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Bioinformatics 2024: all accepted papers

788 papers · page 6 of 8 · the most cited first · ← Bioinformatics 2024

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  1. CrossIsoFun: predicting isoform functions using the integration of multi-omics data ↗Yiwei Liu, Hong-Dong Li, Jianxin Wang4 citations
  2. CyCadas: accelerating interactive annotation and analysis of clustered cytometry data ↗Oliver E. Hunewald, Agnieszka Demczuk, Joseph Longworth et al.4 citations
  3. Deep centroid: a general deep cascade classifier for biomedical omics data classification ↗Kuan Xie, Yuying Hou, Xionghui Zhou4 citations
  4. Efficient protein structure archiving using ProteStAr ↗Sebastian Deorowicz, Adam Gudyś4 citations
  5. Estimating the mean in the space of ranked phylogenetic trees ↗Lars Berling, Lena Collienne, Alex Gavryushkin4 citations
  6. FlexLMM: a Nextflow linear mixed model framework for GWAS ↗Saul Pierotti, Tomas W. Fitzgerald, Ewan Birney4 citations
  7. GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes ↗Vadim A. Pisarenco, Joel Vizueta, Julio Rozas4 citations
  8. GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function ↗Danielle Miller, Ofir Arias, David Burstein4 citations
  9. Generation of a high confidence set of domain–domain interface types to guide protein complex structure predictions by AlphaFold ↗Johanna Lena Geist, Chop Yan Lee, Joelle Morgan Strom et al.4 citations
  10. Generative haplotype prediction outperforms statistical methods for small variant detection in next-generation sequencing data ↗Brendan D. O’Fallon, Ashini Bolia, Jacob Durtschi et al.4 citations
  11. Geometric epitope and paratope prediction ↗Marco Pegoraro, Clémentine Dominé, Emanuele Rodolà et al.4 citations
  12. Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes ↗Florian J. Gisdon, Mariella Zunker, Jan Niclas Wolf et al.4 citations
  13. Gretl—variation GRaph Evaluation TooLkit ↗Sebastian Vorbrugg, Ilja Bezrukov, Zhigui Bao et al.4 citations
  14. Guiding discovery of protein sequence-structure-function modeling ↗Azam Hussain, Charles L. Brooks4 citations
  15. Interpreting protein abundance in Saccharomyces cerevisiae through relational learning ↗Daniel Brunnsåker, Filip Kronström, Ievgeniia Tiukova et al.4 citations
  16. Literature mining discerns latent disease–gene relationships ↗Priyadarshini Rai, Atishay Jain, Shivani Kumar et al.4 citations
  17. MEHunter: transformer-based mobile element variant detection from long reads ↗Yadong Wang, Zuji Zhou, Zhendong Zhang et al.4 citations
  18. MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data ↗Marjan Faizi, Ryan T. Fellers, Dan Lü et al.4 citations
  19. MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification ↗Corrado Pancotti, Cesare Rollo, Francesco Codicè et al.4 citations
  20. Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data ↗Uyen Mai, Gary Hu, Benjamin J. Raphael4 citations
  21. MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data ↗Jackson Barth, Yuqiu Yang, Guanghua Xiao et al.4 citations
  22. MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet ↗Ziqing Wang, Michael Cassidy, Danielle A Wallace et al.4 citations
  23. Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies ↗Jian Zou, Zheqi Li, Neil M. Carleton et al.4 citations
  24. Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana ↗Océane Cassan, Charles‐Henri Lecellier, Antoine Martin et al.4 citations
  25. PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping ↗Hui Sun, Yingfeng Zheng, Haonan Xie et al.4 citations
  26. PlasCAT: Plasmid Cloud Assembly Tool ↗Samuel Peccoud, Casey-Tyler Berezin, Sarah I Hernandez et al.4 citations
  27. PyCoM: a python library for large-scale analysis of residue–residue coevolution data ↗Philipp E Glass, Sabriyeh Alibai, Alessandro Pandini et al.4 citations
  28. Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data ↗Juanru Guo, Wenjin Zhang, Xuhua Chen et al.4 citations
  29. RCPedia: a global resource for studying and exploring retrocopies in diverse species ↗Helena B. Conceição, Rafael L. V. Mercuri, Matheus P. M. de Castro et al.4 citations
  30. Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides ↗Sean J. McIlwain, Anna Hoefges, Amy K. Erbe et al.4 citations
  31. SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes ↗William Boulton, Fatma Rabia Fidan, Hubert Denise et al.4 citations
  32. Sensitivities in protein allocation models reveal distribution of metabolic capacity and flux control ↗Samira van den Bogaard, Pedro A. Saa, Tobias B. Alter4 citations
  33. SpatialOne: end-to-end analysis of visium data at scale ↗Mena Kamel, Amrut Sarangi, Pavel Senin et al.4 citations
  34. T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition ↗Xiaoyu Guan, Wei Shao, Daoqiang Zhang4 citations
  35. Target controllability: a feed-forward greedy algorithm in complex networks, meeting Kalman’s rank condition ↗Seyedeh Fatemeh Khezri, Ali Ebrahimi, Changiz Eslahchi4 citations
  36. Text mining for contexts and relationships in cancer genomics literature ↗Charlotte Collins, Simon Baker, Jason P. Brown et al.4 citations
  37. Transcription factor prediction using protein 3D secondary structures ↗Jeanine Liebold, Fabian Neuhaus, Janina Geiser et al.4 citations
  38. Vcfexpress: flexible, rapid user-expressions to filter and format VCFs ↗Brent S. Pedersen, Aaron R. Quinlan4 citations
  39. deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets ↗Cedric Landerer, Maxim Scheremetjew, HongKee Moon et al.4 citations
  40. gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python ↗Carlos J Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal et al.4 citations
  41. mgikit: demultiplexing toolkit for MGI fastq files ↗Ziad Al Bkhetan, Wang Sen4 citations
  42. msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease ↗Thang V. Pham, Alex A. Henneman, Nam X Truong et al.4 citations
  43. preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology ↗Arik Ermshaus, Michael Piechotta, Gina Rüter et al.4 citations
  44. scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets ↗Leanne S. Whitmore, Jennifer Tisoncik-Go, Michael Gale4 citations
  45. scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision ↗Jue Yang, Weiwen Wang, Xiwen Zhang4 citations
  46. spillR : spillover compensation in mass cytometry data ↗Marco Guazzini, Alexander G. Reisach, Sebastian Weichwald et al.4 citations
  47. A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing ↗Kailing Tu, Xuemei Li, Qi‐Lin Zhang et al.3 citations
  48. Accelerated enumeration of extreme rays through a positive-definite elementarity test ↗Wannes Mores, Satyajeet Sheetal Bhonsale, Filip Logist et al.3 citations
  49. Automated segmentation and recognition of C. elegans whole-body cells ↗Yuanyuan Li, Chuxiao Lai, Meng Wang et al.3 citations
  50. Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool ↗Michael K B Ford, Ananth Hari, Qing-Hui Zhou et al.3 citations
  51. CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution ↗Chiung-Ting Wu, Dongping Du, Lulu Chen et al.3 citations
  52. CELEBRIMBOR: core and accessory genes from metagenomes ↗Joel Hellewell, Samuel Horsfield, Johanna von Wachsmann et al.3 citations
  53. Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes ↗Weizhong Zhao, Junze Wu, Xingpeng Jiang et al.3 citations
  54. Cellular proliferation biases clonal lineage tracing and trajectory inference ↗Becca Bonham-Carter, Geoffrey R. Schiebinger3 citations
  55. Chapter 7 Immunoinformatics: computational keys to immune system secrets ↗Vikas Kushwaha, Anu Prabha, Varruchi Sharma et al.3 citations
  56. Computing linkage disequilibrium aware genome embeddings using autoencoders ↗Gizem Taş, Timo Westerdijk, Eric O. Postma et al.3 citations
  57. DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data ↗Johanna Galvis, Joris Guyon, Benjamin Dartigues et al.3 citations
  58. DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores ↗Umberto Lupo, Damiano Sgarbossa, Martina Milighetti et al.3 citations
  59. Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes ↗Sergio Alías-Segura, Florencio Pazos, Mónica Chagoyen3 citations
  60. Efficient construction and utilization of k-ordered FM-indexes with kISS for ultra-fast read mapping in large genomes ↗Zheng-Dao Yang, Hsuan-Yu Kuo, Po-Wei Hsieh et al.3 citations
  61. EuDockScore: Euclidean graph neural networks for scoring protein–protein interfaces ↗Matthew C. McFee, Jisun Kim, Philip M. Kim3 citations
  62. EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow ↗Yiyang Yu, Shivani Muthukumar, Peter K. Koo3 citations
  63. Facilitating phenotyping from clinical texts: the medkit library ↗Antoine Neuraz, Ghislain Vaillant, Camila Arias et al.3 citations
  64. Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads ↗Dongze He, Yuan Gao, Spencer Skylar Chan et al.3 citations
  65. Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis ↗Zsolt Balázs, Todor Gitchev, Ivna Ivanković et al.3 citations
  66. GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts ↗Donghyung Lee, Silviu‐Alin Bacanu3 citations
  67. GGTyper: genotyping complex structural variants using short-read sequencing data ↗Tim Mirus, Robert Lohmayer, Clementine Döhring et al.3 citations
  68. GUEST : an R package for handling estimation of graphical structure and multiclassification for error-prone gene expression data ↗Li‐Pang Chen, Hui-Shan Tsao3 citations
  69. Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python ↗Malte B. Kuehl, Milagros N. Wong, Nicola Wanner et al.3 citations
  70. Genome-wide analysis and visualization of copy number with CNVpytor in igv.js ↗Arijit Panda, Milovan Šuvakov, Helga Thorvaldsdóttir et al.3 citations
  71. Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases ↗Francesco Gualdi, Baldomero Oliva, Janet Piñero3 citations
  72. HBFormer: a single-stream framework based on hybrid attention mechanism for identification of human-virus protein–protein interactions ↗Liyuan Zhang, Sicong Wang, Yadong Wang et al.3 citations
  73. IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits ↗Daniel Mechtersheimer, Wenze Ding, Xiangnan Xu et al.3 citations
  74. Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing ↗Samson Weiner, Bingjun Li, Sheida Nabavi3 citations
  75. Improving bioinformatics software quality through teamwork ↗Katalin Ferenc, Ieva Rauluševičiūtė, Ladislav Hovan et al.3 citations
  76. Integrating patients in time series clinical transcriptomics data ↗Euxhen Hasanaj, Sachin Mathur, Ziv Bar‐Joseph3 citations
  77. Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition ↗Esmaeil Nouranı, Mikaela Koutrouli, Yijia Xie et al.3 citations
  78. Locuaz: an in silico platform for protein binders optimization ↗German Patricio Barletta, Rika Tandiana, Miguel Angel Soler et al.3 citations
  79. MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems ↗Yue Zhuo, Heng Du, Chenguang Diao et al.3 citations
  80. MSIreg: an R package for unsupervised coregistration of mass spectrometry and H&E images ↗Sai Srikanth Lakkimsetty, Andreas T. Weber, Kylie Ariel Bemis et al.3 citations
  81. MetaHD: a multivariate meta-analysis model for metabolomics data ↗J. Liyanage, Luke A. Prendergast, Robert G. Staudte et al.3 citations
  82. MolPLA: a molecular pretraining framework for learning cores, R-groups and their linker joints ↗Mogan Gim, Jueon Park, Soyon Park et al.3 citations
  83. MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions ↗Rodolphe Loubaton, Nicolas Champagnat, Pierre Vallois et al.3 citations
  84. Optimal phylogenetic reconstruction of insertion and deletion events ↗Sanjana Tule, Gabriel Foley, Chongting Zhao et al.3 citations
  85. PhenoMultiOmics: an enzymatic reaction inferred multi-omics network visualization web server ↗Yuying Shi, Botao Xu, Zhe Wang et al.3 citations
  86. Polyphest: fast polyploid phylogeny estimation ↗Zhi Yan, Zhen Cao, Luay K. Nakhleh3 citations
  87. PredCMB: predicting changes in microbial metabolites based on the gene–metabolite network analysis of shotgun metagenome data ↗Jong Dae Ji, Sungwon Jung3 citations
  88. Protein interaction explorer (PIE): a comprehensive platform for navigating protein–protein interactions and ligand binding pockets ↗Fabien Mareuil, Alexandra Moine-Franel, Anuradha Kar et al.3 citations
  89. QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data ↗Manci Li, Damani N. Bryant, Sarah Gresh et al.3 citations
  90. Quantifying defective and wild-type viruses from high-throughput RNA sequencing ↗Juan C. Muñoz-Sánchez, María J. Olmo-Uceda, José Ángel Oteo et al.3 citations
  91. RNA threading with secondary structure and sequence profile ↗Zongyang Du, Zhenling Peng, Jianyi Yang3 citations
  92. Rapid multiple protein sequence search by parallel and heterogeneous computation ↗Jiefu Li, Ziyuan Wang, Ziyuan Wang et al.3 citations
  93. Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks ↗Jiahao Gao, Mark Gerstein3 citations
  94. Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks ↗Jiating Yu, Jiacheng Leng, Fan Yuan et al.3 citations
  95. SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric ↗Yue Lyu, Steven Hsesheng Lin, Hao Wu et al.3 citations
  96. SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space ↗Hamza Biyuzan, M. Masrour, Lucas Grandmougin et al.3 citations
  97. Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach ↗Yueyu Jiang, Daniel T. McDonald, Daniela S. Perry et al.3 citations
  98. SimReadUntil for benchmarking selective sequencing algorithms on ONT devices ↗Maximilian Mordig, Gunnar Rätsch, André Kahles3 citations
  99. SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments ↗Chitrasen Mohanty, Aman Prasad, Lingxin Cheng et al.3 citations
  100. Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network ↗Jakob Woerner, Vivek Sriram, Yonghyun Nam et al.3 citations

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