RECOMB 2025 Proceedings

Seoul, South Korea, April 26 - 29, 2025.

PC Chair: Sriram Sankararaman, UCLA
Organization Committee: Jihyun F. Kim (co-chair), Martin Steinegger (co-chair), Sungwon Jung, Soon-Kyeong Kwon, Ezgi Ebren, Hyobin Jeong, Hyeshik Chang, Young-suk Lee, Minkyung Baek, Jinhyuk Bhin, Yusook Chung, Mohammed Alser, Jongsik Chun
Keynote Speakers: Peer Bork, Evan E. Eichler, V. Narry Kim, Sang Yup Lee, Lior Pachter, Olga Troyanskaya, Leslie Valiant

List of Publications

• Orientation-Aware Networks for Protein Structure Representation Learning. Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas Guibas, Jian Peng, Jianzhu Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 1-16, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_1
  • Preprint: arXiv:2201.13299
• Active Learning for Protein Structure Prediction. Zexin Xue, Michael Bailey, Abhinav Gupta, Ruijiang Li, Alejandro Corrochano-Navarro, Sizhen Li, Lorenzo Kogler-Anele, Qui Yu, Ziv Bar-Joseph, Sven Jager.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 17-33, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_2
  • Preprint: bioRxiv 2025.04.01.646404
• Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models. Chiho Im, Ryan Zhao, Scott D. Boyd, Anshul Kundaje.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 34-48, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_3
  • Preprint: bioRxiv 2024.10.25.619698
• DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins. Shaojun Wang, Hancheng Liu, Weiqi Zhai, Shanfeng Zhu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 49-67, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_4
• Detecting Antimicrobial Resistance Through MALDI-TOF Mass Spectrometry with Statistical Guarantees Using Conformal Prediction. Nina Corvelo Benz, Lucas Miranda, Dexiong Chen, Janko Sattler, Karsten Borgwardt.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 68-85, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_5
• Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis. Yuxiang Wei, Anees Abrol, Vince D. Calhoun.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 86-98, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_6
  • Preprint: arXiv:2408.13074
• A Phylogenetic Approach to Genomic Language Modeling. Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 99-117, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_7
  • Preprint: arXiv:2503.03773
• Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. Junyan Dai and Erin K. Molloy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 118-133, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_8
  • Preprint: bioRxiv 2024.11.15.623872
  • Journal: StarCDP: Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. Junyan Dai and Erin K. Molloy. Journal of Computational Biology, 33(1): 48-66, 2026.
    • DOI: 10.1177/15578666251386082
• Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 134-152, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_9
  • Preprint: hal-04756160
• Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance. Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 153-174, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_10
  • Preprint: arXiv:2402.17206
• An Exact and Fast SAT Formulation for the DCJ Distance. Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 175-189, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_11
  • Preprint: bioRxiv 2024.11.05.622153
• Improved Pangenomic Classification Accuracy with Chain Statistics. Nathaniel K. Brown, Vikram S. Shivakumar, Ben Langmead.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 190-208, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_12
  • Preprint: bioRxiv 2024.10.29.620953
  • Journal: Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification. Nathaniel K. Brown, Vikram S. Shivakumar, and Ben Langmead. Journal of Computational Biology, 33(1): 168-183, 2025.
    • DOI: 10.1177/15578666251400784
• Dynamic p-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 209-226, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_13
  • Preprint: bioRxiv 2025.02.04.636479
  • Journal: An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data. Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. Journal of Computational Biology, 33(1): 67-89, 2025.
    • DOI: 10.1177/15578666251385570
• Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis. Adam Park and David Koslicki.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 227-249, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_14
  • Preprint: bioRxiv 2023.11.21.568151
  • Journal: Elucidating Transitions of k-mer-Based Objects Across k-mer Sizes. Adam Park and David Koslicki. Journal of Computational Biology, 33(1): 107-133, 2026.
    • DOI: 10.1177/15578666251401600
• Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented Generation. Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, Jianzhu Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 250-254, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_15
  • Preprint: bioRxiv 2024.10.20.619266
  • Journal: Rag2Mol: structure-based drug design based on retrieval augmented generation. Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, and Jianzhu Ma. Briefings in Bioinformatics, 26(3): bbaf265, 2025.
    • DOI: 10.1093/bib/bbaf265
• Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction. Ziang Li and Yunan Luo.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 255-259, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_16
  • Preprint: bioRxiv 2025.02.13.638154
• Learning a CONCISE Language for Small-Molecule Binding. Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 260-263, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_17
  • Preprint: bioRxiv 2025.01.08.632039
• An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 264-267, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_18
  • Preprint: bioRxiv 2025.01.16.633332
  • Journal: An adversarial scheme for integrating multi-modal data on protein function. Rami Nasser, Leah V. Schaffer, Trey Ideker, and Roded Sharan. Cell Systems, 16(11): 101444, 2025.
    • DOI: 10.1016/j.cels.2025.101444
• Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. Sam 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, Lenore Cowen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 268-272, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_19
  • Preprint: bioRxiv 2024.10.25.620267
• The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. Henri Schmidt and Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 273-276, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_20
  • Preprint: bioRxiv 2025.02.14.638328
• 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, Yufeng Wu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 277-280, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_21
  • Preprint: bioRxiv 2024.11.08.622704
  • Journal: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search. Haotian Zhang, Yiming Zhang, Teng Gao, and Yufeng Wu. Genome Research, 35(12): 2781-2791, 2025.
    • DOI: 10.1101/gr.280542.125
• OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders. Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Naz Güleray-Lafci, Jürgen Neesen, Alex Hastie, Andy Wing Chun Pang, Paul Dremsek, Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 281-284, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_22
  • Journal: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities. Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Naz Güleray-Lafci, Jürgen Neesen, Alex Hastie, Alka Chaubey, Andy Wing Chun Pang, Paul Dremsek, and Vineet Bafna. Genome Research, 35(12): 2671-2681, 2025.
    • DOI: 10.1101/gr.280536.125
• TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates. Kemal Inecik, Aleyna Kara, Antony Rose, Muzlifah Haniffa, Fabian J. Theis.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 285-289, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_23
  • Preprint: bioRxiv 2024.06.20.599903
• Devider: Long-Read Reconstruction of Many Diverse Haplotypes. Jim Shaw, Christina Boucher, Yun William Yu, Noelle Noyes, Heng Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 290-293, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_24
  • Preprint: bioRxiv 2024.11.05.621838
  • Journal: Long-read reconstruction of many diverse haplotypes with devider. Jim Shaw, Christina Boucher, Yun William Yu, Noelle Noyes, and Heng Li. Genome Research, 35(12): 2637-2649, 2025.
    • DOI: 10.1101/gr.280510.125
• Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors. Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 294-298, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_25
  • Preprint: bioRxiv 2024.11.17.623950
  • Journal: Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors. Leah L. Weber, Anna Hart, Idoia Ochoa, and Mohammed El-Kebir. Journal of Computational Biology, 33(1): 2-18, 2026.
    • DOI: 10.1177/15578666251374694
• GEM-Finder: Dissecting GWAS Variants via Long-Range Interacting Cis-Regulatory Elements with Differentiationspecific Genes. Gyeongsik Park, Andrew J. Lee, Inkyung Jung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 299-302, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_26
• 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, Graham Heimberg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 303-306, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_27
  • Preprint: bioRxiv 2024.11.18.624166
• 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, Yu Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 307-311, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_28
  • Preprint: bioRxiv 2025.02.11.637663
• Inferring Cell Differentiation Maps from Lineage Tracing Data. Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 312-315, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_29
  • Preprint: bioRxiv 2024.09.09.611835
  • Journal: Inferring cell differentiation maps from lineage tracing data. Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, and Benjamin J. Raphael. Nature Methods, 33(1): 107-133, 2025.
    • DOI: 10.1038/s41592-025-02903-z
• Alignment-Free Estimation of Read to Genome Distances and Its Applications. Ali Osman Berk Şapcı and Siavash Mirarab.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 316-320, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_30
  • Journal: krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement. Ali Osman Berk Şapcı and Siavash Mirarab. Genome Biology, epub, 2026.
    • DOI: 10.1186/s13059-026-03999-y
• ML-MAGES: A Machine Learning Framework for Multivariate Genetic Association Analyses with Genes and Effect Size Shrinkage. Xiran Liu, Lorin Crawford, Sohini Ramachandran.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 321-324, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_31
  • Preprint: bioRxiv 2025.02.11.637655
  • Journal: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage. Xiran Liu, Lorin Crawford, and Sohini Ramachandran. Genome Research, 35(12): 2691-2700, 2025.
    • DOI: 10.1101/gr.280440.125
• TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment. Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, Hyunghoon Cho.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 325-329, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_32
  • Preprint: bioRxiv 2024.09.16.613301
  • Journal: Secure phasing of private genomes in a trusted execution environment with TX-Phase. Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, and Hyunghoon Cho. Genome Research, 35(12): 2626-2636, 2025.
    • DOI: 10.1101/gr.280558.125
• Hyper-k-mers: Efficient Streaming k-mers Representation. Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 330-335, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_33
  • Preprint: bioRxiv 2024.11.06.620789
• Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2. Mrinmoy S. Roddur, Vikram Ramavarapu, Abigail Bunkum, Ariana Huebner, Roman Mineyev, Nicholas McGranahan, Simone Zaccaria, Mohammed El-Kebir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 336-339, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_34
  • Preprint: bioRxiv 2024.11.19.624301
• Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual Inference. Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 340-344, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_35
  • Preprint: bioRxiv 2024.12.11.628077
• Integration and Querying of Multimodal Single-Cell Data with PoE-VAE. Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, Fabian Theis.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 345-348, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_36
  • Preprint: bioRxiv 2022.03.16.484643
• ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly. Enzo Battistella, Anant Maheshwari, Barış Ekim, Bonnie Berger, Victoria Popic.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 349-353, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_37
  • Preprint: bioRxiv 2025.02.17.638151
  • Journal: Graph-based deep reinforcement learning for haplotype assembly with Ralphi. Enzo Battistella, Anant Maheshwari, Barış Ekim, Bonnie Berger, and Victoria Popic. Genome Research, 35(12): 2617-2625, 2025.
    • DOI: 10.1101/gr.280569.125
• GeneCover: A Combinatorial Approach for Label-Free Marker Gene Selection. An Wang, Stephanie Hicks, Donald Geman, Laurent Younes.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 354-357, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_38
  • Preprint: bioRxiv 2024.10.30.621151
  • Journal: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover. An Wang, Stephanie Hicks, Donald Geman, and Laurent Younes. Genome Research, 35(12): 2744-2755, 2025.
    • DOI: 10.1101/gr.280539.125
• Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 358-361, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_39
  • Preprint: bioRxiv 2025.02.17.638195
  • Journal: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms. Hongyu Zheng, Hirak Sarkar, and Benjamin J. Raphael. Genome Research, 35(12): 2734-2743, 2025.
    • DOI: 10.1101/gr.280555.125
• ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads. Rashid Al-Abri and Gamze Gürsoy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 362-366, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_40
  • Preprint: bioRxiv 2025.02.15.638440
  • Journal: Estimating the size of long tandem repeat expansions from short reads with ScatTR. Rashid Al-Abri and Gamze Gürsoy. Genome Research, 35(12): 2701-2713, 2025.
    • DOI: 10.1101/gr.280563.125
• Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 367-370, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_41
  • Preprint: bioRxiv 2025.02.14.638351
• Unified Integration of Spatial Transcriptomics Across Platforms. Ellie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 371-375, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_42
  • Preprint: bioRxiv 2025.03.31.646238
  • Journal: Unified integration of spatial transcriptomics across platforms with LLOKI. Ellie Haber, Ajinkya Deshpande, Jian Ma, and Spencer Krieger. Genome Research, 35(12): 2722-2733, 2025.
    • DOI: 10.1101/gr.280803.125
• Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining. Sebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew G. Jones, Yun S. Song, Nir Yosef.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 376-380, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_43
  • Preprint: bioRxiv 2024.08.27.610007
• mcRigor: A Statistical Method to Enhance the Rigor of Metacell Partitioning in Single-Cell RNA-seq and ATAC-seq Data Analysis. Pan Liu and Jingyi Jessica Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 381-385, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_44
  • Preprint: bioRxiv 2024.10.30.621093
  • Journal: mcRigor: A Statistical Software Package for Evaluating and Optimizing Metacell Partitioning in Single-Cell Data Analysis. Pan Liu and Jingyi Jessica Li. Journal of Computational Biology, 33(1): 43-47, 2026.
    • DOI: 10.1177/15578666251383561
• 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, Mehrtash Babadi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 386-389, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_45
  • Preprint: bioRxiv 2024.11.07.622479
• Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRep. Zhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 390-394, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_46
  • Preprint: bioRxiv 2024.11.05.621953
  • Journal: Accurate detection of tandem repeats from error-prone sequences with EquiRep. Zhezheng Song, Tasfia Zahin, Xiang Li, and Mingfu Shao. Genome Research, 35(12): 2714-2721, 2025.
    • DOI: 10.1101/gr.280750.125
• ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data. Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser, Vicky Yao.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 395-399, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_47
  • Preprint: bioRxiv 2025.02.15.638471
  • Journal: Interpretable phenotype decoding from multicondition sequencing data with ALPINE. Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser, and Vicky Yao. Genome Research, 35(12): 2756-2769, 2025.
    • DOI: 10.1101/gr.280566.125
• 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, Jingyi Jessica Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 400-404, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_48
  • Preprint: bioRxiv 2023.07.21.550107
• Integer Programming Framework for Pangenome-Based Genome Inference. Ghanshyam Chandra, Md Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 405-408, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_49
  • Preprint: bioRxiv 2024.10.27.620212
  • Journal: Pangenome-based genome inference using integer programming. Ghanshyam Chandra, Md Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, and Chirag Jain. Genome Research, 35(12): 2661-2670, 2025.
    • DOI: 10.1101/gr.280567.125
• A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, John D. Bridgers, Eva Pérez-Guijarro, Kerrie L. Marie, Howard H. Yang, Charli Gruen, Chih Hao Wu, Welles Robinson, Huaitian Liu, Can Kizilkale, Michael C. Kelly, Cari Smith, Sung Chin, Jessica Ebersole, Sandra Burkett, Aydin Buluc, Maxwell P. Lee, Erin K. Molloy, Teresa M. Przytycka, Glenn Merlino, Chi-Ping Day, Salem Malikić, Funda Ergun, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 409-413, Springer, Cham.
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• Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach. Yoav Dvir and Sagi Snir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 414-419, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_51
  • Preprint: bioRxiv 2025.01.27.634999
• Learning Maximally Spanning Representations Improves Protein Function Annotation. Jiaqi Luo and Yunan Luo.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 420-423, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_52
  • Preprint: bioRxiv 2025.02.13.638156
• Optimal Marker Genes for c-Separated Cell Types. Bartol Borozan, Luka Borozan, Domagoj Ševerdija, Domagoj Matijević, Stefan Canzar.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 424-427, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_53
  • Preprint: bioRxiv 2025.02.12.637849
  • Journal: Optimal marker genes for c-separated cell types with SepSolve. Bartol Borozan, Tomislav Prusina, Luka Borozan, Domagoj Ševerdija, Francisca Rojas Ringeling, Domagoj Matijević, and Stefan Canzar. Genome Research, 35(12): 2770-2780, 2025.
    • DOI: 10.1101/gr.280637.125
• Bayesian Aggregation of Multiple Annotations Enhances Rare Variant Association Testing. Antonio Nappi, Na Cai, Francesco Paolo Casale.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 428-431, Springer, Cham.
    • DOI: 10.1007/978-3-031-90252-9_54
  • Preprint: bioRxiv 2025.03.02.641062
  • Journal: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations. Antonio Nappi, Liubov Shilova, Theofanis Karaletsos, Na Cai, and Francesco Paolo Casale. Genome Research, 35(12): 2682-2690, 2025.
    • DOI: 10.1101/gr.280689.125
• STEAMBOAT: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues. Shaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 432-436, Springer, Cham.
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