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Bioinformatics 2024: all accepted papers

788 papers · page 2 of 8 · the most cited first · ← Bioinformatics 2024

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  1. MARS: a motif-based autoregressive model for retrosynthesis prediction ↗Jiahan Liu, Chaochao Yan, Yang Yu et al.23 citations
  2. Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution ↗Parsa Ghadermazi, Siu Hung Joshua Chan23 citations
  3. MolLM : a unified language model for integrating biomedical text with 2D and 3D molecular representations ↗Xiangru Tang, Xiangru Tang, Jeffrey Too Chuan Tan et al.23 citations
  4. PHIStruct: improving phage–host interaction prediction at low sequence similarity settings using structure-aware protein embeddings ↗Mark Edward M. Gonzales, Jennifer C. Ureta, Anish Man Singh Shrestha23 citations
  5. Publication-ready single nucleotide polymorphism visualization with snipit ↗Aine Niamh O’Toole, Ammar Aziz, Daniel M. Maloney23 citations
  6. Sigmoni: classification of nanopore signal with a compressed pangenome index ↗Vikram S. Shivakumar, Omar Y. Ahmed, Sam Kovaka et al.23 citations
  7. YACHT : an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample ↗David Koslicki, Stephen White, Chunyu Ma et al.23 citations
  8. Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes ↗Nicholas S. Edmunds, Ahmet G Genc, Liam James McGuffin22 citations
  9. GenoFig: a user-friendly application for the visualization and comparison of genomic regions ↗Maxime Branger, Sébastien O Leclercq22 citations
  10. NFTest: automated testing of Nextflow pipelines ↗Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi et al.22 citations
  11. NeoaPred: a deep-learning framework for predicting immunogenic neoantigen based on surface and structural features of peptide–human leukocyte antigen complexes ↗Dawei Jiang, Binbin Xi, W.C. Tan et al.22 citations
  12. methscore: a comprehensive R function for DNA methylation-based health predictors ↗Zongli Xu, Liang Niu, Jacob K. Kresovich et al.22 citations
  13. Causal enhanced drug–target interaction prediction based on graph generation and multi-source information fusion ↗Guanyu Qiao, Guohua Wang, Yang Li21 citations
  14. DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure ↗Guanglei Yu, Qichang Zhao, Xuehua Bi et al.21 citations
  15. Insights into the inner workings of transformer models for protein function prediction ↗Markus A. Wenzel, Erik Grüner, Nils Strodthoff21 citations
  16. MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning ↗Ruochi Zhang, Chao Wu, Qian Yang et al.21 citations
  17. PheWAS analysis on large-scale biobank data with PheTK ↗Tam C. Tran, David J. Schlueter, Chenjie Zeng et al.21 citations
  18. RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation ↗Xiaoyi Liu, Chengwei Ai, Hongpeng Yang et al.21 citations
  19. Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis ↗Mohammadali Serajian, Simone Marini, Jarno Alanko et al.21 citations
  20. TAWFN: a deep learning framework for protein function prediction ↗Lu Meng, Xiaoran Wang21 citations
  21. TarKG: a comprehensive biomedical knowledge graph for target discovery ↗Cong Zhou, Chuipu Cai, Xiaotian Huang et al.21 citations
  22. Tutorial on survival modeling with applications to omics data ↗Zhi Qiang Zhao, John Zobolas, Manuela Zucknick et al.21 citations
  23. phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data ↗Divya Sharma, Wendy Y. W. Lou, Wei Xu21 citations
  24. scTPC: a novel semisupervised deep clustering model for scRNA-seq data ↗Yushan Qiu, Lingfei Yang, Hao Jiang et al.21 citations
  25. A BLAST from the past: revisiting blastp’s E-value ↗Yang Young Lu, William Stafford Noble, Uri Keich20 citations
  26. Cluster-efficient pangenome graph construction with nf-core/pangenome ↗Simon Heumos, Michael Heuer, Friederike Hanssen et al.20 citations
  27. DeepDR: a deep learning library for drug response prediction ↗Zhengxiang Jiang, Pengyong Li20 citations
  28. FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets ↗Pinglu Zhang, Huan Liu, Yanming Wei et al.20 citations
  29. Geometry-complete perceptron networks for 3D molecular graphs ↗Alex Morehead, Jianlin Jack Cheng20 citations
  30. MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals ↗Joseph Alan Zoller, Steve Horvath20 citations
  31. RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization ↗Can Fırtına, Melina Soysal, Joël Lindegger et al.20 citations
  32. p-IgGen: a paired antibody generative language model ↗Oliver M. Turnbull, Dino Oglić, Rebecca Croasdale-Wood et al.20 citations
  33. ChatMol: interactive molecular discovery with natural language ↗Zheni Zeng, Bangchen Yin, Shipeng Wang et al.19 citations
  34. DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning ↗Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli et al.19 citations
  35. DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning ↗Jun Wang, Marc Horlacher, Lixin Cheng et al.19 citations
  36. FungiFun3: systemic gene set enrichment analysis for fungal species ↗Albert García López, Daniela Albrecht-Eckardt, Gianni Panagiotou et al.19 citations
  37. HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer ↗Xiaopeng Xu, Chencheng Xu, Wenjia He et al.19 citations
  38. HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools ↗Mario Sänger, Samuele Garda, Xing David Wang et al.19 citations
  39. SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis ↗Gohta Aihara, Kalen Clifton, Mayling Chen et al.19 citations
  40. AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification ↗Xiaoshu Zhu, Shuang Meng, Gaoshi Li et al.18 citations
  41. Anti-symmetric framework for balanced learning of protein–protein interactions ↗Tao Tang, Tianyang Li, Weizhuo Li et al.18 citations
  42. AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects ↗Ding Bai, Caleb N. Ellington, Shentong Mo et al.18 citations
  43. Chain-aware graph neural networks for molecular property prediction ↗Honghao Wang, Acong Zhang, Yuan Zhong et al.18 citations
  44. DPNN-ac4C: a dual-path neural network with self-attention mechanism for identification of N4-acetylcytidine (ac4C) in mRNA ↗Jiahao Yuan, Ziyi Wang, Zhuoyu Pan et al.18 citations
  45. MEG-PPIS: a fast protein–protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network ↗Hongzhen Ding, Xue Li, Peifu Han et al.18 citations
  46. MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning ↗Zhijian Huang, Ziyu Fan, Siyuan Shen et al.18 citations
  47. Multi-Omic Graph Diagnosis (MOGDx): a data integration tool to perform classification tasks for heterogeneous diseases ↗Barry Ryan, Riccardo Emilio Marioni, T. Ian Simpson18 citations
  48. Multi-scale topology and position feature learning and relationship-aware graph reasoning for prediction of drug-related microbes ↗Ping Xuan, Jing Gu, Hui Cui et al.18 citations
  49. Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro ↗Zhanhe Chang, Yunfan Xu, Xin Dong et al.18 citations
  50. Advancing mRNA subcellular localization prediction with graph neural network and RNA structure ↗Fuyi Li, Yue Bi, Xudong Guo et al.17 citations
  51. AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification ↗Jung Kim, Ammar S. Naqvi, Ryan J. Corbett et al.17 citations
  52. DESpace : spatially variable gene detection via differential expression testing of spatial clusters ↗Peiying Cai, Mark D. Robinson, Simone Tiberi17 citations
  53. GraphCompass: spatial metrics for differential analyses of cell organization across conditions ↗Mayar Ali, Merel Kuijs, Soroor Hediyeh-zadeh et al.17 citations
  54. GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway–pathway interaction network ↗Teng Ma, Jianxin Wang17 citations
  55. HAlign 4: a new strategy for rapidly aligning millions of sequences ↗Tong Zhou, Pinglu Zhang, Quan Zou et al.17 citations
  56. Improving generalizability of drug–target binding prediction by pre-trained multi-view molecular representations ↗Xike Ouyang, Y. X. Feng, Chen Cui et al.17 citations
  57. MGRN: toward robust drug recommendation via multi-view gating retrieval network ↗Fanjun Meng, Xiaobo Li, Xiaodi Hou et al.17 citations
  58. MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction ↗Fang Wang, Yibin Wang, Xiaofei Zeng et al.17 citations
  59. Protein structure alignment by Reseek improves sensitivity to remote homologs ↗R. C. Edgar17 citations
  60. ReactomeGSA: new features to simplify public data reuse ↗Alexander Grentner, Eliot Ragueneau, Chuqiao Gong et al.17 citations
  61. Ribotin: automated assembly and phasing of rDNA morphs ↗Mikko Rautiainen17 citations
  62. TPepPro: a deep learning model for predicting peptide–protein interactions ↗Jin Xiao-hong, Zimeng Chen, Dan Yu et al.17 citations
  63. Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction ↗Dongmin Bang, Bonil Koo, Sun Kim17 citations
  64. ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets ↗Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas Nordahl Petersen et al.16 citations
  65. An Ensemble Spectral Prediction (ESP) model for metabolite annotation ↗Xinmeng Li, Yan Zhou Chen, Apurva Kalia et al.16 citations
  66. Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers ↗Panagiotis I. Sergouniotis, Adam Diakite, Kumar Gaurav et al.16 citations
  67. CircSI-SSL: circRNA-binding site identification based on self-supervised learning ↗Chao Cao, Chunyu Wang, Shuhong Yang et al.16 citations
  68. Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies ↗William Lees, Swati Saha, Gur Yaari et al.16 citations
  69. Dual-view jointly learning improves personalized drug synergy prediction ↗Xueliang Li, Bihan Shen, Fangyoumin Feng et al.16 citations
  70. Dynamic correlations: exact and approximate methods for mutual information ↗Kemal Demirtaş, Burak Erman, Türkan Haliloǧlu16 citations
  71. Exact global alignment using A* with chaining seed heuristic and match pruning ↗Ragnar Groot Koerkamp, Pesho Ivanov16 citations
  72. Figeno: multi-region genomic figures with long-read support ↗Etienne Sollier, Jessica Heilmann, Clarissa Gerhäuser et al.16 citations
  73. GraphADT: empowering interpretable predictions of acute dermal toxicity with multi-view graph pooling and structure remapping ↗Xinqian Ma, Xiangzheng Fu, Tao Wang et al.16 citations
  74. MVSF-AB: accurate antibody–antigen binding affinity prediction via multi-view sequence feature learning ↗Minghui Li, Yao Shi, Shengqing Hu et al.16 citations
  75. TransGEM: a molecule generation model based on Transformer with gene expression data ↗Yanguang Liu, Hailong Yu, Xinya Duan et al.16 citations
  76. 2dGBH: Two-dimensional group Benjamini–Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data ↗Lu Yang, Pei Wang, Jun Chen15 citations
  77. Are genomic language models all you need? Exploring genomic language models on protein downstream tasks ↗Sam Boshar, Evan Trop, Bernardo P. de Almeida et al.15 citations
  78. Disease gene prioritization with quantum walks ↗Harto Saarinen, Mark Goldsmith, Rui‐Sheng Wang et al.15 citations
  79. Floria: fast and accurate strain haplotyping in metagenomes ↗Jim Shaw, Jean-Sébastien Gounot, Hanrong Chen et al.15 citations
  80. Improved prediction of post-translational modification crosstalk within proteins using DeepPCT ↗Yuxiang Huang, Rong Liu15 citations
  81. Prediction of human O- linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model ↗Subash Chandra Pakhrin, Neha Chauhan, Salman Khan et al.15 citations
  82. PyCoMo: a python package for community metabolic model creation and analysis ↗Michael Predl, Marianne Mießkes, Thomas Rattei et al.15 citations
  83. RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads ↗Peng Ni, Jinrui Xu, Zeyu Zhong et al.15 citations
  84. The FunCoup Cytoscape App: multi-species network analysis and visualization ↗Davide Buzzao, Lukas Steininger, Dimitri Guala et al.15 citations
  85. Using explainable machine learning to uncover the kinase–substrate interaction landscape ↗Zhongliang Zhou, Wayland Yeung, Saber Soleymani et al.15 citations
  86. imputomics: web server and R package for missing values imputation in metabolomics data ↗Jarosław Chilimoniuk, Krystyna Grzesiak, Jakub Kała et al.15 citations
  87. Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization ↗Colin G. Cess, Laleh Haghverdi14 citations
  88. ENKIE: a package for predicting enzyme kinetic parameter values and their uncertainties ↗Mattia G. Gollub, Thierry Backes, Hans‐Michael Kaltenbach et al.14 citations
  89. GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation ↗Huiying Yan, Shaojun Wang, Hancheng Liu et al.14 citations
  90. ICELLNET v2: a versatile method for cell–cell communication analysis from human transcriptomic data ↗Lucile Massenet-Regad, Vassili Soumelis14 citations
  91. Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation ↗Andrew G Duncan, Jennifer A. Mitchell, Alan M Moses14 citations
  92. Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding ↗Yanglan Gan, Jiacheng Yu, Guangwei Xu et al.14 citations
  93. InterLabelGO+: unraveling label correlations in protein function prediction ↗Quancheng Liu, Chengxin Zhang, Lydia Freddolino14 citations
  94. MMOSurv: meta-learning for few-shot survival analysis with multi-omics data ↗Gang Wen, Limin Li14 citations
  95. Metagenomic functional profiling: to sketch or not to sketch? ↗Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei et al.14 citations
  96. Optimizing multi-omics data imputation with NMF and GAN synergy ↗Md. Istiaq Ansari, Khandakar Tanvir Ahmed, Wei Zhang14 citations
  97. PCA-based spatial domain identification with state-of-the-art performance ↗Darius P. Schaub, Behnam Yousefi, Nico Kaiser et al.14 citations
  98. Pitfalls of machine learning models for protein–protein interaction networks ↗Loïc Lannelongue, Michael Inouye14 citations
  99. Predicting single-cell cellular responses to perturbations using cycle consistency learning ↗Wei Huang, Hui Liu14 citations
  100. SCMeTA: a pipeline for single-cell metabolic analysis data processing ↗Xingyu Pan, Si-Yuan Pan, Murong Du et al.14 citations

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