---
title: "Bioinformatics 2024 — all accepted papers, page 7"
description: "All 788 papers of Bioinformatics 2024 · page 7 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 7 of 8 · the most cited first · [← Bioinformatics 2024](https://md.research.elamur.ai/free/en/venues/bioinformatics/2024/)

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601. **[VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation ↗](https://doi.org/10.1093/bioinformatics/btae575)**Yilin Zhu, Guowei Chen, Yanni Sun*3 citations*
602. **[bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties ↗](https://doi.org/10.1093/bioinformatics/btae543)**Jose Gavaldá-García, Adrián Díaz, Wim Vranken*3 citations*
603. **[fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data ↗](https://doi.org/10.1093/bioinformatics/btae314)**Shen Zhang, Huaying Fang, Tao Hu*3 citations*
604. **[nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis ↗](https://doi.org/10.1093/bioinformatics/btae019)**Alexander Peltzer, Christopher Mohr, Kai Bernd Stadermann et al.*3 citations*
605. **[nipalsMCIA : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares ↗](https://doi.org/10.1093/bioinformatics/btaf015)**Max Mattessich, Joaquin Reyna, Edel Aron et al.*3 citations*
606. **[scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model ↗](https://doi.org/10.1093/bioinformatics/btae198)**Sijing An, Jinhui Shi, Runyan Liu et al.*3 citations*
607. **[shinyseg: a web application for flexible cosegregation and sensitivity analysis ↗](https://doi.org/10.1093/bioinformatics/btae201)**Christian Carrizosa, Dag Erik Undlien, Magnus Dehli Vigeland*3 citations*
608. **[skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements ↗](https://doi.org/10.1093/bioinformatics/btae398)**Xiaolei Brian Zhang, Grace Oualline, Jim Shaw et al.*3 citations*
609. **[vSPACE: exploring virtual spatial representation of articular chondrocytes at the single-cell level ↗](https://doi.org/10.1093/bioinformatics/btae568)**Chenyu Zhang, Honglin Wang, Yeonsoo Chung et al.*3 citations*
610. **[A compressive seeding algorithm in conjunction with reordering-based compression ↗](https://doi.org/10.1093/bioinformatics/btae100)**Fahu Ji, Qian Zhou, Jue Ruan et al.*2 citations*
611. **[A deep learning method to predict bacterial ADP-ribosyltransferase toxins ↗](https://doi.org/10.1093/bioinformatics/btae378)**Dandan Zheng, Siyu Zhou, Lihong Chen et al.*2 citations*
612. **[A fast machine learning dataloader for epigenetic tracks from BigWig files ↗](https://doi.org/10.1093/bioinformatics/btad767)**Joren Sebastian Retel, Andreas Poehlmann, Joshua Chiou et al.*2 citations*
613. **[A self-training interpretable cell type annotation framework using specific marker gene ↗](https://doi.org/10.1093/bioinformatics/btae569)**Hegang Chen, Yuyin Lu, Yanghui Rao*2 citations*
614. **[A semi-supervised fracture-attention model for segmenting tubular objects with improved topological connectivity ↗](https://doi.org/10.1093/bioinformatics/btaf013)**Yanfeng Zhou, Liqun Zhong, Zichen Wang et al.*2 citations*
615. **[Analysis of metadynamics simulations by metadynminer.py ↗](https://doi.org/10.1093/bioinformatics/btae614)**Jan Beránek, Aleš Křenek, Vojtěch Spiwok*2 citations*
616. **[BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data ↗](https://doi.org/10.1093/bioinformatics/btae404)**Wei Tian, Wubin Ding, Jiawei Shen et al.*2 citations*
617. **[BTR: a bioinformatics tool recommendation system ↗](https://doi.org/10.1093/bioinformatics/btae275)**Ryan J. Green, Xufeng Qu, Jinze Liu et al.*2 citations*
618. **[BatchFLEX: feature-level equalization of X-batch ↗](https://doi.org/10.1093/bioinformatics/btae587)**Joshua Davis, Alyssa Obermayer, Alex C. Soupir et al.*2 citations*
619. **[Bayesian gene set benchmark dose estimation for “omic” responses ↗](https://doi.org/10.1093/bioinformatics/btaf008)**Daniel Zilber, Kyle P. Messier, John S. House et al.*2 citations*
620. **[BenchStab: a tool for automated querying of web-based stability predictors ↗](https://doi.org/10.1093/bioinformatics/btae553)**Jan Velecký, Matej Berezný, Miloš Musil et al.*2 citations*
621. **[Biomarker identification by interpretable maximum mean discrepancy ↗](https://doi.org/10.1093/bioinformatics/btae251)**Michael F. Adamer, Sarah C. Brüningk, Dexiong Chen et al.*2 citations*
622. **[CASCC: a co-expression-assisted single-cell RNA-seq data clustering method ↗](https://doi.org/10.1093/bioinformatics/btae283)**Lingyi Cai, Dimitris Anastassiou*2 citations*
623. **[CVR-BBI: an open-source VR platform for multi-user collaborative brain to brain interfaces ↗](https://doi.org/10.1093/bioinformatics/btae676)**Di Liu, Yina Wei*2 citations*
624. **[CatReNet: interactive analysis of (auto-) catalytic reaction networks ↗](https://doi.org/10.1093/bioinformatics/btae515)**Daniel H. Huson, Joana C. Xavier, Mike Steel*2 citations*
625. **[Causal relationships between diseases mined from the literature improve the use of polygenic risk scores ↗](https://doi.org/10.1093/bioinformatics/btae639)**Sumyyah Toonsi, Iris Ivy Gauran, Hernando Ombao et al.*2 citations*
626. **[Chapter 6 Computer-aided drug design and drug discovery ↗](https://doi.org/10.1515/9783111568584-006)**Meenakshi Rajpoot, Varruchi Sharma, Shagun Gupta et al.*2 citations*
627. **[Chapter 9 Basic structure of proteins: current paradigms, trends, and perspective ↗](https://doi.org/10.1515/9783111568584-009)**Sheetal Dagar, Anil Panwar, Varruchi Sharma et al.*2 citations*
628. **[Collapsible tree: interactive web app to present collapsible hierarchies ↗](https://doi.org/10.1093/bioinformatics/btae645)**Yuan Gao, Rob Patro, Peng Jiang*2 citations*
629. **[CompariPSSM: a PSSM–PSSM comparison tool for motif-binding determinant analysis ↗](https://doi.org/10.1093/bioinformatics/btae644)**Ifigenia Tsitsa, Izabella Krystkowiak, Norman E. Davey*2 citations*
630. **[DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence ↗](https://doi.org/10.1093/bioinformatics/btae740)**Jesse Durham, Jing Zhang, Richard Dustin Schaeffer et al.*2 citations*
631. **[Damsel: analysis and visualisation of DamID sequencing in R ↗](https://doi.org/10.1093/bioinformatics/btae695)**Caitlin G Page, Andrew Lonsdale, Katrina A. Mitchell et al.*2 citations*
632. **[Designing efficient randstrobes for sequence similarity analyses ↗](https://doi.org/10.1093/bioinformatics/btae187)**Moein Karami, Aryan Soltani Mohammadi, Marcel Martin et al.*2 citations*
633. **[DrugRepPT: a deep pretraining and fine-tuning framework for drug repositioning based on drug’s expression perturbation and treatment effectiveness ↗](https://doi.org/10.1093/bioinformatics/btae692)**Shuyue Fan, Kuo Yang, Kezhi Lu et al.*2 citations*
634. **[Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data ↗](https://doi.org/10.1093/bioinformatics/btae210)**Domagoj Dorešić, Stephan Grein, Jan Hasenauer*2 citations*
635. **[ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining ↗](https://doi.org/10.1093/bioinformatics/btad779)**Jon-Michael T. Beasley, Daniel Korn, Nyssa Tucker et al.*2 citations*
636. **[FEHAT: efficient, large scale and automated heartbeat detection in Medaka fish embryos ↗](https://doi.org/10.1093/bioinformatics/btae664)**Marcio Soares Ferreira, Sebastian Stricker, Tomas W. Fitzgerald et al.*2 citations*
637. **[Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra ↗](https://doi.org/10.1093/bioinformatics/btae149)**Zhaohui Zhan, Lusheng Wang*2 citations*
638. **[GENTANGLE: integrated computational design of gene entanglements ↗](https://doi.org/10.1093/bioinformatics/btae380)**Jose Manuel Martí, Chloe Hsu, Charlotte Rochereau et al.*2 citations*
639. **[Galaxy Helm chart: a standardized method for deploying production Galaxy servers ↗](https://doi.org/10.1093/bioinformatics/btae486)**Nuwan Goonasekera, Alexandru Mahmoud, Keith Suderman et al.*2 citations*
640. **[GateMeClass: Gate Mining and Classification of cytometry data ↗](https://doi.org/10.1093/bioinformatics/btae322)**Simone Caligola, Luca Giacobazzi, Stefania Canè et al.*2 citations*
641. **[GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks ↗](https://doi.org/10.1093/bioinformatics/btae007)**Felix M. Weidner, Nensi Ikonomi, Silke D Werle et al.*2 citations*
642. **[Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure ↗](https://doi.org/10.1093/bioinformatics/btae640)**Ruiting Xu, Dan Li, Wen Yang et al.*2 citations*
643. **[LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies ↗](https://doi.org/10.1093/bioinformatics/btae101)**Melpomeni Kasapi, Kexin Xu, Timothy M. D. Ebbels et al.*2 citations*
644. **[Learning locality-sensitive bucketing functions ↗](https://doi.org/10.1093/bioinformatics/btae228)**Xin Yuan, Ke Chen, Xiang Li et al.*2 citations*
645. **[MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification ↗](https://doi.org/10.1093/bioinformatics/btad757)**Huang Xu, Tian Wang, Yuqi Miao et al.*2 citations*
646. **[Median and small parsimony problems on RNA trees ↗](https://doi.org/10.1093/bioinformatics/btae229)**Bertrand Marchand, Yoann Anselmetti, Manuel Lafond et al.*2 citations*
647. **[Melodia: a Python library for protein structure analysis ↗](https://doi.org/10.1093/bioinformatics/btae468)**Rinaldo W. Montalvão, William R. Pitt, Vitor Bernardes Pinheiro et al.*2 citations*
648. **[Multi-modal contrastive learning of subcellular organization using DICE ↗](https://doi.org/10.1093/bioinformatics/btae387)**Rami Nasser, Leah V. Schaffer, Trey Ideker et al.*2 citations*
649. **[Multi-task deep latent spaces for cancer survival and drug sensitivity prediction ↗](https://doi.org/10.1093/bioinformatics/btae388)**Teemu Rintala, Francesco Napolitano, Vittorio Fortino*2 citations*
650. **[Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples ↗](https://doi.org/10.1093/bioinformatics/btae013)**Zikun Yang, Xin Li, Lele Sheng et al.*2 citations*
651. **[Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification ↗](https://doi.org/10.1093/bioinformatics/btae108)**Kristofer Sandås, Jacob Lewerentz, Edvin Karlsson et al.*2 citations*
652. **[OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs ↗](https://doi.org/10.1093/bioinformatics/btae365)**Yueming Yin, Haifeng Hu, Jitao Yang et al.*2 citations*
653. **[Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes ↗](https://doi.org/10.1093/bioinformatics/btae761)**Andre C. Faubert, Shang Wang*2 citations*
654. **[PCBS: an R package for fast and accurate analysis of bisulfite sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae593)**Kathryn Lande, April E. Williams*2 citations*
655. **[PRONA: an R-package for Patient Reported Outcomes Network Analysis ↗](https://doi.org/10.1093/bioinformatics/btae671)**Brandon Hwa-Lin Bergsneider, Orieta Celiku*2 citations*
656. **[Peptide set test: a peptide-centric strategy to infer differentially expressed proteins ↗](https://doi.org/10.1093/bioinformatics/btae270)**Junmin Wang, Steven J. Novick*2 citations*
657. **[Peptriever: a Bi-Encoder approach for large-scale protein–peptide binding search ↗](https://doi.org/10.1093/bioinformatics/btae303)**Roni Gurvich, Gal Markel, Ziaurrehman Tanoli et al.*2 citations*
658. **[Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data ↗](https://doi.org/10.1093/bioinformatics/btae712)**Jun Zhang, Fan Nie, Feng Luo et al.*2 citations*
659. **[PipeVal: light-weight extensible tool for file validation ↗](https://doi.org/10.1093/bioinformatics/btae079)**Yash Patel, Arpi Beshlikyan, Madison Jordan et al.*2 citations*
660. **[Pod5Viewer: a GUI for inspecting raw nanopore sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae665)**Vincent Dietrich, Nicolò Alagna, Mark Helm et al.*2 citations*
661. **[PredGCN: a Pruning-enabled Gene-Cell Net for automatic cell annotation of single cell transcriptome data ↗](https://doi.org/10.1093/bioinformatics/btae421)**Qi Qi, Yunhe Wang, Yujian Huang et al.*2 citations*
662. **[Proteoform identification and quantification based on alignment graphs ↗](https://doi.org/10.1093/bioinformatics/btaf007)**Zhaohui Zhan, Lusheng Wang*2 citations*
663. **[Ragas: integration and enhanced visualization for single cell subcluster analysis ↗](https://doi.org/10.1093/bioinformatics/btae366)**Uthra Balaji, Juan F. Rodríguez-Alcázar, Preetha Balasubramanian et al.*2 citations*
664. **[Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae336)**Siang Chen, Hao Wang, Dongdong Zhang et al.*2 citations*
665. **[Rnalib: a Python library for custom transcriptomics analyses ↗](https://doi.org/10.1093/bioinformatics/btae751)**Niko P. Popitsch, Stefan Ludwig Ameres*2 citations*
666. **[SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data ↗](https://doi.org/10.1093/bioinformatics/btae454)**Liting Zhang, Xin Zhou, Xian Mallory*2 citations*
667. **[STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication ↗](https://doi.org/10.1093/bioinformatics/btae713)**Jared M. Andrews, Michael W. Lloyd, Steven B. Neuhauser et al.*2 citations*
668. **[Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels ↗](https://doi.org/10.1093/bioinformatics/btae727)**Danqing Yin, Yue Cao, Junyi Chen et al.*2 citations*
669. **[Semblans: automated assembly and processing of RNA-seq data ↗](https://doi.org/10.1093/bioinformatics/btaf003)**Miles D Woodcock-Girard, Eric C Bretz, Holly M Robertson et al.*2 citations*
670. **[Signature Search Polestar: a comprehensive drug repurposing method evaluation assistant for customized oncogenic signature ↗](https://doi.org/10.1093/bioinformatics/btae536)**Jinbo Zhang, Shunling Yuan, Wen Cao et al.*2 citations*
671. **[Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix ↗](https://doi.org/10.1093/bioinformatics/btae701)**Semih Kurt, Alexandre Bouchard‐Côté, Jens Lagergren*2 citations*
672. **[SuperSpot: coarse graining spatial transcriptomics data into metaspots ↗](https://doi.org/10.1093/bioinformatics/btae734)**Matei Teleman, Aurélie AG Gabriel, Léonard Hérault et al.*2 citations*
673. **[The IDSM mass spectrometry extension: searching mass spectra using SPARQL ↗](https://doi.org/10.1093/bioinformatics/btae174)**Jakub Galgonek, Jiřı́ Vondrášek*2 citations*
674. **[The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population ↗](https://doi.org/10.1093/bioinformatics/btae036)**Hagai Levi, Ran Elkon, Ron Shamir A*2 citations*
675. **[VarNMF: non-negative probabilistic factorization with source variation ↗](https://doi.org/10.1093/bioinformatics/btae758)**E. Fallik, Nir Friedman*2 citations*
676. **[ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface ↗](https://doi.org/10.1093/bioinformatics/btae177)**Nicolas Ruffini, Saleh Altahini, Stephan Weißbach et al.*2 citations*
677. **[ViralPrimer: a web server to monitor viral nucleic acid amplification tests’ primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox ↗](https://doi.org/10.1093/bioinformatics/btae657)**Norbert Deutsch, Zsuzsanna Dosztányi, István Csabai et al.*2 citations*
678. **[bnglViz: online visualization of rule-based models ↗](https://doi.org/10.1093/bioinformatics/btae351)**Noah Liguori-Bills, Michael L. Blinov*2 citations*
679. **[metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia ↗](https://doi.org/10.1093/bioinformatics/btae294)**Zulema Rodriguez-Hernandez, Mathias Gorski, María Téllez-Plaza et al.*2 citations*
680. **[scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data ↗](https://doi.org/10.1093/bioinformatics/btae008)**Chih–Yuan Hsu, Chih‐Han Chang, Qi Liu et al.*2 citations*
681. **[scMaSigPro: differential expression analysis along single-cell trajectories ↗](https://doi.org/10.1093/bioinformatics/btae443)**Priyansh Srivastava, Marta Benegas Coll, Stefan Götz et al.*2 citations*
682. **[shinyExprPortal: a configurable ‘shiny’ portal for sharing analysis of molecular expression data ↗](https://doi.org/10.1093/bioinformatics/btae172)**Rafael Henkin, Katriona Goldmann, Myles Lewis et al.*2 citations*
683. **[vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data ↗](https://doi.org/10.1093/bioinformatics/btae099)**Xingyu Bi, Wenbin Ye, Xin Cheng et al.*2 citations*
684. **[A distribution-free and analytic method for power and sample size calculation in single-cell differential expression ↗](https://doi.org/10.1093/bioinformatics/btae540)**Chih–Yuan Hsu, Qi Liu, Yu Shyr*1 citation*
685. **[APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data ↗](https://doi.org/10.1093/bioinformatics/btae689)**Bruno Sousa, Maria João Bessa, Filipa Lopes de Mendonça et al.*1 citation*
686. **[Afpdb: an efficient structure manipulation package for AI protein design ↗](https://doi.org/10.1093/bioinformatics/btae654)**Yingyao Zhou, Jiayi Wu Cox, Bin Zhou et al.*1 citation*
687. **[An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics ↗](https://doi.org/10.1093/bioinformatics/btae233)**Yisu Peng, Shantanu Jain, Predrag Radivojac A*1 citation*
688. **[CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm ↗](https://doi.org/10.1093/bioinformatics/btae345)**Teng-Yu Lin, Szu-Chi Chung*1 citation*
689. **[CLigOpt: controllable ligand design through target-specific optimization ↗](https://doi.org/10.1093/bioinformatics/btae396)**Yutong Li, Pedro Avelar, Xinyue Chen et al.*1 citation*
690. **[Chapter 8 Phylogenetic analysis ↗](https://doi.org/10.1515/9783111568584-008)**Vikas Kumar, Nitin Sharma*1 citation*
691. **[DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion ↗](https://doi.org/10.1093/bioinformatics/btae048)**Momoko Hamano, Toru Nakamura, Ryoku Ito et al.*1 citation*
692. **[Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis ↗](https://doi.org/10.1093/bioinformatics/btae626)**Zelin Li, Dongying Xie, Yiming Ma et al.*1 citation*
693. **[Detecting gene–environment interactions from multiple continuous traits ↗](https://doi.org/10.1093/bioinformatics/btae419)**Wan‐Yu Lin*1 citation*
694. **[Detection and quantification of introgression using Bayesian inference based on conjugate priors ↗](https://doi.org/10.1093/bioinformatics/btae642)**Bastian Pfeifer, Durrell D. Kapan, Sereina Annik Herzog*1 citation*
695. **[DrivR-Base: a feature extraction toolkit for variant effect prediction model construction ↗](https://doi.org/10.1093/bioinformatics/btae197)**Amy Francis, Colin Campbell, Tom R. Gaunt*1 citation*
696. **[EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events ↗](https://doi.org/10.1093/bioinformatics/btaf018)**Yubo Wang, Haoran Zhu, Yansong Wang et al.*1 citation*
697. **[EpiVar Browser: advanced exploration of epigenomics data under controlled access ↗](https://doi.org/10.1093/bioinformatics/btae136)**David R. Lougheed, Hanshi Liu, Katherine A Aracena et al.*1 citation*
698. **[FLAMS: Find Lysine Acylations and other Modification Sites ↗](https://doi.org/10.1093/bioinformatics/btae005)**Hannelore Longin, Nand Broeckaert, Maarten Langen et al.*1 citation*
699. **[FPLS-DC: functional partial least squares through distance covariance for imaging genetics ↗](https://doi.org/10.1093/bioinformatics/btae173)**Wenliang Pan, Yue Shan, Chuang Li et al.*1 citation*
700. **[Fast and scalable querying of eukaryotic linear motifs with gget elm ↗](https://doi.org/10.1093/bioinformatics/btae095)**Laura Luebbert, Chi Hoang, Manjeet Kumar et al.*1 citation*

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