Publications

Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration

Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration

Neuron. . .

Deep learning finds convergent melanocytic morphology despite noisy archival slides

Deep learning finds convergent melanocytic morphology despite noisy archival slides

Cell Rep Methods. . .

  bioRxiv

Cell-type-directed network-correcting combination therapy for Alzheimer's disease

Cell-type-directed network-correcting combination therapy for Alzheimer's disease

Cell. . .

  bioRxiv   Mendeley

The polypharmacology of psychedelics reveals multiple targets for potential therapeutics

The polypharmacology of psychedelics reveals multiple targets for potential therapeutics

Neuron. . .

  Mendeley

Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results

Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results

J Chem Inf Model. . .

  chemRxiv   autoparty

MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures

MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures

Nat Commun. . .

  bioRxiv   MIC   Zenodo

Evolutionary-scale enzymology enables exploration of a rugged catalytic landscape

Evolutionary-scale enzymology enables exploration of a rugged catalytic landscape

Science. . .

  bioRxiv   Zenodo

An improved model for prediction of de novo designed proteins with diverse geometries

An improved model for prediction of de novo designed proteins with diverse geometries

bioRxiv. . .

  bioRxiv

Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation

Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation

J Chem Inf Model. . .

  chemRxiv

ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization

ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization

PLoS Comput Biol. . .

  bioRxiv

Deep phenotypic profiling of neuroactive drugs in larval zebrafish

Deep phenotypic profiling of neuroactive drugs in larval zebrafish

Nat Commun. . .

  bioRxiv   deepfish   Zenodo

Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds

Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds

J Chem Inf Model. . .

  chemRxiv   RAD

Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks

Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks

J Chem Inf Model. . .

  chemRxiv   torch_pgn

Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations

Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations

bioRxiv. . .

  bioRxiv   tangle-tracer   BioStudies

Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles

Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles

Acta Neuropathol Commun. . .

  Google Drive

Autoregressive fragment-based diffusion for pocket-aware ligand design

Autoregressive fragment-based diffusion for pocket-aware ligand design

arXiv - NeurIPS GenBio. . .

  NeurIPS GenBio   autofragdiff

In silico discovery of repetitive elements as key sequence determinants of 3D genome folding

In silico discovery of repetitive elements as key sequence determinants of 3D genome folding

Cell Genom. . .

  bioRxiv

Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels

Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels

Commun Biol. . .

  bioRxiv   OSF

A single-cell gene expression language model

A single-cell gene expression language model

arXiv - NeurIPS LMRL. . .

  NeurIPS LMRL   exceiver

Prioritizing Virtual Screening with Interpretable Interaction Fingerprints

Prioritizing Virtual Screening with Interpretable Interaction Fingerprints

J Chem Inf Model. . .

  bioRxiv   LUNA

Simultaneous analysis of neuroactive compounds in zebrafish

Simultaneous analysis of neuroactive compounds in zebrafish

bioRxiv. . .

  bioRxiv   OSF

Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics

Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics

Nat Mach Intell. . .

  bioRxiv   OSF

Deep learning from multiple experts improves identification of amyloid neuropathologies

Deep learning from multiple experts improves identification of amyloid neuropathologies

Acta Neuropathol Commun. . .

  bioRxiv   OSF

Stress testing reveals gaps in clinic readiness of image-based diagnostic artificial intelligence models

Stress testing reveals gaps in clinic readiness of image-based diagnostic artificial intelligence models

NPJ Digit Med. . .

Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction

Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction

J Chem Inf Model. . .

  bioRxiv

Predicting Cellular Drug Sensitivity using Conditional Modulation of Gene Expression

Predicting Cellular Drug Sensitivity using Conditional Modulation of Gene Expression

bioRxiv - NeurIPS LMRL. . .

  NeurIPS LMRL   film-gex

Attention-Based Learning on Molecular Ensembles

Attention-Based Learning on Molecular Ensembles

arXiv - NeurIPS ML4Molecules. . .

  NeurIPS ML4Molecules

Learning Molecular Representations for Medicinal Chemistry

Learning Molecular Representations for Medicinal Chemistry

J Med Chem. . .

Artificial Intelligence in Dermatology: A Primer

Artificial Intelligence in Dermatology: A Primer

J Invest Dermatol. . .

Robust Semantic Interpretability: Revisiting Concept Activation Vectors

Robust Semantic Interpretability: Revisiting Concept Activation Vectors

arXiv - ICML - WHI. . .

  ICML - WHI   RCAV   Zenodo

Validation of machine learning models to detect amyloid pathologies across institutions

Validation of machine learning models to detect amyloid pathologies across institutions

Acta Neuropathol Commun. . .

  Emory

Global Saliency: Aggregating Saliency Maps to Assess Dataset Artefact Bias

Global Saliency: Aggregating Saliency Maps to Assess Dataset Artefact Bias

arXiv - NeurIPS ML4H. . .

  NeurIPS ML4H

Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation

Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation

Nat Commun. . .

  Zenodo

Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline

Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline

Nat Commun. . .

  bioRxiv   Zenodo

Comment on "Predicting reaction performance in C-N cross-coupling using machine learning"

Comment on "Predicting reaction performance in C-N cross-coupling using machine learning"

Science. . .

Adversarial Controls for Scientific Machine Learning

Adversarial Controls for Scientific Machine Learning

ACS Chem Biol. . .

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders

Cell. . .

  pcmi

Predicted Biological Activity of Purchasable Chemical Space

Predicted Biological Activity of Purchasable Chemical Space

J Chem Inf Model. . .

  ZINC15   files.docking.org

Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior

Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior

Cell Rep. . .

  bioRxiv

A Simple Representation of Three-Dimensional Molecular Structure

A Simple Representation of Three-Dimensional Molecular Structure

J Med Chem. . .

  bioRxiv   E3FP

Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds

Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds

Nat Chem Biol. . .

Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology

Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology

ACS Chem Biol. . .

Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach

Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach

Lancet Psychiatry. . .

Prediction and validation of enzyme and transporter off-targets for metformin

Prediction and validation of enzyme and transporter off-targets for metformin

J Pharmacokinet Pharmacodyn. . .

Systems pharmacology augments drug safety surveillance

Systems pharmacology augments drug safety surveillance

Clin Pharmacol Ther. . .

In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding

In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding

PLoS Biol. . .

Large-scale prediction and testing of drug activity on side-effect targets

Large-scale prediction and testing of drug activity on side-effect targets

Nature. . .

Chemical informatics and target identification in a zebrafish phenotypic screen

Chemical informatics and target identification in a zebrafish phenotypic screen

Nat Chem Biol. . .

The presynaptic component of the serotonergic system is required for clozapine's efficacy

The presynaptic component of the serotonergic system is required for clozapine's efficacy

Neuropsychopharmacology. . .

The chemical basis of pharmacology

The chemical basis of pharmacology

Biochemistry. . .

Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors

Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors

J Med Chem. . .

Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs

Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs

J Med Chem. . .

A pilot study of the pharmacodynamic impact of SSRI drug selection and beta-1 receptor genotype (ADRB1) on cardiac vital signs in depressed patients: a novel pharmacogenetic approach

A pilot study of the pharmacodynamic impact of SSRI drug selection and beta-1 receptor genotype (ADRB1) on cardiac vital signs in depressed patients: a novel pharmacogenetic approach

Psychopharmacol Bull. . .

Predicting new molecular targets for known drugs

Predicting new molecular targets for known drugs

Nature. . .

A mapping of drug space from the viewpoint of small molecule metabolism

A mapping of drug space from the viewpoint of small molecule metabolism

PLoS Comput Biol. . .

Quantifying biogenic bias in screening libraries

Quantifying biogenic bias in screening libraries

Nat Chem Biol. . .

Off-target networks derived from ligand set similarity

Off-target networks derived from ligand set similarity

Methods Mol Biol. . .

Quantifying the relationships among drug classes

Quantifying the relationships among drug classes

J Chem Inf Model. . .

Relating protein pharmacology by ligand chemistry

Relating protein pharmacology by ligand chemistry

Nat Biotechnol. . .