Computational Biology: Publications
Read the latest papers published by our research teams.
Results
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CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens
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NetQuilt: Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity
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Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes
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SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases
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High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy
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Structure-Based Protein Function Prediction using Graph Convolutional Networks
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Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks
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Macromolecular modeling and design in Rosetta: recent methods and frameworks
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Better together: Elements of successful scientific software development in a distributed collaborative community
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Visualizing ’omic feature rankings and log-ratios using Qurro
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Shrinkage improves estimation of microbial associations under different normalization methods
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Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter
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Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection
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Designing Peptides on a Quantum Computer
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Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs
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Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
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A Bayesian nonparametric approach to super-resolution single-molecule localization
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Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling
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Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
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A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV
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Lattices of Hydrodynamically Interacting Flapping Swimmers
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Relating Rheotaxis and Hydrodynamic Actuation using Asymmetric Gold-Platinum Phoretic Rods
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Rotating Membrane Inclusions Crystallize Through Hydrodynamic and Steric Interactions
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The odd free surface flows of a colloidal chiral fluid
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Biologically Plausible Online Principal Component Analysis Without Recurrent Neural Dynamics
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Flexibility in motor timing constrains the topology and dynamics of pattern generator circuits
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Holography, Fractals and the Weyl Anomaly
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Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing
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A clustering neural network model of insect olfaction
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NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data
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Blind Nonnegative Source Separation Using Biological Neural Networks
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OnACID: Online Analysis of Calcium Imaging Data in Real Time, Advances
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A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity
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Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells
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Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models
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Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function
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Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions
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Automated gesture tracking in head-fixed mice
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Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes
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Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ
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The surprising secret identity of the semidefinite relaxation of K-means: manifold learning
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Resource-efficient perceptron has sparse synaptic weight distribution
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The comprehensive connectome of a neural substrate for ‘ON’ motion detection in Drosophila
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
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Phosphotriesterase enzymes, methods and compositions related thereto
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Why do similarity matching objectives lead to Hebbian/anti-Hebbian networks?
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Cerebellar granule cells acquire a widespread predictive feedback signal during motor learning
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Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility