---
title: "Bioinformatics 2024 — all accepted papers, page 5"
description: "All 788 papers of Bioinformatics 2024 · page 5 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 5 of 8 · the most cited first · [← Bioinformatics 2024](https://md.research.elamur.ai/free/en/venues/bioinformatics/2024/)

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401. **[Automated, image-based quantification of peroxisome characteristics with perox-per-cell ↗](https://doi.org/10.1093/bioinformatics/btae442)**Maxwell Lewis Neal, Nandini Shukla, Fred David Mast et al.*6 citations*
402. **[Best practices to evaluate the impact of biomedical research software—metric collection beyond citations ↗](https://doi.org/10.1093/bioinformatics/btae469)**Awan Afiaz, Andrei A. Ivanov, John Chamberlin et al.*6 citations*
403. **[BindingSiteDTI: differential-scale binding site modelling for drug–target interaction prediction ↗](https://doi.org/10.1093/bioinformatics/btae308)**Feng Ming Pan, Chong Yin, Siqi Liu et al.*6 citations*
404. **[Cleavage-stage embryo segmentation using SAM-based dual branch pipeline: development and evaluation with the CleavageEmbryo dataset ↗](https://doi.org/10.1093/bioinformatics/btae617)**Chensheng Zhang, Xintong Shi, Xinyue Yin et al.*6 citations*
405. **[Coding genomes with gapped pattern graph convolutional network ↗](https://doi.org/10.1093/bioinformatics/btae188)**Ruo Han Wang, Yen Kaow Ng, Xianglilan Zhang et al.*6 citations*
406. **[Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework ↗](https://doi.org/10.1093/bioinformatics/btae022)**Gabriel Loyer, Vladimir Reinharz*6 citations*
407. **[CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics ↗](https://doi.org/10.1093/bioinformatics/btae284)**Semih Kurt, Mandi Chen, Hosein Toosi et al.*6 citations*
408. **[DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein–protein complexes upon mutation ↗](https://doi.org/10.1093/bioinformatics/btae309)**Rahul Nikam, Sherlyn Jemimah, M. Michael Gromiha*6 citations*
409. **[DualNetGO: a dual network model for protein function prediction via effective feature selection ↗](https://doi.org/10.1093/bioinformatics/btae437)**Zhuoyang Chen, Qiong Luo*6 citations*
410. **[EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery ↗](https://doi.org/10.1093/bioinformatics/btae178)**Johanna Elena Schmitz, Nihit Aggarwal, Lukas Laufer et al.*6 citations*
411. **[Epigenomics coverage data extraction and aggregation in R with tidyCoverage ↗](https://doi.org/10.1093/bioinformatics/btae487)**Jacques Serizay, Romain Koszul*6 citations*
412. **[Expanding the coverage of spatial proteomics: a machine learning approach ↗](https://doi.org/10.1093/bioinformatics/btae062)**Huangqingbo Sun, Jiayi Li, Robert F. Murphy*6 citations*
413. **[Feature selection by replicate reproducibility and non-redundancy ↗](https://doi.org/10.1093/bioinformatics/btae548)**Tümay Capraz, Wolfgang K. Huber*6 citations*
414. **[Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape ↗](https://doi.org/10.1093/bioinformatics/btae317)**Andreas Wagner*6 citations*
415. **[HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen–Deuterium Exchange Mass-Spectrometry datasets of different protein states ↗](https://doi.org/10.1093/bioinformatics/btae479)**Maria K. Janowska, Katherine H. Reiter, Pearl Magala et al.*6 citations*
416. **[Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy’s outcome for HIV-1 ↗](https://doi.org/10.1093/bioinformatics/btae327)**Giulia Di Teodoro, Martin Pirkl, Francesca Incardona et al.*6 citations*
417. **[Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks ↗](https://doi.org/10.1093/bioinformatics/btae705)**Chao Gao, Joshua D. Welch*6 citations*
418. **[Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper ↗](https://doi.org/10.1093/bioinformatics/btae276)**Charlotte Crauwels, Sophie-Luise Heidig, Adrián Díaz et al.*6 citations*
419. **[LmRaC: a functionally extensible tool for LLM interrogation of user experimental results ↗](https://doi.org/10.1093/bioinformatics/btae679)**Douglas B Craig, Sorin Drăghici*6 citations*
420. **[MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants ↗](https://doi.org/10.1093/bioinformatics/btae578)**Weijia Jin, Yi Xia, Javlon Nizomov et al.*6 citations*
421. **[MR Corge: sensitivity analysis of Mendelian randomization based on the core gene hypothesis for polygenic exposures ↗](https://doi.org/10.1093/bioinformatics/btae666)**Wenmin Zhang, Chen‐Yang Su, Satoshi Yoshiji et al.*6 citations*
422. **[MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation ↗](https://doi.org/10.1093/bioinformatics/btae760)**Farid Chaabane, Trestan Pillonel, Claire Bertelli*6 citations*
423. **[Modeling metastatic progression from cross-sectional cancer genomics data ↗](https://doi.org/10.1093/bioinformatics/btae250)**Kevin Rupp, Andreas Lösch, Y. Linda Hu et al.*6 citations*
424. **[MolDy: molecular dynamics simulation made easy ↗](https://doi.org/10.1093/bioinformatics/btae313)**Mohd Imran Khan, Mohd Imran Khan, Sheetal Pathania et al.*6 citations*
425. **[Nanopore decoding with speed and versatility for data storage ↗](https://doi.org/10.1093/bioinformatics/btaf006)**Kevin Volkel, Paul W. Hook, Albert J. Keung et al.*6 citations*
426. **[PERSEUS: an interactive and intuitive web-based tool for pedigree visualization ↗](https://doi.org/10.1093/bioinformatics/btae060)**Nicole Pradas, Federico Jurado-Ruiz, Carles Onielfa et al.*6 citations*
427. **[Pathway analysis through mutual information ↗](https://doi.org/10.1093/bioinformatics/btad776)**Gustavo S. Jeuken, Lukas Käll*6 citations*
428. **[Prioritization of oligogenic variant combinations in whole exomes ↗](https://doi.org/10.1093/bioinformatics/btae184)**Barbara Gravel, Alexandre Renaux, Sofia Papadimitriou et al.*6 citations*
429. **[SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings ↗](https://doi.org/10.1093/bioinformatics/btae328)**Aysun Urhan, Bianca-Maria Cosma, Ashlee M. Earl et al.*6 citations*
430. **[SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts ↗](https://doi.org/10.1093/bioinformatics/btae344)**Nianqiao Ju, Jiawei Liu, Qixin He*6 citations*
431. **[Scalable integration of multiomic single-cell data using generative adversarial networks ↗](https://doi.org/10.1093/bioinformatics/btae300)**Valentina Giansanti, Francesca Giannese, Oronza Antonietta Botrugno et al.*6 citations*
432. **[Structure-inclusive similarity based directed GNN: a method that can control information flow to predict drug–target binding affinity ↗](https://doi.org/10.1093/bioinformatics/btae563)**Jipeng Huang, Chang Yin Sun, Minglei Li et al.*6 citations*
433. **[Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network ↗](https://doi.org/10.1093/bioinformatics/btae262)**Xiaocheng Zeng, Wei Zheng, Qixiu Du et al.*6 citations*
434. **[Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison ↗](https://doi.org/10.1093/bioinformatics/btae064)**Zhengyang Guo, Yang Wang, Guangshuo Ou*6 citations*
435. **[Virtual tissue expression analysis ↗](https://doi.org/10.1093/bioinformatics/btae709)**Jakob Simeth, Paul Hüttl, Marian Schön et al.*6 citations*
436. **[WatFinder: a ProDy tool for protein–water interactions ↗](https://doi.org/10.1093/bioinformatics/btae516)**James Krieger, Frane Doljanin, Anthony T. Bogetti et al.*6 citations*
437. **[findGSEP: estimating genome size of polyploid species using k -mer frequencies ↗](https://doi.org/10.1093/bioinformatics/btae647)**Laiyi Fu, Yanxin Xie, Shunkang Ling et al.*6 citations*
438. **[k -nonical space: sketching with reverse complements ↗](https://doi.org/10.1093/bioinformatics/btae629)**Guillaume Marçais, C.S. Elder, Carl Kingsford*6 citations*
439. **[learnMSA2: deep protein multiple alignments with large language and hidden Markov models ↗](https://doi.org/10.1093/bioinformatics/btae381)**Felix Becker, Mario Stanke*6 citations*
440. **[q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota ↗](https://doi.org/10.1093/bioinformatics/btae455)**Francesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo et al.*6 citations*
441. **[vcfpp: a C++ API for rapid processing of the variant call format ↗](https://doi.org/10.1093/bioinformatics/btae049)**Zilong Li*6 citations*
442. **[A simple refined DNA minimizer operator enables 2-fold faster computation ↗](https://doi.org/10.1093/bioinformatics/btae045)**Chenxu Pan, Knut Reinert*5 citations*
443. **[Accurate segmentation of intracellular organelle networks using low-level features and topological self-similarity ↗](https://doi.org/10.1093/bioinformatics/btae559)**Jiaxing Huang, Yaoru Luo, Yuanhao Guo et al.*5 citations*
444. **[Adaptive space search-based molecular evolution optimization algorithm ↗](https://doi.org/10.1093/bioinformatics/btae446)**Fei Wang, Xianglong Cheng, Xin Tao Xia et al.*5 citations*
445. **[AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software ↗](https://doi.org/10.1093/bioinformatics/btae616)**Alessandro Lisi, Michael C. Campbell*5 citations*
446. **[BEATRICE: Bayesian fine-mapping from summary data using deep variational inference ↗](https://doi.org/10.1093/bioinformatics/btae590)**Sayan Ghosal, Michael C. Schatz, Archana Venkataraman*5 citations*
447. **[Bayesian modelling of time series data (BayModTS)—a FAIR workflow to process sparse and highly variable data ↗](https://doi.org/10.1093/bioinformatics/btae312)**Sebastian Höpfl, Mohamed Albadry, Uta Dahmen et al.*5 citations*
448. **[BioPred: an R package for biomarkers analysis in precision medicine ↗](https://doi.org/10.1093/bioinformatics/btae592)**Zihuan Liu, Yan Sun, Xin Huang*5 citations*
449. **[CIBRA identifies genomic alterations with a system-wide impact on tumor biology ↗](https://doi.org/10.1093/bioinformatics/btae384)**Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer et al.*5 citations*
450. **[CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences ↗](https://doi.org/10.1093/bioinformatics/btae279)**Nikolaos N. Louros, Frédéric Rousseau, Joost W. H. Schymkowitz*5 citations*
451. **[CParty: hierarchically constrained partition function of RNA pseudoknots ↗](https://doi.org/10.1093/bioinformatics/btae748)**Mateo Gray, Luke Trinity, Ulrike Stege et al.*5 citations*
452. **[CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data ↗](https://doi.org/10.1093/bioinformatics/btae063)**Xiao Wang, Ziyi Chai, Shaohua Li et al.*5 citations*
453. **[Chemical reaction enhanced graph learning for molecule representation ↗](https://doi.org/10.1093/bioinformatics/btae558)**Anchen Li, Elena Casiraghi, Juho Rousu*5 citations*
454. **[Controlled noise: evidence of epigenetic regulation of single-cell expression variability ↗](https://doi.org/10.1093/bioinformatics/btae457)**Yan Zhong, Siwei Cui, Yongjian Yang et al.*5 citations*
455. **[DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance ↗](https://doi.org/10.1093/bioinformatics/btae427)**Michael Payne, Dalong Hu, Qinning Wang et al.*5 citations*
456. **[Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition ↗](https://doi.org/10.1093/bioinformatics/btae245)**Charles Broadbent, Tianci Song, Rui Kuang*5 citations*
457. **[DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data ↗](https://doi.org/10.1093/bioinformatics/btae434)**Guangzhi Xiong, Nathan J. LeRoy, Stefan Bekiranov et al.*5 citations*
458. **[DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity ↗](https://doi.org/10.1093/bioinformatics/btae306)**Hang Wei, Lin Gao, Shuai Wu et al.*5 citations*
459. **[D’or: deep orienter of protein–protein interaction networks ↗](https://doi.org/10.1093/bioinformatics/btae355)**Daniel Pirak, Roded Sharan*5 citations*
460. **[Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions ↗](https://doi.org/10.1093/bioinformatics/btae235)**Daniel E. Platt, Aritra Bose, Kahn Rhrissorrakrai et al.*5 citations*
461. **[ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities ↗](https://doi.org/10.1093/bioinformatics/btae507)**Dongjia Li, Zhuochao Min, Jia Qi Guo et al.*5 citations*
462. **[Fast and exact gap-affine partial order alignment with POASTA ↗](https://doi.org/10.1093/bioinformatics/btae757)**Lucas R. van Dijk, Abigail L. Manson, Ashlee M. Earl et al.*5 citations*
463. **[Funmap: integrating high-dimensional functional annotations to improve fine-mapping ↗](https://doi.org/10.1093/bioinformatics/btaf017)**Yuekai Li, Jiashun Xiao, Jingsi Ming et al.*5 citations*
464. **[Heterogeneous entity representation for medicinal synergy prediction ↗](https://doi.org/10.1093/bioinformatics/btae750)**Jiawei Wu, Jun Wen, Mingyuan Yan et al.*5 citations*
465. **[High-dimensional quantile mediation analysis with application to a birth cohort study of mother–newborn pairs ↗](https://doi.org/10.1093/bioinformatics/btae055)**Haixiang Zhang, Xiumei Hong, Yinan Zheng et al.*5 citations*
466. **[Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation ↗](https://doi.org/10.1093/bioinformatics/btae246)**Jiyu Chen, Benjamin Goudey, Nicholas Geard et al.*5 citations*
467. **[Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae231)**Palash Sashittal, Viola Chen, Amey P. Pasarkar et al.*5 citations*
468. **[Label-guided seed-chain-extend alignment on annotated De Bruijn graphs ↗](https://doi.org/10.1093/bioinformatics/btae226)**Harun Mustafa, Mikhail Karasikov, Nika Mansouri Ghiasi et al.*5 citations*
469. **[MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification ↗](https://doi.org/10.1093/bioinformatics/btae601)**Ruipeng Lu, Tim Dumonceaux, Muhammad Anzar et al.*5 citations*
470. **[MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD ↗](https://doi.org/10.1093/bioinformatics/btae726)**Tim Cadman, Mariska K. Slofstra, Marije A. van der Geest et al.*5 citations*
471. **[MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins ↗](https://doi.org/10.1093/bioinformatics/btae741)**Nicholas E. Newell*5 citations*
472. **[Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell ↗](https://doi.org/10.1093/bioinformatics/btae662)**Remco L. van den Broek, Xabier Bello, Rebecca V Küpper et al.*5 citations*
473. **[MetaboReport: from metabolomics data analysis to comprehensive reporting ↗](https://doi.org/10.1093/bioinformatics/btae373)**Yonghui Dong, Sergey Malitsky*5 citations*
474. **[NIEND: neuronal image enhancement through noise disentanglement ↗](https://doi.org/10.1093/bioinformatics/btae158)**Zuo-Han Zhao, Lijuan Liu, Yufeng Liu*5 citations*
475. **[NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations ↗](https://doi.org/10.1093/bioinformatics/btae585)**Wenqian Yu, Hongwu Yu, Jingjing Zhao et al.*5 citations*
476. **[PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks ↗](https://doi.org/10.1093/bioinformatics/btae389)**Tobias Pietz, Sukrit Gupta, Christoph N. Schlaffner et al.*5 citations*
477. **[Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications ↗](https://doi.org/10.1093/bioinformatics/btae526)**Steven B. Cannon, Hyun Oh Lee, Nathan T. Weeks et al.*5 citations*
478. **[PathwayNexus: a tool for interactive metabolic data analysis ↗](https://doi.org/10.1093/bioinformatics/btae310)**Philipp Eberhard, Martin Kern, Michael Aichem et al.*5 citations*
479. **[PhysioFit: a software to quantify cell growth parameters and extracellular fluxes ↗](https://doi.org/10.1093/bioinformatics/btae488)**Loïc Le Grégam, Yann Guitton, Floriant Bellvert et al.*5 citations*
480. **[PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature ↗](https://doi.org/10.1093/bioinformatics/btae672)**Shubo Tian, Qingyu Chen, Donald C. Comeau et al.*5 citations*
481. **[QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images ↗](https://doi.org/10.1093/bioinformatics/btae026)**Carles Pons, Caroline Mauvezin*5 citations*
482. **[RecGraph: recombination-aware alignment of sequences to variation graphs ↗](https://doi.org/10.1093/bioinformatics/btae292)**Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella et al.*5 citations*
483. **[SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network ↗](https://doi.org/10.1093/bioinformatics/btae433)**Yongjie Wang, Fengfan Zhou, Jinting Guan*5 citations*
484. **[SST-editing: in silico spatial transcriptomic editing at single-cell resolution ↗](https://doi.org/10.1093/bioinformatics/btae077)**Jiqing Wu, Viktor Hendrik Koelzer*5 citations*
485. **[TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator ↗](https://doi.org/10.1093/bioinformatics/btae051)**Fatih Karaoğlanoğlu, Baraa Orabi, Ryan Kendrick Flannigan et al.*5 citations*
486. **[TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference ↗](https://doi.org/10.1093/bioinformatics/btae502)**Anqi Wang, Peixin Tian, Yan Zhang*5 citations*
487. **[Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students ↗](https://doi.org/10.1093/bioinformatics/btae208)**Pavlin G. Poličar, Martin Špendl, Tomaž Curk et al.*5 citations*
488. **[ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment ↗](https://doi.org/10.1093/bioinformatics/btae093)**Zuher Jahshan, Leonid Yavits*5 citations*
489. **[Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments ↗](https://doi.org/10.1093/bioinformatics/btae608)**Benjamin Strope, Katherine E. Pendleton, William Bowie et al.*5 citations*
490. **[pipesnake : generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci ↗](https://doi.org/10.1093/bioinformatics/btae195)**Ian G. Brennan, Sonal Singhal, Ziad Al Bkhetan*5 citations*
491. **[pycofitness—Evaluating the fitness landscape of RNA and protein sequences ↗](https://doi.org/10.1093/bioinformatics/btae074)**Fabrizio Pucci, Mehari B. Zerihun, Marianne J. Rooman et al.*5 citations*
492. **[scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression ↗](https://doi.org/10.1093/bioinformatics/btae223)**Ghulam Murtaza, Byron Butaney, Justin Wagner et al.*5 citations*
493. **[A multi-modality and multi-granularity collaborative learning framework for identifying spatial domains and spatially variable genes ↗](https://doi.org/10.1093/bioinformatics/btae607)**Xiao Liang, Pei Liu, Li Xue et al.*4 citations*
494. **[A near-tight lower bound on the density of forward sampling schemes ↗](https://doi.org/10.1093/bioinformatics/btae736)**Bryce L. Kille, Ragnar Groot Koerkamp, Drake McAdams et al.*4 citations*
495. **[Accurate assembly of multiple RNA-seq samples with Aletsch ↗](https://doi.org/10.1093/bioinformatics/btae215)**Qian Shi, Qimin Zhang, Mingfu Shao*4 citations*
496. **[BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images ↗](https://doi.org/10.1093/bioinformatics/btae052)**Xinyuan Huang, Xiujuan Gao, Ling Fu*4 citations*
497. **[BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model ↗](https://doi.org/10.1093/bioinformatics/btae461)**Hanyu Luo, Li Jie Tang, Min Zeng et al.*4 citations*
498. **[CLAUDIO: automated structural analysis of cross-linking data ↗](https://doi.org/10.1093/bioinformatics/btae146)**Alexander Röhl, Eugen Netz, Oliver Kohlbacher et al.*4 citations*
499. **[Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data ↗](https://doi.org/10.1093/bioinformatics/btae417)**Yichi Zhang, Chenghui Hu, Xiaohui Wu et al.*4 citations*
500. **[Chapter 4 Tools used in sequence alignment ↗](https://doi.org/10.1515/9783111568584-004)**Varruchi Sharma, Imran Sheikh, Vikas Kushwaha et al.*4 citations*

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