Publications
Lab members and alumni in bold. Google Scholar
2026
- Dual-graph deconvolution of enzyme fitness: an interpretable framework to identify and explain catalytic modulators
bioRxiv
- Generative model of patient health states and pan-cancer risk stratification
medRxiv
- Unified sampling framework and experimental benchmarking of sequence- and structure-based protein models
bioRxiv
- Hypervariable loop profiling decodes sequence determinants of antibody stability
Nature Structural & Molecular Biology
- In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer
Nature Communications
- Transition from infectivity and immune escape to pure escape as an evolutionary strategy during the COVID-19 pandemic
bioRxiv
- evedesign: accessible biosequence design with a unified framework
bioRxiv
- Protein structure, a genetic constraint on glycosylation
bioRxiv
- Evaluating Variant Effect Prediction Across Viruses
bioRxiv
- Machine learning enables efficient and effective affinity maturation of nanobodies
bioRxiv
- Machine Learning Reveals Hidden Dimensions of Functional Similarity
PNAS Commentary
2025
- Biological Sequence Kernels with Guaranteed Flexibility
Journal of Machine Learning Research
- Proteome-wide model for human disease genetics
Nature Genetics
- Democratizing protein language model training, sharing and collaboration
Nature Biotechnology
- A Genomic Language Model for Zero-Shot Prediction of Promoter Indel Effects
Proceedings of Machine Learning Research
- Pancreatic cancer risk prediction using deep sequential modeling of longitudinal diagnostic and medication records
Cell Reports Medicine
- Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design
Proteins
- Evolutionary-Scale Enzymology Enables Biochemical Constant Prediction Across a Multi-Peaked Catalytic Landscape
Science
- Computationally designed proteins mimic antibody immune evasion in viral evolution
Immunity
- High-Throughput Machine Learning-Aided Antibody Discovery for Cell Surface Antigens
bioRxiv
- Machine learning prediction of enzyme optimum pH
Nature Machine Intelligence
- Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning
Nature
- Sequence-Based Protein Models for the Prediction of Mutations Across Priority Viruses
GEM workshop, ICLR
- Evolutionary-Scale Enzymology Enables Biochemical Constant Prediction Across a Multi-Peaked Catalytic Landscape
bioRxiv
- MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays
Genome Biology
- Multi-megabase scale genome interpretation with genetic language models
bioRxiv
2024
- Multi-Scale Representation Learning for Protein Fitness Prediction
NeurIPS
- Toward trustable use of machine learning models of variant effects in the clinic
American Journal of Human Genetics
- Continuous evolution of user-defined genes at 1 million times the genomic mutation rate
Science
- An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome
Alzheimer’s & Dementia
- Future-Proof Vaccine Design with a Generative Model of Antibody Cross-Reactivity
GEM workshop, ICLR
- SaprotHub: Making Protein Modeling Accessible to All Biologists
bioRxiv
- Protein design using structure-based residue preferences
Nature Communications
- Machine Learning for Functional Protein Design
Nature Biotechnology
- GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway
Nature Structural & Molecular Biology
- scPerturb: harmonized single-cell perturbation data
Nature Methods
2023
- ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers
NeurIPS
- ProteinGym: Large-scale Benchmarks for Protein Fitness Prediction and Design
NeurIPS
- Combining Structure and Sequence for Superior Fitness Prediction
NeurIPS 2023 GenBio Workshop
- An Energy Based Model for Incorporating Sequence Priors for Target-Specific Antibody Design
NeurIPS 2023 GenBio Workshop
- Learning from pre-pandemic data to forecast viral antibody escape
Nature
- Removing bias in sequence models of protein fitness
bioRxiv
- A kernelized Stein discrepancy for biological sequences
International Conference on Machine Learning
- An Atlas of Variant Effects to understand the genome at nucleotide resolution
Genome Biology
- Simultaneous enhancement of multiple functional properties using evolution-informed protein design
PubMed
- A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories
Nature Medicine
- The relaxin receptor RXFP1 signals through a mechanism of autoinhibition
Nature Chemical Biology
- Coordination of bacterial cell wall and outer membrane biosynthesis
Nature
2022
- An In Silico Method to Assess Antibody Fragment Polyreactivity
Nature Communications
- Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval
arXiv
- Natural and designed proteins inspired by extremotolerant organisms can form condensates and attenuate apoptosis in human cells
ACS Synthetic Biology
2021
- A Structured Observation Distribution for Generative Biological Sequence Prediction and Forecasting
Proceedings of the 38th International Conference on Machine Learning
- MaveDB v2: a curated community database with over three million variant effects from multiplexed functional assays
bioRxiv
- Optimal Design of Stochastic DNA Synthesis Protocols based on Generative Sequence Models
bioRxiv
- Dormant spores sense amino acids through the B subunits of their germination receptors
bioRxiv
- Disease variant prediction with deep generative models of evolutionary data
Nature
- Coevolution of interacting proteins through non-contacting and non-specific mutations
bioRxiv
- A generative nonparametric Bayesian model for whole genomes
NeurIPS
- Pancreatic cancer risk predicted from disease trajectories using deep learning
bioRxiv
- Rapid generation of potent antibodies by autonomous hypermutation in yeast
Nature Chemical Biology
- Protein design and variant prediction using autoregressive generative models
Nature Communications
- Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences
Nature Communications
- CellBox: interpretable machine learning for perturbation biology with application to the design of cancer combination therapy
Cell Systems
- High-content screening of coronavirus genes for innate immune suppression reveals enhanced potency of SARS-CoV-2 proteins
bioRxiv
- A structured observation distribution for generative biological sequence prediction and forecasting
bioRxiv
2020
- Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning
bioRxiv
- Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact
eLife
- Interpretable machine learning for perturbation biology
Cancer Research
- Structural coordination of polymerization and crosslinking by a SEDS–bPBP peptidoglycan synthase complex
Nature Microbiology
- Protein structure from experimental evolution
Cell Systems
2019
- Generative models for codon prediction and optimization
Machine Learning in Computational Biology
- Proteome-scale discovery of protein interactions with residue-level resolution using sequence coevolution
bioRxiv
- Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis
PNAS
- Inferring protein 3D structure from deep mutation scans
Nature Genetics
- Protein structure from experimental evolution
bioRxiv
- The EVcouplings Python framework for coevolutionary sequence analysis
Bioinformatics
- Combining evolutionary covariance and NMR data for protein structure determination
Academic Press
- Sequence Data
Integrative Structural Biology with Hybrid Methods
2018
- Cryo–electron microscopy structure of the lipid droplet–formation protein seipin
Journal of Cell Biology
- Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings
Nature Microbiology
- Deep generative models of genetic variation capture the effects of mutations
Nature Methods
- Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli
PNAS
- 3D protein structure from genetic epistasis experiments
bioRxiv
- Population-specific design of de-immunized protein biotherapeutics
PLOS Comp Bio
- Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis
Nature
- Genome-wide discovery of epistatic loci affecting antibiotic resistance using evolutionary couplings
bioRxiv
2017
- Deep Generative models of genetic variation capture mutation effects
arXiv· ^ joint first authors
- Population-specific design of de-immunized protein biotherapeutics
arXiv
- Variational inference for sparse and undirected models
ICML
- Genetic variation in human drug related genes
Genome Medicine
- Mutation effects predicted from sequence co-variation
Nature Biotechnology· ^ joint first authors
2016
- Structured states of disordered proteins from genomic sequences
Cell· ^ joint first authors
- Genomic epidemiology of gonoccal resistance to extend Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the US, 2000-2013
J Infect Dis.
- Antiparallel protocadherin homodimers use distinct affinity and specificity-mediating regions in cadherin repeats 1-4
eLife
- 3D RNA and functional interactions from evolutionary couplings
Cell
- Target mRNA abundance dilutes microRNA and siRNA activity
Molecular Systems Biology
2015
- Structure and sequence analyses of clustered protocadherins reveal antiparallel interactions that mediate homophilic specificity
Cell Press
- Quantification of the effects of mutations using a global probability model of natural sequence variation
arXiv· ^ joint first authors
- Protein Structure determinationby combining sparse NMR data with evolutionary couplings
Nature Methods· ^ corresponding authors
- Inferring pairwise interactions from biological data using maximum-entropy probability models
PLoS Comput Biol
- All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences
PNAS
- MicroRNA control of protein expression noise
Science
- Evolutionary Couplings and protein 3D structure prediction
bioRxiv
2014
- Amino acid coevolution reveals three-dimensional strucutre and functional domains of insect odorant receptors
Nature Communications
- Sequence co-evolution gives 3D contacts and structures of protein complexes
eLife· ^ joint first authors
2012
2011
- Protein 3D structure computed from evolutionary sequence variation
PLoS ONE· ^ joint first authors
2009
- Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
Nature Biotechnology
2004
- Human microRNA targets
PLoS Biology