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

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

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701. **[Fast multiple sequence alignment via multi-armed bandits ↗](https://doi.org/10.1093/bioinformatics/btae225)**Kayvon Mazooji, Ilan Shomorony*1 citation*
702. **[Fast polypharmacy side effect prediction using tensor factorization ↗](https://doi.org/10.1093/bioinformatics/btae706)**Oliver Lloyd, Yi Liu, Tom R. Gaunt*1 citation*
703. **[FastTENET: an accelerated TENET algorithm based on manycore computing in Python ↗](https://doi.org/10.1093/bioinformatics/btae699)**Rakbin Sung, Hyeonkyu Kim, Junil Kim et al.*1 citation*
704. **[GEEES: inferring cell-specific gene–enhancer interactions from multi-modal single-cell data ↗](https://doi.org/10.1093/bioinformatics/btae638)**Shuyang Chen, Sündüz Keleş*1 citation*
705. **[GTAM: A Molecular Pretraining Model with Geometric Triangle Awareness ↗](https://doi.org/10.1093/bioinformatics/btae524)**Xiaoyang Hou, Tian Zhu, Milong Ren et al.*1 citation*
706. **[GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization ↗](https://doi.org/10.1093/bioinformatics/btae462)**Julián Montoto-Louzao, Alberto Gómez‐Carballa, Xabier Bello et al.*1 citation*
707. **[HCS—hierarchical algorithm for simulation of omics datasets ↗](https://doi.org/10.1093/bioinformatics/btae392)**Piotr Stomma, Witold Remigiusz Rudnicki*1 citation*
708. **[Highly efficient clustering of long-read transcriptomic data with GeLuster ↗](https://doi.org/10.1093/bioinformatics/btae059)**Junchi Ma, Xiaoyu Zhao, Enfeng Qi et al.*1 citation*
709. **[KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction ↗](https://doi.org/10.1093/bioinformatics/btae090)**Haoliang Xue, Mélina Gallopin, Camille Marchet et al.*1 citation*
710. **[KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs ↗](https://doi.org/10.1093/bioinformatics/btae538)**Dhruv Khatri, Shivani A. Yadav, Chaitanya A. Athale*1 citation*
711. **[Knowledge mining of brain connectivity in massive literature based on transfer learning ↗](https://doi.org/10.1093/bioinformatics/btae648)**Xiaokang Chai, Sile An, Simeng Chen et al.*1 citation*
712. **[M2ara : unraveling metabolomic drug responses in whole-cell MALDI mass spectrometry bioassays ↗](https://doi.org/10.1093/bioinformatics/btae694)**Thomas Enzlein, Alexander Geisel, Carsten Hopf et al.*1 citation*
713. **[Metadata-guided feature disentanglement for functional genomics ↗](https://doi.org/10.1093/bioinformatics/btae403)**Alexander Rakowski, Remo Monti, Viktoriia Huryn et al.*1 citation*
714. **[Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method ↗](https://doi.org/10.1093/bioinformatics/btae728)**Duo Xi, Minjianan Zhang, Muheng Shang et al.*1 citation*
715. **[MotGen: a closed-loop bacterial motility control framework using generative adversarial networks ↗](https://doi.org/10.1093/bioinformatics/btae170)**BoGeum Seo, DoHee Lee, Heung Jin Jeon et al.*1 citation*
716. **[OneSC: a computational platform for recapitulating cell state transitions ↗](https://doi.org/10.1093/bioinformatics/btae703)**Da Peng, Patrick Cahan*1 citation*
717. **[Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling ↗](https://doi.org/10.1093/bioinformatics/btae399)**Srijay Deshpande, Sokratia Georgaka, Michael Haley et al.*1 citation*
718. **[PERFUMES: pipeline to extract RNA functional motifs and exposed structures ↗](https://doi.org/10.1093/bioinformatics/btae056)**Arnaud Chol, Roman Sarrazin‐Gendron, Éric Lécuyer et al.*1 citation*
719. **[Polyphonia: detecting inter-sample contamination in viral genomic sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae698)**Lydia Andreyevna Krasilnikova, Christopher H. Tomkins-Tinch, Alton C. Gayton et al.*1 citation*
720. **[PostFocus: automated selective post-acquisition high-throughput focus restoration using diffusion model for label-free time-lapse microscopy ↗](https://doi.org/10.1093/bioinformatics/btae467)**Kwan-Ling Wu, Melisa J. Montalvo, Prashant S. Menon et al.*1 citation*
721. **[Quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning ↗](https://doi.org/10.1093/bioinformatics/btae658)**Seonghwan Park, Min Young Kim, Min Young Kim et al.*1 citation*
722. **[RUCova: Removal of Unwanted Covariance in mass cytometry data ↗](https://doi.org/10.1093/bioinformatics/btae669)**Rosario Astaburuaga-García, Thomas Sell, Samet Mutlu et al.*1 citation*
723. **[SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality ↗](https://doi.org/10.1093/bioinformatics/btae016)**Xin Liu, Jieni Hu, Jie Zheng*1 citation*
724. **[SampleExplorer: using language models to discover relevant transcriptome data ↗](https://doi.org/10.1093/bioinformatics/btae759)**Wee Loong Chin, Timo Lassmann*1 citation*
725. **[Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes ↗](https://doi.org/10.1093/bioinformatics/btae040)**Louise Ryan, Colleen Lawless, Graham M. Hughes*1 citation*
726. **[Shu: visualization of high-dimensional biological pathways ↗](https://doi.org/10.1093/bioinformatics/btae140)**Jorge Carrasco Muriel, Nicholas Luke Cowie, Shannara Kayleigh Taylor Parkins et al.*1 citation*
727. **[SimService: a lightweight library for building simulation services in Python ↗](https://doi.org/10.1093/bioinformatics/btae009)**T. J. Sego*1 citation*
728. **[Subset scanning for multi-trait analysis using GWAS summary statistics ↗](https://doi.org/10.1093/bioinformatics/btad777)**Rui Cao, EVAN A. OLAWSKY, Edward McFowland et al.*1 citation*
729. **[The 2024 ISCB Accomplishments by a Senior Scientist Award—Dr Tandy Warnow ↗](http://dx.doi.org/10.1093/bioinformatics/btae289)**Mallory L Wiper*1 citation*
730. **[The 2024 ISCB Innovator Award—Dr Su-In Lee ↗](https://doi.org/10.1093/bioinformatics/btae287)**Mallory L Wiper*1 citation*
731. **[Uncertainty quantification in high-dimensional linear models incorporating graphical structures with applications to gene set analysis ↗](https://doi.org/10.1093/bioinformatics/btae541)**Xiangyong Tan, Xiao Zhang, Yuehua Cui et al.*1 citation*
732. **[Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference ↗](http://dx.doi.org/10.1093/bioinformatics/btae120)**Hamed Vasei, Mohammad-Hadi Foroughmand-Araabi, Amir Daneshgar*1 citation*
733. **[ceas: an R package for Seahorse data analysis and visualization ↗](https://doi.org/10.1093/bioinformatics/btae503)**Rachel J. House, James Eapen, Hui Shen et al.*1 citation*
734. **[easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis ↗](https://doi.org/10.1093/bioinformatics/btae710)**Haoyun Zhang, Wentao Zhang, Shuai Zhao et al.*1 citation*
735. **[pyTWMR: transcriptome-wide Mendelian randomization in python ↗](https://doi.org/10.1093/bioinformatics/btae505)**Sergey Oreshkov, Kaido Lepik, Federico Andrea Santoni*1 citation*
736. **[rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments ↗](https://doi.org/10.1093/bioinformatics/btae193)**Jonathan L. Price, Omer Ziv, Malte L. Pinckert et al.*1 citation*
737. **[scCross: efficient search for rare subpopulations across multiple single-cell samples ↗](https://doi.org/10.1093/bioinformatics/btae371)**Alexander Gerniers, Siegfried Nijssen, Pierre Dupont*1 citation*
738. **[3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures ↗](https://doi.org/10.1093/bioinformatics/btae171)**Victoria Ruiz‐Serra, Samuel Valentini, Sergi Madroñero et al.
739. **[A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae431)**Mo Li, Xing Hua, Shuai Cheng Li et al.
740. **[ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression ↗](https://doi.org/10.1093/bioinformatics/btae660)**Alex C.H. Liu, Steven M. Chan
741. **[ALLSTAR: inference of reliAble causaL ruLes between Somatic muTAtions and canceR phenotypes ↗](https://doi.org/10.1093/bioinformatics/btae449)**Dario Simionato, Antonio Collesei, Federica Miglietta et al.
742. **[BindCompare: a novel integrated protein–nucleic acid binding analysis platform ↗](https://doi.org/10.1093/bioinformatics/btae668)**Pranav Mahableshwarkar, Jasmine Shum, Mukulika Ray et al.
743. **[Chapter 1 Introduction to bioinformatics ↗](https://doi.org/10.1515/9783111568584-001)**Nitin Sharma, Manika Choudhary, Vikas Kumar
744. **[Chapter 2 Biological databases and bioinformatics tools ↗](https://doi.org/10.1515/9783111568584-002)**Varruchi Sharma, Imran Sheikh, Vikas Kushwaha et al.
745. **[Chapter 3 Fundamentals of bioinformatics ↗](https://doi.org/10.1515/9783111568584-003)**Varruchi Sharma, Poonam Bansal, Imran Sheikh et al.
746. **[Chapter 5 Recent advances in the discovery of drug molecules: trends, scope, and relevance ↗](https://doi.org/10.1515/9783111568584-005)**Ramesh Chand Thakur, Akshay Sharma, Renuka Sharma
747. **[ClusterMatch aligns single-cell RNA-sequencing data at the multi-scale cluster level via stable matching ↗](https://doi.org/10.1093/bioinformatics/btae480)**Teer Ba, Miao Hao, Lirong Zhang et al.
748. **[Crypt4GH-JS: securely storing sensitive data online with client-side encryption ↗](https://doi.org/10.1093/bioinformatics/btae763)**Fabienne Thelen, Jannis Hochmuth, Sven Griep et al.
749. **[ECCB2024: The 23rd European Conference on Computational Biology ↗](http://dx.doi.org/10.1093/bioinformatics/btae422)**Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F. Heil et al.
750. **[Eliater: a Python package for estimating outcomes of perturbations in biomolecular networks ↗](https://doi.org/10.1093/bioinformatics/btae527)**Sara Mohammad-Taheri, Pruthvi Prakash Navada, Charles Tapley Hoyt et al.
751. **[Enabling Population Protein Dynamics Through Bayesian Modeling ↗](https://doi.org/10.1093/bioinformatics/btae484)**Sylvain Lehmann, Jérôme Vialaret, Audrey Gabelle et al.
752. **[Expression of Concern: Cleavage-Stage Embryo Segmentation Using SAM-Based Dual Branch Pipeline: Development and Evaluation with the CleavageEmbryo Dataset ↗](https://doi.org/10.1093/bioinformatics/btaf001)**
753. **[GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data ↗](https://doi.org/10.1093/bioinformatics/btae152)**Eric Odle, Samuel E. Kahng, Siratee Riewluang et al.
754. **[GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies ↗](https://doi.org/10.1093/bioinformatics/btae489)**James V. Talwar, Adam Klie, Meghana S. Pagadala et al.
755. **[Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks ↗](https://doi.org/10.1093/bioinformatics/btae650)**Sam F. L. Windels, Daniel Tello Velasco, Mikhail Rotkevich et al.
756. **[ISMB 2024 Proceedings ↗](https://doi.org/10.1093/bioinformatics/btae286)**Tijana Milenković, Yann Ponty
757. **[ITree: a user-driven tool for interactive decision-making with classification trees ↗](https://doi.org/10.1093/bioinformatics/btae273)**Hubert Sokołowski, Marcin Czajkowski, Anna Czajkowska et al.
758. **[Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence ↗](https://doi.org/10.1093/bioinformatics/btae131)**Jason Y. Cain, Jacob I. Evarts, Jessica S. Yu et al.
759. **[Integrative annotation scores of variants for impact on RNA binding protein activities ↗](https://doi.org/10.1093/bioinformatics/btae181)**Jingqi Duan, Audrey P. Gasch, Sündüz Keleş
760. **[Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique ↗](https://doi.org/10.1093/bioinformatics/btae566)**Hang Yang, Xiaoxin Lu, Jiaxing Chang et al.
761. **[MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species ↗](https://doi.org/10.1093/bioinformatics/btae429)**Zhiming Zhang, Jing Fei Ren, Lili Ren et al.
762. **[Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions ↗](https://doi.org/10.1093/bioinformatics/btae667)**Ruoqian Liu, Yue Wang, Dan Cheng
763. **[New GO-based measures in multiple network alignment ↗](https://doi.org/10.1093/bioinformatics/btae476)**Kimia Yazdani, Reza Mousapour, Wayne B. Hayes
764. **[OpenVariant: a toolkit to parse and operate multiple input file formats ↗](https://doi.org/10.1093/bioinformatics/btae714)**David Martínez-Millán, Federica Brando, Miguel L. Grau et al.
765. **[Optimal sequencing budget allocation for trajectory reconstruction of single cells ↗](https://doi.org/10.1093/bioinformatics/btae258)**Noa Moriel, Edvin Memet, Mor Nitzan
766. **[PONYTA: prioritization of phenotype-related genes from mouse KO events using PU learning on a biological network ↗](https://doi.org/10.1093/bioinformatics/btae634)**Jun Hyeong Kim, Bonil Koo, Sun Kim
767. **[Peer Review Report For: From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure version 1; peer review: 3 approved with reservations ↗](https://doi.org/10.5256/f1000research.168851.r321797)**Bogdan Andrei Mirauta, Cătălina Zenoaga-Barbăroşie, Monica I. Abrudan et al.
768. **[Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems ↗](https://doi.org/10.1093/bioinformatics/btae465)**Mauro Silberberg, Henning Hermjakob, Rahuman S. Malik‐Sheriff et al.
769. **[Probabilistic pathway-based multimodal factor analysis ↗](https://doi.org/10.1093/bioinformatics/btae216)**Alexander Immer, Stefan G. Stark, Francis Jacob et al.
770. **[PySNV for complex intra-host variation detection ↗](https://doi.org/10.1093/bioinformatics/btae116)**Liandong Li, Haoyi Fu, Wentai Ma et al.
771. **[R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species ↗](https://doi.org/10.1093/bioinformatics/btae682)**Sri Devan Appasamy, Craig L. Zirbel
772. **[RTF: an R package for modelling time course data ↗](https://doi.org/10.1093/bioinformatics/btae597)**Eva Brombacher, Clemens Kreutz
773. **[Regional analysis to delineate intrasample heterogeneity with RegionalST ↗](https://doi.org/10.1093/bioinformatics/btae186)**Yue Lyu, Chong Wu, Wei Sun et al.
774. **[SWGTS—a platform for stream-based host DNA depletion ↗](https://doi.org/10.1093/bioinformatics/btae332)**Philipp Spohr, Max Ried, Laura C. Kühle et al.
775. **[SciDataFlow: a tool for improving the flow of data through science ↗](https://doi.org/10.1093/bioinformatics/btad754)**Vince Buffalo
776. **[Supervised learning of enhancer–promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning ↗](https://doi.org/10.1093/bioinformatics/btae367)**Dylan Barth, Richard Van, Jonathan Cardwell et al.
777. **[SurvBal: compositional microbiome balances for survival outcomes ↗](https://doi.org/10.1093/bioinformatics/btae612)**Ying Li, Teresa Lee, Kai Marin et al.
778. **[TARO: tree-aggregated factor regression for microbiome data integration ↗](https://doi.org/10.1093/bioinformatics/btae321)**Aditya K. Mishra, Iqbal Mahmud, Philip L. Lorenzi et al.
779. **[TRAITER: transformer-guided diagnosis and prognosis of heart failure using cell nuclear morphology and DNA damage marker ↗](https://doi.org/10.1093/bioinformatics/btae610)**Hiromu Hayashi, Toshiyuki Ko, Zhehao Dai et al.
780. **[The 2024 ISCB Overton Prize Award—Dr Martin Steinegger ↗](http://dx.doi.org/10.1093/bioinformatics/btae288)**Mallory L Wiper
781. **[The 2024 Outstanding Contributions to ISCB Award—Dr Scott Markel ↗](http://dx.doi.org/10.1093/bioinformatics/btae285)**Mallory L Wiper
782. **[VSS-Hi-C: variance-stabilized signals for chromatin contacts ↗](https://doi.org/10.1093/bioinformatics/btae715)**Neda Shokraneh, Faezeh Bayat, Maxwell W. Libbrecht
783. **[biotextgraph: graphical summarization of functional similarities from textual information ↗](https://doi.org/10.1093/bioinformatics/btae357)**Noriaki Sato, Yaozhong Zhang, Zuguang Gu et al.
784. **[cloudrna SP Ades : isoform assembly using bulk barcoded RNA sequencing data ↗](https://doi.org/10.1093/bioinformatics/btad781)**Dmitry Meleshko, Andrey D. Prjbelski, Mikhail Raiko et al.
785. **[cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment ↗](https://doi.org/10.1093/bioinformatics/btae511)**Shilin Yu, Guanqun Meng, Wen Tang et al.
786. **[greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets ↗](https://doi.org/10.1093/bioinformatics/btae307)**Sheikh Nizamuddin, H. T. Marc Timmers
787. **[quaqc: efficient and quick ATAC-seq quality control and filtering ↗](https://doi.org/10.1093/bioinformatics/btae649)**Benjamin J.-M. Tremblay, Julia I. Qüesta
788. **[snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics ↗](https://doi.org/10.1093/bioinformatics/btae377)**Kim L. Vertacnik, Oksana V. Vernygora, Julian R. Dupuis

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