Bioinformatics 2024: all accepted papers
- The scalable variant call representation: enabling genetic analysis beyond one million genomes ↗Timothy Poterba, Christopher Vittal, Daniel A. King et al.14 citations
- VirusPredictor: XGBoost-based software to predict virus-related sequences in human data ↗Guangchen Liu, Xun Chen, Yihui Luan et al.14 citations
- m5c-iEnsem: 5-methylcytosine sites identification through ensemble models ↗Anas Bilal, Fawaz Khaled Alarfaj, Rafaqat Alam Khan et al.14 citations
- AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides ↗Shengli Zhang, Ya Zhao, Yunyun Liang13 citations
- ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation ↗Irenaeus C.C. Chan, Alex Panchot, Evelyn Schmidt et al.13 citations
- Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models ↗Francesca Cuturello, Marco Celoria, Alessio Ansuini et al.13 citations
- Estimation of inbreeding and kinship coefficients via latent identity-by-descent states ↗Yongtao Guan, Daniel A Levy13 citations
- FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology ↗Tudor Groza, Dylan Gration, Gareth S Baynam et al.13 citations
- From cell lines to cancer patients: personalized drug synergy prediction ↗Halil İbrahim Kuru, A. Ercüment Çiçek, Öznur Taştan13 citations
- HAT: de novo variant calling for highly accurate short-read and long-read sequencing data ↗Jeffrey K. Ng, Tychele N. Turner13 citations
- Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction ↗Yurui Chen, Louxin Zhang13 citations
- Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data ↗Valérie Marot-Lassauzaie, Sergi Beneyto‐Calabuig, Benedikt Obermayer et al.13 citations
- Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks ↗Chao Deng, Hong‐Dong Li, Lishen Zhang et al.13 citations
- MoleMCL: a multi-level contrastive learning framework for molecular pre-training ↗Xinyi Zhang, Yanni Xu, Changzhi Jiang et al.13 citations
- Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS ↗Rémi Trimbour, Ina Maria Deutschmann, Laura Cantini13 citations
- RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction ↗Clément Bernard, Guillaume Postic, Sahar Ghannay et al.13 citations
- SCARAP: scalable cross-species comparative genomics of prokaryotes ↗Stijn Wittouck, Tom Eilers, Vera van Noort et al.13 citations
- SpatialQC: automated quality control for spatial transcriptome data ↗Guangyao Mao, Yi Yang, Zhuojuan Luo et al.13 citations
- Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics ↗Yanfang Li, Shihua Zhang13 citations
- Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data ↗Marco Stock, Niclas Popp, Jonathan Fiorentino et al.13 citations
- A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling ↗Iain G. Johnston, Ramón Díaz‐Uriarte12 citations
- A machine-readable specification for genomics assays ↗A. Sina Booeshaghi, Xi Xian Chen, Lior S. Pachter12 citations
- AbFlex: designing antibody complementarity determining regions with flexible CDR definition ↗Woosung Jeon, Dongsup Kim12 citations
- An empirical study on KDIGO-defined acute kidney injury prediction in the intensive care unit ↗Xinrui Lyu, Bowen Fan, Matthias Hüser et al.12 citations
- Approximating facial expression effects on diagnostic accuracy via generative AI in medical genetics ↗Tanviben Patel, Amna A. Othman, Ömer Sümer et al.12 citations
- AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality ↗Usman Rashid, Chen Wu, Jason B. Shiller et al.12 citations
- BIMSA: accelerating long sequence alignment using processing-in-memory ↗Alejandro Alonso-Marín, Ivan Fernandez, Quim Aguado-Puig et al.12 citations
- BetaAlign: a deep learning approach for multiple sequence alignment ↗Edo Dotan, Elya Wygoda, Noa Ecker et al.12 citations
- CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing ↗Ali Osman Berk Şapcı, Eleonora Rachtman, Siavash Mirarab12 citations
- DDN3.0: determining significant rewiring of biological network structure with differential dependency networks ↗Yingzhou Lu, Yingzhou Lu, Yizhi Wang et al.12 citations
- Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module ↗Jianyuan Yuan, Fengyu Zhang, Yimeng Qiu et al.12 citations
- Drawing mitochondrial genomes with circularMT ↗Simon J. Goodman, Ian Carr12 citations
- Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools ↗Artuur Couckuyt, Benjamin Rombaut, Yvan Saeys et al.12 citations
- FAIRsoft—a practical implementation of FAIR principles for research software ↗Eva Martín del Pico, Josep Lluis Gelpí, Salvador Capella-Gutiérrez12 citations
- FAPM: functional annotation of proteins using multimodal models beyond structural modeling ↗Wenkai Xiang, Zhaoping Xiong, Huan Chen et al.12 citations
- Fine-tuning protein embeddings for functional similarity evaluation ↗Andrew M. Dickson, Mohammad R. K. Mofrad12 citations
- HyperGen: compact and efficient genome sketching using hyperdimensional vectors ↗Weihong Xu, Po-Kai Hsu, Niema Moshiri et al.12 citations
- LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors ↗Koichiro Majima, Yasuhiro Kojima, Kodai Minoura et al.12 citations
- MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2 ↗Ho Yeung Chim, Arne Elofsson12 citations
- Partial RNA design ↗Frederic Runge, Jörg K. H. Franke, Daniel Fertmann et al.12 citations
- STRPsearch: fast detection of structured tandem repeat proteins ↗Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel et al.12 citations
- Time-efficient filtering of imaging polarimetric data by checking physical realizability of experimental Mueller matrices ↗Tatiana Novikova, Alexey Ovchinnikov, Gleb Pogudin et al.12 citations
- VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs ↗Philippe Charron, Mingsong Kang12 citations
- methyLImp2: faster missing value estimation for DNA methylation data ↗Anna Plaksienko, Pietro Di Lena, Christine Nardini et al.12 citations
- popDMS infers mutation effects from deep mutational scanning data ↗Zhenchen Hong, Kai S Shimagaki, John P. Barton12 citations
- spread.gl: visualizing pathogen dispersal in a high-performance browser application ↗Yimin Li, Nena Bollen, Samuel Leandro Hong et al.12 citations
- A count-based model for delineating cell–cell interactions in spatial transcriptomics data ↗Hirak Sarkar, Uthsav Chitra, Julian Gold et al.11 citations
- A supervised Bayesian factor model for the identification of multi-omics signatures ↗Jeremy P. Gygi, Jeremy P. Gygi, Anna Konstorum et al.11 citations
- Assessing citation integrity in biomedical publications: corpus annotation and NLP models ↗Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna et al.11 citations
- BELHD: improving biomedical entity linking with homonym disambiguation ↗Samuele Garda, Ulf Leser11 citations
- Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis ↗Sofia Mongardi, Silvia Cascianelli, Marco Masseroli11 citations
- Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets ↗Igor Martayan, Bastien Cazaux, Antoine Limasset et al.11 citations
- FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data ↗Mikaela Koutrouli, Katerina C. Nastou, Pau Piera Líndez et al.11 citations
- Federated unsupervised random forest for privacy-preserving patient stratification ↗Bastian Pfeifer, Christel Sirocchi, Marcus D. Bloice et al.11 citations
- Genome-wide detection of somatic mosaicism at short tandem repeats ↗Aarushi Sehgal, Helyaneh Ziaei Jam, Andrew Shen et al.11 citations
- Guide assignment in single-cell CRISPR screens using crispat ↗Jana M. Braunger, Britta Velten11 citations
- Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation ↗Ziheng Duan, Dylan Riffle, Ren Li et al.11 citations
- Improving the performance and interpretability on medical datasets using graphical ensemble feature selection ↗Enzo Battistella, Susan Dina Ghiassian, Albert-Ĺaszló Barabási11 citations
- JARVIS3: an efficient encoder for genomic data ↗Maria J P Sousa, Armando J. Pinho, Diogo Pratas11 citations
- Mariner: explore the Hi-Cs ↗Eric S. Davis, Sarah M Parker, Nicole E Kramer et al.11 citations
- Predicting protein functions using positive-unlabeled ranking with ontology-based priors ↗Fernando Zhapa-Camacho, Zhenwei Tang, Maxat Kulmanov et al.11 citations
- Protein language models meet reduced amino acid alphabets ↗Ioan Ieremie, Rob M. Ewing, Mahesan Niranjan11 citations
- R2Dtool: integration and visualization of isoform-resolved RNA features ↗Aditya J. Sethi, Pablo Acera Mateos, Rippei Hayashi et al.11 citations
- Sitetack: a deep learning model that improves PTM prediction by using known PTMs ↗Clair S. Gutierrez, Alia A. Kassim, Benjamin D. Gutierrez et al.11 citations
- SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS ↗Emese I. Végh, Katerina Douka11 citations
- StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides ↗Ding Wang, Junru Jin, Zhongshen Li et al.11 citations
- SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models ↗Ketrin Gjoni, Katherine S. Pollard11 citations
- Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation ↗Minzhu Xie, Yabin Kuang, Mengyun Song et al.11 citations
- The Naïve Bayes classifier++ for metagenomic taxonomic classification—query evaluation ↗Haozhe (Neil) Duan, Gavin Hearne, Robi Polikar A et al.11 citations
- hictk: blazing fast toolkit to work with .hic and .cool files ↗Roberto Rossini, Jonas Paulsen11 citations
- iSeq: an integrated tool to fetch public sequencing data ↗Haoyu Chao, Z Li, Dijun Chen et al.11 citations
- mLiftOver: harmonizing data across Infinium DNA methylation platforms ↗Brian H. Chen, Wanding Zhou11 citations
- A survey of BWT variants for string collections ↗Davide Cenzato, Zsuzsanna Lipták10 citations
- BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities ↗Telmo Blasco, Francesco Balzerani, Luis V. Valcárcel et al.10 citations
- Flexible parsing, interpretation, and editing of technical sequences with splitcode ↗Delaney K. Sullivan, Lior S. Pachter10 citations
- For antibody sequence generative modeling, mixture models may be all you need ↗Jonathan Parkinson, Wei Wang10 citations
- GammaGateR: semi-automated marker gating for single-cell multiplexed imaging ↗Jiangmei Xiong, Harsimran Kaur, Cody N. Heiser et al.10 citations
- Improving dictionary-based named entity recognition with deep learning ↗Katerina C. Nastou, Mikaela Koutrouli, Sampo Pyysalo et al.10 citations
- LarvaTagger: manual and automatic tagging of Drosophila larval behaviour ↗François Laurent, Alexandre Blanc, Lilly May et al.10 citations
- MPH: fast REML for large-scale genome partitioning of quantitative genetic variation ↗Jicai Jiang10 citations
- MSDAFL: molecular substructure-based dual attention feature learning framework for predicting drug–drug interactions ↗Chao Hou, Guihua Duan, Cheng Yan10 citations
- Many-core algorithms for high-dimensional gradients on phylogenetic trees ↗Karthik Gangavarapu, Xiang Ji, Guy Baele et al.10 citations
- MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing ↗Antoine Passemiers, Stefania Tuveri, Dhanya Sudhakaran et al.10 citations
- MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data ↗Ana Mendes, Jesper Foged Havelund, Jonas Lemvig et al.10 citations
- MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability ↗Yunxiang Yu, Mengyun Gu, Hai Yang Guo et al.10 citations
- PanEffect: a pan-genome visualization tool for variant effects in maize ↗Carson M. Andorf, Olivia C. Haley, Rita K. Hayford et al.10 citations
- Pangenome graph layout by Path-Guided Stochastic Gradient Descent ↗Simon Heumos, Andrea Guarracino, Jan-Niklas M. Schmelzle et al.10 citations
- PhiHER2: phenotype-informed weakly supervised model for HER2 status prediction from pathological images ↗Chaoyang Yan, Jialiang Sun, Yiming Guan et al.10 citations
- Reference-free structural variant detection in microbiomes via long-read co-assembly graphs ↗Kristen D. Curry, Feiqiao Brian Yu, Summer E. Vance et al.10 citations
- RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution ↗Jonathan Chacko, Hakan Özadam, Can Cenik10 citations
- Towards more accurate microbial source tracking via non-negative matrix factorization (NMF) ↗Ziyi Huang, Dehan Cai, Yanni Sun10 citations
- mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations ↗Anna Sintsova, Hans‐Joachim Ruscheweyh, Christopher M. Field et al.10 citations
- scToppR: a coding-friendly R interface to ToppGene ↗Bryan Granger, Stefano Berto10 citations
- A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data ↗Sarah Samorodnitsky, Katie Marie Campbell, Antoni Ribas et al.9 citations
- A deep learning architecture for metabolic pathway prediction ↗Mayank Baranwal, Abram Magner, Paolo Elvati et al.9 citations
- A dual-rule encoding DNA storage system using chaotic mapping to control GC content ↗Xuncai Zhang, Baonan Qi, Ying Niu9 citations
- A hybrid constrained continuous optimization approach for optimal causal discovery from biological data ↗Yuehua Zhu, Panayiotis V. Benos, Maria D. Chikina9 citations
- ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models ↗Mukai Wang, Simon Fontaine, Hui Jiang et al.9 citations
- AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions ↗Zachary A. Rollins, Talal Widatalla, Andrew B. Waight et al.9 citations
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