Publications · 81 papers

Papers

From Cell and Nature Methods to NeurIPS, ICML, and ICLR. For citation counts, see Google Scholar. Blue dots mark papers in Nature- and Cell-family journals and at NeurIPS, ICML, and ICLR.

Every paper, by year · hover a dot

2026

2026
The AI Neuroscientist: An Interactive Agentic Interface for Neuroimaging Analysis
Patel A, Ketonis P, Saxena S, Krishnaswamy S, van Dijk D

AgentsNeuroscience

arXiv
2026
MoRSE: Task-Oriented Multi-Agent System with Mixture of Role-Subtask Experts
Li P, Zhang S, Zhang Y, He S, van Dijk D, Ying R

AgentsML methods

NeurIPS 2026
2026
Variational Learning for Insertion-based Generation
Zhang Y, Wang Z, Gretton A, Ying R, van Dijk D, Titsias MK, Shi J

ML methods

ICML 2026
2026
Learning Permutation Distributions via Reflected Diffusion on Ranks
He S, Zhang Y, Zhang S, van Dijk D

ML methods

ICML 2026
2026
STRIDE: Post-Training LLMs to Reason and Refine Bio-Sequences via Edit Trajectories
Zhang D, Zhang S, He S, Zhang Y, Rizvi SA, van Dijk D

Foundation modelsAgents

ICML 2026
2026
SciDesignBench: Benchmarking and Improving Language Models for Scientific Inverse Design
van Dijk D, Vrkic I

AgentsML methods

arXiv
2026
TANTE: Time-Adaptive Operator Learning via Neural Taylor Expansion
Wu Z, Wang S, Zhang S, He S, Zhu M, Jiao A, Lu L, van Dijk D

Dynamics & operators

Journal of Computational Physics

2025

2025
Scaling Large Language Models for Next-Generation Single-Cell Analysis (C2S-Scale)
Rizvi SA, Levine D, Patel A, Zhang S, Wang E, Perry CJ, Vrkic I, … Perozzi B, Ishizuka J, Azizi S, van Dijk D

Foundation modelsSingle-cell

bioRxiv Code / weights ↗
2025
Non-Markovian Discrete Diffusion with Causal Language Models (CaDDi)
Zhang Y, He S, Levine D, Zhao L, Zhang D, Rizvi SA, Zhang S, Zappala E, Ying R, van Dijk D

ML methods

NeurIPS 2025
2025
Intelligence at the Edge of Chaos
Zhang S, Patel A, Rizvi SA, Liu N, He S, Karbasi A, Zappala E, van Dijk D

ML methods

ICLR 2025 Code / weights ↗
2025
GeoFunFlow: Geometric Function Flow Matching for Inverse Operator Learning over Complex Geometries
Wang S, Wu Z, van Dijk D, Lu L

Dynamics & operators

arXiv
2025
Transformer-Based Foundation Model for Functional Neuroimaging
Akiki et al.

NeuroscienceFoundation models

Biological Psychiatry

2024

2024
HEART: Learning better representation of EHR data with a heterogeneous relation-aware transformer
Huang et al.

Clinical

J. Biomedical Informatics
2024
Cell2Sentence: Teaching Large Language Models the Language of Biology
Levine et al.

Foundation modelsSingle-cell

ICML 2024
2024
BrainLM: A Foundation Model for Brain Activity Recordings
Ortega Caro et al.

Foundation modelsNeuroscience

ICLR 2024
2024
FIMP: Foundation Model-Informed Message Passing for Graph Neural Networks
Rizvi et al.

ML methods

arXiv
2024
Learning integral operators via neural integral equations
Zappala et al.

Dynamics & operators

Nature Machine Intelligence
2024
CaLMFlow: Volterra Flow Matching Using Causal Language Models
He et al.

ML methodsDynamics & operators

arXiv
2024
The Role of Epstein-Barr Virus in Long COVID
Tabachnikova et al.

Clinical

J. Immunology

2023

2023
Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study
Cheemarla et al.

Clinical

Lancet Microbe
2023
Continuous Spatiotemporal Transformers
Fonseca et al.

Dynamics & operatorsNeuroscience

ICML 2023
2023
A machine learning method for the identification and characterization of novel COVID-19 drug targets
Schultz et al.

Clinical

Scientific Reports
2023
Neural Integro-Differential Equations
Zappala et al.

Dynamics & operators

AAAI 2023
2023
Operator Learning Meets Numerical Analysis: Improving Neural Networks through Iterative Methods
Zappala et al.

Dynamics & operators

arXiv
2023
Causal identification of single-cell experimental perturbation effects with CINEMA-OT
Dong et al.

CausalitySingle-cell

Nature Methods
2023
Distinguishing features of Long COVID identified through immune profiling
Klein et al.

Clinical

Nature
2023
Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1
Tejwani et al.

Single-cellNeuroscience

Neuron

2022

2022
Interspecies commensal interactions have nonlinear impacts on host immunity
Rice et al.

Single-cell

Cell Host & Microbe
2022
Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones
Collora et al.

Single-cell

Immunity
2022
Prdm6 controls heart development by regulating neural crest cell differentiation and migration
Hong et al.

Single-cell

JCI Insight
2022
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19
Unterman et al.

Single-cellClinical

Nature Communications

2021

2021
Generating hard-to-obtain information from easy-to-obtain information: Applications in drug discovery and clinical inference
Amodio et al.

ML methodsClinical

Patterns
2021
A phenomapping-derived tool to personalize the selection of anatomical vs. functional testing in evaluating chest pain (ASSIST)
Oikonomou et al.

Clinical

European Heart Journal
2021
Single-Cell Transcriptional Profiling of the Adult Corticospinal Tract Reveals Forelimb and Hindlimb Molecular Specialization
Golan et al.

Single-cellNeuroscience

bioRxiv
2021
A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization
Schultz et al.

Clinical

Scientific Reports
2021
Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children
Ramaswamy et al.

Single-cellClinical

Immunity
2021
Single-cell immune profiling reveals the impact of antiretroviral therapy on HIV-1-induced immune dysfunction, T cell clonal expansion, and HIV-1 persistence in vivo
Collora et al.

Single-cell

bioRxiv
2021
Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes
Ravindra et al.

Single-cell

PLoS Biology
2021
Permutation invariant networks to learn Wasserstein metrics
Sehanobish et al.

ML methods

NeurIPS TDA Workshop
2021
Gaining Insight into SARS-CoV-2 Infection and COVID-19 Severity Using Self-supervised Edge Features and Graph Neural Networks
Sehanobish et al.

ML methodsSingle-cell

AAAI 2021
2021
Learning Potentials of Quantum Systems using Deep Neural Networks
Sehanobish et al.

Dynamics & operators

arXiv
2021
Quantifying the effect of experimental perturbations at single-cell resolution
Burkhardt et al.

CausalitySingle-cell

Nature Biotechnology
2021
Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection
Wei et al.

Single-cell

Cell

2020

2020
Learning General Transformations of Data for Out-of-Sample Extensions
Amodio et al.

ML methods

IEEE MLSP 2020
2020
Development and Validation of the Quick COVID-19 Severity Index: A Prognostic Tool for Early Clinical Decompensation
Haimovich et al.

Clinical

Annals of Emergency Medicine
2020
Patient factors associated with SARS-CoV-2 in an admitted emergency department population
Haimovich et al.

Clinical

JACEP Open
2020
Self-supervised edge features for improved Graph Neural Network training
Sehanobish et al.

ML methods

arXiv
2020
Disease State Prediction From Single-Cell Data Using Graph Attention Networks
Ravindra et al.

ML methodsSingle-cell

ACM CHIL 2020
2020
Circulating Markers of Angiogenesis and Endotheliopathy in COVID-19
Meizlish et al.

Clinical

Pulmonary Circulation
2020
Learning aligned embeddings for semi-supervised word translation using Maximum Mean Discrepancy
Fonseca et al.

ML methods

arXiv
2020
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
Tong et al.

Dynamics & operatorsSingle-cell

ICML 2020
2020
Interpretable Neuron Structuring with Graph Spectral Regularization
Tong et al.

ML methods

IDA 2020
2020
Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity
Ramaswamy et al.

Clinical

medRxiv
2020
Transcriptomic and clonal characterization of T cells in the human central nervous system
Pappalardo et al.

Single-cellNeuroscience

Science Immunology
2020
A neutrophil activation signature predicts critical illness and mortality in COVID-19
Meizlish et al.

Clinical

Blood Advances
2020
Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures
Zhao et al.

Single-cell

PLoS Neglected Tropical Diseases
2020
Uncovering axes of variation among single-cell cancer specimens
Chen et al.

Single-cell

Nature Methods
2020
Neurohormonal Blockade and Clinical Outcomes in Patients With Heart Failure Supported by Left Ventricular Assist Devices
McCullough et al.

Clinical

JAMA Cardiology
2020
Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells
Ravindra et al.

Single-cell

bioRxiv
2020
Neuroinvasion of SARS-CoV-2 in human and mouse brain
Song et al.

Single-cellNeuroscience

J. Experimental Medicine

2019

2019
Coarse Graining of Data via Inhomogeneous Diffusion Condensation
Brugnone et al.

ML methods

IEEE Big Data 2019
2019
Finding Archetypal Spaces Using Neural Networks
van Dijk et al.

ML methods

IEEE Big Data 2019
2019
Compressed Diffusion
Gigante et al.

ML methods

SampTA 2019
2019
Visualizing structure and transitions in high-dimensional biological data (PHATE)
Moon et al.

ML methodsSingle-cell

Nature Biotechnology
2019
Exploring single-cell data with deep multitasking neural networks (SAUCIE)
Amodio et al.

ML methodsSingle-cell

Nature Methods
2019
Modeling Global Dynamics from Local Snapshots with Deep Generative Neural Networks
Gigante et al.

Dynamics & operators

SampTA 2019

2018

2018
Recovering gene interactions from single-cell data using data diffusion (MAGIC)
van Dijk et al.

ML methodsSingle-cell

Cell
2018
Out-of-sample extrapolation with neuron editing
Amodio et al.

ML methods

arXiv
2018
Embedding the single-cell sample manifold to reveal insights into cancer pathogenesis and disease heterogeneity
Chen et al.

Single-cell

bioRxiv

2017

2017
Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
van Dijk et al.

Single-cell

Genome Research
2017
Manifold learning-based methods for analyzing single-cell RNA-sequencing data
Moon et al.

ML methodsSingle-cell

Current Opinion in Systems Biology

2016

2016
PD-1 marks dysfunctional regulatory T cells in malignant gliomas
Lowther et al.

Single-cell

JCI Insight

2015

2015
Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage
van Dijk et al.

Single-cell

Nature Communications
2015
Noise in gene expression is coupled to growth rate
Keren et al.

Single-cell

Genome Research

2014

2014
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
Sharon et al.

Single-cell

Genome Research
2014
Publication metrics and success on the academic job market
van Dijk et al.

ML methods

Current Biology

2013

2013
Promoter sequence determines the relationship between expression level and noise
Carey et al.

Single-cell

PLoS Biology
2013
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
Dadiani et al.

Single-cell

Genome Research

2010

2010
Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks
van Dijk et al.

Single-cell

BMC Systems Biology
2010
Individual-based simulation of sexual selection: A quantitative genetic approach
van Dijk et al.

Dynamics & operators

ICCS 2010
2010
Inference of surface membrane factors of HIV-1 infection through functional interaction networks
Jaeger et al.

Single-cell

PLoS One