Program


Accepted Papers


  • Ghanshyam Chandra and Chirag Jain. "Sequence to graph alignment using gap-sensitive co-linear chaining".
  • Nathan LaPierre, Boyang Fu, Steven Turnbull, Eleazar Eskin and Sriram Sankararaman. "Leveraging family data to design Mendelian Randomization that is provably robust to population stratification".
  • Yasamin Tabatabaee, Sebastien Roch and Tandy Warnow. "Statistically Consistent Rooting of Species Trees under the Multi-Species Coalescent Model".
  • Jiacheng Lin, Hanwen Xu, Addie Woicik, Jianzhu Ma and Sheng Wang. "Pisces: A combo-wise contrastive learning approach to synergistic drug combination prediction".
  • Uyen Mai, Eduardo Charvel and Siavash Mirarab. "MD-Cat: Phylogenetic dating under a flexible categorical model using Expectation-Maximization".
  • Louxin Zhang, Niloufar Abhari, Caroline Colijn and Yufeng Wu. "A Fast and Scalable Method for Inferring Phylogenetic Networks from Trees via Aligning the Ancestor Sequences of Taxa".
  • Xiaogen Zhou, Zhiqiang Li and Tong Tong. "DM-Net: A Dual-Model Network for Automated Biomedical Image Diagnosis".
  • Jim Shaw and Yun William Yu. "Seed-chain-extend alignment is accurate and runs in close to O(m log n) time for similar sequences: a rigorous average-case analysis".
  • Soufiane M.C. Mourragui, Marco Loog, Mirrelijn van Nee, Mark van de Wiel, Marcel J.T. Reinders and Lodewyk F.A. Wessels. "Percolate: an exponential family JIVE model to design DNA-based predictors of drug response".
  • Amir Joudaki, Alexandru Meterez, Harun Mustafa, Ragnar Groot Koerkamp, André Kahles and Gunnar Rätsch. "Aligning Distant Sequences to Graphs using Long Seed Sketches".
  • Daniel Baker and Ben Langmead. "Dashing 2: genomic sketching with multiplicities and locality-sensitive hashing".
  • Bing-Xue Du, Yi Xu, Siu-Ming Yiu, Hui Yu and Jian-Yu Shi. "MTGL-ADMET: A Novel Multi-Task Graph Learning Framework for ADMET Prediction Enhanced by Status-Theory and Maximum Flow".
  • Andrea Cracco and Alexandru I. Tomescu. "Extremely-fast construction and querying of compacted and colored de Bruijn graphs with GGCAT".
  • Sara C. Schulte, Alexander Dilthey and Gunnar W. Klau. "HOGVAX: Exploiting Peptide Overlaps to Maximize Population Coverage in Vaccine Design with Application to SARS-CoV-2".
  • Benjamin Maier and Kristoffer Sahlin. "Entropy predicts fuzzy-seed sensitivity".
  • Rıza Özçelik, Alperen Bağ, Berk Atıl, Melih Barsbey, Arzucan Ozgur and Elif Ozkirimli. "DebiasedDTA: Improving the Generalizability of Drug-Target Affinity Prediction Models".
  • Mahmudur Rahman Hera, N. Tessa Pierce-Ward and David Koslicki. "Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash".
  • David Pellow, Lianrong Pu, Baris Ekim, Lior Kotlar, Ron Shamir and Yaron Orenstein. "Efficient minimizer orders for large values of k using minimum decycling sets".
  • Shuvom Sadhuka, Daniel Fridman, Bonnie Berger and Hyunghoon Cho. "Accurate evaluation of transcriptomic re-identification risks using discriminative sequence models".
  • Jason Fan, Jamshed Khan, Giulio Pibiri and Rob Patro. "Spectrum preserving tilings enable sparse and modular reference indexing".
  • Omar Ahmed, Massimiliano Rossi, Christina Boucher and Ben Langmead. "Efficient taxa identification using a pangenome index".
  • Baris Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger and Rayan Chikhi. "hifimap: Efficient low-divergence mapping of long reads in minimizer space".
  • Stefan Ivanovic and Mohammed El-Kebir. "Modeling and Predicting Cancer Clonal Evolution with Reinforcement Learning".
  • Palash Sashittal, Henri Schmidt, Michelle Chan and Benjamin Raphael. "Startle: a star homoplasy approach for CRISPR-Cas9 lineage tracing".
  • Yudi Zhang, Ha Vu, Karin Dorman and Geetu Tuteja. "Unsupervised Deep Peak Caller for ATAC-seq".
  • Ahsan Sanaullah, Degui Zhi and Shaojie Zhang. "Minimal Positional Substring Cover: A Haplotype Threading Alternative to Li & Stephens Model".
  • Yunheng Han and Erin Molloy. "TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees".
  • Aditya Gorla, Sriram Sankararaman, Esteban Burchard, Jonathan Flint, Noah Zaitlen and Elior Rahmani. "Phenotypic subtyping via contrastive learning".
  • Shikha Mallick and Sahely Bhadra. "CDGCN: Conditional de novo Drug generative model using Graph Convolution Networks".
  • Hao Chen, Dongshunyi Li and Ziv Bar-Joseph. "Cell segmentation for high-resolution spatial transcriptomics".
  • Regev Schweiger and Richard Durbin. "Ultra-fast genome-wide inference of pairwise coalescence times".
  • Weizhong Zheng, John H.C. Fong, Yuk Kei Wan, Athena H.Y. Chu, Yuanhua Huang, Alan S.L. Wong and Joshua W.K. Ho. "Translation rate prediction and regulatory motif discovery with multi-task learning".
  • Runpeng Luo and Yu Lin. "VStrains: De Novo Reconstruction of Viral Strains Via Iterative Path Extraction From Assembly Graphs".
  • Ziqi Chen, Martin Min, Hongyu Guo, Chao Cheng, Trevor Clancy and Xia Ning. "T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy".
  • Rajagopal Venkatesaramani, Zhiyu Wan, Bradley Malin and Yevgeniy Vorobeychik. "Enabling Trade-offs in Privacy and Utility in Genomic Data Beacons and Summary Statistics".
  • Ardalan Naseri, William Yue, Shaojie Zhang and Degui Zhi. "FastRecomb: Fast inference of genetic recombination rates in biobank scale data".
  • Spencer Krieger and John Kececioglu. "Computing shortest hyperpaths for pathway inference in cellular reaction networks".
  • Claire McWhite and Mona Singh. "Vector-clustering Multiple Sequence Alignment: Aligning into twilight zone of protein sequence similarity with protein language models".
  • Rohit Singh, Alexander Wu, Anish Mudide and Bonnie Berger. "Unraveling causal gene regulation from the RNA velocity graph using Velorama".
  • Xinhao Liu, Ron Zeira and Benjamin J. Raphael. "PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data".
  • Yuelin Liu, Xuan C. Li, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew Pratt, David R. Crawford, Salem Malikić, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape and S. Cenk Sahinalp. "Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models".
  • Vtalii Stebliankin, Azam Shirali, Prabin Baral, Prem Chapagain and Giri Narasimhan. "PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks".
  • Chihao Zhang, Yiling Elaine Chen, Shihua Zhang and Jingyi Jessica Li. "Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification".
  • Zhihang Hu, Qinze Yu, Yucheng Guo, Taifeng Wang, Irwin King, Xin Gao, Le Song and Yu Li. "Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning".