---
title: "Bioinformatics 2024 — all accepted papers, page 6"
description: "All 788 papers of Bioinformatics 2024 · page 6 of 8, the most cited first; those with our summary link to it."
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---
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# Bioinformatics 2024: all accepted papers

788 papers · page 6 of 8 · the most cited first · [← Bioinformatics 2024](https://md.research.elamur.ai/free/en/venues/bioinformatics/2024/)

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501. **[CrossIsoFun: predicting isoform functions using the integration of multi-omics data ↗](https://doi.org/10.1093/bioinformatics/btae742)**Yiwei Liu, Hong-Dong Li, Jianxin Wang*4 citations*
502. **[CyCadas: accelerating interactive annotation and analysis of clustered cytometry data ↗](https://doi.org/10.1093/bioinformatics/btae595)**Oliver E. Hunewald, Agnieszka Demczuk, Joseph Longworth et al.*4 citations*
503. **[Deep centroid: a general deep cascade classifier for biomedical omics data classification ↗](https://doi.org/10.1093/bioinformatics/btae039)**Kuan Xie, Yuying Hou, Xionghui Zhou*4 citations*
504. **[Efficient protein structure archiving using ProteStAr ↗](https://doi.org/10.1093/bioinformatics/btae428)**Sebastian Deorowicz, Adam Gudyś*4 citations*
505. **[Estimating the mean in the space of ranked phylogenetic trees ↗](https://doi.org/10.1093/bioinformatics/btae514)**Lars Berling, Lena Collienne, Alex Gavryushkin*4 citations*
506. **[FlexLMM: a Nextflow linear mixed model framework for GWAS ↗](https://doi.org/10.1093/bioinformatics/btaf021)**Saul Pierotti, Tomas W. Fitzgerald, Ewan Birney*4 citations*
507. **[GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes ↗](https://doi.org/10.1093/bioinformatics/btae439)**Vadim A. Pisarenco, Joel Vizueta, Julio Rozas*4 citations*
508. **[GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function ↗](https://doi.org/10.1093/bioinformatics/btae034)**Danielle Miller, Ofir Arias, David Burstein*4 citations*
509. **[Generation of a high confidence set of domain–domain interface types to guide protein complex structure predictions by AlphaFold ↗](https://doi.org/10.1093/bioinformatics/btae482)**Johanna Lena Geist, Chop Yan Lee, Joelle Morgan Strom et al.*4 citations*
510. **[Generative haplotype prediction outperforms statistical methods for small variant detection in next-generation sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae565)**Brendan D. O’Fallon, Ashini Bolia, Jacob Durtschi et al.*4 citations*
511. **[Geometric epitope and paratope prediction ↗](https://doi.org/10.1093/bioinformatics/btae405)**Marco Pegoraro, Clémentine Dominé, Emanuele Rodolà et al.*4 citations*
512. **[Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes ↗](https://doi.org/10.1093/bioinformatics/btae112)**Florian J. Gisdon, Mariella Zunker, Jan Niclas Wolf et al.*4 citations*
513. **[Gretl—variation GRaph Evaluation TooLkit ↗](https://doi.org/10.1093/bioinformatics/btae755)**Sebastian Vorbrugg, Ilja Bezrukov, Zhigui Bao et al.*4 citations*
514. **[Guiding discovery of protein sequence-structure-function modeling ↗](https://doi.org/10.1093/bioinformatics/btae002)**Azam Hussain, Charles L. Brooks*4 citations*
515. **[Interpreting protein abundance in Saccharomyces cerevisiae through relational learning ↗](https://doi.org/10.1093/bioinformatics/btae050)**Daniel Brunnsåker, Filip Kronström, Ievgeniia Tiukova et al.*4 citations*
516. **[Literature mining discerns latent disease–gene relationships ↗](https://doi.org/10.1093/bioinformatics/btae185)**Priyadarshini Rai, Atishay Jain, Shivani Kumar et al.*4 citations*
517. **[MEHunter: transformer-based mobile element variant detection from long reads ↗](https://doi.org/10.1093/bioinformatics/btae557)**Yadong Wang, Zuji Zhou, Zhendong Zhang et al.*4 citations*
518. **[MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data ↗](https://doi.org/10.1093/bioinformatics/btae335)**Marjan Faizi, Ryan T. Fellers, Dan Lü et al.*4 citations*
519. **[MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification ↗](https://doi.org/10.1093/bioinformatics/btae320)**Corrado Pancotti, Cesare Rollo, Francesco Codicè et al.*4 citations*
520. **[Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data ↗](https://doi.org/10.1093/bioinformatics/btae221)**Uyen Mai, Gary Hu, Benjamin J. Raphael*4 citations*
521. **[MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data ↗](https://doi.org/10.1093/bioinformatics/btae024)**Jackson Barth, Yuqiu Yang, Guanghua Xiao et al.*4 citations*
522. **[MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet ↗](https://doi.org/10.1093/bioinformatics/btae410)**Ziqing Wang, Michael Cassidy, Danielle A Wallace et al.*4 citations*
523. **[Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies ↗](https://doi.org/10.1093/bioinformatics/btae696)**Jian Zou, Zheqi Li, Neil M. Carleton et al.*4 citations*
524. **[Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana ↗](https://doi.org/10.1093/bioinformatics/btae415)**Océane Cassan, Charles‐Henri Lecellier, Antoine Martin et al.*4 citations*
525. **[PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping ↗](https://doi.org/10.1093/bioinformatics/btae323)**Hui Sun, Yingfeng Zheng, Haonan Xie et al.*4 citations*
526. **[PlasCAT: Plasmid Cloud Assembly Tool ↗](https://doi.org/10.1093/bioinformatics/btae299)**Samuel Peccoud, Casey-Tyler Berezin, Sarah I Hernandez et al.*4 citations*
527. **[PyCoM: a python library for large-scale analysis of residue–residue coevolution data ↗](https://doi.org/10.1093/bioinformatics/btae166)**Philipp E Glass, Sabriyeh Alibai, Alessandro Pandini et al.*4 citations*
528. **[Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data ↗](https://doi.org/10.1093/bioinformatics/btae070)**Juanru Guo, Wenjin Zhang, Xuhua Chen et al.*4 citations*
529. **[RCPedia: a global resource for studying and exploring retrocopies in diverse species ↗](https://doi.org/10.1093/bioinformatics/btae530)**Helena B. Conceição, Rafael L. V. Mercuri, Matheus P. M. de Castro et al.*4 citations*
530. **[Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides ↗](https://doi.org/10.1093/bioinformatics/btae637)**Sean J. McIlwain, Anna Hoefges, Amy K. Erbe et al.*4 citations*
531. **[SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes ↗](https://doi.org/10.1093/bioinformatics/btae532)**William Boulton, Fatma Rabia Fidan, Hubert Denise et al.*4 citations*
532. **[Sensitivities in protein allocation models reveal distribution of metabolic capacity and flux control ↗](https://doi.org/10.1093/bioinformatics/btae691)**Samira van den Bogaard, Pedro A. Saa, Tobias B. Alter*4 citations*
533. **[SpatialOne: end-to-end analysis of visium data at scale ↗](https://doi.org/10.1093/bioinformatics/btae509)**Mena Kamel, Amrut Sarangi, Pavel Senin et al.*4 citations*
534. **[T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition ↗](https://doi.org/10.1093/bioinformatics/btae083)**Xiaoyu Guan, Wei Shao, Daoqiang Zhang*4 citations*
535. **[Target controllability: a feed-forward greedy algorithm in complex networks, meeting Kalman’s rank condition ↗](https://doi.org/10.1093/bioinformatics/btae630)**Seyedeh Fatemeh Khezri, Ali Ebrahimi, Changiz Eslahchi*4 citations*
536. **[Text mining for contexts and relationships in cancer genomics literature ↗](https://doi.org/10.1093/bioinformatics/btae021)**Charlotte Collins, Simon Baker, Jason P. Brown et al.*4 citations*
537. **[Transcription factor prediction using protein 3D secondary structures ↗](https://doi.org/10.1093/bioinformatics/btae762)**Jeanine Liebold, Fabian Neuhaus, Janina Geiser et al.*4 citations*
538. **[Vcfexpress: flexible, rapid user-expressions to filter and format VCFs ↗](https://doi.org/10.1093/bioinformatics/btaf097)**Brent S. Pedersen, Aaron R. Quinlan*4 citations*
539. **[deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets ↗](https://doi.org/10.1093/bioinformatics/btae424)**Cedric Landerer, Maxim Scheremetjew, HongKee Moon et al.*4 citations*
540. **[gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python ↗](https://doi.org/10.1093/bioinformatics/btae318)**Carlos J Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal et al.*4 citations*
541. **[mgikit: demultiplexing toolkit for MGI fastq files ↗](https://doi.org/10.1093/bioinformatics/btae554)**Ziad Al Bkhetan, Wang Sen*4 citations*
542. **[msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease ↗](https://doi.org/10.1093/bioinformatics/btae432)**Thang V. Pham, Alex A. Henneman, Nam X Truong et al.*4 citations*
543. **[preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology ↗](https://doi.org/10.1093/bioinformatics/btae085)**Arik Ermshaus, Michael Piechotta, Gina Rüter et al.*4 citations*
544. **[scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets ↗](https://doi.org/10.1093/bioinformatics/btae145)**Leanne S. Whitmore, Jennifer Tisoncik-Go, Michael Gale*4 citations*
545. **[scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision ↗](https://doi.org/10.1093/bioinformatics/btae091)**Jue Yang, Weiwen Wang, Xiwen Zhang*4 citations*
546. **[spillR : spillover compensation in mass cytometry data ↗](https://doi.org/10.1093/bioinformatics/btae337)**Marco Guazzini, Alexander G. Reisach, Sebastian Weichwald et al.*4 citations*
547. **[A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing ↗](https://doi.org/10.1093/bioinformatics/btae206)**Kailing Tu, Xuemei Li, Qi‐Lin Zhang et al.*3 citations*
548. **[Accelerated enumeration of extreme rays through a positive-definite elementarity test ↗](https://doi.org/10.1093/bioinformatics/btae723)**Wannes Mores, Satyajeet Sheetal Bhonsale, Filip Logist et al.*3 citations*
549. **[Automated segmentation and recognition of C. elegans whole-body cells ↗](https://doi.org/10.1093/bioinformatics/btae324)**Yuanyuan Li, Chuxiao Lai, Meng Wang et al.*3 citations*
550. **[Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool ↗](https://doi.org/10.1093/bioinformatics/btae622)**Michael K B Ford, Ananth Hari, Qing-Hui Zhou et al.*3 citations*
551. **[CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution ↗](https://doi.org/10.1093/bioinformatics/btae107)**Chiung-Ting Wu, Dongping Du, Lulu Chen et al.*3 citations*
552. **[CELEBRIMBOR: core and accessory genes from metagenomes ↗](https://doi.org/10.1093/bioinformatics/btae542)**Joel Hellewell, Samuel Horsfield, Johanna von Wachsmann et al.*3 citations*
553. **[Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes ↗](https://doi.org/10.1093/bioinformatics/btae180)**Weizhong Zhao, Junze Wu, Xingpeng Jiang et al.*3 citations*
554. **[Cellular proliferation biases clonal lineage tracing and trajectory inference ↗](https://doi.org/10.1093/bioinformatics/btae483)**Becca Bonham-Carter, Geoffrey R. Schiebinger*3 citations*
555. **[Chapter 7 Immunoinformatics: computational keys to immune system secrets ↗](https://doi.org/10.1515/9783111568584-007)**Vikas Kushwaha, Anu Prabha, Varruchi Sharma et al.*3 citations*
556. **[Computing linkage disequilibrium aware genome embeddings using autoencoders ↗](https://doi.org/10.1093/bioinformatics/btae326)**Gizem Taş, Timo Westerdijk, Eric O. Postma et al.*3 citations*
557. **[DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data ↗](https://doi.org/10.1093/bioinformatics/btae282)**Johanna Galvis, Joris Guyon, Benjamin Dartigues et al.*3 citations*
558. **[DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores ↗](https://doi.org/10.1093/bioinformatics/btae738)**Umberto Lupo, Damiano Sgarbossa, Martina Milighetti et al.*3 citations*
559. **[Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes ↗](https://doi.org/10.1093/bioinformatics/btae646)**Sergio Alías-Segura, Florencio Pazos, Mónica Chagoyen*3 citations*
560. **[Efficient construction and utilization of k-ordered FM-indexes with kISS for ultra-fast read mapping in large genomes ↗](https://doi.org/10.1093/bioinformatics/btae409)**Zheng-Dao Yang, Hsuan-Yu Kuo, Po-Wei Hsieh et al.*3 citations*
561. **[EuDockScore: Euclidean graph neural networks for scoring protein–protein interfaces ↗](https://doi.org/10.1093/bioinformatics/btae636)**Matthew C. McFee, Jisun Kim, Philip M. Kim*3 citations*
562. **[EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow ↗](https://doi.org/10.1093/bioinformatics/btae092)**Yiyang Yu, Shivani Muthukumar, Peter K. Koo*3 citations*
563. **[Facilitating phenotyping from clinical texts: the medkit library ↗](https://doi.org/10.1093/bioinformatics/btae681)**Antoine Neuraz, Ghislain Vaillant, Camila Arias et al.*3 citations*
564. **[Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads ↗](https://doi.org/10.1093/bioinformatics/btae207)**Dongze He, Yuan Gao, Spencer Skylar Chan et al.*3 citations*
565. **[Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis ↗](https://doi.org/10.1093/bioinformatics/btae017)**Zsolt Balázs, Todor Gitchev, Ivna Ivanković et al.*3 citations*
566. **[GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts ↗](https://doi.org/10.1093/bioinformatics/btae203)**Donghyung Lee, Silviu‐Alin Bacanu*3 citations*
567. **[GGTyper: genotyping complex structural variants using short-read sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae391)**Tim Mirus, Robert Lohmayer, Clementine Döhring et al.*3 citations*
568. **[GUEST : an R package for handling estimation of graphical structure and multiclassification for error-prone gene expression data ↗](https://doi.org/10.1093/bioinformatics/btae731)**Li‐Pang Chen, Hui-Shan Tsao*3 citations*
569. **[Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python ↗](https://doi.org/10.1093/bioinformatics/btae700)**Malte B. Kuehl, Milagros N. Wong, Nicola Wanner et al.*3 citations*
570. **[Genome-wide analysis and visualization of copy number with CNVpytor in igv.js ↗](https://doi.org/10.1093/bioinformatics/btae453)**Arijit Panda, Milovan Šuvakov, Helga Thorvaldsdóttir et al.*3 citations*
571. **[Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases ↗](https://doi.org/10.1093/bioinformatics/btae379)**Francesco Gualdi, Baldomero Oliva, Janet Piñero*3 citations*
572. **[HBFormer: a single-stream framework based on hybrid attention mechanism for identification of human-virus protein–protein interactions ↗](https://doi.org/10.1093/bioinformatics/btae724)**Liyuan Zhang, Sicong Wang, Yadong Wang et al.*3 citations*
573. **[IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits ↗](https://doi.org/10.1093/bioinformatics/btae702)**Daniel Mechtersheimer, Wenze Ding, Xiangnan Xu et al.*3 citations*
574. **[Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing ↗](https://doi.org/10.1093/bioinformatics/btae506)**Samson Weiner, Bingjun Li, Sheida Nabavi*3 citations*
575. **[Improving bioinformatics software quality through teamwork ↗](https://doi.org/10.1093/bioinformatics/btae632)**Katalin Ferenc, Ieva Rauluševičiūtė, Ladislav Hovan et al.*3 citations*
576. **[Integrating patients in time series clinical transcriptomics data ↗](https://doi.org/10.1093/bioinformatics/btae241)**Euxhen Hasanaj, Sachin Mathur, Ziv Bar‐Joseph*3 citations*
577. **[Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition ↗](https://doi.org/10.1093/bioinformatics/btae613)**Esmaeil Nouranı, Mikaela Koutrouli, Yijia Xie et al.*3 citations*
578. **[Locuaz: an in silico platform for protein binders optimization ↗](https://doi.org/10.1093/bioinformatics/btae492)**German Patricio Barletta, Rika Tandiana, Miguel Angel Soler et al.*3 citations*
579. **[MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems ↗](https://doi.org/10.1093/bioinformatics/btae044)**Yue Zhuo, Heng Du, Chenguang Diao et al.*3 citations*
580. **[MSIreg: an R package for unsupervised coregistration of mass spectrometry and H&E images ↗](https://doi.org/10.1093/bioinformatics/btae624)**Sai Srikanth Lakkimsetty, Andreas T. Weber, Kylie Ariel Bemis et al.*3 citations*
581. **[MetaHD: a multivariate meta-analysis model for metabolomics data ↗](https://doi.org/10.1093/bioinformatics/btae470)**J. Liyanage, Luke A. Prendergast, Robert G. Staudte et al.*3 citations*
582. **[MolPLA: a molecular pretraining framework for learning cores, R-groups and their linker joints ↗](https://doi.org/10.1093/bioinformatics/btae256)**Mogan Gim, Jueon Park, Soyon Park et al.*3 citations*
583. **[MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions ↗](https://doi.org/10.1093/bioinformatics/btae315)**Rodolphe Loubaton, Nicolas Champagnat, Pierre Vallois et al.*3 citations*
584. **[Optimal phylogenetic reconstruction of insertion and deletion events ↗](https://doi.org/10.1093/bioinformatics/btae254)**Sanjana Tule, Gabriel Foley, Chongting Zhao et al.*3 citations*
585. **[PhenoMultiOmics: an enzymatic reaction inferred multi-omics network visualization web server ↗](https://doi.org/10.1093/bioinformatics/btae623)**Yuying Shi, Botao Xu, Zhe Wang et al.*3 citations*
586. **[Polyphest: fast polyploid phylogeny estimation ↗](https://doi.org/10.1093/bioinformatics/btae390)**Zhi Yan, Zhen Cao, Luay K. Nakhleh*3 citations*
587. **[PredCMB: predicting changes in microbial metabolites based on the gene–metabolite network analysis of shotgun metagenome data ↗](https://doi.org/10.1093/bioinformatics/btaf020)**Jong Dae Ji, Sungwon Jung*3 citations*
588. **[Protein interaction explorer (PIE): a comprehensive platform for navigating protein–protein interactions and ligand binding pockets ↗](https://doi.org/10.1093/bioinformatics/btae414)**Fabien Mareuil, Alexandra Moine-Franel, Anuradha Kar et al.*3 citations*
589. **[QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data ↗](https://doi.org/10.1093/bioinformatics/btae752)**Manci Li, Damani N. Bryant, Sarah Gresh et al.*3 citations*
590. **[Quantifying defective and wild-type viruses from high-throughput RNA sequencing ↗](https://doi.org/10.1093/bioinformatics/btae651)**Juan C. Muñoz-Sánchez, María J. Olmo-Uceda, José Ángel Oteo et al.*3 citations*
591. **[RNA threading with secondary structure and sequence profile ↗](https://doi.org/10.1093/bioinformatics/btae080)**Zongyang Du, Zhenling Peng, Jianyi Yang*3 citations*
592. **[Rapid multiple protein sequence search by parallel and heterogeneous computation ↗](https://doi.org/10.1093/bioinformatics/btae151)**Jiefu Li, Ziyuan Wang, Ziyuan Wang et al.*3 citations*
593. **[Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks ↗](https://doi.org/10.1093/bioinformatics/btae463)**Jiahao Gao, Mark Gerstein*3 citations*
594. **[Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks ↗](https://doi.org/10.1093/bioinformatics/btae435)**Jiating Yu, Jiacheng Leng, Fan Yuan et al.*3 citations*
595. **[SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric ↗](https://doi.org/10.1093/bioinformatics/btae537)**Yue Lyu, Steven Hsesheng Lin, Hao Wu et al.*3 citations*
596. **[SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space ↗](https://doi.org/10.1093/bioinformatics/btae105)**Hamza Biyuzan, M. Masrour, Lucas Grandmougin et al.*3 citations*
597. **[Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach ↗](https://doi.org/10.1093/bioinformatics/btae361)**Yueyu Jiang, Daniel T. McDonald, Daniela S. Perry et al.*3 citations*
598. **[SimReadUntil for benchmarking selective sequencing algorithms on ONT devices ↗](https://doi.org/10.1093/bioinformatics/btae199)**Maximilian Mordig, Gunnar Rätsch, André Kahles*3 citations*
599. **[SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments ↗](https://doi.org/10.1093/bioinformatics/btae117)**Chitrasen Mohanty, Aman Prasad, Lingxin Cheng et al.*3 citations*
600. **[Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network ↗](https://doi.org/10.1093/bioinformatics/btae126)**Jakob Woerner, Vivek Sriram, Yonghyun Nam et al.*3 citations*

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