotation of the human genome |
Communications Biology |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2019 |
Substrate complex competition – a regulatory motif that allows NFkB RelA to license but not amplify NFkB/RelA |
PNAS |
Link |
Mathematical Biology |
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| Savage |
2019 |
Stressor interaction networks suggest antibiotic resistance co-opted from stress responses to temperature |
The ISME Journal |
Link |
Mathematical Biology |
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| Horvath |
2019 |
Reversal of epigenetic aging and immunosenescent trends in humans |
Aging Cell |
Link |
Comp Genetics & Genomics |
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| Venugopal |
2019 |
Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons |
PLoS |
Link |
Systems & Synthetic Biology |
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| Coller |
2019 |
RECK isoforms differentially regulate fibroblast migration by modulating tubulin post-translational modifications |
BBRC |
Link |
Systems & Synthetic Biology |
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| Kruglyak |
2019 |
Rare variants contribute disproportionately to quantitative trait variation in yeast |
eLIFE |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2019 |
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes |
Genome Biology |
Link |
Systems & Synthetic Biology |
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| Yang |
2019 |
Prenatal Bisphenol A Exposure in Mice Induces Multi-tissue Multi-omics Disruptions Linking to Cardiometabolic Disorders |
Endocrinology |
Link |
Comp Genetics & Genomics |
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| DiStefano III |
2019 |
Predicting Optimal Combination LT4 + LT3 Therapy for Hypothyroidism Based on Residual Thyroid Function |
Frontiers in Endocrinology |
Link |
Mathematical Biology |
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| Garud |
2019 |
Population genetics in the Human Microbiome |
Trends in Genetics |
Link |
Comp Genetics & Genomics |
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| Wilson |
2019 |
PathFXweb: a web application for identifying drug safety and efficacy phenotypes |
Bioinformatics |
Link |
Systems & Synthetic Biology |
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| Graeber |
2019 |
Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies |
Cancer Cell |
Link |
Comp Genetics & Genomics |
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| Xiao |
2019 |
mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq |
Cell Systems |
Link |
Comp Genetics & Genomics |
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| Boutros |
2019 |
Molecular landmarks of tumor hypoxia across cancer types |
Nature Genetics |
Link |
Medical Informatics |
Download PDF |
| Halperin |
2019 |
Modeling the temporal dynamics of the gut microbial community in adults and infants |
PLoS Computational Biology |
Link |
Systems & Synthetic Biology |
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| Lloyd-Smith |
2019 |
Mechanistic dose-response modelling of animal challenge data shows that intact skin is a crucial barrier to leptospiral infection |
Philosophical Transactions of the Royal Society B |
Link |
Mathematical Biology |
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| Li, JJ |
2019 |
Matched Bipartite Block Model with Covariates |
Journal of Machine Learning Research |
Link |
Comp Genetics & Genomics |
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| Eskin |
2019 |
Leveraging allelic imbalance to refine fine-mapping for eQTL studies |
PLoS Genetics |
Link |
Comp Genetics & Genomics |
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| Sul |
2019 |
Interrogating the Genetic Determinants of Tourette’s Syndrome and Other Tic Disorders Through Genome-Wide Association Studies |
The American Journal of Psychiatry |
Link |
Comp Genetics & Genomics |
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| Geschwind |
2019 |
Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks |
Cell |
Link |
Systems & Synthetic Biology |
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| Hoffmann |
2019 |
Identifying determinants of persistent MRSA bacteremia using mathematical modeling |
PLoS Comp |
Link |
Mathematical Biology |
Download PDF |
| Geschwind |
2019 |
Human evolved regulatory elements modulate genes involved in cortical expansion and neurodevelopmental disease susceptibility |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Pellegrini |
2019 |
Human epigenetic ageing is logarithmic with time across the entire lifespan |
Epigenetics |
Link |
Comp Genetics & Genomics |
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| Kruglyak |
2019 |
Highly parallel genome variant engineering with CRISPR-Cas9 |
Nature Genetics |
Link |
Systems & Synthetic Biology |
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| Boutros |
2019 |
Genome-wide germline correlates of the epigenetic landscape of prostate cancer |
Nature Medicine |
Link |
Comp Genetics & Genomics |
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| Geschwind |
2019 |
Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms |
Cell |
Link |
Comp Genetics & Genomics |
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| Sul |
2019 |
ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest. |
PLoS Computational Biology |
Link |
Comp Genetics & Genomics |
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| Halperin |
2019 |
FEAST: fast expectation-maximization for microbial source tracking |
Nature Methods |
Link |
Comp Genetics & Genomics |
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| Hsu |
2019 |
External validation and recalibration of the Brock model to predict probability of cancer in pulmonary nodules using NLST data |
BMJ Journals |
Link |
Medical Informatics |
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| Wang, S |
2019 |
Evolving generalists in switching rugged landscapes |
PLoS Computational Biology |
Link |
Mathematical Biology |
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| Garud |
2019 |
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts |
Plos Biology |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2019 |
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences |
Nucleic Acids Research |
Link |
Comp Genetics & Genomics |
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| Horvath |
2019 |
DNA methylation GrimAge strongly predicts lifespan and healthspan |
Aging Cell |
Link |
Comp Genetics & Genomics |
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| Pellegrini |
2019 |
DNA Methylation Changes More Slowly Than Physiological States in Response to Weight Loss in Genetically Diverse Mouse Strains |
Front Endocrinol |
Link |
Comp Genetics & Genomics |
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| Alber |
2019 |
De Novo Structural Pattern Mining in Cellular Electron Cryotomograms |
Structure |
Link |
Systems & Synthetic Biology |
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| Halperin |
2019 |
CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasets |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Suchard |
2019 |
Comprehensive comparative effectiveness and safety of first-line antihypertensive drug classes: a systematic, multinational, large-scale analysis |
Lancet |
Link |
Mathematical Biology |
Download PDF |
| Bell |
2019 |
Clinical Characteristics of and Risk Factors for Chronic Kidney Disease Among Adults and Children: An Analysis of the CURE-CKD Registry |
JAMA Network Open |
Link |
Medical Informatics |
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| Savage |
2019 |
Climate shapes and shifts functional biodiversity in forests worldwide |
PNAS |
Link |
Mathematical Biology |
Download PDF |
| Venugopal |
2019 |
Circuit-Specific Early Impairment of Proprioceptive Sensory Neurons in the SOD1 G93A Mouse Model for ALS |
The Journal of Neuroscience |
Link |
Systems & Synthetic Biology |
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| Lloyd-Smith |
2019 |
Childhood immune imprinting to influenza A shapes birth year-specific risk during seasonal H1N1 and H3N2 epidemics |
PLoS Pathogens |
Link |
Mathematical Biology |
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| Halperin |
2019 |
Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Hsu |
2019 |
An interpretable deep hierarchical semantic convolutional neural network for lung nodule malignancy classification |
Expert Systems with Applications |
Link |
Medical Informatics |
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| Halperin |
2019 |
An automated machine learning-based model predicts postoperative mortality using readily-extractable preoperative electronic health record data |
BJA |
Link |
Comp Genetics & Genomics |
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| Xiao |
2019 |
Allele-specific Binding of RNA-binding Proteins Reveals Functional Genetic Variants in the RNA |
Nature Communications |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2019 |
AIDE: annotation-assisted isoform discovery with high precision |
Genome Research |
Link |
Comp Genetics & Genomics |
Download PDF |
| Li, JJ |
2019 |
A statistical simulator scDesign for rational scRNA-seq experimental design |
Bioinformatics |
Link |
Systems & Synthetic Biology |
Download PDF |
| Sankararaman |
2019 |
A statistical model for reference-free inference of archaic local ancestry |
PLoS Genetics |
Link |
Comp Genetics & Genomics |
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| Geschwind |
2019 |
A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation |
Neuron |
Link |
Systems & Synthetic Biology |
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| Hoffmann |
2019 |
A regulatory circuit controlling the Dynamics of NFkB cRel transitions B-cells from proliferation to plasma cell differentiation |
Immunity |
Link |
Systems & Synthetic Biology |
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| Chou |
2019 |
A Mathematical Model of the Effects of Aging on Naive T Cell Populations and Diversity |
Society for Mathematical Biology |
Link |
Mathematical Biology |
Download PDF |
| Arnold |
2019 |
A Machine Learning Approach to Classifying Self-Reported Health Status in a cohort of Patients with Heart Disease using Activity Tracker Data |
IEEE Journal of Biomedical and Health Informatics |
Link |
Medical Informatics |
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| Arnold |
2019 |
A Machine Learning Approach for Classifying Ischemic Stroke Onset Time from Imaging |
IEEE Transactions on Medical Imaging |
Link |
Medical Informatics |
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| Pinter-Wollman |
2018 |
The impact of the built environment on health behaviours and disease transmission in social systems |
Philosophical Transactions B |
Link |
Systems & Synthetic Biology |
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| Pinter-Wollman |
2018 |
Social interactions shape individual and collective personality in social spiders |
Proceedings B |
Link |
Mathematical Biology |
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| Yang |
2018 |
Single cell molecular alterations reveal target cells and pathways of concussive brain injury |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Hsu |
2018 |
Researchmaps.org for integrating and planning research |
PLoS One |
Link |
Medical Informatics |
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| Graeber |
2018 |
Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage |
Science |
Link |
Systems & Synthetic Biology |
Download PDF |
| Coller |
2018 |
RECK isoforms have opposing effects on cell migration |
Molecular Biology of the Cell |
Link |
Systems & Synthetic Biology |
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| Alber |
2018 |
Producing genome structure populations with the dynamic and automated PGS software |
Nature Protocols |
Link |
Systems & Synthetic Biology |
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| Bell |
2018 |
Primary Care Provider Adherence to an Alert for Intensification of Diabetes Blood Pressure Medications Before and After the Addition of a “Chart Closure” Hard Stop |
Journal of American Medical Informatics Association |
Link |
Medical Informatics |
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| Savage |
2018 |
Prevalence and patterns of higher-order drug interactions in Escherichia coli |
NPJ Systems Biology and Applications |
Link |
Systems & Synthetic Biology |
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| Boutros |
2018 |
Pathway-based subnetworks enable cross-disease biomarker discovery |
Nature Communications |
Link |
Medical Informatics |
Download PDF |
| Wilson |
2018 |
PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development |
PLoS Computational Biology |
Link |
Systems & Synthetic Biology |
Download PDF |
| Arnold |
2018 |
Path R-CNN for Prostate Cancer Diagnosis and Gleason Grading of Histological Images |
IEEE Transactions on Medical Imaging |
Link |
Medical Informatics |
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| Hoffmann |
2018 |
Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation |
PNAS |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2018 |
Neyman-Pearson classification algorithms and NP receiver operating characteristics |
Science Advances |
Link |
Comp Genetics & Genomics |
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| Graeber |
2018 |
Multi-stage differentiation defines melanoma subtypes with differential vulnerability to drug-induced iron-dependent oxidative stress |
Cancer Cell |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2018 |
MSIQ: Joint modeling of multiple RNA-seq samples for accurate isoform quantification |
Annals of Applied Statistics |
Link |
Systems & Synthetic Biology |
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| Chou |
2018 |
Modeling large fluctuations of thousands of clones during hematopoiesis: the role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque |
PLoS Computational Biology |
Link |
Mathematical Biology |
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| Li, JJ |
2018 |
Modeling and analysis of RNA-seq data: a review from a statistical perspective |
Quantitative Biology |
Link |
Systems & Synthetic Biology |
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| Hoffmann |
2018 |
Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing |
NAR |
Link |
Mathematical Biology |
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| Hsu |
2018 |
Longitudinal patterns in clinical and imaging measurements predict residual survival in glioblastoma patients |
Scientific Reports |
Link |
Medical Informatics |
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| Pinter-Wollman |
2018 |
Interdisciplinary approaches for uncovering the impacts of architecture on collective behaviour |
Philosophical Transactions B |
Link |
Mathematical Biology |
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| Coller |
2018 |
Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer |
Scientific Reports |
Link |
Systems & Synthetic Biology |
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| Yang |
2018 |
Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-Alcoholic Fatty Liver Disease |
Cell Systems |
Link |
Comp Genetics & Genomics |
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| Bell |
2018 |
Improving admission medication reconciliation with pharmacists or pharmacy technicians in the emergency department; a randomized controlled trial |
BMJ Quality and Safety |
Link |
Medical Informatics |
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| Horvath |
2018 |
GWAS of epigenetic aging rates in blood reveals a critical role for TERT |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Kruglyak |
2018 |
Genetics of trans-regulatory variation in gene expression |
eLIFE |
Link |
Comp Genetics & Genomics |
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| Jamshidi |
2018 |
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting |
PLOS Computational Biology |
Link |
Systems & Synthetic Biology |
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| Chou |
2018 |
Exact steady-state distributions of multispecies birth-death-immigration processes: effects of mutations and carrying capacity on diversity |
Journal of Statistical Physics |
Link |
Mathematical Biology |
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| Pellegrini |
2018 |
Epigenome-wide association in adipose tissue from the METSIM cohort |
Human Molecular Genetics |
Link |
Comp Genetics & Genomics |
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| Horvath |
2018 |
DNA methylation-based biomarkers and the epigenetic clock theory of ageing |
Nature Reviews Genetics |
Link |
Comp Genetics & Genomics |
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| Meyer |
2018 |
Dissecting FcγR Regulation through a Multivalent Binding Model |
Cell Systems |
Link |
Systems & Synthetic Biology |
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| Zhou |
2018 |
Detecting early-warning signals of influenza outbreak based on dynamic network marker |
Journal of Cellular and Molecular Medicine |
Link |
Medical Informatics |
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| Geschwind |
2018 |
Comprehensive functional genomic resource and integrative model for the human brain |
Science |
Link |
Systems & Synthetic Biology |
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| Ernst |
2018 |
ChromTime: modeling spatio-temporal dynamics of chromatin marks |
Genome Biology |
Link |
Systems & Synthetic Biology |
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| Bell |
2018 |
Characteristics of the National Applicant Pool for Clinical Informatics Fellowships (2016-2017) |
Proceedings of the AMIA Annual Symposium |
Link |
Medical Informatics |
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| Zhou |
2018 |
CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data |
Oxford Academic |
Link |
Medical Informatics |
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| Pinter-Wollman |
2018 |
Can multilayer networks advance animal behavior research |
Trends in Ecololy and Evolution |
Link |
Mathematical Biology |
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| Arnold |
2018 |
An EM-based Semi-supervised Deep Learning Approach for Semantic Segmentation of Histopathological Images from Radical Prostatectomies |
Computerized Medical Imaging and Graphics |
Link |
Medical Informatics |
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| Li, JJ |
2018 |
An accurate and robust imputation method scImpute for single-cell RNA-seq data |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Coller |
2018 |
Alternative polyadenylation factors link cell cycle to migration |
Genome Biology |
Link |
Systems & Synthetic Biology |
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| Wang, S |
2018 |
Active Tuning of Synaptic Patterns Enhances Immune Discrimination |
Physical Review Letters |
Link |
Mathematical Biology |
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| Pellegrini |
2018 |
A multi-tissue full lifespan epigenetic clock for mice |
Aging |
Link |
Comp Genetics & Genomics |
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| Chou |
2018 |
A Dynamical Bifurcation Model of Bipolar Disorder Based on Learned Expectation and Asymmetry in Mood Sensitivity |
Computational Psychiatry |
Link |
Mathematical Biology |
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| Li, JJ |
2017 |
TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples |
Statistics in Biosciences |
Link |
Comp Genetics & Genomics |
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| Alber |
2017 |
The three-dimensional genome organization of Drosophila melanogaster through data integration |
Genome Biology |
Link |
Systems & Synthetic Biology |
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| Jamshidi |
2017 |
Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism |
Scientific Reports |
Link |
Systems & Synthetic Biology |
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| Ernst |
2017 |
Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression |
Cell Reports |
Link |
Comp Genetics & Genomics |
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| Xiao |
2017 |
Structure-mediated Modulation of mRNA Abundance by A-to-I Editing |
Nature Communications |
Link |
Comp Genetics & Genomics |
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| Yang |
2017 |
Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States |
PLoS Genetics |
Link |
Comp Genetics & Genomics |
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| Graeber |
2017 |
Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures |
Molecular Systems Biology |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2017 |
Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them |
Nucleic Acids Research |
Link |
Systems & Synthetic Biology |
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| Wang, S |
2017 |
Optimal Sequential Immunization Can Focus Antibody Responses against Diversity Loss and Distraction |
PLoS Computational Biology |
Link |
Mathematical Biology |
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| Jamshidi |
2017 |
Multiregional Radiogenomic Assessment of Prostate Microenvironments with Multiparametric MR Imaging and DNA Whole-Exome Sequencing of Prostate Glands with Adenocarcinoma |
Radiology |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2017 |
Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states |
Nucleic Acids Research |
Link |
Comp Genetics & Genomics |
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| Hoffmann |
2017 |
Iterative modeling reveals sequential transcriptional control mechanisms |
Cell Systems |
Link |
Systems & Synthetic Biology |
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| DiStefano III |
2017 |
DISTING: A web application for fast algorithmic computation of alternative indistinguishable linear compartmental models |
Computer Methods and Programs in Biomedicine |
Link |
Mathematical Biology |
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| Lloyd-Smith |
2017 |
Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions as a case study |
Journal of Animal Ecology |
Link |
Mathematical Biology |
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| Li, JJ |
2017 |
Correspondence of D. melanogaster and C. elegansdevelopmental stages revealed by alternative splicing characteristics of conserved exons |
BMC Genomics |
Link |
Systems & Synthetic Biology |
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| Ernst |
2017 |
Cooperative Binding of Transcription Factors Orchestrates Reprogramming |
Cell Reports |
Link |
Systems & Synthetic Biology |
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| Zhou |
2017 |
CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA |
Genome Biology |
Link |
Medical Informatics |
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| Kruglyak |
2017 |
A maternal-effect selfish genetic element in Caenorhabditis elegans |
Science |
Link |
Comp Genetics & Genomics |
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| Kruglyak |
2017 |
A genetic signature of the evolution of loss of flight in the Galapagos cormorant |
Science |
Link |
Comp Genetics & Genomics |
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| Distefano III |
2016 |
THYROSIM App for Education and Research Predicts Potential Health Risks of Over-the-Counter Thyroid Supplements |
Thyroid |
Link |
Mathematical Biology |
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| Yang |
2016 |
Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders |
EBioMedicine |
Link |
Comp Genetics & Genomics |
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| Meyer |
2016 |
Systems biology approaches to measure and model phenotypic heterogeneity in cancer |
Cancer Research |
Link |
Systems & Synthetic Biology |
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| Meyer |
2016 |
Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance |
Cancer Discovery |
Link |
Systems & Synthetic Biology |
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| Bui |
2016 |
Prediction of lung cancer incidence on the LDCT arm of the National Lung Screening Trial: A dynamic Bayesian network |
Artif Intell Medicine |
Link |
Medical Informatics |
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| Lloyd-Smith |
2016 |
Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting |
Science |
Link |
Mathematical Biology |
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| Alber |
2016 |
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization |
Proceedings of the National Academy of Sciences USA |
Link |
Systems & Synthetic Biology |
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| Li, JJ |
2016 |
NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data |
BMC Genomics |
Link |
Comp Genetics & Genomics |
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| Zhou |
2016 |
Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities |
Nature Communications |
Link |
Systems & Synthetic Biology |
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| Alber |
2016 |
Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities |
Nature Communications |
Link |
Systems & Synthetic Biology |
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| Meyer |
2016 |
JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2-Targeted Therapies |
Cancer Research |
Link |
Systems & Synthetic Biology |
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| Sul |
2016 |
Increasing generality and power of rare variant tests utilizing extended pedigrees |
AJHG |
Link |
Comp Genetics & Genomics |
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| Ernst |
2016 |
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions |
Nature Biotechnology |
Link |
Comp Genetics & Genomics |
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| Li, JJ |
2016 |
Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states |
BMC Genomics |
Link |
Comp Genetics & Genomics |
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| Garud |
2016 |
Elevated linkage disequilibrium and signatures of soft sweeps are common in Drosophila melanogaster |
Genetics |
Link |
Comp Genetics & Genomics |
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| Savage |
2016 |
Do Vascular Networks Branch Optimally or Randomly across Spatial Scales? |
PLOS Computational Biology |
Link |
Mathematical Biology |
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| Horvath |
2016 |
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease |
Genome Biology |
Link |
Comp Genetics & Genomics |
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| Xiao |
2016 |
Alternative Splicing Modulated by Genetic Variants Demonstrates Accelerated Evolution Regulated by Highly Conserved Proteins |
Genome Research |
Link |
Comp Genetics & Genomics |
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| Chou |
2016 |
A hierarchical kinetic theory of birth, death, and fission in age-structured interacting populations |
Journal of Statistical Physics |
Link |
Mathematical Biology |
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| Jamshidi |
2015 |
The Radiogenomic Risk Score: Construction of a Prognostic Quantitative, Noninvasive Image-based Molecular Assay for Renal Cell Carcinoma |
Radiology |
Link |
Systems & Synthetic Biology |
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| Meyer |
2015 |
The AXL Receptor is a Sensor of Ligand Spatial Heterogeneity |
Cell Systems |
Link |
Systems & Synthetic Biology |
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| Savage |
2015 |
Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks |
PLoS Computational Biology |
Link |
Mathematical Biology |
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| Savage |
2015 |
Scaling from traits to ecosystems: Developing a general Trait Driver Theory via integrating trait-based and metabolic scaling theories |
Advances in Ecological Research |
Link |
Mathematical Biology |
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| Jamshidi |
2015 |
Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics |
Cell Systems |
Link |
Systems & Synthetic Biology |
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| Wang, S |
2015 |
Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies |
Cell |
Link |
Mathematical Biology |
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| Xiao |
2015 |
Genome Sequence-Independent Identification of RNA Editing Sites |
Nature Methods |
Link |
Comp Genetics & Genomics |
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| Jamshidi |
2015 |
Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods |
Frontiers in Microbiology |
Link |
Systems & Synthetic Biology |
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| Chou |
2015 |
Bayesian Uncertainty Quantification for Bond Energies and Mobilities Using Path Integral Analysis |
Biophysical Journal |
Link |
Mathematical Biology |
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| Sul |
2015 |
Accurate and fast multiple-testing correction in eQTL studies |
AJHG |
Link |
Comp Genetics & Genomics |
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| DiStefano III |
2014 |
On Finding and Using Identifiable Parameter Combinations in Nonlinear Dynamic Systems Biology Models and COMBOS: A Novel Web Implementation |
PloS one |
Link |
Mathematical Biology |
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| Bui |
2013 |
Imaging-based observational data-bases for clinical problem solving: The role of informatics |
J Am Med Inform Assoc |
Link |
Medical Informatics |
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| Bui |
2012 |
Context-based electronic health records: Towards patient-specific healthcare |
IEEE Trans Inf Technol Biomed |
Link |
Medical Informatics |
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| DiStefano III |
2011 |
Finding identifiable parameter combinations in nonlinear ODE models and the rational reparameterization of their input-output equations |
Math Biosciences |
Link |
Mathematical Biology |
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| DiStefano III |
2010 |
Chronic exposure to Mn inhalation may have lasting effects: A physiologically-based toxicokinetic model in rats |
Toxicological & Environmental Chemistry |
Link |
Mathematical Biology |
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| DiStefano III |
2009 |
An algorithm for finding globally identifiable parameter combinations of nonlinear ODE models using Gröbner Bases |
Mathematical Biosciences |
Link |
Mathematical Biology |
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