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28th RECOMB 2024: Cambridge, MA, USA
- Jian Ma
:
Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings. Lecture Notes in Computer Science 14758, Springer 2024, ISBN 978-1-0716-3988-7 - Kapil Devkota
Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks. 1-16 - Kexin Huang, Romain Lopez, Jan-Christian Hütter, Takamasa Kudo, Antonio Rios, Aviv Regev:
Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors. 17-37 - Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová:
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. 38-53 - Alexander T. Leighton
Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography. 54-67 - Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Özlem Özmen Garibay:
FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation. 68-85 - Shani Jacobson, Roded Sharan:
An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. 86-98 - Yuxuan Du
ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. 99-114 - Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford:
Graph-Based Genome Inference from Hi-C Data. 115-130 - Giulio Ermanno Pibiri
Meta-colored Compacted de Bruijn Graphs. 131-146 - Taher Yacoub, Roy González-Alemán
Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. 147-163 - Luca Renders
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. 164-184 - Emaad Khwaja, Yun S. Song, Bo Huang
CELL-E: A Text-to-Image Transformer for Protein Image Prediction. 185-200 - C. S. Elder
A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements. 201-216 - Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel:
Overcoming Observation Bias for Cancer Progression Modeling. 217-234 - Holly R. Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew J. Hirn, Michael Perlmutter, Smita Krishnaswamy:
Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning. 235-252 - Spencer Krieger, John D. Kececioglu:
Computing Robust Optimal Factories in Metabolic Reaction Networks. 253-269 - Tianshuo Zhou
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. 270-287 - Paolo Pellizzoni, Carlos G. Oliver, Karsten M. Borgwardt:
Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching. 288-307 - Matthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho:
Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. 308-313 - Yimin Fan, Yu Li, Jun Ding, Yue Li:
GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. 314-319 - Jianyu Yang, Kuangyu Yen, Shaun Mahony:
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. 320-323 - Li Song
Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification. 324-327 - Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Kimberly Glass, Dawn L. DeMeo, Camila Miranda Lopes-Ramos, John Quackenbush:
BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. 328-331 - Avantika Lal
regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models. 332-335 - Nathan Guerin, Henry Childs, Pei Zhou, Bruce Randall Donald:
DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors. 336-339 - Ali Osman Berk Sapci, Siavash Mirarab:
Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. 340-343 - Stefan Schrod
SpaCeNet: Spatial Cellular Networks from Omics Data. 344-347 - Ziting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang:
Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models. 348-351 - Myson C. Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas:
MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies. 352-355 - Fatemeh Mohebbi
Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes. 356-359 - Uyen Mai, Gillian Chu, Benjamin J. Raphael:
Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. 360-363 - Leah L. Weber
TRIBAL: Tree Inference of B Cell Clonal Lineages. 364-367 - Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael:
Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. 368-371 - Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra:
GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. 372-376 - Han Li
PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. 377-380 - Ghanshyam Chandra, Daniel Gibney, Chirag Jain:
Haplotype-Aware Sequence Alignment to Pangenome Graphs. 381-384 - Ludwig Gräf, Daniel Sens, Liubov Shilova, Francesco Paolo Casale:
Disease Risk Predictions with Differentiable Mendelian Randomization. 385-389 - Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Satyen Gohil, Shuqiang Li, Teddy Huang, David A. Knowles, Catherine J. Wu, Elham Azizi:
DIISCO: A Bayesian Framework for Inferring Dynamic Intercellular Interactions from Time-Series Single-Cell Data. 390-395 - Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao:
Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach. 396-399 - Shuai Zeng
Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction. 400-405 - Madalina Giurgiu
Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. 406-411 - Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia:
Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency. 412-416 - Yichen Gu, Jialin Liu, Chen Li, Joshua D. Welch:
Mapping Cell Fate Transition in Space and Time. 417-420 - Benjamin Giovanni Iovino
Protein Domain Embeddings for Fast and Accurate Similarity Search. 421-424 - George I. Austin
Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction Models. 425-428 - Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren:
VICTree - A Variational Inference Method for Clonal Tree Reconstruction. 429-433 - Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael:
DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. 434-437 - Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic:
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History. 438-443 - Tasfia Zahin, Qian Shi
Accurate Assembly of Circular RNAs with TERRACE. 444-447 - Jack Freestone, Lukas Käll
Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. 448-453 - Kaiyuan Zhu
CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing. 454-457 - Boyang Fu, Prateek Anand, Aakarsh Anand, Joel Mefford, Sriram Sankararaman:
A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits. 458-461 - Shayesteh Arasti
Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. 462-465 - Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael:
Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. 466-469 - Junming Zhao, Chao Zhang, Yunan Luo
Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape. 470-474 - Moonseong Jeong, Ali Pazokitoroudi, Zhengtong Liu, Sriram Sankararaman:
Scalable Summary Statistics-Based Heritability Estimation Method with Individual Genotype Level Accuracy. 475-478 - Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei, Xuegong Zhang:
scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis. 479-482
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