Presenting Author

Abstract Title

Talk/Poster

Aerts, Stein

Modeling genome regulation using single-cell atlases

talk

Ahrend, Franziska

Modeling nucleotide-resolution piRNA production from precursor sequences across species using machine learning

poster

Ak, Cigdem

scMKL—Interpretable integration of single-cell multi-omics for cancer biology

poster

Akmese, Safa Mert M

Modeling terpene synthase biochemistry with machine learning

poster

Alam, Shahul

STeep—A toolkit for graph-aware subsampling of spatially-resolved transcriptomics data

poster

Ali, Hira

Scalable single-cell segmentation and morphological profiling of microglial states

poster

AlQuraishi, Mohammed

Some observations on how AlphaFold predicts structures and how it learns to predict structure

talk

Angelo, Murphy C

Addressing the generalization gap in RNA dynamics with differentiable folding

poster

Aninta, Sambina Islam

Position-dependent variant effects reveal importance of context in genomic regulation

poster

Avsec, Ziga

Advancing regulatory variant effect prediction with AlphaGenome

talk

Azizi, Elham

Generative AI models of cellular dynamics in the tumor microenvironment

talk

Baali, Ilyes

Bridging the Gap—Recalibrating in vitro models for accurate in vivo RBP binding predictions

poster

Baral, Jessika

Advancing peptide-HLA class I prediction with active and iterative deep learning for improved cancer vaccine design

poster

Barbosa, Leonardo S

Learning to calibrate—Few-shot cross-probe generalization for sub-second neurochemical decoding in humans

poster

Bear, Daniel

Solving clinical translation with foundation models of human biology

talk

Benegas, Gonzalo

Data curation strategies for genomic language models

poster

Benjamin, Ari

TissueFormer—Extending single-cell foundation models to predict population-level phenotypes

poster

Berreby, Yohai-Eliel

CanViT—Toward active-vision foundation models

poster

Bhalodia, Aashik

Determining heterogeneously active regulatory elements using entropy

poster

Bhattacharyya, Nirjhar

System-level mapping of antimalarial drug responses reveals conserved stress programs, lineage-specific rewiring, and a multiomics multimodal architecture in Plasmodium falciparum

poster

Birney, Ewan

Genomics, imaging and AI—Three technologies which are changing our understanding of living systems

talk

Blainey, Paul C

High content interventional data resources for training cellular models

poster

Bonneau, Richard A

Integrating generative AI with active learning to power next-generation drug discovery

talk

Bono, Hidemasa

AI-based meta-analysis of omics data from public databases

poster

Booeshaghi, A. Sina

Automatic extraction and evaluation of marker genes

poster

Booeshaghi, A. Sina

Science should be machine-readable

poster

Bossel Ben-Moshe, Noa

Integrative single-cell analysis reveals hypoxic immune states following Salmonella Typhi gut invasion associated with disease outcome

poster

Bowman, Derek

scVIGR—Interpretable single-cell variational inference of gene regulation for perturbation prediction

poster

Brady, Lauren K

SCOPE-MIA—Scale-consistent PDE-optimized encoding in 3D medical imaging analysis

poster

Brandes, Nadav

Genomic heterogeneity inflates the performance of variant pathogenicity predictions

poster

Braun, Rosemary

Variational inference reveals dynamics and hidden topological structures in single-cell RNAseq data

poster

Brbic, Maria

Many views, one cell—Multimodal models for decoding cellular complexity

talk

Bronstein, Michael

Black box data in the AI era

talk

Buckler, Edward S

Using artificial intelligence to learn across flowering plant genomes

talk

Bunne, Charlotte

Virtual patient labs—AI-driven simulation and diagnostics for precision oncology

talk

Cao, Peijian

iPscDB—A versatile platform of plant cell atlases at the single-cell level

poster

Casco-Rodriguez, Josue

Modular computation in multi-area cortical-like networks

poster

Chakraborty, Monoswi

Integrative functional population genomics for predictive engineering of next-generation yeast chassis for chemical production

poster

Chapfuwa, Paidamoyo

Mechanisms matter—Transportability in cellular perturbation response prediction

poster

Char, Erin

PRC2 loss rewires 3D genome to activate druggable imprinted genes in cancer

poster

Chen, Leo Tianlai

Centaur—Bridging continuous and discrete generation for protein sequence structure co-design

poster

Chen, Szu-Ping

Cross-species modeling of nucleosome positioning in plants

poster

Chen, Tingjun

Integrating DNA sequence priors and morphological context via feature-wise linear modulation for spatial transcriptomics prediction

poster

Chklovskii, Dmitri

Toward biologically inspired AI—Predicting and controlling a dynamical world

talk

Chougule, Kapeel M

An incremental multi-agent AI pipeline for marker knowledge extraction and ontology harmonization to support sorghum genotyping array design

poster

Christensen, Trevor

Iterative design of training datasets for generalizable sequence-to-function models

poster

Chu, Shane

Identifying motif combinations with extreme expression

poster

Chyr, Jacqueline

Deep learning meets high-throughput CRISPR editing—Utilizing novel CHANCE-net and CHANCE-seq platforms for safe and precise genome editing

poster

Clarke, Joseph

Gigascale in silico and megascale experimental discovery and testing of splicing regulatory mechanisms

poster

Conde Paredes, Margaret-Estefani

Inferring interneuron molecular identity from functional correlation structure using AI-driven model discovery

poster

Cong, Le

Building LabOS AI co‑scientists to accelerate biomedical innovation from molecules to machines

talk

Cool, Jonah

Frontier AI as a thinking partner for biological discovery

talk

Creeggan, Finn

Multi-omic regulatory modelling defines a novel reactive ependymal cell state in multiple sclerosis

poster

Cunha, Cesar

AlphaGenome unveils non-CNS etiology of Alzheimer's disease

poster

Daakour, Sarah

Experimental and AI-augmented interactome of the high-light-adapted cyanobacterium Prochlorococcus marinus MED4

poster

De, Subhajyoti

Interactive, personalized summarization of cancer diagnostics data

poster

Debnath, Tanmay

Decoding mammalian regulatory grammar—Deep learning sequence-to-function models trained on large-scale cross-species MPRA data

poster

DeGroat, William B

Learning transferable cis-regulatory grammar across neuronal cell types from massively parallel reporter assays

poster

Demetci, Pinar

Generative modeling of multi-scale tissue remodeling dynamics with flow matching reveals niche-mediated drivers of cell state transitions

poster

Deng, Pan

Modeling and navigating cell state transitions with deep learning

poster

Deng, Wei

PGx-3D—A structure-guided framework for pharmacogenomic phenotype prediction

poster

Dimitrova, Nevenka

Discrete representation learning for spatial tissue modeling in multiplex imaging

poster

Diplock, Nathan

Simple models outperform AI when predicting the fitness of highly diverse, new-to-nature protein sequences

poster

Dobbins, Sarah

Characterizing noncoding variant effects in amyotrophic lateral sclerosis through deep learning models

poster

d'Oelsnitz, Simon

Using enantioselective biosensors to evolve asymmetric biocatalysts

poster

Doudna, Jennifer

Design of functional unnatural RNA-guided nucleases

talk

Du, Yuanqi

Accelerating scientific discovery with autonomous goal-evolving agents

poster

Dufault, Cameron

Learning functional representations of bacterial regulatory sequences with contrastive promoter-protein pretraining

poster

Dyer, Eva

Multimodal foundation models for neural data

talk

El-Shimy, Ismail

Cell-type-resolved mapping of disease mechanisms and therapeutic rescue in SMA using single-nucleus RNA sequencing

poster

Eraslan, Gokcen

Disease vector fields—An agentic experiment in disease transport modeling from single-cell atlases

poster

Eschbach, Ethan

Sequence-based evolutionary models conditioned on structure identify mutations that affect enzyme activity

poster

Escola, Sean

Cognitive dark matter and human-like AI

talk

Farh, Kyle

A quick progress update on the 1 billion cell atlas—Findings from the first 300 million cells of genome-wide perturb-seq

talk

Farooq, Hammad

Linking noncoding variants to target genes through polymer modeling of 3D genome architecture and sequence-based modeling

poster

Fenske, Sam

Decoding vascular tissue architecture through multimodal representation learning of histology

poster

Fife, James

Systematic evaluation of protein language models highlights strengths and limitations

poster

Ford, Willard W

From residuals to risk—Beyond linear PRS with interpretable machine learning of common and rare genetic interactions

poster

Forster, Duncan T

The CellMap 2.0—An integrated model of yeast gene function

poster

Ganguli, Surya

From explainable AI to conceptual understanding in neuroscience

talk

Ganguly, Aniruddha

LUMPS—Leveraging uncertainty for morphological priors in smoothing improves quality of spatial transcriptomics data

poster

Garcia Busto, Sergio

evedesign—Accessible biosequence design with a unified framework

poster

Guckelberger, Philine P

AI-guided discovery of selective enhancer-gene regulatory rewiring in cancer

poster

Guo, David

Lightweight sequence to conservation modeling for causal variant prediction

poster

Guo, Juanru

Benchmarking diffusion-based models for cross-context generalization in single-cell response prediction

poster

Gupta, Kavi

Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing

poster

Gupta, Saumya

Weakly-supervised topology-preserving 3D mitochondria segmentation

poster

Gurev, Sarah

Learning from prepandemic data to design and test future-proof vaccines

poster

Gurev, Sarah

Pitfalls of current protein-protein interaction predictors for viral spillover risk prediction

poster

Gurevitch, Oren

Investigation of long COVID effects on the central autonomic network using 7T multi-contrast MRI and deep learning

poster

Hang, Shengqi

Puget predicts gene expression across cell types using sequence and 3D chromatin organization data

poster

Harsh, Moshir

Multi-cancer risk prediction from large-scale longitudinal EHR data

poster

He, Chujun

Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy

poster

He, Yichun

An agentic AI spatial molecular foundation model of the mouse brain

poster

Healy, Shawn

Synthera—An agentic AI system for blood-brain barrier permeability prediction

poster

Hermosillo, Dylan G

From birth mode to feeding status—Benchmarking LLM-based metadata extraction strategies across a difficulty gradient in infant gut metagenomics

poster

Higgs, Aidan

Recurrent neural networks with heterogenous time constants adapt efficiently to tasks with diverse timescales

poster

Hill, Barnaby

Accurately modelling gapmer ASOs across the preclinical pipeline

poster

Hou, Chao

Understanding language model scaling on protein fitness prediction

poster

Huo, Bing-Xing

multiVIB—A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data

poster

Hwang, Yunha

Linear-time prediction of proteome-scale microbial protein interactions

talk

Ikonomova, Svetlana P

Probing mutability of TEV protease through comprehensive deep mutational scanning with GROQ-Seq

poster

Issa, Habon

Scaling laws of biological insight—Quantifying the interpretability and diversity of neural population codes

poster

Ivancevic, Atma

Virtual CRISPR—Benchmarking sequence-to-function models on complex regulatory elements

poster

Jain, Navami

Designing Long-lasting flu vaccines with AI

poster

Jakimo, Alan L.

Validating an integrated organoid/machine intelligence non-clinical new approach methodology for drug development

poster

Jaureguy, Jeff.

Single-cell sequence-to-function modeling of pancreas and immune cells for large-scale variant effect prediction in type 1 diabetes

poster

Jeon, Eun Young

Bridging the gap in rare neurological disease treatment—Pharmacoscopy enables systematic drug repurposing for MELAS and sphingolipidoses

poster

Jeong, Chang-Uk

CytoJEPA—Interpretable immune phenotyping via inducing point joint embedding predictive architecture

poster

Jha, Anupama

ChromeZoo reveals chromatin organization across mammalian evolution

poster

Jhutty, Anjeet

Orion’s belt by Prima Mente and Automata—The first end-to-end agentic biological intelligence platform applied to neurodegenerative disease and liquid biopsy

poster

Jiang, Jialong

Inferring dynamic regulatory network models from time-course scRNA-seq data

poster

Jiang, Shaowen

Protein language models for adaptive immune repertoire analysis via spatial transcriptomics

poster

Jimenez, Daniel

AI-guided enzyme specificity modulation and property optimization

poster

Jonsson, Benedikt

Training on 13,000 transcriptomes increases prediction accuracy in sequence-to-function models

poster

Jony, Saifur

Modeling epigenetic drug-induced transposable element expression from pre-treatment genomic and epigenomic landscape

poster

Kang, Yijie

Decoding the sequence basis of Pol II elongation with deep learning

poster

Kanpa, Vivek N

Multi-task learning to identify pan-cancerous and tissue-specific plasma protein biomarkers in a pre-diagnostic multi-cancer cohort

poster

Karbalayghareh, Alireza

Causal transformer for gene perturbation

poster

Karim, Shaamil

Virtual cells via discrete diffusion—From perturbation prediction to patient stratification

poster

Kasukawa, Takeya

A ground-truth atlas of active cis-regulatory elements (CREs) in human and mouse

poster

Kato, Daniel D

Contrastive self-supervised learning in high-level visual cortex

poster

Kedzierska, Kasia Z

Benchmarking sequence-to-function models for designing cell-type-specific synthetic enhancers across species

poster

Kelley, David

Borzoi—A sequence-to-expression model for gene regulation and genetic variant interpretation

talk

Khan, Mohammad Asif

Multi-cancer risk stratification from longitudinal health records using parameter-efficient fine-tuning of a generative foundation model

poster

Kim, Minju

Integrative machine learning and deep learning framework for rice phenotype prediction—generalization tests and consilience with association studies

poster

Kimmel, Jacob C

In silico design of epigenetic reprogramming payloads

talk

Kinger, Savik

Inferring active neural circuits using diffusion scores

poster

Kobos, William C

Predicting perturbation-induced program shifts in glioma-infiltrating T cells

poster

Kodali, Vamsi

Scaling eukaryotic genome annotation using NCBI EGAP and EGAPx

poster

Kohli, Pushmeet

Leveraging AI to advance biology

talk

Koo, Peter

Improving genomic deep learning with perturbation data

talk

Koulakov, Alexei

Grounding olfactory perception in language—Benchmarks and models for generating natural language odor descriptions

talk

Kubilius, Jonas

Systematic engineering of guide RNA repeats to optimize Cas12a editing efficiency

poster

Kudo, Shuichi N

Systematic identification of Cis-regulatory motifs modulating gene expression in fluctuating environments

poster

Kundaje, Anshul B

Decoding regulatory DNA with deep learning models

talk

Kwon, Ohbin

Modeling stem cell niche dependencies and their bypass in gastric tumorigenesis

poster

Lai, Ben

De novo design of antigen-specific T cell receptors using compositional protein language modeling

poster

Lakhani, Chirag

Integration of deep learning annotations with functional genomics improves identification of causal Alzheimer's disease variants

poster

Lash, Blake

Multi-agent reasoning for automated exploration of the protein universe

poster

Lee, Alice Eunjung

Predicting Alu-mediated loop-out exon skipping events with deep learning

poster

Lee, Jodi

Structural variants in human congenital heart disease disrupt distal genomic regulatory contacts of developmental genes

poster

Lee, Matthew E

Deep learning representations of human Immune Health for precision immunology

poster

Lee, Su-In

Explainable AI for biomedicine—Where we are and how to move forward

talk

Lehner, Ben

Mutate everything—Mapping the energetic and allosteric landscapes of proteins at scale

talk

Lei, Bo

Brainμ—Toward a universal foundation model for neuroscience through pre-trained multimodal world models

poster

Li, Dongshunyi

Unraveling tissue assembly with hierarchical transformers

poster

Li, Jiada

Leveraging the fine-tuned vision foundation model for precise mycobacterial cell segmentation and fluorescence event classification in multi-channel time-lapse microscopy images

poster

Li, Qianzi

Allele-specific sequence modeling with Siamese training improves regulatory variant prediction

poster

Li, Ronghan

Benchmarking diffusion models of single-cell perturbation prediction for generalization to unseen perturbations

poster

Lightstone, Felice

MuMMI—A machine learning-driven modeling infrastructure for coupling different scales, showcased for RAS-RAF activation

poster

Liu, Changchang

Improving molecular glue ternary complex reconstruction via integrative finetuning of co-folding models using structural and proteomics data

poster

Liu, Fan

Building structural interactomics by cross-linking mass spectrometry

talk

Liu, Feng

Epilepsy domain adapted large language models enhance epileptogenic zone prediction from seizure semiology

poster

Liu, Sunny

Superposition confounds representational alignment in neural systems

poster

Liu, Yunhe

A unified framework for cross-platform spatial omics analysis and deep spatial profiling

poster

Liu, Zhihan

S2F—A package for deep and mechanistic sequence-to-function modeling

poster

Liu, Zong-Yan

GeneCAD—Biologically constrained decoding for plant gene annotation with DNA foundation models

poster

Lo, Yucheng

GO2Symptom—A path-based causal GNN on biological knowledge graphs bridges molecular function to clinical phenotype

poster

Londhe, Shubhankar

Assessing variant deleteriousness using whole genomes and phenotypes of half a million individuals

poster

Lorenzi, Valentina

Learning spatial structure in endometriosis lesions

poster

Lundberg, Emma

Decoding human cell architecture – from spatial proteomics to cell modeling

talk

Lwin-Munger, Pancy T

Harnessing the single-cell RNA-seq data for immune digital twins

poster

Ly, Kevin Chi Hao

Predicting how perturbations reshape cellular trajectories with PerturbGen

poster

Lyman, Edward

Predicting membrane protein localization by deep learning on structure and chemistry

poster

Ma, Jian

AI for cellular organization and function across scales

talk

Mahmood, Faisal

Multimodal, generative, and agentic AI for pathology

talk

Mahood, Elizabeth

Multi-objective flow matching for generation and optimization of plant enhancers

poster

Majila, Kartik

Disobind—A sequence-based, partner-dependent contact map and interface residue predictor for intrinsically disordered regions

poster

Maneshgar, Behnam

GeneExpert—A foundation model for gene expression understanding

poster

Mantilla Puccetti, Pablo J

Dissecting the cis-regulatory code beyond motif syntax with genomic AI as virtual platforms

poster

Manzo, Gaetano

DeepFootprinting—Motif-level inference of transcription factor co-occupancy across active enhancers

poster

Marks, Debora S

AI methods to solve protein engineering and human genetics

talk

Martí-Gómez, Carlos

Inference of fitness landscapes with heterogenous patterns of epistasis across sites

poster

Martinez-Carrasco, Alejandro

A deep learning framework to identify drugs that restore cellular states

poster

Martín-Zamora, Francisco M

PARTHENON—Virtual cell models for causal discovery in Alzheimer's disease

talk

Martín-Zamora, Francisco M

Pleiades—Human whole-genome epigenomic foundation modelling for clinical diagnostics and biological discovery

poster

Mathis, Mackenzie

Measuring and modeling behavior with AI

talk

Matthias, Jan

A systematic benchmark evaluation of 3D tissue alignment algorithms for spatial omics

poster

Mazzarella, Luca

Seed variation impacts clustering stability in Single-Cell RNA-Seq and can be mitigated by StAbility-BasEd-Reassignment (SABER)

poster

Meza-Llamosas, Jose

Spatiotemporal mapping of the pancreatic ductal adenocarcinoma microenvironment under treatment using fused gromov-wasserstein divergences

poster

Miller, David

ContrasTED—Resolving protein dark matter with supervised contrastive learning

poster

Mishra, Reet

Decoding microglial state dynamics via CRISPR perturbations and multi-modal single-cell modeling

poster

Molen, Ricky

Pathway-resolved spatial niche analysis via graph-based masked autoencoding

poster

Mosso, Carson

From GWAS to function—Gaussian copula haplotype perturbations and AlphaGenome predictions validated by scRNA-seq

poster

Murphy, Alan

Modular transfer of AlphaGenome to short regulatory sequences

poster

Nagai, Masayuki

Causal refinement—Improving genomic deep learning models with perturbation data through continual learning

poster

Nagle, Roma

Evaluating mutagenesis strategies for inferring higher-order sequence–Function relationships

poster

Nair, Surag

Agentic systems are adept at solving well-scoped problems in computational genomics

poster

Nargund, Siddhi

Deep learning models of transcription factor activity in human immune aging

poster

Narykov, Oleksandr

Contrastive transfer learning on small datasets—Uncovering common representations for biological models

poster

Nawaz, Urwah

Towards proteome-driven precision oncology—Large-scale standardized cancer proteomics and AI modelling at ProCan

poster

Nelson, David R

Protein language model classification and satellite embeddings reveal microalgal genome-environment coupling across 221 million sequences on a global manifold

poster

Nishimura, Toru

Practical use of LLM-based AI agents for data analysis in drug discovery

poster

Nordenstorm, Olof

Mechanism constrained deep learning model for pan cancer drug responses

poster

Norman, Thomas

Reconstructing cellular transcriptional states using systematic transcription factor perturbations

poster

Ogden, Pierce

Toward the virtual organism—Predicting in vivo biology from millions of de novo protein designs

poster

Oku, Ali

DECONVersation—Single cell foundation model-derived embeddings for robust cell type deconvolution of bulk RNA-seq Data

poster

Olson, Andrew

AI agents for plant genomics research via model context protocol integration with Gramene and complementary biological databases

poster

Oneto, Alessandro

Establishing an empirical neutral model of endosymbiont evolution using Bayesian machine learning

poster

Orenbuch, Rose

A multi-modal approach to cancer risk prediction

poster

Pang, Kuan

PULSAR—A foundation model for multi-scale and multicellular biology

poster

Pang, Minxing

Query-driven generative AI synthesizes multi-modal spatial omics from histology

poster

Pasani, Satwik

How many DNN features are needed to predict neural responses?

poster

Pauli, Andrea

Life's first kiss—New insights into the mechanism of fertilization

talk

Peikon, Evan

A multi-layered biological knowledge graph framework for phenotype prediction following physiological perturbation

poster

Peng, Jiahui

A neuroscience discovery paradigm for mechanistic interpretability of neural networks

poster

Pielies Avelli, Marc

Modeling nascent transcription from chromatin landscape and structure with CLASTER

poster

Pierrot, Thomas

NTv3—A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction

talk

Pinello, Luca

Chorus—Agentic AI meets sequence-to-function oracles for comparative regulatory genomics

poster

Pinello, Luca

ChromCodes—Interpretable discrete representations enable controllable design of cell-type-specific regulatory DNA sequences

poster

Piva, Annamaria

Synthetic transcriptomic augmentation for robust prognostic signature discovery in small cohorts

poster

Podobedov, Nikita

Characterizing cellular functional landscapes with label-free imaging in optical pooled screening

poster

Poon, Hoifung

Towards virtual patient—AI for accelerating medical discovery

talk

Pratt, Nicholas B

Identifying learnable structure in genomic sequence with compute bounded models

poster

Priyadarshi, Satyam

GAME—Genomic API for model evaluation

poster

Qin, Yue

Towards functional maps of human cells by bridging molecular and morphological profiles

poster

Qu, Fiona

Modeling to learn patterns of antibody-antigen recognition

poster

Qu, Yiming

Terminal Anchor Variants (TAV)—ASVs beyond read-merge constraints with higher taxonomic resolution

poster

Quake, Stephen

Understanding the mysteries of the cell—How do many cell types arise from one genome?

talk

Rafi, Abdul Muntakim

Characterizing homology-induced data leakage and memorization in genome-trained sequence models

poster

Rafi, Abdul Muntakim

Evaluation of active learning selection strategies and characterization of informative sequences for sequence-to-expression models

poster

Rafi, Abdul Muntakim

gRely—Reliability estimation of variant effect predictions for genome trained sequence-to-expression models

poster

Raoufi, Sadaf

Machine learning for viral inference in metagenomes—Progress, pitfalls, and emerging directions

poster

Ren, Yunxiao

Neuronal and microglial fine-tuned 3D DNA foundation models dissect genetic variants in Alzheimer’s disease

poster

Rizzo, Kaeli

STEDD—Resource-efficient ensemble distillation for uncertainty-aware genomic deep learning

poster

Robinson, Kassidy

Convolutional neural network–based model for inferring transcriptional regulatory networks in maize

poster

Robinson, Andrew

AIRRchat—A natural language agent for structural exploration and sequence-to-structure mapping across predicted TCR-pMHC complexes

poster

Roblin, Elvire

PEARL—Predicting locus-specific chromatin accessibility from cell-free DNA whole-genome sequencing to identify molecular signatures of cancer heterogeneity

poster

Rochefort-Boulanger, Camille

Deep learning on genetic data with Diet Networks for genetic ancestry inference

poster

Rose, Nicholas

TRIOPS—Deep learning predicts peptide-independent TCR–MHC restriction from sequence

poster

Ross, David

A strategy for data collection to solve the protein function problem

poster

Sabri, Shan

Paired single-cell imaging and transcriptomics provide a functional alignment layer for virtual cell models

poster

Sachdev, Nina

Incorporating human genetic variation into protein language models

poster

Sarkar, Anirban S

Designing DNA with tunable regulatory activity using discrete diffusion

poster

Sarkar, Anirban S

Generative population annealing for biological sequence design

poster

Sarker, Drishty Badhon B

Machine learning-based prediction of drug sensitivity from ATRT transcriptomic signatures

poster

Schmidt, Megan

Computational techniques for harmonizing cancer cell line and tumor transcriptomes

poster

Sejnowski, Terrence

Brains and AI

talk

Shaw, John F

COPHI—A classifier to identify phospho-regulated protein-protein interactions

poster

Shelley, Kathryn

De novo design of light-driven protein motor domains

poster

Shen, Siqi

Morphology-to-transcriptome—Using foundation models and xenium data to discover prognostic H&E biomarkers in colorectal cancer

poster

Shewchuk, Alexandra

Integrating protein and DNA conformational dynamics into prediction of transcription factor binding specificity

poster

Shultes, Paulameena V

Cell-cell fusion in NSCLC—Novel transcriptomic features yield promising first classifiers

poster

Sinha, Riya

An agentic platform for phenotype-aware prioritization and interpretation of noncoding genetic variants

poster

Sirtori, Riccardo

Blood-based detection of sporadic amyotrophic lateral sclerosis by coupling single-walled carbon nanotube biosensing with deep learning

poster

Sledzieski, Samuel

MIMIC—A generative multimodal foundation model for biomolecules

poster

Soldat, Matous

De novo generation of terpene synthases with desired catalytic activity

poster

Song, Yun S.

Learning from evolutionary trajectories to predict variant effects and generate realistic biomolecules

talk

Soto-Ugaldi, Luis F

Deep learning reveals CpG dinucleotide density as the sequence-intrinsic determinant of epigenetic memory persistence

poster

Stanton, Alice

Engineered brain models for enhanced causal inference of disease

poster

Stark, Rory

Biologically grounded by design—Winning the ARC Virtual Cell Challenge Generalist Prize with PRiMeFlow

poster

Steinegger, Martin

Exploring the protein universe, from structural motifs to proteome-scale complexes

talk

Sternke, Matt

De novo protein domain engineering to aid structure determination of an integral membrane protein drug target

poster

Sui, Yanan

Human sensory-musculoskeletal modeling and control of whole-body movements

poster

Sui, Yanan

Whole-body mouse sensory-musculoskeletal modeling and control for movement

poster

Sui, Yanan

Whole-brain connectomic graph model enables whole-body locomotion control in fruit fly

poster

Sun, Mengyi

Predictive AI and shifting research focus—Lessons from structural biology

poster

Swanson, Erik

The EpiTome—Systematic de novo antibody design across every addressable epitope in the human proteome

poster

Tahmid, Md Toki

Beyond the consensus—Learning transcription factor-specific dna binding within the homeodomain family via deep learning and generative sequence design

poster

Tang, Wei Yu

Improving structure-based prediction of protein–DNA binding specificity using AlphaFold 3–predicted complexes

poster

Tegner, Jesper N

AI-driven 4D biology—Towards spatio-temporal deconvolution of life

poster

Tian, Ruiyi

Temporal evolution of early signs and symptoms of early-onset colorectal cancer—Integrating epidemiologic and transformer-based analyses

poster

Tiwari, Sarthak

Cis-Mamba integrates base-pair accessibility and DNA sequence for zero-shot in silico prediction of CRISPR enhancer perturbations

poster

Tolias, Andreas

Foundation models of the brain

talk

Toneyan, Shushan

Assessing codon language models for codon optimization in nucleic acid-based medicines

poster

Tsui, Kristin Chung Ying

Clinical data-driven CAR T cell therapy design with attention-based multiple instance learning

poster

Tu, Xinming

A modality gap in personal-genome prediction by sequence-to-function models

poster

Turner-Evans, Daniel

From the bench to the beltway—A view of the AI for biology funding landscape

poster

Uhler, Caroline

Integrating multimodal data—From biomarkers to mechanisms

talk

Van Valen, David A

Acceleration biological discovery with AI enabled measurements

talk

Vardanian, Erik

AI-driven characterization of chromatin architecture landscapes in triple-negative breast cancer

poster

Venkatraman, Divya Lakshmi

PRISM—Contrastive metric learning for T cell receptor embedding with intrinsic uncertainty estimation

poster

Voitov, Ivan

Fast intrinsic dynamics decouple stability and flexibility in neural sequence generation

poster

Walter, Johannes

Proteome-wide in silico screening for human protein-protein interactions

talk

Wang, Bo

Co‑discovery at scale—Digital twins, xAI, and collaborative biomedical workflows

poster

Wang, Jianrong

High-resolution reconstruction of single-cell specific spatial genome architectures in 3D space reveals context-specific gene regulation

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Wang, Junqiang

Decoding malignant blast cell state heterogeneity in acute leukemia using single-cell multi-omics

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Wang, Meng

Fast and scalable synthetic gene circuit design via transformer-based inverse modeling

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Wang, Xiaotong

Predicting rates of genome size change following polyploidy in angiosperms

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Wang, Xuefeng

A 1,000-region lymphoid aggregate atlas reveals functional and prognostic tertiary lymphoid structure states defined by virtual staining in metastatic melanoma

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Wang, Yilan

De novo computational design of pMHCI minibinders targeting the KRAS G12D neoantigen

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Webster, Dylan

Democratizing single cell and spatial omics analysis with cloud infrastructure and agentic workflows

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Wengert, Simon

Genomics-based multi-task foundation models for large-scale biomedical data analysis

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Wong, Wilfred

Bayesian multiscale models for epigenomic applications

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Wu, Haojia

CellPilot—A serverless, ai-powered desktop application for chat-based single-cell and spatial transcriptomics analysis

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Wu, Yujiao

Decoding regulatory grammar using long random DNA libraries and single-molecule chromatin profiling

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Xiao, Yao

Learning sequence-dependent cohesin kinetics via physics-informed neural networks

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Xie, Xiaoman

GEMS (GWAS effect mechanisms via sequence-to-function)—Unveiling cell type-specific mechanisms for GWAS variants

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Xing, Eric P

A world model of the virtual cell

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Xing, Jiawei

LaVOUS—Lineage-aware variational ornstein-uhlenbeck stochastics linking single-cell lineage tracing with dynamic gene expression

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Xu, Feihong

Toward trustworthy AI in biology with a well-calibrated similarity measure for arbitrary neural networks

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Xu, Jielin

A scalable human brain cell atlas dissects the microglial immune codes and cognitive resilience

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Xue, Yu

Inferring transcriptomic recovery from gene editing outcomes in SMARCB1-mutant ATRT

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Yamins, Daniel

A fruitful reciprocity; the past, present, and future of NeuroAI

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Yang, Rui

MethylPrint—A counterfactual deep learning framework for interpreting regulatory effects of DNA methylation

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Yao, Jiahui

TF-BindNet—Modeling transcription factor DNA binding specificity from sequence using PBM data

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Ye, Li

Discovering gut virome dynamics across dietary and surgical perturbations with the AI-based tool geNomad

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Yi, Stephen

eSIG-Net—Accurate prediction of single-mutation induced perturbations on protein interactions using a language model

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Yin, Liangying

A scalable invariant causal discovery framework reveals direct genetic and clinical determinants of complex human traits

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Youssef, Noor

Reliable mutation effect prediction across pandemic-threat viruses

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Yuste, Rafael M.

Neurorights—Human rights guidelines for neurotechnology and AI

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Zador, Anthony

What can neuroscience still teach AI?

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Zhai, Jingjing

Exploring regulatory rewiring underlying cold tolerance in grasses by fine-tuning a DNA language model

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Zhan, Yinxiu

A machine learning assay to predict disease recurrence in hormone receptor-positive breast cancer

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Zhang, Chen

Machine learning-based prediction of olfactory tendency in mice from chemical structure

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Zhang, Harrison G

The Virtual Biotech—A multi-agent AI framework for therapeutic discovery and development

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Zhang, Wenjin

Towards a pan-epigenome—AI-driven inference of multi-omics regulatory landscapes on complete genomes

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Zheng, Cici Xingyu

Priming-OT—Leveraging chromatin priming to resolve neuronal fate trajectories via optimal transport

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Zhong, Ellen

Algorithms for biomolecular structure determination at the proteome scale

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Zhong, Guojie

EpiBRAIN—A sequence-to-function model to understand cell type specific gene regulatory mechanisms in human brain

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Zhou, Jian

From predictive to mechanistic models of regulatory DNA sequence

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Zhou, Jingtian

Bolero—Predicting cell-state- and species-specific gene regulation from DNA sequence

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Zhou, Juannan

Measuring epistatic effects of mutations with exact, scalable Shapley values

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Zitnik, Marinka

Collaborative AI agents for biology

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Zuppas, Niko

Learning distributional corrections for undersampled populations with domain adaptation

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