RECOMB 2026 Proceedings

Thessaloniki, Greece, May 26 - 29, 2026.

PC Chair: Rayan Chikhi, Institut Pasteur
Organization Committee: Christos Ouzounis (chair), Ezgi Ebren
Keynote Speakers:

List of Publications

  • Quartet-based species tree methods enable fast and consistent tree of blobs reconstruction under the network multispecies coalescent. Junyan Dai, Yunheng Han, 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, 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, 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, Chang-Yu Hsieh.
  • POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets. Sara C. Käufler, Henri Schmidt, Martin Jürgens, Gunnar W. Klau, Palash Sashittal, Benjamin J. Raphael.
  • SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design. Peidong Zhang, Rong Han, Xiangzhe Kong, Ting Chen, 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, 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, Conrado Martínez.
  • Evolutionary dynamics under phenotypic uncertainty. Vaibhav Mohanty, Anna Sappington, Eugene Shakhnovich, Bonnie Berger.
  • Deconvolving Phylogenetic Distance Mixtures. Shayesteh Arasti, Ali Osman Berk Şapcı, Eleonora Rachtman, Mohammed El-Kebir, Siavash Mirarab.
  • Achieving spatial multi-omics integration from unaligned serial sections with DIME. Pengyu Sun, Tian Mou, Xubin Zheng, 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, Sara Mostafavi.
  • On Deriving Synteny Blocks by Compacting Elements. Leonard Bohnenkämper, Luca Parmigiani, Cedric Chauve, Jens Stoye.
  • PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks. Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, 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, Hongyi Xin.
  • Bacterial protein function prediction via multimodal deep learning. Giulia Muzio, Michael Adamer, Leyden Fernandez, Lukas Miklautz, Karsten Borgwardt, Kemal Avican.
  • Alternet: Alternative splicing-aware gene regulatory network inference. Juliane Hoffmann, Julia Wallnig, Ziheng Dai, Olga Tsoy, David B. Blumenthal, Anne Hartebrodt.
  • Bias in genome-wide association test statistics due to omitted interactions. Burak Yelmen, Merve Nur Güler, Tõnu Kollo, Märt Möls, Guillaume Charpiat, 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, Jing Li.
  • Sequence-to-graph alignment based copy number calling using a network flow formulation. Hugo Magalhães, Jonas Weber, Gunnar W. Klau, Tobias Marschall, Timofey Prodanov.
  • Fast, accurate construction of multiple sequence alignments from protein language embeddings. Minh Hoang, Isabel Armour-Garb, Mona Singh.
  • SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores. Ardalan Naseri, Ahsan Sanaullah, Shaojie Zhang, Degui Zhi.
  • Compressed inverted indexes for scalable sequence similarity. Florian Ingels, Lea Vandamme, Mathilde Girard, Clément Agret, Bastien Cazaux, Antoine Limasset.
  • Minimizer Density revisited: Models and Multiminimizers. Florian Ingels, Lucas Robidou, Igor Martayan, Camille Marchet, 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, Yuval Kluger.
  • bronko: ultrarapid, alignment-free detection of viral genome variation. Ryan Doughty, Michael Tisza, 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, Peter Van Loo.
  • Causal gene regulatory network inference from Perturb-seq via adaptive instrumental variable modeling. Zhongxuan Sun, Hyunseung Kang, Sunduz Keles.
  • Summarizing RNA Structural Ensembles via Maximum Agreement Secondary Structures. Xinyu Gu, Stefan Ivanovic, Daniel Feng, Mohammed El-Kebir.
  • CAMP: Coreset Accelerated Metacell Partitioning enables scalable analysis of single-cell data. Danrong Li, Young Kun Ko, Stefan Canzar.
  • Multi-modal tissue-aware graph neural network for in silico genetic discovery. Anusha Aggarwal, Ksenia Sokolova, Olga Troyanskaya.
  • CLADES — Contrastive Learning Augmented DifferEntial Splicing with Orthologous Positive Pairs. Arghamitra Talukder, Nicholas Keung, Itsik Pe’Er, David A. Knowles.
  • MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-Omics. Chang Lu, Yuval Kluger, Rong Ma.
  • GOPHER: Optimization-based Phenotype Randomization for Genome-Wide Association Studies with Differential Privacy. Anupama Nandi, Seth Neel, Hyunghoon Cho.
  • Identifying Robust Subclonal Structures Through Tumor Progression Tree Alignment. Chih Hao Wu, Jacob Gilbert, Salem Malikić, S. Cenk Sahinalp.
  • DeltaNMF: A Two-Stage Neural NMF for Differential Gene Program Discovery. Anish Karpurapu, Charles Gersbach, Rohit Singh.
  • Transforming Biological Foundation Model Representations for Out-of-Distribution Data. Aditya Pratapa, Rohit Singh, 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, Sriram Sankararaman.
  • Integrative Inference of Spatially Informed Cell Lineage Trees using LineageMap. Xinhai Pan, Yiru Chen, Xiuwei Zhang.
  • Uncertainty-aware synthetic lethality prediction with pretrained foundation models. Kailey Hua, Ellie Haber, Jian Ma.
  • Evolutionary profile enhancement improves protein function annotation. Shitong Dai, Jiaqi Luo, Yunan Luo.
  • Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3. Jamshed Khan, Laxman Dhulipala, Prashant Pandey, 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, Jingyi Jessica Li.
  • Gene-First Identity Construction for Robust Cell Identification in Single-Cell Transcriptomics. Luqi Yang, Zhenwei Huang, Hongyi Xin, 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, Jingyi Jessica Li.
  • Error Correction Algorithms for Efficient Gene Quantification in Single Cell Transcriptomics. Jens Zentgraf, Johanna Schmitz, Andreas Keller, Sven Rahmann.
  • CycleGRN: Inferring Gene Regulatory Networks from Cyclic Flow Dynamics in Single-Cell RNA-seq. Wenjun Zhao, Elana Fertig, Genevieve Stein-O’Brien.
  • Protein Compositional Ratio Representation (PCRR) Systematically Improves Human Disease Prediction. Adithya Madduri, Randall Ellis, Chirag Patel.
  • Constrained diffusion as a paradigm for evolution. Daniel Lazarev, Anna Sappington, Grant Chau, Ruochi Zhang, Bonnie Berger.
  • Integrative Multi‑Scale Sequence–Structure Modeling for Antimicrobial Peptide Prediction and Design. Jiayi Li, Yanruisheng Shao, Yu Li, Qinze Yu.
  • Integrating morphology and gene expression in unpaired single-cell data using GeoAdvAE. Jinqiu Du, Kevin Z. Lin.
  • Deconvolving mutation effects on protein stability and function with disentangled protein language models. Kerr Ding, Ziang Li, Tony Tu, Jiaqi Luo, Yunan Luo.
  • Fast and accurate resolution of ecDNA sequence using Cycle-Extractor. Mahsa Faizrahnemoon, Jens Luebeck, King L. Hung, Suhas Rao, Matthew G. Jones, Paul S. Mischel, Howard Y. Chang, Kaiyuan Zhu, Vineet Bafna.
  • pHapCompass: Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase. Marjan Hosseini, Ella Veiner, Thomas Bergendahl, Tala Yasenpoor, Zane Smith, Margaret Staton, Derek Aguiar.
  • scProfiterole: Clustering of Single-Cell Proteomic Data Using Graph Contrastive Learning via Spectral Filters. Mustafa Coşkun, Filipa Blasco Lopes, Pınar Kubilay Tolunay, Mark R. Chance, Mehmet Koyutürk.
  • Generating Hybrid Proteins with the MSA-Transformer. Sanjana Tule, Samuel Davis, Ivan Koludarov, Ariane Mora, Mikael Boden.
  • Modeling Multi-Modal Brain Connectomes for Brain Disorder Diagnosis via Graph Diffusion Optimal Transport Network. Xiaoqi Sheng, Jiawen Liu, Jiaming Liang, Yiheng Zhang, Sankar Mondal, Yutong Li, Tinghe Zhang, Bing Liu, Jiangning Song, Hongmin Cai.
  • Multimodal spatial alignment and morphology mapping with MOSAICField. Xinhao Liu, Hongyu Zheng, Peter Halmos, Julian Gold, Erik Storrs, Li Ding, Ben Raphael.