RECOMB 2026 Accepted Papers

• Quartet-based species tree methods enable fast and consistent tree of blobs reconstruction under the network multispecies coalescent
  Junyan Dai, Yunheng Han and Erin Molloy

• Fast and Flexible Flow Decompositions in General Graphs via Dominators
  Francisco Sena and Alexandru I. Tomescu

• Predicting interaction-specific protein–protein interaction perturbations by missense variants with MutPred-PPI
  Ross Stewart, Florent Laval, Michael Calderwood, Matthew Mort, David Cooper, Marc Vidal and Predrag Radivojac

• KuPID: Kmer-based Upstream Preprocessing of Long Reads for Isoform Discovery
  Molly Borowiak and Yun William Yu

• Private Information Leakage from Polygenic Risk Scores
  Kirill Nikitin and Gamze Gursoy

• Privacy-Preserving Pangenome Graphs
  Jacob Blindenbach, Shaunak Soni and Gamze Gursoy

• ProtFlow: Flow Matching-based Protein Sequence Design with Comprehensive Protein Semantic Distribution Learning and High-quality Generation
  Zitai Kong, Yiheng Zhu, Yinlong Xu, Mingze Yin, Tingjun Hou, Jian Wu, Hongxia Xu and Chang-Yu Hsieh

• POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets
  Sara C. Schulte, Henri Schmidt, Martin Jürgens, Gunnar W. Klau, Palash Sashittal and Benjamin J. Raphael

• SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design
  Peidong Zhang, Rong Han, Xiangzhe Kong, Ting Chen and Jianzhu Ma

• STELAR-X: Scaling Coalescent-Based Species Tree Inference to 100,000 Species and Beyond
  Anik Saha and Md Shamsuzzoha Bayzid

• A Cophylogenetic Approach for Virus-Host Interaction Prediction
  Md Zarzees Uddin Shah Chowdhury, T. M. Murali and Palash Sashittal

• Denoising single-cell transcriptomic data with sparse PCA
  Victor Chardès

• Prediction of lifetime disease liability from EHR features
  Yazheng Di and Na Cai

• Quantum and Temporal Graph Neural Networks Reveal New Accuracy Limits in Predicting Protein–Ligand Dissociation Kinetics
  Azamat Salamatov and Gowtham Atluri

• MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements
  Mahmudur Rahman Hera, David Koslicki and Conrado Martínez

• Evolutionary dynamics under phenotypic uncertainty
  Vaibhav Mohanty, Anna Sappington, Eugene Shakhnovich and Bonnie Berger

• Deconvolving Phylogenetic Distance Mixtures
  Shayesteh Arasti, Ali Osman Berk Şapcı, Eleonora Rachtman, Mohammed El-Kebir and Siavash Mirarab

• Achieving spatial multi-omics integration from unaligned serial sections with DIME
  Pengyu Sun, Tian Mou, Xubin Zheng and Xinlei Huang

• Deep genomic models of allele-specific measurements
  Xinming Tu, Alexander Sasse, Kaitavjeet Chowdhary, Anna E. Spiro, Liang Yang, Maria Chikina, Christophe O. Benoist and Sara Mostafavi

• On Deriving Synteny Blocks by Compacting Elements
  Leonard Bohnenkämper, Luca Parmigiani, Cedric Chauve and Jens Stoye

• PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks
  Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami and Jannik Schestag

• Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic Analysis
  Jinpu Cai, Yuxuan Wang, Yunhao Qiao, Cheng Wang, Ziqi Rong, Luting Zhou, Haoyang Liu, Meng Jiang, Hongbin Shen, Jingyi Jessica Li and Hongyi Xin

• Bacterial protein function prediction via multimodal deep learning
  Giulia Muzio, Michael Adamer, Leyden Fernandez, Lukas Miklautz, Karsten Borgwardt and Kemal Avican

• Alternet: Alternative splicing-aware gene regulatory network inference
  Juliane Hoffmann, Julia Wallnig, Ziheng Dai, Olga Tsoy, David B. Blumenthal and Anne Hartebrodt

• Bias in genome-wide association test statistics due to omitted interactions
  Burak Yelmen, Merve Nur Güler, Tõnu Kollo, Märt Möls, Guillaume Charpiat and Flora Jay

• Joint Learning of Drug-Drug Combination and Drug-Drug Interaction via Coupled Tensor-Tensor Factorization with Side Information
  Xiaoge Zhang, Zhengyu Fang, Kaiyu Tang, Huiyuan Chen and Jing Li

• Sequence-to-graph alignment based copy number calling using a network flow formulation
  Hugo Magalhães, Jonas Weber, Gunnar W. Klau, Tobias Marschall and Timofey Prodanov

• Fast, accurate construction of multiple sequence alignments from protein language embeddings
  Minh Hoang, Isabel Armour-Garb and Mona Singh

• SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores
  Ardalan Naseri, Ahsan Sanaullah, Shaojie Zhang and Degui Zhi

• Compressed inverted indexes for scalable sequence similarity
  Florian Ingels, Lea Vandamme, Mathilde Girard, Clément Agret, Bastien Cazaux and Antoine Limasset

• Minimizer Density revisited: Models and Multiminimizers
  Florian Ingels, Lucas Robidou, Igor Martayan, Camille Marchet and Antoine Limasset

• DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data
  Ruiqi Li, Junchen Yang, Pei-Chun Su, Ariel Jaffe, Ofir Lindenbaum and Yuval Kluger

• bronko: ultrarapid, alignment-free detection of viral genome variation
  Ryan Doughty, Michael Tisza and Todd Treangen

• Arborist: Prioritizing Bulk DNA Inferred Tumor Phylogenies via Low-pass Single-cell DNA Sequencing Data
  Leah Weber, Chi Yin Ching, Chrisopher Ly, Yixiao Cheng, Chunxu Gao and Peter Van Loo

• Causal gene regulatory network inference from Perturb-seq via adaptive instrumental variable modeling
  Zhongxuan Sun, Hyunseung Kang and Sunduz Keles

• Summarizing RNA Structural Ensembles via Maximum Agreement Secondary Structures
  Xinyu Gu, Stefan Ivanovic, Daniel Feng and Mohammed El-Kebir

• CAMP: Coreset Accelerated Metacell Partitioning enables scalable analysis of single-cell data
  Danrong Li, Young Kun Ko and Stefan Canzar

• Multi-modal tissue-aware graph neural network for in silico genetic discovery
  Anusha Aggarwal, Ksenia Sokolova and Olga Troyanskaya

• CLADES — Contrastive Learning Augmented DifferEntial Splicing with Orthologous Positive Pairs
  Arghamitra Talukder, Nicholas Keung, Itsik Pe’Er and David A. Knowles

• MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-Omics
  Chang Lu, Yuval Kluger and Rong Ma

• GOPHER: Optimization-based Phenotype Randomization for Genome-Wide Association Studies with Differential Privacy
  Anupama Nandi, Seth Neel and Hyunghoon Cho

• Identifying Robust Subclonal Structures Through Tumor Progression Tree Alignment
  Chih Hao Wu, Jacob Gilbert, Salem Malikić and S. Cenk Sahinalp

• DeltaNMF: A Two-Stage Neural NMF for Differential Gene Program Discovery
  Anish Karpurapu, Charles Gersbach and Rohit Singh

• Transforming Biological Foundation Model Representations for Out-of-Distribution Data
  Aditya Pratapa, Rohit Singh and Purushothama Rao Tata

• A biobank-scale method for learning environmental modulators of gene–environment interaction underlying complex traits
  Zhengtong Liu, Arush Ramteke, Aakarsh Anand, Aditya Gorla, Moonseong Jeong and Sriram Sankararaman

• Integrative Inference of Spatially Informed Cell Lineage Trees using LineageMap
  Xinhai Pan, Yiru Chen and Xiuwei Zhang

• Uncertainty-aware synthetic lethality prediction with pretrained foundation models
  Kailey Hua, Ellie Haber and Jian Ma

• Evolutionary profile enhancement improves protein function annotation
  Shitong Dai, Jiaqi Luo and Yunan Luo

• Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3
  Jamshed Khan, Laxman Dhulipala, Prashant Pandey and Rob Patro

• Nullstrap-DE: A General Framework for Calibrating FDR and Preserving Power in Differential Expression Methods, with Applications to DESeq2 and edgeR
  Chenxin Flora Jiang, Changhu Wang and Jingyi Jessica Li

• Gene-First Identity Construction for Robust Cell Identification in Single-Cell Transcriptomics
  Luqi Yang, Zhenwei Huang, Hongyi Xin and Jinpu Cai

• scDesignPop generates population-scale single-cell RNA-seq data for power analysis, method benchmarking, and privacy protection
  Chris Dong, Yihui Cen, Dongyuan Song and Jingyi Jessica Li

• Error Correction Algorithms for Efficient Gene Quantification in Single Cell Transcriptomics
  Jens Zentgraf, Johanna Schmitz, Andreas Keller and Sven Rahmann