| 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 |
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| Xiao |
2021 |
Allele-specific alternative splicing and its functional genetic variants in human tissues |
Genome Biology |
Link |
Comp Genetics & Genomics |
|
| Boutros |
2021 |
A practical guide to cancer subclonal reconstruction from DNA sequencing |
Nature Methods |
Link |
Comp Genetics & Genomics |
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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 |
Download PDF |
| 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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| 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 |
|
| Pellegrini |
2020 |
The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework |
Bioinformatics |
Link |
Comp Genetics & Genomics |
|
| 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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| Pellegrini |
2020 |
Targeted bisulfite sequencing for biomarker discovery |
Methods |
Link |
Comp Genetics & Genomics |
|
| 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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| 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 |
|
| Boutros |
2020 |
Sex differences in oncogenic mutational processes |
Nature Communications |
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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| 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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| Yang |
2020 |
Multi-tissue Multi-omics Systems Biology of Complex Diseases |
Trends in Molecular Medicine |
Link |
Comp Genetics & Genomics |
|
| 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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| 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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| 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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| 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 |
|
| Xiao |
2020 |
Extracellular microRNA 3’ end modification across diverse body fluids |
Epigenetics |
Link |
Comp Genetics & Genomics |
|
| 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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| 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 |
|
| 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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| 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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| 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 |
|
| 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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| 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 |
|
| Bell |
2020 |
Accuracy of an Electronic Health Record Patient Linkage Module Evaluated between Neighboring Academic Health Care Centers |
Applied clinical informatics |
Link |
Medical Informatics |
|
| Plath |
2020 |
A protein assembly mediates Xist localization and gene silencing |
Nature |
Link |
Systems & Synthetic Biology |
|
| 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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| Geschwind |
2019 |
Widespread RNA editing dysregulation in brains from autistic individuals |
Nature Neuroscience |
Link |
Comp Genetics & Genomics |
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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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| 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 |
Download PDF |
| 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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| Kruglyak |
2019 |
Rare variants contribute disproportionately to quantitative trait variation in yeast |
eLIFE |
Link |
Comp Genetics & Genomics |
Download PDF |
| 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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| 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 |
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| 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 |
Download PDF |
| 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 Systems |
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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| 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 |
Download PDF |
| Garud |
2019 |
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts |
Plos Biology |
Link |
Comp Genetics & Genomics |
Download PDF |
| Li, JJ |
2019 |
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences |
Nucleic Acids Research |
Link |
Comp Genetics & Genomics |
Download PDF |
| Horvath |
2019 |
DNA methylation GrimAge strongly predicts lifespan and healthspan |
Aging Cell |
Link |
Comp Genetics & Genomics |
Download PDF |
| 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 |
Download PDF |
| 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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| 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 |
| 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 |
Download PDF |
| 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 |
Download PDF |
| Geschwind |
2019 |
A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation |
Neuron |
Link |
Systems & Synthetic Biology |
Download PDF |
| 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 |
Download PDF |
| 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 |
|
| 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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| Geschwind |
2019 |
A genome-wide association study of shared risk across psychiatric disorders implicates gene regulation during fetal neurodevelopment |
Nature Neuroscience |
Link |
Comp Genetics & Genomics |
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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 |
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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 |
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| 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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| 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 |
Download PDF |
| 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 |
Download PDF |
| 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 |
|
| 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 |
Download PDF |
| Ernst |
2018 |
ChromTime: modeling spatio-temporal dynamics of chromatin marks |
Genome Biology |
Link |
Systems & Synthetic Biology |
Download PDF |
| Bell |
2018 |
Characteristics of the National Applicant Pool for Clinical Informatics Fellowships (2016-2017) |
Proceedings of the AMIA Annual Symposium |
Link |
Medical Informatics |
Download PDF |
| 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 |
Download PDF |
| 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 |
Download PDF |
| 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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| Wang, S |
2018 |
Active Tuning of Synaptic Patterns Enhances Immune Discrimination |
Physical Review Letters |
Link |
Mathematical Biology |
Download PDF |
| Pellegrini |
2018 |
A multi-tissue full lifespan epigenetic clock for mice |
Aging |
Link |
Comp Genetics & Genomics |
Download PDF |
| Chou |
2018 |
A Dynamical Bifurcation Model of Bipolar Disorder Based on Learned Expectation and Asymmetry in Mood Sensitivity |
Computational Psychiatry |
Link |
Mathematical Biology |
Download PDF |
| 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 |
Download PDF |
| 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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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Medical Informatics |
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| Kruglyak |
2017 |
A maternal-effect selfish genetic element in Caenorhabditis elegans |
Science |
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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 |
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Mathematical Biology |
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| Horvath |
2016 |
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease |
Genome Biology |
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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 |
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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 |
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Systems & Synthetic Biology |
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| Meyer |
2015 |
The AXL Receptor is a Sensor of Ligand Spatial Heterogeneity |
Cell Systems |
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Systems & Synthetic Biology |
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| Savage |
2015 |
Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks |
PLoS Computational Biology |
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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 |
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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 |
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Medical Informatics |
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| Bui |
2012 |
Context-based electronic health records: Towards patient-specific healthcare |
IEEE Trans Inf Technol Biomed |
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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 |
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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 |
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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 |
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Mathematical Biology |
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