09:25 – 09:30
Welcome
Welcome speech
09:30 – 10:20
Keynote — Ben Raphael, PhD (Princeton University)
40 min + 10 min Q&A
10:20 – 10:40
Chuhanwen Sun and Yi Zhang
STHD: probabilistic cell typing of single Spots in whole Transcriptome spatial data with High Definition
10:40 – 11:00
Haoyu Wang, Brittany Cody, Manuel Saavedra, Lanuza Faccioli, Rodrigo Florentino, Alejandro Soto-Gutierrez and Hatice Ulku Osmanbeyoglu
DGAT: A Dual-Graph Attention Network for Inferring Spatial Protein Landscapes from Transcriptomics
11:00 – 11:40
Midmorning coffee break
11:40 – 12:00
Seokmin Ha and Bonnie Berger
Inferring Direct Causal Regulation in Branching Lineages via Geometric Deconfounding
12:00 – 12:20
Elizabeth Gilfeather, Maria Chikina and Dennis Kostka
When Less Is Enough: Low-Rank Structure in DNA Sequence-to-Function Models
12:20 – 12:40
Jieni Hu, Julianne Fetter, David Ryan Koes and Maria Chikina
InfluenceNet: Encoding Motif Influence for Interpretable Modeling of Cis-Regulatory Syntax
12:40 – 12:50
Noam Shimshoviz, Safwan Butto and Yaron Orenstein
NPBIP: Predicting Binding Preferences of Uncharacterized Nucleic-Acid-Binding Proteins
12:50 – 13:00
Fabian Woller, Paul Martini, Souptik Sen, David B. Blumenthal and Anne Hartebrodt
SignifiKANTE: Efficient P-value computation for gene regulatory networks
13:00 – 14:30
Lunch break
14:30 – 14:50
Abrar Rahman Abir, Sajib Acharjee Dip and Liqing Zhang
CFM-GP: Unified Conditional Flow Matching to Learn Gene Perturbation Across Cell Types
14:50 – 15:10
Hechen Li and Xiuwei Zhang
scModCompare: Disentangling Shared Identity and Modality-Specific Regulatory Programs in Multimodal Single-Cell Data
15:10 – 15:30
Hui Cheng, Yunhao Qiao, Yufan Feng, Yuyang Wei, Jinpu Cai, Xinzhu Jiang, Qiuyu Lian and Hongyi Xin
VeloTrace Reconciles Divergent Velocity and Trajectory in Single-cell Transcriptomics with Deep Neural ODE
15:30 – 15:40
Anna Möller, Miriam Schnitzerlein, Eric Greto, Vasily Zaburdaev, Stefan Uderhardt and David B. Blumenthal
Quantifying distribution shifts in single-cell data with scXMatch
15:40 – 15:50
Kristina Sungeun Song, Marianne Cyr, Laurence Faucher-Giguère, Bernice Yeo Hwee Ting, Vivian Kaiyan Seow, Gabrielle Deschamps-Francoeur, Sherif Abou Elela and Michelle S. Scott
snoFlake: A network model for discovering novel snoRNA-RBP regulatory complexes in human post-transcriptional regulation
15:50 – 16:00
Sobhan Shukueian Tabrizi, Helyasadat Hashemi Aghdam and A. Ercument Cicek
RNA–X: Modeling RNA interactions to design binder RNA and simultaneously target multiple molecules of different types
16:00 – 16:40
Afternoon coffee break
16:40 – 17:00
Ruyi Chen, Nathan Palpant, Gabriel Foley and Mikael Boden
Coupling codon and protein constraints decouples drivers of variant pathogenicity
17:00 – 17:20
Pia Keukeleire, Coline Arnould, Martin Kircher and Nadav Ahituv
Simultaneously characterizing promoter interactions and regulatory activity using Capture-C MPRA
17:20 – 17:25
Closing remarks
17:30 – 19:00
Poster session