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Bioinformatics 2024: all accepted papers

788 papers · page 5 of 8 · the most cited first · ← Bioinformatics 2024

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  1. Automated, image-based quantification of peroxisome characteristics with perox-per-cell ↗Maxwell Lewis Neal, Nandini Shukla, Fred David Mast et al.6 citations
  2. Best practices to evaluate the impact of biomedical research software—metric collection beyond citations ↗Awan Afiaz, Andrei A. Ivanov, John Chamberlin et al.6 citations
  3. BindingSiteDTI: differential-scale binding site modelling for drug–target interaction prediction ↗Feng Ming Pan, Chong Yin, Siqi Liu et al.6 citations
  4. Cleavage-stage embryo segmentation using SAM-based dual branch pipeline: development and evaluation with the CleavageEmbryo dataset ↗Chensheng Zhang, Xintong Shi, Xinyue Yin et al.6 citations
  5. Coding genomes with gapped pattern graph convolutional network ↗Ruo Han Wang, Yen Kaow Ng, Xianglilan Zhang et al.6 citations
  6. Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework ↗Gabriel Loyer, Vladimir Reinharz6 citations
  7. CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics ↗Semih Kurt, Mandi Chen, Hosein Toosi et al.6 citations
  8. DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein–protein complexes upon mutation ↗Rahul Nikam, Sherlyn Jemimah, M. Michael Gromiha6 citations
  9. DualNetGO: a dual network model for protein function prediction via effective feature selection ↗Zhuoyang Chen, Qiong Luo6 citations
  10. EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery ↗Johanna Elena Schmitz, Nihit Aggarwal, Lukas Laufer et al.6 citations
  11. Epigenomics coverage data extraction and aggregation in R with tidyCoverage ↗Jacques Serizay, Romain Koszul6 citations
  12. Expanding the coverage of spatial proteomics: a machine learning approach ↗Huangqingbo Sun, Jiayi Li, Robert F. Murphy6 citations
  13. Feature selection by replicate reproducibility and non-redundancy ↗Tümay Capraz, Wolfgang K. Huber6 citations
  14. Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape ↗Andreas Wagner6 citations
  15. HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen–Deuterium Exchange Mass-Spectrometry datasets of different protein states ↗Maria K. Janowska, Katherine H. Reiter, Pearl Magala et al.6 citations
  16. Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy’s outcome for HIV-1 ↗Giulia Di Teodoro, Martin Pirkl, Francesca Incardona et al.6 citations
  17. Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks ↗Chao Gao, Joshua D. Welch6 citations
  18. Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper ↗Charlotte Crauwels, Sophie-Luise Heidig, Adrián Díaz et al.6 citations
  19. LmRaC: a functionally extensible tool for LLM interrogation of user experimental results ↗Douglas B Craig, Sorin Drăghici6 citations
  20. MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants ↗Weijia Jin, Yi Xia, Javlon Nizomov et al.6 citations
  21. MR Corge: sensitivity analysis of Mendelian randomization based on the core gene hypothesis for polygenic exposures ↗Wenmin Zhang, Chen‐Yang Su, Satoshi Yoshiji et al.6 citations
  22. MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation ↗Farid Chaabane, Trestan Pillonel, Claire Bertelli6 citations
  23. Modeling metastatic progression from cross-sectional cancer genomics data ↗Kevin Rupp, Andreas Lösch, Y. Linda Hu et al.6 citations
  24. MolDy: molecular dynamics simulation made easy ↗Mohd Imran Khan, Mohd Imran Khan, Sheetal Pathania et al.6 citations
  25. Nanopore decoding with speed and versatility for data storage ↗Kevin Volkel, Paul W. Hook, Albert J. Keung et al.6 citations
  26. PERSEUS: an interactive and intuitive web-based tool for pedigree visualization ↗Nicole Pradas, Federico Jurado-Ruiz, Carles Onielfa et al.6 citations
  27. Pathway analysis through mutual information ↗Gustavo S. Jeuken, Lukas Käll6 citations
  28. Prioritization of oligogenic variant combinations in whole exomes ↗Barbara Gravel, Alexandre Renaux, Sofia Papadimitriou et al.6 citations
  29. SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings ↗Aysun Urhan, Bianca-Maria Cosma, Ashlee M. Earl et al.6 citations
  30. SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts ↗Nianqiao Ju, Jiawei Liu, Qixin He6 citations
  31. Scalable integration of multiomic single-cell data using generative adversarial networks ↗Valentina Giansanti, Francesca Giannese, Oronza Antonietta Botrugno et al.6 citations
  32. Structure-inclusive similarity based directed GNN: a method that can control information flow to predict drug–target binding affinity ↗Jipeng Huang, Chang Yin Sun, Minglei Li et al.6 citations
  33. Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network ↗Xiaocheng Zeng, Wei Zheng, Qixiu Du et al.6 citations
  34. Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison ↗Zhengyang Guo, Yang Wang, Guangshuo Ou6 citations
  35. Virtual tissue expression analysis ↗Jakob Simeth, Paul Hüttl, Marian Schön et al.6 citations
  36. WatFinder: a ProDy tool for protein–water interactions ↗James Krieger, Frane Doljanin, Anthony T. Bogetti et al.6 citations
  37. findGSEP: estimating genome size of polyploid species using k -mer frequencies ↗Laiyi Fu, Yanxin Xie, Shunkang Ling et al.6 citations
  38. k -nonical space: sketching with reverse complements ↗Guillaume Marçais, C.S. Elder, Carl Kingsford6 citations
  39. learnMSA2: deep protein multiple alignments with large language and hidden Markov models ↗Felix Becker, Mario Stanke6 citations
  40. q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota ↗Francesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo et al.6 citations
  41. vcfpp: a C++ API for rapid processing of the variant call format ↗Zilong Li6 citations
  42. A simple refined DNA minimizer operator enables 2-fold faster computation ↗Chenxu Pan, Knut Reinert5 citations
  43. Accurate segmentation of intracellular organelle networks using low-level features and topological self-similarity ↗Jiaxing Huang, Yaoru Luo, Yuanhao Guo et al.5 citations
  44. Adaptive space search-based molecular evolution optimization algorithm ↗Fei Wang, Xianglong Cheng, Xin Tao Xia et al.5 citations
  45. AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software ↗Alessandro Lisi, Michael C. Campbell5 citations
  46. BEATRICE: Bayesian fine-mapping from summary data using deep variational inference ↗Sayan Ghosal, Michael C. Schatz, Archana Venkataraman5 citations
  47. Bayesian modelling of time series data (BayModTS)—a FAIR workflow to process sparse and highly variable data ↗Sebastian Höpfl, Mohamed Albadry, Uta Dahmen et al.5 citations
  48. BioPred: an R package for biomarkers analysis in precision medicine ↗Zihuan Liu, Yan Sun, Xin Huang5 citations
  49. CIBRA identifies genomic alterations with a system-wide impact on tumor biology ↗Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer et al.5 citations
  50. CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences ↗Nikolaos N. Louros, Frédéric Rousseau, Joost W. H. Schymkowitz5 citations
  51. CParty: hierarchically constrained partition function of RNA pseudoknots ↗Mateo Gray, Luke Trinity, Ulrike Stege et al.5 citations
  52. CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data ↗Xiao Wang, Ziyi Chai, Shaohua Li et al.5 citations
  53. Chemical reaction enhanced graph learning for molecule representation ↗Anchen Li, Elena Casiraghi, Juho Rousu5 citations
  54. Controlled noise: evidence of epigenetic regulation of single-cell expression variability ↗Yan Zhong, Siwei Cui, Yongjian Yang et al.5 citations
  55. DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance ↗Michael Payne, Dalong Hu, Qinning Wang et al.5 citations
  56. Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition ↗Charles Broadbent, Tianci Song, Rui Kuang5 citations
  57. DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data ↗Guangzhi Xiong, Nathan J. LeRoy, Stefan Bekiranov et al.5 citations
  58. DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity ↗Hang Wei, Lin Gao, Shuai Wu et al.5 citations
  59. D’or: deep orienter of protein–protein interaction networks ↗Daniel Pirak, Roded Sharan5 citations
  60. Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions ↗Daniel E. Platt, Aritra Bose, Kahn Rhrissorrakrai et al.5 citations
  61. ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities ↗Dongjia Li, Zhuochao Min, Jia Qi Guo et al.5 citations
  62. Fast and exact gap-affine partial order alignment with POASTA ↗Lucas R. van Dijk, Abigail L. Manson, Ashlee M. Earl et al.5 citations
  63. Funmap: integrating high-dimensional functional annotations to improve fine-mapping ↗Yuekai Li, Jiashun Xiao, Jingsi Ming et al.5 citations
  64. Heterogeneous entity representation for medicinal synergy prediction ↗Jiawei Wu, Jun Wen, Mingyuan Yan et al.5 citations
  65. High-dimensional quantile mediation analysis with application to a birth cohort study of mother–newborn pairs ↗Haixiang Zhang, Xiumei Hong, Yinan Zheng et al.5 citations
  66. Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation ↗Jiyu Chen, Benjamin Goudey, Nicholas Geard et al.5 citations
  67. Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data ↗Palash Sashittal, Viola Chen, Amey P. Pasarkar et al.5 citations
  68. Label-guided seed-chain-extend alignment on annotated De Bruijn graphs ↗Harun Mustafa, Mikhail Karasikov, Nika Mansouri Ghiasi et al.5 citations
  69. MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification ↗Ruipeng Lu, Tim Dumonceaux, Muhammad Anzar et al.5 citations
  70. MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD ↗Tim Cadman, Mariska K. Slofstra, Marije A. van der Geest et al.5 citations
  71. MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins ↗Nicholas E. Newell5 citations
  72. Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell ↗Remco L. van den Broek, Xabier Bello, Rebecca V Küpper et al.5 citations
  73. MetaboReport: from metabolomics data analysis to comprehensive reporting ↗Yonghui Dong, Sergey Malitsky5 citations
  74. NIEND: neuronal image enhancement through noise disentanglement ↗Zuo-Han Zhao, Lijuan Liu, Yufeng Liu5 citations
  75. NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations ↗Wenqian Yu, Hongwu Yu, Jingjing Zhao et al.5 citations
  76. PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks ↗Tobias Pietz, Sukrit Gupta, Christoph N. Schlaffner et al.5 citations
  77. Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications ↗Steven B. Cannon, Hyun Oh Lee, Nathan T. Weeks et al.5 citations
  78. PathwayNexus: a tool for interactive metabolic data analysis ↗Philipp Eberhard, Martin Kern, Michael Aichem et al.5 citations
  79. PhysioFit: a software to quantify cell growth parameters and extracellular fluxes ↗Loïc Le Grégam, Yann Guitton, Floriant Bellvert et al.5 citations
  80. PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature ↗Shubo Tian, Qingyu Chen, Donald C. Comeau et al.5 citations
  81. QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images ↗Carles Pons, Caroline Mauvezin5 citations
  82. RecGraph: recombination-aware alignment of sequences to variation graphs ↗Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella et al.5 citations
  83. SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network ↗Yongjie Wang, Fengfan Zhou, Jinting Guan5 citations
  84. SST-editing: in silico spatial transcriptomic editing at single-cell resolution ↗Jiqing Wu, Viktor Hendrik Koelzer5 citations
  85. TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator ↗Fatih Karaoğlanoğlu, Baraa Orabi, Ryan Kendrick Flannigan et al.5 citations
  86. TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference ↗Anqi Wang, Peixin Tian, Yan Zhang5 citations
  87. Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students ↗Pavlin G. Poličar, Martin Špendl, Tomaž Curk et al.5 citations
  88. ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment ↗Zuher Jahshan, Leonid Yavits5 citations
  89. Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments ↗Benjamin Strope, Katherine E. Pendleton, William Bowie et al.5 citations
  90. pipesnake : generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci ↗Ian G. Brennan, Sonal Singhal, Ziad Al Bkhetan5 citations
  91. pycofitness—Evaluating the fitness landscape of RNA and protein sequences ↗Fabrizio Pucci, Mehari B. Zerihun, Marianne J. Rooman et al.5 citations
  92. scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression ↗Ghulam Murtaza, Byron Butaney, Justin Wagner et al.5 citations
  93. A multi-modality and multi-granularity collaborative learning framework for identifying spatial domains and spatially variable genes ↗Xiao Liang, Pei Liu, Li Xue et al.4 citations
  94. A near-tight lower bound on the density of forward sampling schemes ↗Bryce L. Kille, Ragnar Groot Koerkamp, Drake McAdams et al.4 citations
  95. Accurate assembly of multiple RNA-seq samples with Aletsch ↗Qian Shi, Qimin Zhang, Mingfu Shao4 citations
  96. BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images ↗Xinyuan Huang, Xiujuan Gao, Ling Fu4 citations
  97. BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model ↗Hanyu Luo, Li Jie Tang, Min Zeng et al.4 citations
  98. CLAUDIO: automated structural analysis of cross-linking data ↗Alexander Röhl, Eugen Netz, Oliver Kohlbacher et al.4 citations
  99. Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data ↗Yichi Zhang, Chenghui Hu, Xiaohui Wu et al.4 citations
  100. Chapter 4 Tools used in sequence alignment ↗Varruchi Sharma, Imran Sheikh, Vikas Kushwaha et al.4 citations

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