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Bioinformatics 2024: all accepted papers

788 papers · page 7 of 8 · the most cited first · ← Bioinformatics 2024

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  1. VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation ↗Yilin Zhu, Guowei Chen, Yanni Sun3 citations
  2. bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties ↗Jose Gavaldá-García, Adrián Díaz, Wim Vranken3 citations
  3. fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data ↗Shen Zhang, Huaying Fang, Tao Hu3 citations
  4. nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis ↗Alexander Peltzer, Christopher Mohr, Kai Bernd Stadermann et al.3 citations
  5. nipalsMCIA : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares ↗Max Mattessich, Joaquin Reyna, Edel Aron et al.3 citations
  6. scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model ↗Sijing An, Jinhui Shi, Runyan Liu et al.3 citations
  7. shinyseg: a web application for flexible cosegregation and sensitivity analysis ↗Christian Carrizosa, Dag Erik Undlien, Magnus Dehli Vigeland3 citations
  8. skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements ↗Xiaolei Brian Zhang, Grace Oualline, Jim Shaw et al.3 citations
  9. vSPACE: exploring virtual spatial representation of articular chondrocytes at the single-cell level ↗Chenyu Zhang, Honglin Wang, Yeonsoo Chung et al.3 citations
  10. A compressive seeding algorithm in conjunction with reordering-based compression ↗Fahu Ji, Qian Zhou, Jue Ruan et al.2 citations
  11. A deep learning method to predict bacterial ADP-ribosyltransferase toxins ↗Dandan Zheng, Siyu Zhou, Lihong Chen et al.2 citations
  12. A fast machine learning dataloader for epigenetic tracks from BigWig files ↗Joren Sebastian Retel, Andreas Poehlmann, Joshua Chiou et al.2 citations
  13. A self-training interpretable cell type annotation framework using specific marker gene ↗Hegang Chen, Yuyin Lu, Yanghui Rao2 citations
  14. A semi-supervised fracture-attention model for segmenting tubular objects with improved topological connectivity ↗Yanfeng Zhou, Liqun Zhong, Zichen Wang et al.2 citations
  15. Analysis of metadynamics simulations by metadynminer.py ↗Jan Beránek, Aleš Křenek, Vojtěch Spiwok2 citations
  16. BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data ↗Wei Tian, Wubin Ding, Jiawei Shen et al.2 citations
  17. BTR: a bioinformatics tool recommendation system ↗Ryan J. Green, Xufeng Qu, Jinze Liu et al.2 citations
  18. BatchFLEX: feature-level equalization of X-batch ↗Joshua Davis, Alyssa Obermayer, Alex C. Soupir et al.2 citations
  19. Bayesian gene set benchmark dose estimation for “omic” responses ↗Daniel Zilber, Kyle P. Messier, John S. House et al.2 citations
  20. BenchStab: a tool for automated querying of web-based stability predictors ↗Jan Velecký, Matej Berezný, Miloš Musil et al.2 citations
  21. Biomarker identification by interpretable maximum mean discrepancy ↗Michael F. Adamer, Sarah C. Brüningk, Dexiong Chen et al.2 citations
  22. CASCC: a co-expression-assisted single-cell RNA-seq data clustering method ↗Lingyi Cai, Dimitris Anastassiou2 citations
  23. CVR-BBI: an open-source VR platform for multi-user collaborative brain to brain interfaces ↗Di Liu, Yina Wei2 citations
  24. CatReNet: interactive analysis of (auto-) catalytic reaction networks ↗Daniel H. Huson, Joana C. Xavier, Mike Steel2 citations
  25. Causal relationships between diseases mined from the literature improve the use of polygenic risk scores ↗Sumyyah Toonsi, Iris Ivy Gauran, Hernando Ombao et al.2 citations
  26. Chapter 6 Computer-aided drug design and drug discovery ↗Meenakshi Rajpoot, Varruchi Sharma, Shagun Gupta et al.2 citations
  27. Chapter 9 Basic structure of proteins: current paradigms, trends, and perspective ↗Sheetal Dagar, Anil Panwar, Varruchi Sharma et al.2 citations
  28. Collapsible tree: interactive web app to present collapsible hierarchies ↗Yuan Gao, Rob Patro, Peng Jiang2 citations
  29. CompariPSSM: a PSSM–PSSM comparison tool for motif-binding determinant analysis ↗Ifigenia Tsitsa, Izabella Krystkowiak, Norman E. Davey2 citations
  30. DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence ↗Jesse Durham, Jing Zhang, Richard Dustin Schaeffer et al.2 citations
  31. Damsel: analysis and visualisation of DamID sequencing in R ↗Caitlin G Page, Andrew Lonsdale, Katrina A. Mitchell et al.2 citations
  32. Designing efficient randstrobes for sequence similarity analyses ↗Moein Karami, Aryan Soltani Mohammadi, Marcel Martin et al.2 citations
  33. DrugRepPT: a deep pretraining and fine-tuning framework for drug repositioning based on drug’s expression perturbation and treatment effectiveness ↗Shuyue Fan, Kuo Yang, Kezhi Lu et al.2 citations
  34. Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data ↗Domagoj Dorešić, Stephan Grein, Jan Hasenauer2 citations
  35. ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining ↗Jon-Michael T. Beasley, Daniel Korn, Nyssa Tucker et al.2 citations
  36. FEHAT: efficient, large scale and automated heartbeat detection in Medaka fish embryos ↗Marcio Soares Ferreira, Sebastian Stricker, Tomas W. Fitzgerald et al.2 citations
  37. Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra ↗Zhaohui Zhan, Lusheng Wang2 citations
  38. GENTANGLE: integrated computational design of gene entanglements ↗Jose Manuel Martí, Chloe Hsu, Charlotte Rochereau et al.2 citations
  39. Galaxy Helm chart: a standardized method for deploying production Galaxy servers ↗Nuwan Goonasekera, Alexandru Mahmoud, Keith Suderman et al.2 citations
  40. GateMeClass: Gate Mining and Classification of cytometry data ↗Simone Caligola, Luca Giacobazzi, Stefania Canè et al.2 citations
  41. GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks ↗Felix M. Weidner, Nensi Ikonomi, Silke D Werle et al.2 citations
  42. Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure ↗Ruiting Xu, Dan Li, Wen Yang et al.2 citations
  43. LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies ↗Melpomeni Kasapi, Kexin Xu, Timothy M. D. Ebbels et al.2 citations
  44. Learning locality-sensitive bucketing functions ↗Xin Yuan, Ke Chen, Xiang Li et al.2 citations
  45. MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification ↗Huang Xu, Tian Wang, Yuqi Miao et al.2 citations
  46. Median and small parsimony problems on RNA trees ↗Bertrand Marchand, Yoann Anselmetti, Manuel Lafond et al.2 citations
  47. Melodia: a Python library for protein structure analysis ↗Rinaldo W. Montalvão, William R. Pitt, Vitor Bernardes Pinheiro et al.2 citations
  48. Multi-modal contrastive learning of subcellular organization using DICE ↗Rami Nasser, Leah V. Schaffer, Trey Ideker et al.2 citations
  49. Multi-task deep latent spaces for cancer survival and drug sensitivity prediction ↗Teemu Rintala, Francesco Napolitano, Vittorio Fortino2 citations
  50. Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples ↗Zikun Yang, Xin Li, Lele Sheng et al.2 citations
  51. Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification ↗Kristofer Sandås, Jacob Lewerentz, Edvin Karlsson et al.2 citations
  52. OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs ↗Yueming Yin, Haifeng Hu, Jitao Yang et al.2 citations
  53. Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes ↗Andre C. Faubert, Shang Wang2 citations
  54. PCBS: an R package for fast and accurate analysis of bisulfite sequencing data ↗Kathryn Lande, April E. Williams2 citations
  55. PRONA: an R-package for Patient Reported Outcomes Network Analysis ↗Brandon Hwa-Lin Bergsneider, Orieta Celiku2 citations
  56. Peptide set test: a peptide-centric strategy to infer differentially expressed proteins ↗Junmin Wang, Steven J. Novick2 citations
  57. Peptriever: a Bi-Encoder approach for large-scale protein–peptide binding search ↗Roni Gurvich, Gal Markel, Ziaurrehman Tanoli et al.2 citations
  58. Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data ↗Jun Zhang, Fan Nie, Feng Luo et al.2 citations
  59. PipeVal: light-weight extensible tool for file validation ↗Yash Patel, Arpi Beshlikyan, Madison Jordan et al.2 citations
  60. Pod5Viewer: a GUI for inspecting raw nanopore sequencing data ↗Vincent Dietrich, Nicolò Alagna, Mark Helm et al.2 citations
  61. PredGCN: a Pruning-enabled Gene-Cell Net for automatic cell annotation of single cell transcriptome data ↗Qi Qi, Yunhe Wang, Yujian Huang et al.2 citations
  62. Proteoform identification and quantification based on alignment graphs ↗Zhaohui Zhan, Lusheng Wang2 citations
  63. Ragas: integration and enhanced visualization for single cell subcluster analysis ↗Uthra Balaji, Juan F. Rodríguez-Alcázar, Preetha Balasubramanian et al.2 citations
  64. Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data ↗Siang Chen, Hao Wang, Dongdong Zhang et al.2 citations
  65. Rnalib: a Python library for custom transcriptomics analyses ↗Niko P. Popitsch, Stefan Ludwig Ameres2 citations
  66. SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data ↗Liting Zhang, Xin Zhou, Xian Mallory2 citations
  67. STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication ↗Jared M. Andrews, Michael W. Lloyd, Steven B. Neuhauser et al.2 citations
  68. Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels ↗Danqing Yin, Yue Cao, Junyi Chen et al.2 citations
  69. Semblans: automated assembly and processing of RNA-seq data ↗Miles D Woodcock-Girard, Eric C Bretz, Holly M Robertson et al.2 citations
  70. Signature Search Polestar: a comprehensive drug repurposing method evaluation assistant for customized oncogenic signature ↗Jinbo Zhang, Shunling Yuan, Wen Cao et al.2 citations
  71. Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix ↗Semih Kurt, Alexandre Bouchard‐Côté, Jens Lagergren2 citations
  72. SuperSpot: coarse graining spatial transcriptomics data into metaspots ↗Matei Teleman, Aurélie AG Gabriel, Léonard Hérault et al.2 citations
  73. The IDSM mass spectrometry extension: searching mass spectra using SPARQL ↗Jakub Galgonek, Jiřı́ Vondrášek2 citations
  74. The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population ↗Hagai Levi, Ran Elkon, Ron Shamir A2 citations
  75. VarNMF: non-negative probabilistic factorization with source variation ↗E. Fallik, Nir Friedman2 citations
  76. ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface ↗Nicolas Ruffini, Saleh Altahini, Stephan Weißbach et al.2 citations
  77. ViralPrimer: a web server to monitor viral nucleic acid amplification tests’ primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox ↗Norbert Deutsch, Zsuzsanna Dosztányi, István Csabai et al.2 citations
  78. bnglViz: online visualization of rule-based models ↗Noah Liguori-Bills, Michael L. Blinov2 citations
  79. metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia ↗Zulema Rodriguez-Hernandez, Mathias Gorski, María Téllez-Plaza et al.2 citations
  80. scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data ↗Chih–Yuan Hsu, Chih‐Han Chang, Qi Liu et al.2 citations
  81. scMaSigPro: differential expression analysis along single-cell trajectories ↗Priyansh Srivastava, Marta Benegas Coll, Stefan Götz et al.2 citations
  82. shinyExprPortal: a configurable ‘shiny’ portal for sharing analysis of molecular expression data ↗Rafael Henkin, Katriona Goldmann, Myles Lewis et al.2 citations
  83. vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data ↗Xingyu Bi, Wenbin Ye, Xin Cheng et al.2 citations
  84. A distribution-free and analytic method for power and sample size calculation in single-cell differential expression ↗Chih–Yuan Hsu, Qi Liu, Yu Shyr1 citation
  85. APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data ↗Bruno Sousa, Maria João Bessa, Filipa Lopes de Mendonça et al.1 citation
  86. Afpdb: an efficient structure manipulation package for AI protein design ↗Yingyao Zhou, Jiayi Wu Cox, Bin Zhou et al.1 citation
  87. An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics ↗Yisu Peng, Shantanu Jain, Predrag Radivojac A1 citation
  88. CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm ↗Teng-Yu Lin, Szu-Chi Chung1 citation
  89. CLigOpt: controllable ligand design through target-specific optimization ↗Yutong Li, Pedro Avelar, Xinyue Chen et al.1 citation
  90. Chapter 8 Phylogenetic analysis ↗Vikas Kumar, Nitin Sharma1 citation
  91. DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion ↗Momoko Hamano, Toru Nakamura, Ryoku Ito et al.1 citation
  92. Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis ↗Zelin Li, Dongying Xie, Yiming Ma et al.1 citation
  93. Detecting gene–environment interactions from multiple continuous traits ↗Wan‐Yu Lin1 citation
  94. Detection and quantification of introgression using Bayesian inference based on conjugate priors ↗Bastian Pfeifer, Durrell D. Kapan, Sereina Annik Herzog1 citation
  95. DrivR-Base: a feature extraction toolkit for variant effect prediction model construction ↗Amy Francis, Colin Campbell, Tom R. Gaunt1 citation
  96. EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events ↗Yubo Wang, Haoran Zhu, Yansong Wang et al.1 citation
  97. EpiVar Browser: advanced exploration of epigenomics data under controlled access ↗David R. Lougheed, Hanshi Liu, Katherine A Aracena et al.1 citation
  98. FLAMS: Find Lysine Acylations and other Modification Sites ↗Hannelore Longin, Nand Broeckaert, Maarten Langen et al.1 citation
  99. FPLS-DC: functional partial least squares through distance covariance for imaging genetics ↗Wenliang Pan, Yue Shan, Chuang Li et al.1 citation
  100. Fast and scalable querying of eukaryotic linear motifs with gget elm ↗Laura Luebbert, Chi Hoang, Manjeet Kumar et al.1 citation

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