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Bioinformatics 2024: all accepted papers

788 papers · page 4 of 8 · the most cited first · ← Bioinformatics 2024

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  1. AmplificationTimeR: an R package for timing sequential amplification events ↗G. Maria Jakobsdottir, Stefan C. Dentro, Robert Glen Bristow et al.9 citations
  2. CSV-Filter: a deep learning-based comprehensive structural variant filtering method for both short and long reads ↗Zeyu Xia, Weiming Xiang, Qingzhe Wang et al.9 citations
  3. CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis ↗Liang Wang, Chenyang Hong, Jiangning Song et al.9 citations
  4. Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model ↗Xin Ma, Sai Ritesh Thela, Fengdi Zhao et al.9 citations
  5. Detecting transposable elements in long-read genomes using sTELLeR ↗Kristine Bilgrav Sæther, Jesper Eisfeldt9 citations
  6. Dynamic category-sensitive hypergraph inferring and homo-heterogeneous neighbor feature learning for drug-related microbe prediction ↗Ping Xuan, Zelong Xu, Hui Cui et al.9 citations
  7. FateNet: an integration of dynamical systems and deep learning for cell fate prediction ↗Mehrshad Sadria, Thomas M. Bury9 citations
  8. GNN4DM: a graph neural network-based method to identify overlapping functional disease modules ↗András Gézsi, Péter Antal9 citations
  9. HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data ↗Xingjian Chen, Jiecong Lin, Yuchen Wang et al.9 citations
  10. Higher-order correction of persistent batch effects in correlation networks ↗Soel Micheletti, Daniel Schlauch, John Quackenbush et al.9 citations
  11. ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells ↗Andrew Jiang, Russell G. Snell, Klaus Lehnert9 citations
  12. Icarust, a real-time simulator for Oxford Nanopore adaptive sampling ↗Rory Munro, Satrio Haryo Benowo Wibowo, Alexander Payne et al.9 citations
  13. Identification and annotation of centromeric hypomethylated regions with CDR-Finder ↗Francesco Kumara Mastrorosa, Keisuke K. Oshima, Allison N. Rozanski et al.9 citations
  14. Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network ↗Baixue Qiao, Shuda Wang, Mingjun Hou et al.9 citations
  15. Interactive visualization of nanopore sequencing signal data with Squigualiser ↗Hiruna Samarakoon, Kisaru Liyanage, James M. Ferguson et al.9 citations
  16. MCDHGN: heterogeneous network-based cancer driver gene prediction and interpretability analysis ↗Lexiang Wang, Jingli Zhou, Xuan Wang et al.9 citations
  17. Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries ↗Jochen Weile, Gabrielle Ferra, Gabriel E. Boyle et al.9 citations
  18. Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of Plasmodium falciparum genes ↗Chiyun Lee, Eyyüb S. Ünlü, Nina F. D. White et al.9 citations
  19. Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation ↗David Ferreiro, Catarina Branco, Miguel Arenas9 citations
  20. Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences ↗Osamu Gotoh9 citations
  21. SpecEncoder: deep metric learning for accurate peptide identification in proteomics ↗Kaiyuan Liu, Chenghua Tao, Yuzhen Ye et al.9 citations
  22. TargetSA: adaptive simulated annealing for target-specific drug design ↗Zhe Xue, Chenwei Sun, Wenhao Zheng et al.9 citations
  23. Unraveling spatial domain characterization in spatially resolved transcriptomics with robust graph contrastive clustering ↗Yingxi Zhang, Zhuohan Yu, Ka‐Chun Wong et al.9 citations
  24. ViralWasm: a client-side user-friendly web application suite for viral genomics ↗Daniel Ji, Robert Aboukhalil, Niema Moshiri9 citations
  25. Zero is not absence: censoring-based differential abundance analysis for microbiome data ↗Lap Sum Chan, Gen Li9 citations
  26. pyM2aia: Python interface for mass spectrometry imaging with focus on deep learning ↗Jonas Cordes, Thomas Enzlein, Carsten Hopf et al.9 citations
  27. tstrait : a quantitative trait simulator for ancestral recombination graphs ↗Daiki Tagami, Gertjan Bisschop, Jerome Kelleher9 citations
  28. A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies ↗Tasbiraha Athaya, Xiaoman Li, Haiyan Hu8 citations
  29. A learned score function improves the power of mass spectrometry database search ↗Varun Ananth, Justin Sanders, Melih Yilmaz et al.8 citations
  30. BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework ↗Xiangxin Zhan, Yanbin Yin, Han Zhang8 citations
  31. BS-clock, advancing epigenetic age prediction with high-resolution DNA methylation bisulfite sequencing data ↗Congcong Hu, Yunxiao Li, Longhui Li et al.8 citations
  32. Bigtools: a high-performance BigWig and BigBed library in Rust ↗Jack D. Huey, Nezar A. Abdennur8 citations
  33. Computational prediction of multiple antigen epitopes ↗Rajalakshmi Viswanathan, Moshe Carroll, A. Roffe et al.8 citations
  34. ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements ↗Orit Adato, Anna Sloutskin, Hodaya Komemi et al.8 citations
  35. Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model ↗Tangqi Fang, Yifeng Liu, Addie Woicik et al.8 citations
  36. Enhancing generalizability and performance in drug–target interaction identification by integrating pharmacophore and pre-trained models ↗Zuolong Zhang, Xin He, Dazhi Long et al.8 citations
  37. GradHC: highly reliable gradual hash-based clustering for DNA storage systems ↗Dvir Ben Shabat, Adar Hadad, Avital Boruchovsky et al.8 citations
  38. Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport ↗Zizhan Gao, Kai Cao, Lin Wan8 citations
  39. Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences ↗Hannes Hauswedell, Sara Hetzel, Simon Gene Gottlieb et al.8 citations
  40. Learning meaningful representation of single-neuron morphology via large-scale pre-training ↗Yimin Fan, Yaxuan Li, Yaxuan Li et al.8 citations
  41. NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data ↗Yunlu Chen, Feng Ruan, Ji-Ping Wang8 citations
  42. Oncotree2vec — a method for embedding and clustering of tumor mutation trees ↗Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel8 citations
  43. Optimizing representations for integrative structural modeling using Bayesian model selection ↗Shreyas M. Arvindekar, Aditi Pathak, Kartik Majila et al.8 citations
  44. PhosX: data-driven kinase activity inference from phosphoproteomics experiments ↗Alessandro Lussana, Sophia Müller‐Dott, Julio Sáez-Rodríguez et al.8 citations
  45. Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning ↗Azza Althagafi, Fernando Zhapa-Camacho, Robert Hoehndorf8 citations
  46. Representing mutations for predicting cancer drug response ↗Patrick Wall, Trey Ideker8 citations
  47. SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein–protein complexes ↗Prawin Rimal, Shailesh Kumar Panday, Xu Wang et al.8 citations
  48. SPRITE: improving spatial gene expression imputation with gene and cell networks ↗Eric Sun, Rong Ma, James Zou8 citations
  49. SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks ↗Diego Mañanes, Inés Rivero-García, Carlos Relaño‐Rupérez et al.8 citations
  50. Statistical framework to determine indel-length distribution ↗Elya Wygoda, Gil Loewenthal, Asher Moshe et al.8 citations
  51. TPepRet: a deep learning model for characterizing T-cell receptors–antigen binding patterns ↗Meng Wang, Wei Fan, Tianrui Wu et al.8 citations
  52. Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins ↗Javier González-Delgado, Pau Bernadó, Pierre Neuvial et al.8 citations
  53. hopsy — a methods marketplace for convex polytope sampling in Python ↗Richard Dominik Paul, Johann F. Jadebeck, Anton Stratmann et al.8 citations
  54. longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types ↗Jonas Hagenberg, Monika Budde, Teodora Pandeva et al.8 citations
  55. scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution ↗Zeyu Chen, Yuxin Miao, Zhiyuan Tan et al.8 citations
  56. scDRMAE: integrating masked autoencoder with residual attention networks to leverage omics feature dependencies for accurate cell clustering ↗Tianjiao Zhang, Hongfei Zhang, Jixiang Ren et al.8 citations
  57. 3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties ↗Diogo A. C. Narciso, Ana Pereira, Nuno O Dias et al.7 citations
  58. A curated rotamer library for common post-translational modifications of proteins ↗Oufan Zhang, Shubhankar A Naik, Zi Hao Liu et al.7 citations
  59. A model-based hierarchical Bayesian approach to Sholl analysis ↗Erik D. VonKaenel, Alexis M. Feidler, Rebecca L. Lowery et al.7 citations
  60. Adaptive digital tissue deconvolution ↗Franziska Görtler, Malte Mensching-Buhr, Ørjan Skaar et al.7 citations
  61. AltGosling: automatic generation of text descriptions for accessible genomics data visualization ↗Thomas Chris Smits, Sehi L’Yi, Andrew Patrick Mar et al.7 citations
  62. CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations ↗Stefan Schrod, Helena U. Zacharias, Tim Beißbarth et al.7 citations
  63. Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data ↗Richard Mayne, Shannah Secret, Cyndi G. Geoghegan et al.7 citations
  64. Closing the computational biology ‘knowledge gap’: Spanish Wikipedia as a case study ↗Nelly Selem Mojica, Tülay Karakulak, Audra Anjum et al.7 citations
  65. Combined LC-MS/MS feature grouping, statistical prioritization, and interactive networking in msFeaST ↗Kevin Mildau, Christoph Büschl, Jürgen Zanghellini et al.7 citations
  66. Deep coupled registration and segmentation of multimodal whole-brain images ↗Tingting Han, Jun Wu, Pengpeng Sheng et al.7 citations
  67. DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins ↗Xiaokun Li, Qiang Yang, Long Xu et al.7 citations
  68. Dynamic modelling of signalling pathways when ordinary differential equations are not feasible ↗Timo Rachel, Eva Brombacher, Svenja Wöhrle et al.7 citations
  69. End-to-end simulation of nanopore sequencing signals with feed-forward transformers ↗Denis Beslic, Martin Kucklick, Susanne Engelmann et al.7 citations
  70. EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data ↗Sijie Li, Yuxi Li, Yu Sun et al.7 citations
  71. GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console ↗Anindita Nath, Savannah Mwesigwa, Yulin Dai et al.7 citations
  72. HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies ↗Milind Misra, Jeffy Jeffy, Charis Liao et al.7 citations
  73. Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection ↗Erhu Liu, Hongqiang Lyu, Yuan Liu et al.7 citations
  74. Information-incorporated gene network construction with FDR control ↗Hao Wang, Yumou Qiu, Hongqing Guo et al.7 citations
  75. Integrating physics in deep learning algorithms: a force field as a PyTorch module ↗Gabriele Orlando, Luis G. Serrano, Joost W. H. Schymkowitz et al.7 citations
  76. Learning to explain is a good biomedical few-shot learner ↗Peng Chen, Jian Wang, Ling Luo et al.7 citations
  77. Ligand identification in CryoEM and X-ray maps using deep learning ↗Jacek Karolczak, Anna Przybyłowska, Konrad Szewczyk et al.7 citations
  78. Multi-indicator comparative evaluation for deep learning-based protein sequence design methods ↗Jinyu Yu, Junxi Mu, Ting Wei et al.7 citations
  79. NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data ↗Michael D. Linderman, Jacob Wallace, Alderik van der Heyde et al.7 citations
  80. NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population ↗Anja Mösch, Filippo Grazioli, Pierre Machart et al.7 citations
  81. NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph ↗Antonio Di Maria, Lorenzo Bellomo, Fabrizio Billeci et al.7 citations
  82. OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling ↗Qiuyue Hu, Zechen Wang, Jintao Meng et al.7 citations
  83. Pair-EGRET: enhancing the prediction of protein–protein interaction sites through graph attention networks and protein language models ↗Ramisa Alam, Sazan Mahbub, Md. Shamsuzzoha Bayzid7 citations
  84. Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs ↗Tianci Song, Eric Cosatto, Gaoyuan Wang et al.7 citations
  85. REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data ↗Yang Yang, Dana Pe’er7 citations
  86. Scalable CNN-based classification of selective sweeps using derived allele frequencies ↗Sjoerd van den Belt, Hanqing Zhao, Nikolaos Alachiotis7 citations
  87. Scbean: a python library for single-cell multi-omics data analysis ↗Haohui Zhang, Yuwei Wang, Bin Lian et al.7 citations
  88. Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing ↗Peter De Rijk, Tijs Watzeels, Fahri Küçükali et al.7 citations
  89. Second-order group knockoffs with applications to genome-wide association studies ↗Benjamin B. Chu, Jiaqi Gu, Zhaomeng Chen et al.7 citations
  90. TSpred: a robust prediction framework for TCR–epitope interactions using paired chain TCR sequence data ↗Ha Young Kim, Sungsik Kim, Woong‐Yang Park et al.7 citations
  91. TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups ↗Pallavi Surana, Pratik Dutta, Ramana V. Davuluri7 citations
  92. Triangulating evidence in health sciences with Annotated Semantic Queries ↗Yi Liu, Tom R. Gaunt7 citations
  93. Uncertainty-aware single-cell annotation with a hierarchical reject option ↗Lauren Theunissen, Thomas Mortier, Yvan Saeys et al.7 citations
  94. isolateR: an R package for generating microbial libraries from Sanger sequencing data ↗Brendan A. Daisley, Sarah J. Vancuren, Dylan J. L. Brettingham et al.7 citations
  95. sparsesurv: a Python package for fitting sparse survival models via knowledge distillation ↗David Wissel, Nikita Janakarajan, Julius Schulte et al.7 citations
  96. A machine-learning-based alternative to phylogenetic bootstrap ↗Noa Ecker, Dorothée Huchon, Yishay Mansour et al.6 citations
  97. A signal-diffusion-based unsupervised contrastive representation learning for spatial transcriptomics analysis ↗Nan Chen, Yu Xiao, Weimin Li et al.6 citations
  98. Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca ↗Eric Weine, Peter S. Carbonetto, Matthew Stephens6 citations
  99. Accurate and efficient protein embedding using multi-teacher distillation learning ↗Jiayu Shang, Cheng Peng, Yongxin Ji et al.6 citations
  100. Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep ↗Teng Liu, Zhaoyu Fang, Xin Li et al.6 citations

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