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Volume 40 Issue Supplement_2
September 2024
Editorial
ECCB2024: The 23rd European Conference on Computational Biology
Anu Kukkonen-Macchi
,
Sampsa Hautaniemi
,
Katharina F Heil
,
Merja Heinäniemi
,
Lars Juhl Jensen
...
Genomes
Metadata-guided feature disentanglement for functional genomics
Alexander Rakowski
,
Remo Monti
,
Viktoriia Huryn
,
Marta Lemanczyk
,
Uwe Ohler
...
GGTyper: genotyping complex structural variants using short-read sequencing data
Tim Mirus
,
Robert Lohmayer
,
Clementine Döhring
,
Bjarni V Halldórsson
,
Birte Kehr
Polyphest: fast polyploid phylogeny estimation
Zhi Yan
,
Zhen Cao
,
Luay Nakhleh
Scalable CNN-based classification of selective sweeps using derived allele frequencies
Sjoerd van den Belt
,
Hanqing Zhao
,
Nikolaos Alachiotis
CIBRA identifies genomic alterations with a system-wide impact on tumor biology
Soufyan Lakbir
,
Caterina Buranelli
,
Gerrit A Meijer
,
Jaap Heringa
,
Remond J A Fijneman
...
Proteins
Improving dictionary-based named entity recognition with deep learning
Katerina Nastou
,
Mikaela Koutrouli
,
Sampo Pyysalo
,
Lars Juhl Jensen
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation
Huiying Yan
,
Shaojun Wang
,
Hancheng Liu
,
Hiroshi Mamitsuka
,
Shanfeng Zhu
CLigOpt: controllable ligand design through target-specific optimization
Yutong Li
,
Pedro Henrique da Costa Avelar
,
Xinyue Chen
,
Li Zhang
,
Min Wu
...
PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks
Tobias Pietz
,
Sukrit Gupta
,
Christoph N Schlaffner
,
Saima Ahmed
,
Hanno Steen
...
learnMSA2: deep protein multiple alignments with large language and hidden Markov models
Felix Becker
,
Mario Stanke
Systems Biology and Multiomics
A hybrid constrained continuous optimization approach for optimal causal discovery from biological data
Yuehua Zhu
,
Panayiotis V Benos
,
Maria Chikina
HCS'hierarchical algorithm for simulation of omics datasets
Piotr Stomma
,
Witold R Rudnicki
Multi-modal contrastive learning of subcellular organization using DICE
Rami Nasser
,
Leah V Schaffer
,
Trey Ideker
,
Roded Sharan
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs
Tianci Song
,
Eric Cosatto
,
Gaoyuan Wang
,
Rui Kuang
,
Mark Gerstein
...
Single-cell Omics
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data
Qi Jiang
,
Lin Wan
Learning meaningful representation of single-neuron morphology via large-scale pre-training
Yimin Fan
,
Yaxuan Li
,
Yunhua Zhong
,
Liang Hong
,
Lei Li
...
Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport
Zizhan Gao
,
Kai Cao
,
Lin Wan
scNODE
: generative model for temporal single cell transcriptomic data prediction
Jiaqi Zhang
,
Erica Larschan
,
Jeremy Bigness
,
Ritambhara Singh
Microbiomes and Planetary Health
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements
Xiaolei Brian Zhang
,
Grace Oualline
,
Jim Shaw
,
Yun William Yu
Metagenomic functional profiling: to sketch or not to sketch?
Mahmudur Rahman Hera
,
Shaopeng Liu
,
Wei Wei
,
Judith S Rodriguez
,
Chunyu Ma
...
Digital Health
Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling
Srijay Deshpande
,
Sokratia Georgaka
,
Michael Haley
,
Robert Sellers
,
James Minshull
...
Multi-task deep latent spaces for cancer survival and drug sensitivity prediction
Teemu J Rintala
,
Francesco Napolitano
,
Vittorio Fortino
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning
Zhijian Huang
,
Ziyu Fan
,
Siyuan Shen
,
Min Wu
,
Lei Deng
Federated unsupervised random forest for privacy-preserving patient stratification
Bastian Pfeifer
,
Christel Sirocchi
,
Marcus D Bloice
,
Markus Kreuzthaler
,
Martin Urschler
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