{
  "title": "30th Annual International Conference on Research in Computational Molecular Biology",
  "location": "Thessaloniki, Greece",
  "dates": "May 26 - 29, 2026",
  "pc_chair": "Rayan Chikhi",
  "organization_committee": "Christos Ouzounis (chair), Ezgi Ebren",
  "keynotes": "Sara Mostafavi, Paul Medvedev, Manolis Kellis, Alexandros Stamatakis",
  "website": "https://recomb.org/recomb2026/",
  "papers": [
    {
      "author": "Junyan Dai, Yunheng Han, Erin Molloy",
      "title": "Quartet-based species tree methods enable fast and consistent tree of blobs reconstruction under the network multispecies coalescent",
      "preprint_id": "bioRxiv 2025.11.05.686850",
      "preprint_doi": "10.1101/2025.11.05.686850"
    },
    {
      "author": "Francisco Sena and Alexandru I. Tomescu",
      "title": "Fast and Flexible Flow Decompositions in General Graphs via Dominators",
      "preprint_id": "arXiv:2511.19153",
      "preprint_doi": "10.48550/arXiv.2511.19153"
    },
    {
      "author": "Ross Stewart, Florent Laval, Michael Calderwood, Matthew Mort, David Cooper, Marc Vidal, Predrag Radivojac",
      "title": "Predicting interaction-specific protein–protein interaction perturbations by missense variants with MutPred-PPI",
      "preprint_id": "bioRxiv 2025.12.20.695738",
      "preprint_doi": "10.64898/2025.12.20.695738"
    },
    {
      "author": "Molly Borowiak and Yun William Yu",
      "title": "KuPID: Kmer-based Upstream Preprocessing of Long Reads for Isoform Discovery",
      "preprint_id": "bioRxiv 2025.12.05.692400",
      "preprint_doi": "10.64898/2025.12.05.692400"
    },
    {
      "author": "Kirill Nikitin and Gamze Gursoy",
      "title": "Private Information Leakage from Polygenic Risk Scores",
      "preprint_id": "bioRxiv 2026.02.16.706191",
      "preprint_doi": "10.64898/2026.02.16.706191"
    },
    {
      "author": "Jacob Blindenbach, Shaunak Soni, Gamze Gursoy",
      "title": "Privacy-Preserving Pangenome Graphs",
      "preprint_id": "bioRxiv 2026.02.16.706152",
      "preprint_doi": "10.64898/2026.02.16.706152"
    },
    {
      "author": "Zitai Kong, Yiheng Zhu, Yinlong Xu, Mingze Yin, Tingjun Hou, Jian Wu, Hongxia Xu, Chang-Yu Hsieh",
      "title": "ProtFlow: Flow Matching-based Protein Sequence Design with Comprehensive Protein Semantic Distribution Learning and High-quality Generation",
      "preprint_id": "bioRxiv 2026.02.14.705870",
      "preprint_doi": "10.64898/2026.02.14.705870"
    },
    {
      "author": "Sara C. Käufler, Henri Schmidt, Martin Jürgens, Gunnar W. Klau, Palash Sashittal, Benjamin J. Raphael",
      "title": "POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets",
      "preprint_id": "bioRxiv 2026.02.25.707960",
      "preprint_doi": "10.64898/2026.02.25.707960"
    },
    {
      "author": "Peidong Zhang, Rong Han, Xiangzhe Kong, Ting Chen, Jianzhu Ma",
      "title": "SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design",
      "preprint_id": "bioRxiv 2025.11.06.687093",
      "preprint_doi": "10.1101/2025.11.06.687093"
    },
    {
      "author": "Anik Saha and Md Shamsuzzoha Bayzid",
      "title": "STELAR-X: Scaling Coalescent-Based Species Tree Inference to 100,000 Species and Beyond",
      "preprint_id": "bioRxiv 2025.11.22.689894",
      "preprint_doi": "10.1101/2025.11.22.689894"
    },
    {
      "author": "Md Zarzees Uddin Shah Chowdhury, T. M. Murali, Palash Sashittal",
      "title": "A Cophylogenetic Approach for Virus-Host Interaction Prediction",
      "preprint_id": "bioRxiv 2026.02.26.708038",
      "preprint_doi": "10.64898/2026.02.26.708038"
    },
    {
      "author": "Victor Chardès",
      "title": "Denoising single-cell transcriptomic data with sparse PCA",
      "preprint_id": "arXiv:2509.15429",
      "preprint_doi": "10.48550/arXiv.2509.15429"
    },
    {
      "author": "Yazheng Di and Na Cai",
      "title": "Prediction of lifetime disease liability from EHR features",
      "preprint_id": "medRxiv 2026.02.15.26346336",
      "preprint_doi": "10.64898/medRxiv 2026.02.15.26346336"
    },
    {
      "author": "Azamat Salamatov and Gowtham Atluri",
      "title": "Quantum and Temporal Graph Neural Networks Reveal New Accuracy Limits in Predicting Protein–Ligand Dissociation Kinetics",
      "preprint_id": "bioRxiv 2025.11.20.689635",
      "preprint_doi": "10.1101/2025.11.20.689635"
    },
    {
      "author": "Mahmudur Rahman Hera, David Koslicki, Conrado Martínez",
      "title": "MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements",
      "preprint_id": "bioRxiv 2025.11.11.687920",
      "preprint_doi": "10.1101/2025.11.11.687920"
    },
    {
      "author": "Vaibhav Mohanty, Anna Sappington, Eugene Shakhnovich, Bonnie Berger",
      "title": "Evolutionary dynamics under phenotypic uncertainty",
      "preprint_id": "bioRxiv 2026.03.15.711953",
      "preprint_doi": "10.64898/2026.03.15.711953"
    },
    {
      "author": "Shayesteh Arasti, Ali Osman Berk Şapcı, Eleonora Rachtman, Mohammed El-Kebir, Siavash Mirarab",
      "title": "Deconvolving Phylogenetic Distance Mixtures",
      "preprint_id": "bioRxiv 2026.01.18.700179",
      "preprint_doi": "10.64898/2026.01.18.700179"
    },
    {
      "author": "Pengyu Sun, Xinlei Huang, Tian Mou, Xubin Zheng",
      "title": "Achieving spatial multi-omics integration from unaligned serial sections with DIME",
      "preprint_id": "bioRxiv 2026.02.25.707961",
      "preprint_doi": "10.64898/2026.02.25.707961"
    },
    {
      "author": "Xinming Tu, Alexander Sasse, Kaitavjeet Chowdhary, Anna E. Spiro, Liang Yang, Maria Chikina, Christophe O. Benoist, Sara Mostafavi",
      "title": "Deep genomic models of allele-specific measurements",
      "preprint_id": "bioRxiv 2025.04.09.648060",
      "preprint_doi": "10.1101/2025.04.09.648060"
    },
    {
      "author": "Leonard Bohnenkämper, Luca Parmigiani, Cedric Chauve, Jens Stoye",
      "title": "On Deriving Synteny Blocks by Compacting Elements",
      "preprint_id": "bioRxiv 2025.12.15.694404",
      "preprint_doi": "10.64898/2025.12.15.694404"
    },
    {
      "author": "Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, Jannik Schestag",
      "title": "PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks",
      "preprint_id": "bioRxiv 2025.11.14.688467",
      "preprint_doi": "10.1101/2025.11.14.688467"
    },
    {
      "author": "Jinpu Cai, Yuxuan Wang, Yunhao Qiao, Cheng Wang, Ziqi Rong, Luting Zhou, Haoyang Liu, Meng Jiang, Hongbin Shen, Jingyi Jessica Li, Hongyi Xin",
      "title": "Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic Analysis",
      "preprint_id": "bioRxiv 2026.02.25.707866",
      "preprint_doi": "10.64898/2026.02.25.707866"
    },
    {
      "author": "Giulia Muzio, Michael Adamer, Leyden Fernandez, Lukas Miklautz, Karsten Borgwardt, Kemal Avican",
      "title": "Bacterial protein function prediction via multimodal deep learning",
      "preprint_id": "bioRxiv 2024.10.30.621035",
      "preprint_doi": "10.1101/2024.10.30.621035"
    },
    {
      "author": "Juliane Hoffmann, Julia Wallnig, Ziheng Dai, Olga Tsoy, David B. Blumenthal, Anne Hartebrodt",
      "title": "Alternet: Alternative splicing-aware gene regulatory network inference",
      "preprint_id": "bioRxiv 2025.11.21.689745",
      "preprint_doi": "10.1101/2025.11.21.689745"
    },
    {
      "author": "Burak Yelmen, Merve Nur Güler, Tõnu Kollo, Märt Möls, Guillaume Charpiat, Flora Jay",
      "title": "Bias in genome-wide association test statistics due to omitted interactions",
      "preprint_id": "bioRxiv 2025.11.21.689603",
      "preprint_doi": "10.1101/2025.11.21.689603"
    },
    {
      "author": "Xiaoge Zhang, Zhengyu Fang, Kaiyu Tang, Huiyuan Chen, Jing Li",
      "title": "Joint Learning of Drug-Drug Combination and Drug-Drug Interaction via Coupled Tensor-Tensor Factorization with Side Information",
      "preprint_id": "bioRxiv 2026.02.13.705792",
      "preprint_doi": "10.64898/2026.02.13.705792"
    },
    {
      "author": "Hugo Magalhães, Jonas Weber, Gunnar W. Klau, Tobias Marschall, Timofey Prodanov",
      "title": "Sequence-to-graph alignment based copy number calling using a network flow formulation",
      "preprint_id": "bioRxiv 2025.11.21.689771",
      "preprint_doi": "10.1101/2025.11.21.689771"
    },
    {
      "author": "Minh Hoang, Isabel Armour-Garb, Mona Singh",
      "title": "Fast, accurate construction of multiple sequence alignments from protein language embeddings",
      "preprint_id": "bioRxiv 2026.01.02.697423",
      "preprint_doi": "10.64898/2026.01.02.697423"
    },
    {
      "author": "Ardalan Naseri, Ahsan Sanaullah, Shaojie Zhang, Degui Zhi",
      "title": "SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores",
      "preprint_id": "bioRxiv 2026.03.16.712201",
      "preprint_doi": "10.64898/2026.03.16.712201"
    },
    {
      "author": "Florian Ingels, Lea Vandamme, Mathilde Girard, Clément Agret, Bastien Cazaux, Antoine Limasset",
      "title": "Compressed inverted indexes for scalable sequence similarity",
      "preprint_id": "bioRxiv 2025.11.21.689685",
      "preprint_doi": "10.1101/2025.11.21.689685"
    },
    {
      "author": "Florian Ingels, Lucas Robidou, Igor Martayan, Camille Marchet, Antoine Limasset",
      "title": "Minimizer Density revisited: Models and Multiminimizers",
      "preprint_id": "bioRxiv 2025.11.21.689688",
      "preprint_doi": "10.1101/2025.11.21.689688"
    },
    {
      "author": "Ruiqi Li, Junchen Yang, Pei-Chun Su, Ariel Jaffe, Ofir Lindenbaum, Yuval Kluger",
      "title": "DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data",
      "preprint_id": "bioRxiv 2025.11.23.689932",
      "preprint_doi": "10.1101/2025.11.23.689932"
    },
    {
      "author": "Ryan Doughty, Michael Tisza, Todd Treangen",
      "title": "bronko: ultrarapid, alignment-free detection of viral genome variation",
      "preprint_id": "bioRxiv 2025.12.01.691650",
      "preprint_doi": "10.64898/2025.12.01.691650"
    },
    {
      "author": "Leah Weber, Chi Yin Ching, Chrisopher Ly, Yixiao Cheng, Chunxu Gao, Peter Van Loo",
      "title": "Arborist: Prioritizing Bulk DNA Inferred Tumor Phylogenies via Low-pass Single-cell DNA Sequencing Data",
      "preprint_id": "bioRxiv 2026.02.26.707773",
      "preprint_doi": "10.64898/2026.02.26.707773"
    },
    {
      "author": "Zhongxuan Sun, Hyunseung Kang, Sunduz Keles",
      "title": "Causal gene regulatory network inference from Perturb-seq via adaptive instrumental variable modeling",
      "preprint_id": "bioRxiv 2026.02.18.706642",
      "preprint_doi": "10.64898/2026.02.18.706642"
    },
    {
      "author": "Xinyu Gu, Stefan Ivanovic, Daniel Feng, Mohammed El-Kebir",
      "title": "Summarizing RNA Structural Ensembles via Maximum Agreement Secondary Structures",
      "preprint_id": "bioRxiv 2026.02.25.708069",
      "preprint_doi": "10.64898/2026.02.25.708069"
    },
    {
      "author": "Danrong Li, Young Kun Ko, Stefan Canzar",
      "title": "CAMP: Coreset Accelerated Metacell Partitioning enables scalable analysis of single-cell data",
      "preprint_id": "bioRxiv 2025.12.11.693725",
      "preprint_doi": "10.64898/2025.12.11.693725"
    },
    {
      "author": "Anusha Aggarwal, Ksenia Sokolova, Olga Troyanskaya",
      "title": "Multi-modal tissue-aware graph neural network for in silico genetic discovery",
      "preprint_id": "bioRxiv 2026.02.17.706433",
      "preprint_doi": "10.64898/2026.02.17.706433"
    },
    {
      "author": "Arghamitra Talukder, Nicholas Keung, Itsik Pe'Er, David A. Knowles",
      "title": "CLADES — Contrastive Learning Augmented DifferEntial Splicing with Orthologous Positive Pairs",
      "preprint_id": "bioRxiv 2026.02.20.707118",
      "preprint_doi": "10.64898/2026.02.20.707118"
    },
    {
      "author": "Chang Lu, Yuval Kluger, Rong Ma",
      "title": "MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-Omics",
      "preprint_id": "bioRxiv 2026.02.10.705077",
      "preprint_doi": "10.64898/2026.02.10.705077"
    },
    {
      "author": "Anupama Nandi, Seth Neel, Hyunghoon Cho",
      "title": "GOPHER: Optimization-based Phenotype Randomization for Genome-Wide Association Studies with Differential Privacy",
      "preprint_id": "arXiv:2512.04225",
      "preprint_doi": "10.48550/arXiv.2512.04225"
    },
    {
      "author": "Chih Hao Wu, Jacob Gilbert, Salem Malikić, S. Cenk Sahinalp",
      "title": "Identifying Robust Subclonal Structures Through Tumor Progression Tree Alignment",
      "preprint_id": "bioRxiv 2026.02.25.708046",
      "preprint_doi": "10.64898/2026.02.25.708046"
    },
    {
      "author": "Anish Karpurapu, Charles Gersbach, Rohit Singh",
      "title": "DeltaNMF: A Two-Stage Neural NMF for Differential Gene Program Discovery",
      "preprint_id": "bioRxiv 2026.01.22.701049",
      "preprint_doi": "10.64898/2026.01.22.701049"
    },
    {
      "author": "Aditya Pratapa, Rohit Singh, Purushothama Rao Tata",
      "title": "Transforming Biological Foundation Model Representations for Out-of-Distribution Data",
      "preprint_id": "bioRxiv 2025.11.20.689462",
      "preprint_doi": "10.1101/2025.11.20.689462"
    },
    {
      "author": "Zhengtong Liu, Arush Ramteke, Aakarsh Anand, Aditya Gorla, Moonseong Jeong, Sriram Sankararaman",
      "title": "A biobank-scale method for learning environmental modulators of gene–environment interaction underlying complex traits",
      "preprint_id": "bioRxiv 2026.03.13.711725",
      "preprint_doi": "10.64898/2026.03.13.711725"
    },
    {
      "author": "Xinhai Pan, Yiru Chen, Xiuwei Zhang",
      "title": "Integrative Inference of Spatially Informed Cell Lineage Trees using LineageMap",
      "preprint_id": "bioRxiv 2026.01.19.700383",
      "preprint_doi": "10.64898/2026.01.19.700383"
    },
    {
      "author": "Kailey Hua, Ellie Haber, Jian Ma",
      "title": "Uncertainty-aware synthetic lethality prediction with pretrained foundation models",
      "preprint_id": "bioRxiv 2026.02.25.708096",
      "preprint_doi": "10.64898/2026.02.25.708096"
    },
    {
      "author": "Shitong Dai, Jiaqi Luo, Yunan Luo",
      "title": "Evolutionary profile enhancement improves protein function annotation",
      "preprint_id": "bioRxiv 2026.03.03.709280",
      "preprint_doi": "10.64898/2026.03.03.709280"
    },
    {
      "author": "Jamshed Khan, Laxman Dhulipala, Prashant Pandey, Rob Patro",
      "title": "Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3",
      "preprint_id": "bioRxiv 2025.02.02.636161",
      "preprint_doi": "10.1101/2025.02.02.636161"
    },
    {
      "author": "Chenxin Flora Jiang, Changhu Wang, Jingyi Jessica Li",
      "title": "Nullstrap-DE: A General Framework for Calibrating FDR and Preserving Power in Differential Expression Methods, with Applications to DESeq2 and edgeR",
      "preprint_id": "arXiv:2507.20598",
      "preprint_doi": "10.48550/arXiv.2507.20598"
    },
    {
      "author": "Luqi Yang, Zhenwei Huang, Jinpu Cai, Hongyi Xin",
      "title": "Gene-First Identity Construction for Robust Cell Identification in Single-Cell Transcriptomics",
      "preprint_id": "bioRxiv 2026.02.25.707869",
      "preprint_doi": "10.64898/2026.02.25.707869"
    },
    {
      "author": "Chris Dong, Yihui Cen, Dongyuan Song, Jingyi Jessica Li",
      "title": "scDesignPop generates population-scale single-cell RNA-seq data for power analysis, method benchmarking, and privacy protection",
      "preprint_id": "bioRxiv 2026.02.23.707578",
      "preprint_doi": "10.64898/2026.02.23.707578"
    },
    {
      "author": "Jens Zentgraf, Johanna Schmitz, Andreas Keller, Sven Rahmann",
      "title": "Error Correction Algorithms for Efficient Gene Quantification in Single Cell Transcriptomics",
      "preprint_id": "bioRxiv 2025.11.27.690682",
      "preprint_doi": "10.1101/2025.11.27.690682"
    },
    {
      "author": "Wenjun Zhao, Elana Fertig, Genevieve Stein-O'Brien",
      "title": "CycleGRN: Inferring Gene Regulatory Networks from Cyclic Flow Dynamics in Single-Cell RNA-seq",
      "preprint_id": "bioRxiv 2025.11.12.688126",
      "preprint_doi": "10.1101/2025.11.12.688126"
    },
    {
      "author": "Adithya Madduri, Randall Ellis, Chirag Patel",
      "title": "Protein Compositional Ratio Representation (PCRR) Systematically Improves Human Disease Prediction",
      "preprint_id": "bioRxiv 2025.11.29.691286",
      "preprint_doi": "10.1101/2025.11.29.691286"
    },
    {
      "author": "Daniel Lazarev, Anna Sappington, Grant Chau, Ruochi Zhang, Bonnie Berger",
      "title": "Constrained diffusion as a paradigm for evolution",
      "preprint_id": "bioRxiv 2026.03.10.710948",
      "preprint_doi": "10.64898/2026.03.10.710948"
    },
    {
      "author": "Jiayi Li, Yanruisheng Shao, Yu Li, Qinze Yu",
      "title": "Integrative Multi‑Scale Sequence–Structure Modeling for Antimicrobial Peptide Prediction and Design",
      "preprint_id": "bioRxiv 2026.02.24.707610",
      "preprint_doi": "10.64898/2026.02.24.707610"
    },
    {
      "author": "Jinqiu Du, Kevin Z. Lin",
      "title": "Integrating morphology and gene expression in unpaired single-cell data using GeoAdvAE",
      "preprint_id": "bioRxiv 2025.11.19.689368",
      "preprint_doi": "10.1101/2025.11.19.689368"
    },
    {
      "author": "Kerr Ding, Ziang Li, Tony Tu, Jiaqi Luo, Yunan Luo",
      "title": "Deconvolving mutation effects on protein stability and function with disentangled protein language models",
      "preprint_id": "bioRxiv 2026.02.03.703560",
      "preprint_doi": "10.64898/2026.02.03.703560"
    },
    {
      "author": "Mahsa Faizrahnemoon, Jens Luebeck, King L. Hung, Suhas Rao, Matthew G. Jones, Paul S. Mischel, Howard Y. Chang, Kaiyuan Zhu, Vineet Bafna",
      "title": "Fast and accurate resolution of ecDNA sequence using Cycle-Extractor",
      "preprint_id": "bioRxiv 2026.03.10.710955",
      "preprint_doi": "10.64898/2026.03.10.710955"
    },
    {
      "author": "Marjan Hosseini, Ella Veiner, Thomas Bergendahl, Tala Yasenpoor, Zane Smith, Margaret Staton, Derek Aguiar",
      "title": "pHapCompass: Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase",
      "preprint_id": "arXiv:2512.04393",
      "preprint_doi": "10.48550/arXiv.2512.04393"
    },
    {
      "author": "Mustafa Coşkun, Filipa Blasco Lopes, Pınar Kubilay Tolunay, Mark R. Chance, Mehmet Koyutürk",
      "title": "scProfiterole: Clustering of Single-Cell Proteomic Data Using Graph Contrastive Learning via Spectral Filters",
      "preprint_id": "bioRxiv 2026.02.26.708196",
      "preprint_doi": "10.64898/2026.02.26.708196"
    },
    {
      "author": "Sanjana Tule, Samuel Davis, Ivan Koludarov, Ariane Mora, Mikael Boden",
      "title": "Generating Hybrid Proteins with the MSA-Transformer",
      "preprint_id": "bioRxiv 2025.11.20.689447",
      "preprint_doi": "10.1101/2025.11.20.689447"
    },
    {
      "author": "Xiaoqi Sheng, Jiawen Liu, Jiaming Liang, Yiheng Zhang, Sankar Mondal, Yutong Li, Tinghe Zhang, Bing Liu, Jiangning Song, Hongmin Cai",
      "title": "Modeling Multi-Modal Brain Connectomes for Brain Disorder Diagnosis via Graph Diffusion Optimal Transport Network",
      "preprint_id": "bioRxiv 2026.03.05.709693",
      "preprint_doi": "10.64898/2026.03.05.709693"
    },
    {
      "author": "Xinhao Liu, Hongyu Zheng, Peter Halmos, Julian Gold, Erik Storrs, Li Ding, Ben Raphael",
      "title": "Multimodal spatial alignment and morphology mapping with MOSAICField",
      "preprint_id": "bioRxiv 2026.03.10.710931",
      "preprint_doi": "10.64898/2026.03.10.710931"
    }
  ]
}