RECOMB 2025 Accepted Papers

• Dynamic programming algorithms for fast and accurate cell lineage tree reconstruction from CRISPR-based lineage tracing data
  Junyan Dai and Erin Molloy


• Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-cell DNA Sequencing of Tumors
  Leah Weber, Anna Hart, Idoia Ochoa and Mohammed El-Kebir


• TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment
  Natnatee Dokmai, Kaiyuan Zhu, Cenk Sahinalp and Hyunghoon Cho


• mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis
  Pan Liu and Jingyi Jessica Li


• Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses
  Dongyuan Song, Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge and Jingyi Jessica Li


• Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining
  Sebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew Jones, Yun Song and Nir Yosef


• TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates
  Kemal Inecik, Aleyna Kara, Antony Rose, Muzlifah Haniffa and Fabian Theis


• Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis
  Yuxiang Wei, Anees Abrol and Vince Calhoun


• devider: long-read reconstruction of many diverse haplotypes
  Jim Shaw, Christina Boucher, Yun William Yu, Noelle Noyes and Heng Li


• Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states
  Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang, Minsheng Hao, Hector Corrada Bravo, Gabriele Scalia, Aviv Regev and Graham Heimberg


• Rag2Mol: Structure-based drug design based on Retrieval Augmented Generation
  Peidong Zhang, Xingang Peng, Rong Han, Ting Chen and Jianzhu Ma


• ML-MAGES: A machine learning framework for multivariate genetic association analyses with genes and effect size shrinkage
  Xiran Liu, Lorin Crawford and Sohini Ramachandran


• Untying rates of gene gain and loss leads to a new phylogenetic approach
  Yoav Dvir and Sagi Snir


• Hyper-k-mers: efficient streaming k-mers representation
  Igor Martayan, Lucas Robidou, Yoshihiro Shibuya and Antoine Limasset


• Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC
  Samuel Sledzieski, Charlotte Versavel, Rohit Singh, Faith Ocitti, Kapil Devkota, Lokender Kumar, Polina Shpilker, Liza Roger, Jinkyu Yang, Nastassja Lewinski, Hollie Putnam, Bonnie Berger, Judith Klein-Seetharaman and Lenore Cowen


• ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads
  Rashid Al-Abri and Gamze Gürsoy


• TissueMosaic enables cross-sample differential analysis of spatial transcriptomics datasets through self-supervised representation learning
  Sandeep Kambhampati, Luca D'Alessio, Fedor Grab, Stephen Fleming, Fei Chen and Mehrtash Babadi


• Inferring cell differentiation maps from lineage tracing data
  Palash Sashittal, Richard Zhang, Benjamin Law, Alexander Strzalkowski, Henri Schmidt, Adriano Bolondi, Michelle Chan and Ben Raphael


• OMKar: optical map based automated karyotyping of genomes to identify constitutional abnormalities
  Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Paul Dremsek, Alex Hastie, Andy Wing Chun Pang and Vineet Bafna


• An Exact and Fast SAT Formulation for the DCJ Distance
  Aaryan Mahesh Sarnaik, Ke Chen, Austin Diaz and Mingfu Shao


• cfDecon: Accurate and Interpretable methylation-based cell type deconvolution for cell-free DNA
  Yixuan Wang, Jiayi Li, Jingqi Li, Shen Yang, Yuhan Huang, Xinyuan Liu, Yimin Fan, Irwin King, Yumei Li and Yu Li


• Orientation-Aware Graph Neural Networks for Protein Structure Representation Learning
  Jiahan Li, Shitong Luo, Cengyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas Guibas, Jian Peng and Jianzhu Ma


• Sequence-based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-tuning of Protein Language Models
  Chiho Im, Ryan Zhao, Scott Boyd and Anshul Kundaje


• Integer programming framework for pangenome-based genome inference
  Ghanshyam Chandra, Md Helal Hossen, Stephan Scholz, Alexander T Dilthey, Daniel Gibney and Chirag Jain


• DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins
  Shaojun Wang, Hancheng Liu, Weiqi Zhai and Shanfeng Zhu


• Active Learning for Protein Structure Prediction
  Zexin Xue, Michael Bailey, Abhinav Gupta, Alejandro Corrochano-Navarro, Sizhen Li, Ruijiang Li, Qiu Yu, Ziv Bar-Joseph, Sven Jager and Lorenzo Kogler-Anele


• A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement.
  Ali Osman Berk Şapcı and Siavash Mirarab


• An adversarial scheme for integrating multi-modal data on protein function
  Rami Nasser, Leah Schaffer, Trey Ideker and Roded Sharan


• Accurate Detection of Tandem Repeats from Error-Prone Long Reads with EquiRep
  Zhezheng Song, Tasfia Zahin, Xiang Li and Mingfu Shao


• Learning a CoNCISE language for small molecule binding and function
  Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen and Rohit Singh


• Optimal marker genes for c-separated cell types
  Bartol Borozn, Luka Borozan, Domagoj Severdija, Domagoj Matijevic and Stefan Canzar


• Old dog, new tricks: Exact seeding strategy improves RNA design performances
  Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty and Hua-Ting Yao


• Integration and querying of multimodal single-cell data with product-of-experts VAE
  Anastasia Litinetskaya, Maiia Shulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi and Fabian Theis


• Causal disentanglement of treatment effects in single-cell RNA Sequencing through counterfactual inference
  Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg and Lin Wan


• ScisTree2: An Improved Method for Large-scale Inference of Cell Lineage Trees and Genotype Calling from Noisy Single Cell Data
  Haotian Zhang, Yiming Zhang, Teng Gao and Yufeng Wu


• Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2
  Mrinmoy Saha Roddur, Vikram Ramavarapu, Abi Bunkum, Ariana Huebner, Roman Mineyev, Nicholas McGranahan, Simone Zaccaria and Mohammed El-Kebir


• BayesRVAT: Bayesian Aggregation of Multiple Annotations Enhances Rare Variant Association Testing
  Antonio Nappi, Na Cai and Francesco Paolo Casale


• Dynamic mu-PBWT: Dynamic Run-length Compressed PBWT for Biobank Scale Data
  Pramesh Shakya, Ahsan Sanaullah, Degui Zhi and Shaojie Zhang


• The tree labeling polytope: a unified approach to ancestral reconstruction problems
  Henri Schmidt and Benjamin Raphael


• Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
  Hongyu Zheng, Hirak Sarkar and Benjamin Raphael


• STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues
  Shaoheng Liang, Junjie Tang, Guanghan Wang and Jian Ma


• Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport
  Peter Halmos, Julian Gold, Xinhao Liu and Benjamin Raphael


• Improved pangenomic classification accuracy with chain statistics
  Nathaniel K. Brown, Vikram Shivakumar and Ben Langmead


• Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance
  Tianshuo Zhou, Wei Yu Tang, Apoorv Malik, David H. Mathews and Liang Huang


• Unified integration of spatial transcriptomics across platforms
  Ellie Haber, Ajinkya Deshpande, Jian Ma and Spencer Krieger


• ALPINE: an interpretable approach for decoding phenotypes from multicondition sequencing data
  Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser and Vicky Yao


• ralphi: a deep reinforcement learning framework for haplotype assembly
  Enzo Battistella, Anant Maheshwari, Barış Ekim, Bonnie Berger and Victoria Popic


• A Phylogenetic Approach to Genomic Language Modeling
  Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye and Yun S. Song


• A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single Cell Sequencing Datasets
  Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, John Bridgers, Salem Malikic, A. Funda Ergun and S. Cenk Sahinalp


• Prokrustean Graph: A substring index for rapid k-mer size analysis
  Adam Park and David Koslicki


• GeneCover: A Combinatorial Approach for Label-free Marker Gene Selection
  An Wang, Stephanie Hicks, Donald Geman and Laurent Younes


• Learning maximally spanning representations improves protein function annotation
  Jiaqi Luo and Yunan Luo


• Rewiring protein sequence and structure generative models to enhance protein stability prediction
  Ziang Li and Yunan Luo


• Antimicrobial drug recommendation from MALDI-TOF mass spectrometry with statistical guarantees using conformal prediction
  Nina Corvelo Benz, Lucas Miranda, Dexiong Chen, Janko Sattler and Karsten Borgwardt