RECOMB 2024 Proceedings

Cambridge, MA, USA, April 29 - May 2, 2024.

PC Chair: Jian Ma, Carnegie Mellon University
Organization Committee: Bonnie Berger (co-chair), Lenore Cowen (co-chair), Iman Hajirasouliha
Keynote Speakers: Jim Collins, Shafi Goldwasser, Bob Langer, Xihong Lin, Steven Salzberg

List of Publications

• Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks. Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 1-16, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_1
  • Preprint: bioRxiv 2023.03.13.532445
  • Journal: Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks. Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen. Journal of Computational Biology, 31(10):990-1007, 2024.
    • DOI: 10.1089/cmb.2024.0673
• Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors. Kexin Huang, Romain Lopez, Jan-Christian Hütter, Takamasa Kudo, Antonio Rios, Aviv Regev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 17-37, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_2
  • Preprint: bioRxiv 2023.12.12.571389
• Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. Askar Gafurov, Tomáš Vinař, Paul Medvedev, Broňa Brejová.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 38-53, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_3
  • Preprint: bioRxiv 2023.11.22.568259
  • Journal: Fast Context-Aware Analysis of Genome Annotation Colocalization. Askar Gafurov, Tomáš Vinař, Paul Medvedev, Broňa Brejová. Journal of Computational Biology, 31(10):946-964, 2024.
    • DOI: 10.1089/cmb.2024.0667
• Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography. Alexander T. Leighton, Yun William Yu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 54-67, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_4
  • Preprint: bioRxiv 2021.11.10.468090
• FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation. Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Ozlem Ozmen Garibay.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 68-85, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_5
  • Preprint: arXiv:2311.02326
• An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. Shani Jacobson, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 86-98, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_6
• ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. Yuxuan Du, Wenxuan Zuo, Fengzhu Sun.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 99-114, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_7
  • Preprint: bioRxiv 2023.12.06.570492
  • Journal: Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Ra…. Yuxuan Du, Wenxuan Zuo, Fengzhu Sun. Journal of Computational Biology, 31(10):1008-1021, 2024.
    • DOI: 10.1089/cmb.2024.0663
• Graph-Based Genome Inference from Hi-C Data. Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 115-130, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_8
  • Preprint: bioRxiv 2023.11.08.566275
• Meta-colored Compacted de Bruijn Graphs. Giulio Ermanno Pibiri, Jason Fan, Rob Patro.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 131-146, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_9
  • Preprint: bioRxiv 2023.07.21.550101
  • Journal: Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs. Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro. Journal of Computational Biology, 31(10):1022-1044, 2024.
    • DOI: 10.1089/cmb.2024.0714
• Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 147-163, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_10
  • Preprint: hal-03816423v3
• Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 164-184, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_11
  • Journal: Lossless approximate pattern matching: Automated design of efficient search schemes. Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier. Journal of Computational Biology, 31(10):975-989, 2024.
    • DOI: 10.1089/cmb.2024.0664
• CELL-E: A Text-to-Image Transformer for Protein Image Prediction. Emaad Khwaja, Yun S. Song, Bo Huang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 185-200, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_12
  • Preprint: bioRxiv 2022.05.27.493774
• A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements. C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 201-216, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_13
  • Preprint: bioRxiv 2024.02.15.580520
  • Journal: Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements. C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford. Journal of Computational Biology, 31(10):908-926, 2024.
    • DOI: 10.1089/cmb.2024.0661
• Overcoming Observation Bias for Cancer Progression Modeling. Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 217-234, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_14
  • Preprint: bioRxiv 2023.12.03.569824
  • Journal: Correcting for Observation Bias in Cancer Progression Modeling. Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel. Journal of Computational Biology, 31(10):927-945, 2024.
    • DOI: 10.1089/cmb.2024.0666
• Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning. Holly R. Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew Hirn, Michael Perlmutter, Smita Krishnaswamy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 235-252, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_15
  • Preprint: bioRxiv 2023.12.05.570153
• Computing Robust Optimal Factories in Metabolic Reaction Networks. Spencer Krieger, John Kececioglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 253-269, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_16
  • Journal: Robust Optimal Metabolic Factories. Spencer Krieger, John Kececioglu. Journal of Computational Biology, 31(10):1045-1086, 2024.
    • DOI: 10.1089/cmb.2024.0748
• Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 270-287, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_17
  • Preprint: arXiv:2311.08339
• Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching. Paolo Pellizzoni, Carlos Oliver, Karsten Borgwardt.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 288-307, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_18
• Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. Matthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 308-313, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_19
  • Preprint: bioRxiv 2024.02.16.580613
  • Journal: Secure discovery of genetic relatives across large-scale and distributed genomic data sets. Secure discovery of genetic relatives across large-scale and distributed genomic data sets. Genome Research, 34(9): 1312–1323, 2024.
    • DOI: 10.1101/gr.279057.124
• GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. Yimin Fan, Yu Li, Jun Ding, Yue Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 314-319, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_20
  • Preprint: bioRxiv 2023.11.09.566403
• SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. Jianyu Yang, Kuangyu Yen, Shaun Mahony.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 320-323, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_21
  • Preprint: bioRxiv 2023.10.17.562727
  • Journal: Size-based expectation maximization for characterizing nucleosome positions and subtypes. Jianyu Yang, Kuangyu Yen, Shaun Mahony. Genome Research, 34(9): 1334–1343, 2024.
    • DOI: 10.1101/gr.279138.124
• Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification. Li Song, Ben Langmead.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 324-327, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_22
  • Preprint: bioRxiv 2023.11.15.567129
  • Journal: Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. Li Song, Ben Langmead. Genome Biology, 25(1):106, 2024.
    • DOI: 10.1186/s13059-024-03244-4
• BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine Shutta, Kimberly Glass, Dawn DeMeo, Camila Lopes Ramos, John Quackenbush.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 328-331, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_23
  • Preprint: bioRxiv 2023.11.16.567119
  • Journal: Bayesian Inference of Sample-Specific Coexpression Networks. Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Dawn L. DeMeo, Camila M. Lopes-Ramos, John Quackenbush. Genome Research, 34:1397–1410, 2024.
    • DOI: 10.1101/gr.279117.124
• regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models. Avantika Lal, David Garfield, Tommaso Biancalani, Gokcen Eraslan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 332-335, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_24
  • Preprint: bioRxiv 2024.02.14.580373
  • Journal: Designing realistic regulatory DNA with autoregressive language models. Avantika Lal, David Garfield, Tommaso Biancalani, Gokcen Eraslan. Genome Research, 34(9): 1411–1420, 2024.
    • DOI: 10.1101/gr.279142.124
• DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors. Nathan Guerin, Henry Childs, Pei Zhou, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 336-339, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_25
  • Preprint: bioRxiv 2024.02.12.579944
  • Journal: Protocol for Designing De Novo Noncanonical Peptide Binders in OSPREY. Henry Childs, Nathan Guerin, Pei Zhou, Bruce R. Donald. Journal of Computational Biology, 31(10):965-974, 2024.
    • DOI: 10.1089/cmb.2024.0669
• Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. Ali Osman Berk Şapcı, Siavash Mirarab.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 340-343, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_26
  • Preprint: bioRxiv 2024.02.12.580015
  • Journal: Memory-Bound k-Mer Selection for Large and Evolutionary Diverse Reference Libraries. Ali Osman Berk Şapcı and Siavash Mirarab. Genome Research, 34(9): 1455–1467, 2024.
    • DOI: 10.1101/gr.279339.124
• SpaCeNet: Spatial Cellular Networks from Omics Data. Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 344-347, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_27
  • Preprint: bioRxiv 2022.09.01.506219
  • Journal: Spatial Cellular Networks from omics data with SpaCeNet. Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Dennis Völkl, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger. Genome Research, 34(9): 1371–1383, 2024.
    • DOI: 10.1101/gr.279125.124
• Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models. Ziting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 348-351, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_28
  • Preprint: bioRxiv 2024.02.07.579420
• MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies. Myson Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 352-355, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_29
  • Preprint: bioRxiv 2023.11.13.23298469
  • Journal: Matrix sketching framework for linear mixed models in association studies. Myson Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas. Genome Research, 34(9): 1304–1311, 2024.
    • DOI: 10.1101/gr.279230.124
• Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes. Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 356-359, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_30
  • Preprint: bioRxiv 2023.04.02.535277
• Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. Uyen Mai, Gillian Chu, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 360-363, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_31
  • Preprint: bioRxiv 2024.03.05.583638
  • Journal: Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML. Gillian Chu, Uyen Mai, Henri Schmidt, Benjamin J. Raphael. Genome Biology, 26: 189, 2025.
    • DOI: 10.1186/s13059-025-03649-9
• TRIBAL: Tree Inference of B Cell Clonal Lineages. Leah L. Weber, Derek Reiman, Mrinmoy S. Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 364-367, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_32
  • Preprint: bioRxiv 2023.11.27.568874
• Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. Uthsav Chitra, Brian Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Ben Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 368-371, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_33
  • Preprint: bioRxiv 2023.10.10.561757
  • Journal: Mapping the topography of spatial gene expression with interpretable deep learning. Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Kohei Sanno, Cong Ma, Sereno Lopez-Darwin, Benjamin J. Raphael. Nature Methods, 22: 298-309, 2025.
    • DOI: 10.1038/s41592-024-02503-3
• GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 372-376, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_34
  • Preprint: arXiv:2402.09381
  • Journal: Graph-based self-supervised learning for repeat detection in metagenomic assembly. Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra. Genome Research, 34(9): 1468–1476, 2024.
    • DOI: 10.1101/gr.279136.124
• PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 377-380, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_35
  • Preprint: bioRxiv 2024.02.13.580211
  • Journal: Modeling gene interactions in polygenic prediction via geometric deep learning. Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang. Genome Research, 35(1):178-187, 2025.
    • DOI: 10.1101/gr.279694.124
• Haplotype-Aware Sequence Alignment to Pangenome Graphs. Ghanshyam Chandra, Daniel Gibney, Chirag Jain.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 381-384, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_36
  • Preprint: bioRxiv 2023.11.15.566493
  • Journal: Haplotype-aware sequence alignment to pangenome graphs. Ghanshyam Chandra, Daniel Gibney, and Chirag Jain. Genome Research, 34(9):1265–1275, 2024.
    • DOI: 10.1101/gr.279143.124
• Disease Risk Predictions with Differentiable Mendelian Randomization. Ludwig Gräf, Daniel Sens, Liubov Shilova, Francesco Paolo Casale.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 385-389, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_37
  • Preprint: bioRxiv 2024.03.06.583727
  • Journal: Genetics-driven risk predictions leveraging the Mendelian randomization framework. Daniel Sens, Liubov Shilova, Ludwig Gräf, Maria Grebenshchikova, Bjoern M. Eskofier, Francesco Paolo Casale. Genome Research, 34(9): 1276–1285, 2024.
    • DOI: 10.1101/gr.279252.124
• DIISCO: A Bayesian Framework for Inferring Dynamic Intercellular Interactions from Time-Series Single-Cell Data. Cameron Park, Shouvik Mani, Nicolas Beltran, Katie Maurer, Satyen Gohil, Shuqiang Li, Teddy Huang, David Knowles, Catherine Wu, Elham Azizi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 390-395, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_38
  • Preprint: bioRxiv 2023.11.14.566956
  • Journal: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Teddy Huang, Shuqiang Li, Satyen Gohil, Kenneth J. Livak, David A. Knowles, Catherine J. Wu, Elham Azizi. Genome Research, 34(9): 1384–1396, 2024.
    • DOI: 10.1101/gr.279126.124
• Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach. Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 396-399, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_39
  • Preprint: bioRxiv 2023.11.21.568145
  • Journal: A best-match approach for gene set analyses in embedding spaces. Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao. Genome Research, 34(9): 1421–1433, 2024.
    • DOI: 10.1101/gr.279141.124
• Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction. Shuai Zeng, Duolin Wang, Lei Jiang, Dong Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 400-405, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_40
  • Preprint: bioRxiv 2023.11.04.565642
  • Journal: Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction. Shuai Zeng, Duolin Wang, Lei Jiang, Dong Xu. Genome Research, 34(9): 1445–1454, 2024.
    • DOI: 10.1101/gr.279132.124
• Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. Madalina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocio Chamorro-Gonzalez, Lotte Brueckner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Richard P. Koche, Kerstin Haase, Knut Reinert, Anton G. Henssen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 406-411, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_41
  • Preprint: bioRxiv 2023.11.15.567169
  • Journal: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Mădălina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocío Chamorro González, Lotte Brückner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Philipp Euskirchen, Richard P. Koche, Kerstin Haase, Knut Reinert, Anton G. Henssen . Genome Research, 34(9): 1355–1364, 2024.
    • DOI: 10.1101/gr.279123.124
• Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency. Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 412-416, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_42
  • Preprint: bioRxiv 2024.02.15.580590
  • Journal: Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption. Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia. Genome Research, 34(9): 1324–1333, 2024.
    • DOI: 10.1101/gr.279071.124
• Mapping Cell Fate Transition in Space and Time. Yichen Gu, Jialin Liu, Chen Li, Joshua D. Welch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 417-420, Springer, Cham.
    • DOI: 10.1007/978-1-0716-3989-4_43
  • Preprint: bioRxiv 2024.02.12.579941
  • Journal: Topological velocity inference from spatial transcriptomic data. Yichen Gu, Jialin Liu, Kun H. Lee, Chen Li, Lu Lu, Jaimee Moline, Renxiang Guan, Joshua D. Welch. Nature Biotechnology, Online ahead of print, 2025.
    • DOI: 10.1038/s41587-025-02688-8
• Protein Domain Embeddings for Fast and Accurate Similarity Search. Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye.
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• Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction Models. George I. Austin, Aya Brown Kav, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Tal Korem.
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• VICTree - A Variational Inference Method for Clonal Tree Reconstruction. Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren.
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• DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael.
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• Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History. Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, S. Cenk Sahinalp, Salem Malikic.
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• Accurate Assembly of Circular RNAs with TERRACE. Tasfia Zahin, Qian Shi, Xiaofei Carl Zang, Mingfu Shao.
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• Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich.
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• CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing. Kaiyuan Zhu, Matthew Jones, Jens Luebeck, Xinxin Bu, Hyerim Yi, King L. Hung, Ivy Tsz-Lo Wong, Shu Zhang, Paul Mischel, Howard Chang, Vineet Bafna.
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• A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits. Boyang Fu, Prateek Anand, Aakarsh Anand, Joel Mefford, Sriram Sankararaman.
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• Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab.
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• Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael.
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• Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape. Junming Zhao, Chao Zhang, Yunan Luo.
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• Scalable Summary Statistics-Based Heritability Estimation Method with Individual Genotype Level Accuracy. Moonseong Jeong, Ali Pazokitoroudi, Zhengtong Liu, Sriram Sankararaman.
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