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ORCID29th RECOMB 2025: Seoul, South Korea
- Sriram Sankararaman
:
Research in Computational Molecular Biology - 29th International Conference, RECOMB 2025, Seoul, South Korea, April 26-29, 2025, Proceedings. Lecture Notes in Computer Science 15647, Springer 2025, ISBN 978-3-031-90251-2 - Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma:
Orientation-Aware Networks for Protein Structure Representation Learning. 1-16 - Zexin Xue, Michael Bailey, Abhinav Gupta, Ruijiang Li, Alejandro Corrochano-Navarro, Sizhen Li, Lorenzo Kogler-Anele, Qui Yu, Ziv Bar-Joseph, Sven Jager:
Active Learning for Protein Structure Prediction. 17-33 - Chiho Im, Ryan Zhao, Scott D. Boyd, Anshul Kundaje:
Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models. 34-48 - Shaojun Wang, Hancheng Liu, Weiqi Zhai, Shanfeng Zhu:
DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins. 49-67 - Nina Corvelo Benz, Lucas Miranda, Dexiong Chen, Janko Sattler, Karsten M. Borgwardt:
Detecting Antimicrobial Resistance Through MALDI-TOF Mass Spectrometry with Statistical Guarantees Using Conformal Prediction. 68-85 - Yuxiang Wei, Anees Abrol, Vince D. Calhoun:
Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis. 86-98 - Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song:
A Phylogenetic Approach to Genomic Language Modeling. 99-117 - Junyan Dai, Erin K. Molloy:
Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. 118-133 - Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao:
Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. 134-152 - Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang:
Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance. 153-174 - Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao:
An Exact and Fast SAT Formulation for the DCJ Distance. 175-189 - Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead:
Improved Pangenomic Classification Accuracy with Chain Statistics. 190-208 - Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. 209-226 - Adam Park, David Koslicki:
Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis. 227-249 - Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, Jianzhu Ma:
Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented Generation. 250-254 - Ziang Li, Yunan Luo:
Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction. 255-259 - Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh:
Learning a CoNCISE Language for Small-Molecule Binding. 260-263 - Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan:
An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. 264-267 - 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, Lenore Cowen:
Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. 268-272 - Henri Schmidt, Benjamin J. Raphael:
The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. 273-276 - Haotian Zhang, Yiming Zhang, Teng Gao, Yufeng Wu:
ScisTree2: An Improved Method for Large-Scale Inference of Cell Lineage Trees and Genotype Calling from Noisy Single Cell Data. 277-280 - 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:
OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders. 281-284 - Kemal Inecik, Aleyna Kara, Antony Rose, Muzlifah Haniffa, Fabian J. Theis:
TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates. 285-289 - Jim Shaw, Christina Boucher, Yun William Yu, Noelle R. Noyes, Heng Li:
Devider: Long-Read Reconstruction of Many Diverse Haplotypes. 290-293 - Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir:
Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors. 294-298 - Gyeongsik Park, Andrew J. Lee, Inkyung Jung:
GEM-Finder: Dissecting GWAS Variants via Long-Range Interacting Cis-Regulatory Elements with Differentiationspecific Genes. 299-302 - Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang, Minsheng Hao, Héctor Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg:
Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States. 303-306 - Yixuan Wang, Jiayi Li, Jingqi Li, Shen Yang, Yuhan Huang, Xinyuan Liu, Yimin Fan, Irwin King, Yumei Li, Yu Li:
cfDecon: Accurate and Interpretable Methylation-Based Cell Type Deconvolution for Cell-Free DNA. 307-311 - Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael:
Inferring Cell Differentiation Maps from Lineage Tracing Data. 312-315 - Ali Osman Berk Sapci, Siavash Mirarab:
Alignment-Free Estimation of Read to Genome Distances and Its Applications. 316-320 - Xiran Liu, Lorin Crawford, Sohini Ramachandran:
ML-MAGES: A Machine Learning Framework for Multivariate Genetic Association Analyses with Genes and Effect Size Shrinkage. 321-324 - Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, Hyunghoon Cho:
TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment. 325-329 - Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset:
Hyper-k-mers: Efficient Streaming k-mers Representation. 330-335 - Mrinmoy Saha Roddur, Vikram Ramavarapu, Abigail Bunkum, Ariana Huebner, Roman Mineyev, Nicholas McGranahan, Simone Zaccaria, Mohammed El-Kebir:
Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2. 336-339 - Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan:
Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual Inference. 340-344 - Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, Fabian J. Theis:
Integration and Querying of Multimodal Single-Cell Data with PoE-VAE. 345-348 - Enzo Battistella, Anant Maheshwari, Baris Ekim, Bonnie Berger, Victoria Popic:
ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly. 349-353 - An Wang, Stephanie Hicks, Donald Geman, Laurent Younes:
GeneCover: A Combinatorial Approach for Label-Free Marker Gene Selection. 354-357 - Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael:
Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. 358-361 - Rashid Al-Abri, Gamze Gürsoy:
ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads. 362-366 - Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael:
Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. 367-370 - Ellie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger:
Unified Integration of Spatial Transcriptomics Across Platforms. 371-375 - Sebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew G. Jones, Yun S. Song, Nir Yosef:
Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining. 376-380 - Pan Liu, Jingyi Jessica Li:
mcRigor: A Statistical Method to Enhance the Rigor of Metacell Partitioning in Single-Cell RNA-seq and ATAC-seq Data Analysis. 381-385 - Sandeep Kambhampati, Luca D'Alessio, Fedor Grab, Stephen Fleming, Fei Chen, Mehrtash Babadi:
TissueMosaic Enables Cross-Sample Differential Analysis of Spatial Transcriptomics Datasets Through Self-supervised Representation Learning. 386-389 - Zhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao:
Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRep. 390-394 - Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser, Vicky Yao:
ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data. 395-399 - Dongyuan Song, Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge, Jingyi Jessica Li:
Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses. 400-404 - Ghanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain:
Integer Programming Framework for Pangenome-Based Genome Inference. 405-408 - Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, John D. Bridgers, Eva Pérez-Guijarro, Kerrie 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 Buluç, Maxwell P. Lee, Erin K. Molloy, Teresa M. Przytycka, Glenn Merlino, Chi-Ping Day, Salem Malikic, Funda Ergün, S. Cenk Sahinalp:
A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. 409-413 - Yoav Dvir, Sagi Snir:
Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach. 414-419 - Jiaqi Luo, Yunan Luo:
Learning Maximally Spanning Representations Improves Protein Function Annotation. 420-423 - Bartol Borozan, Luka Borozan, Domagoj Severdija, Domagoj Matijevic, Stefan Canzar:
Optimal Marker Genes for c-Separated Cell Types. 424-427 - Antonio Nappi, Na Cai, Francesco Paolo Casale:
Bayesian Aggregation of Multiple Annotations Enhances Rare Variant Association Testing. 428-431 - Shaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma:
Steamboat: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues. 432-436
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last updated on 2025-11-13 21:53 CET by the dblp team
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