RECOMB

Publications

2024

Alexander T. Leighton, Yun William Yu
Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography. RECOMB (2024)
Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich
Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. RECOMB (2024)
Shani Jacobson, Roded Sharan
An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. RECOMB (2024)
Uyen Mai, Gillian Chu, Benjamin J. Raphael
Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. RECOMB (2024)
Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab
Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. RECOMB (2024)
Leah L. Weber, Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan
TRIBAL: Tree Inference of B Cell Clonal Lineages. RECOMB (2024)
Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. RECOMB (2024)
Ali Osman Berk Sapci, Siavash Mirarab
Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. RECOMB (2024)
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. RECOMB (2024)
Spencer Krieger, John D. Kececioglu
Computing Robust Optimal Factories in Metabolic Reaction Networks. RECOMB (2024)
Myson C. Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas
MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies. RECOMB (2024)
Avantika Lal, David Garfield, Tommaso Biancalani, Gökcen Eraslan
regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models. RECOMB (2024)
Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao
Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach. RECOMB (2024)
Emaad Khwaja, Yun S. Song, Bo Huang
CELL-E: A Text-to-Image Transformer for Protein Image Prediction. RECOMB (2024)
Nathan Guerin, Henry Childs, Pei Zhou, Bruce Randall Donald
DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors. RECOMB (2024)
Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. RECOMB (2024)
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. RECOMB (2024)
Yimin Fan, Yu Li, Jun Ding, Yue Li
GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. RECOMB (2024)
C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford
A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements. RECOMB (2024)
Junming Zhao, Chao Zhang, Yunan Luo
Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape. RECOMB (2024)
Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen
Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks. RECOMB (2024)
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. RECOMB (2024)
Giulio Ermanno Pibiri, Jason Fan, Rob Patro
Meta-colored Compacted de Bruijn Graphs. RECOMB (2024)
Yuxuan Du, Wenxuan Zuo, Fengzhu Sun
ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. RECOMB (2024)
Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang
PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. RECOMB (2024)
Jianyu Yang, Kuangyu Yen, Shaun Mahony
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. RECOMB (2024)
Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye
Protein Domain Embeddings for Fast and Accurate Similarity Search. RECOMB (2024)
Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra
GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. RECOMB (2024)
Kaiyuan Zhu, Matthew G. Jones, Jens Luebeck, Xinxin Bu, Hyerim Yi, King L. Hung, Ivy Tsz-Lo Wong, Shu Zhang, Paul S. Mischel, Howard Y. Chang, Vineet Bafna
CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing. RECOMB (2024)
Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty
Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. RECOMB (2024)
Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford
Graph-Based Genome Inference from Hi-C Data. RECOMB (2024)
Moonseong Jeong, Ali Pazokitoroudi, Zhengtong Liu, Sriram Sankararaman
Scalable Summary Statistics-Based Heritability Estimation Method with Individual Genotype Level Accuracy. RECOMB (2024)
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. RECOMB (2024)
Ghanshyam Chandra, Daniel Gibney, Chirag Jain
Haplotype-Aware Sequence Alignment to Pangenome Graphs. RECOMB (2024)
Tasfia Zahin, Qian Shi, Xiaofei Carl Zang, Mingfu Shao
Accurate Assembly of Circular RNAs with TERRACE. RECOMB (2024)
Li Song, Ben Langmead
Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification. RECOMB (2024)
George I. Austin, Aya Brown Kav, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Tal Korem
Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction Models. RECOMB (2024)
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. RECOMB (2024)
Ludwig Gräf, Daniel Sens, Liubov Shilova, Francesco Paolo Casale
Disease Risk Predictions with Differentiable Mendelian Randomization. RECOMB (2024)
Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia
Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency. RECOMB (2024)
Boyang Fu, Prateek Anand, Aakarsh Anand, Joel Mefford, Sriram Sankararaman
A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits. RECOMB (2024)
Yichen Gu, Jialin Liu, Chen Li, Joshua D. Welch
Mapping Cell Fate Transition in Space and Time. RECOMB (2024)
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. RECOMB (2024)
Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren
VICTree - A Variational Inference Method for Clonal Tree Reconstruction. RECOMB (2024)
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. RECOMB (2024)
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. RECOMB (2024)
Madalina 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
Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. RECOMB (2024)
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. RECOMB (2024)
Shuai Zeng, Duolin Wang, Lei Jiang, Dong Xu
Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction. RECOMB (2024)

volume 14758, 2024

Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings RECOMB 14758 (2024)