---
title: "Bioinformatics 2024 — all accepted papers, page 3"
description: "All 788 papers of Bioinformatics 2024 · page 3 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 3 of 8 · the most cited first · [← Bioinformatics 2024](https://md.research.elamur.ai/free/en/venues/bioinformatics/2024/)

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201. **[The scalable variant call representation: enabling genetic analysis beyond one million genomes ↗](https://doi.org/10.1093/bioinformatics/btae746)**Timothy Poterba, Christopher Vittal, Daniel A. King et al.*14 citations*
202. **[VirusPredictor: XGBoost-based software to predict virus-related sequences in human data ↗](https://doi.org/10.1093/bioinformatics/btae192)**Guangchen Liu, Xun Chen, Yihui Luan et al.*14 citations*
203. **[m5c-iEnsem: 5-methylcytosine sites identification through ensemble models ↗](https://doi.org/10.1093/bioinformatics/btae722)**Anas Bilal, Fawaz Khaled Alarfaj, Rafaqat Alam Khan et al.*14 citations*
204. **[AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides ↗](https://doi.org/10.1093/bioinformatics/btae142)**Shengli Zhang, Ya Zhao, Yunyun Liang*13 citations*
205. **[ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation ↗](https://doi.org/10.1093/bioinformatics/btae121)**Irenaeus C.C. Chan, Alex Panchot, Evelyn Schmidt et al.*13 citations*
206. **[Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models ↗](https://doi.org/10.1093/bioinformatics/btae447)**Francesca Cuturello, Marco Celoria, Alessio Ansuini et al.*13 citations*
207. **[Estimation of inbreeding and kinship coefficients via latent identity-by-descent states ↗](https://doi.org/10.1093/bioinformatics/btae082)**Yongtao Guan, Daniel A Levy*13 citations*
208. **[FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology ↗](https://doi.org/10.1093/bioinformatics/btae406)**Tudor Groza, Dylan Gration, Gareth S Baynam et al.*13 citations*
209. **[From cell lines to cancer patients: personalized drug synergy prediction ↗](https://doi.org/10.1093/bioinformatics/btae134)**Halil İbrahim Kuru, A. Ercüment Çiçek, Öznur Taştan*13 citations*
210. **[HAT: de novo variant calling for highly accurate short-read and long-read sequencing data ↗](https://doi.org/10.1093/bioinformatics/btad775)**Jeffrey K. Ng, Tychele N. Turner*13 citations*
211. **[Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction ↗](https://doi.org/10.1093/bioinformatics/btae204)**Yurui Chen, Louxin Zhang*13 citations*
212. **[Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data ↗](https://doi.org/10.1093/bioinformatics/btae512)**Valérie Marot-Lassauzaie, Sergi Beneyto‐Calabuig, Benedikt Obermayer et al.*13 citations*
213. **[Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks ↗](https://doi.org/10.1093/bioinformatics/btae257)**Chao Deng, Hong‐Dong Li, Lishen Zhang et al.*13 citations*
214. **[MoleMCL: a multi-level contrastive learning framework for molecular pre-training ↗](https://doi.org/10.1093/bioinformatics/btae164)**Xinyi Zhang, Yanni Xu, Changzhi Jiang et al.*13 citations*
215. **[Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS ↗](https://doi.org/10.1093/bioinformatics/btae143)**Rémi Trimbour, Ina Maria Deutschmann, Laura Cantini*13 citations*
216. **[RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction ↗](https://doi.org/10.1093/bioinformatics/btaf004)**Clément Bernard, Guillaume Postic, Sahar Ghannay et al.*13 citations*
217. **[SCARAP: scalable cross-species comparative genomics of prokaryotes ↗](https://doi.org/10.1093/bioinformatics/btae735)**Stijn Wittouck, Tom Eilers, Vera van Noort et al.*13 citations*
218. **[SpatialQC: automated quality control for spatial transcriptome data ↗](https://doi.org/10.1093/bioinformatics/btae458)**Guangyao Mao, Yi Yang, Zhuojuan Luo et al.*13 citations*
219. **[Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics ↗](https://doi.org/10.1093/bioinformatics/btae611)**Yanfang Li, Shihua Zhang*13 citations*
220. **[Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data ↗](https://doi.org/10.1093/bioinformatics/btae267)**Marco Stock, Niclas Popp, Jonathan Fiorentino et al.*13 citations*
221. **[A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling ↗](https://doi.org/10.1093/bioinformatics/btae737)**Iain G. Johnston, Ramón Díaz‐Uriarte*12 citations*
222. **[A machine-readable specification for genomics assays ↗](https://doi.org/10.1093/bioinformatics/btae168)**A. Sina Booeshaghi, Xi Xian Chen, Lior S. Pachter*12 citations*
223. **[AbFlex: designing antibody complementarity determining regions with flexible CDR definition ↗](https://doi.org/10.1093/bioinformatics/btae122)**Woosung Jeon, Dongsup Kim*12 citations*
224. **[An empirical study on KDIGO-defined acute kidney injury prediction in the intensive care unit ↗](https://doi.org/10.1093/bioinformatics/btae212)**Xinrui Lyu, Bowen Fan, Matthias Hüser et al.*12 citations*
225. **[Approximating facial expression effects on diagnostic accuracy via generative AI in medical genetics ↗](https://doi.org/10.1093/bioinformatics/btae239)**Tanviben Patel, Amna A. Othman, Ömer Sümer et al.*12 citations*
226. **[AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality ↗](https://doi.org/10.1093/bioinformatics/btae477)**Usman Rashid, Chen Wu, Jason B. Shiller et al.*12 citations*
227. **[BIMSA: accelerating long sequence alignment using processing-in-memory ↗](https://doi.org/10.1093/bioinformatics/btae631)**Alejandro Alonso-Marín, Ivan Fernandez, Quim Aguado-Puig et al.*12 citations*
228. **[BetaAlign: a deep learning approach for multiple sequence alignment ↗](https://doi.org/10.1093/bioinformatics/btaf009)**Edo Dotan, Elya Wygoda, Noa Ecker et al.*12 citations*
229. **[CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing ↗](https://doi.org/10.1093/bioinformatics/btae150)**Ali Osman Berk Şapcı, Eleonora Rachtman, Siavash Mirarab*12 citations*
230. **[DDN3.0: determining significant rewiring of biological network structure with differential dependency networks ↗](https://doi.org/10.1093/bioinformatics/btae376)**Yingzhou Lu, Yingzhou Lu, Yizhi Wang et al.*12 citations*
231. **[Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module ↗](https://doi.org/10.1093/bioinformatics/btae418)**Jianyuan Yuan, Fengyu Zhang, Yimeng Qiu et al.*12 citations*
232. **[Drawing mitochondrial genomes with circularMT ↗](https://doi.org/10.1093/bioinformatics/btae450)**Simon J. Goodman, Ian Carr*12 citations*
233. **[Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools ↗](https://doi.org/10.1093/bioinformatics/btae179)**Artuur Couckuyt, Benjamin Rombaut, Yvan Saeys et al.*12 citations*
234. **[FAIRsoft—a practical implementation of FAIR principles for research software ↗](https://doi.org/10.1093/bioinformatics/btae464)**Eva Martín del Pico, Josep Lluis Gelpí, Salvador Capella-Gutiérrez*12 citations*
235. **[FAPM: functional annotation of proteins using multimodal models beyond structural modeling ↗](https://doi.org/10.1093/bioinformatics/btae680)**Wenkai Xiang, Zhaoping Xiong, Huan Chen et al.*12 citations*
236. **[Fine-tuning protein embeddings for functional similarity evaluation ↗](https://doi.org/10.1093/bioinformatics/btae445)**Andrew M. Dickson, Mohammad R. K. Mofrad*12 citations*
237. **[HyperGen: compact and efficient genome sketching using hyperdimensional vectors ↗](https://doi.org/10.1093/bioinformatics/btae452)**Weihong Xu, Po-Kai Hsu, Niema Moshiri et al.*12 citations*
238. **[LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors ↗](https://doi.org/10.1093/bioinformatics/btae520)**Koichiro Majima, Yasuhiro Kojima, Kodai Minoura et al.*12 citations*
239. **[MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2 ↗](https://doi.org/10.1093/bioinformatics/btae329)**Ho Yeung Chim, Arne Elofsson*12 citations*
240. **[Partial RNA design ↗](https://doi.org/10.1093/bioinformatics/btae222)**Frederic Runge, Jörg K. H. Franke, Daniel Fertmann et al.*12 citations*
241. **[STRPsearch: fast detection of structured tandem repeat proteins ↗](https://doi.org/10.1093/bioinformatics/btae690)**Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel et al.*12 citations*
242. **[Time-efficient filtering of imaging polarimetric data by checking physical realizability of experimental Mueller matrices ↗](https://doi.org/10.1093/bioinformatics/btae348)**Tatiana Novikova, Alexey Ovchinnikov, Gleb Pogudin et al.*12 citations*
243. **[VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs ↗](https://doi.org/10.1093/bioinformatics/btae066)**Philippe Charron, Mingsong Kang*12 citations*
244. **[methyLImp2: faster missing value estimation for DNA methylation data ↗](https://doi.org/10.1093/bioinformatics/btae001)**Anna Plaksienko, Pietro Di Lena, Christine Nardini et al.*12 citations*
245. **[popDMS infers mutation effects from deep mutational scanning data ↗](https://doi.org/10.1093/bioinformatics/btae499)**Zhenchen Hong, Kai S Shimagaki, John P. Barton*12 citations*
246. **[spread.gl: visualizing pathogen dispersal in a high-performance browser application ↗](https://doi.org/10.1093/bioinformatics/btae721)**Yimin Li, Nena Bollen, Samuel Leandro Hong et al.*12 citations*
247. **[A count-based model for delineating cell–cell interactions in spatial transcriptomics data ↗](https://doi.org/10.1093/bioinformatics/btae219)**Hirak Sarkar, Uthsav Chitra, Julian Gold et al.*11 citations*
248. **[A supervised Bayesian factor model for the identification of multi-omics signatures ↗](https://doi.org/10.1093/bioinformatics/btae202)**Jeremy P. Gygi, Jeremy P. Gygi, Anna Konstorum et al.*11 citations*
249. **[Assessing citation integrity in biomedical publications: corpus annotation and NLP models ↗](https://doi.org/10.1093/bioinformatics/btae420)**Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna et al.*11 citations*
250. **[BELHD: improving biomedical entity linking with homonym disambiguation ↗](https://doi.org/10.1093/bioinformatics/btae474)**Samuele Garda, Ulf Leser*11 citations*
251. **[Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis ↗](https://doi.org/10.1093/bioinformatics/btae605)**Sofia Mongardi, Silvia Cascianelli, Marco Masseroli*11 citations*
252. **[Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets ↗](https://doi.org/10.1093/bioinformatics/btae217)**Igor Martayan, Bastien Cazaux, Antoine Limasset et al.*11 citations*
253. **[FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data ↗](https://doi.org/10.1093/bioinformatics/btae010)**Mikaela Koutrouli, Katerina C. Nastou, Pau Piera Líndez et al.*11 citations*
254. **[Federated unsupervised random forest for privacy-preserving patient stratification ↗](https://doi.org/10.1093/bioinformatics/btae382)**Bastian Pfeifer, Christel Sirocchi, Marcus D. Bloice et al.*11 citations*
255. **[Genome-wide detection of somatic mosaicism at short tandem repeats ↗](https://doi.org/10.1093/bioinformatics/btae485)**Aarushi Sehgal, Helyaneh Ziaei Jam, Andrew Shen et al.*11 citations*
256. **[Guide assignment in single-cell CRISPR screens using crispat ↗](https://doi.org/10.1093/bioinformatics/btae535)**Jana M. Braunger, Britta Velten*11 citations*
257. **[Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation ↗](https://doi.org/10.1093/bioinformatics/btae339)**Ziheng Duan, Dylan Riffle, Ren Li et al.*11 citations*
258. **[Improving the performance and interpretability on medical datasets using graphical ensemble feature selection ↗](https://doi.org/10.1093/bioinformatics/btae341)**Enzo Battistella, Susan Dina Ghiassian, Albert-Ĺaszló Barabási*11 citations*
259. **[JARVIS3: an efficient encoder for genomic data ↗](https://doi.org/10.1093/bioinformatics/btae725)**Maria J P Sousa, Armando J. Pinho, Diogo Pratas*11 citations*
260. **[Mariner: explore the Hi-Cs ↗](https://doi.org/10.1093/bioinformatics/btae352)**Eric S. Davis, Sarah M Parker, Nicole E Kramer et al.*11 citations*
261. **[Predicting protein functions using positive-unlabeled ranking with ontology-based priors ↗](https://doi.org/10.1093/bioinformatics/btae237)**Fernando Zhapa-Camacho, Zhenwei Tang, Maxat Kulmanov et al.*11 citations*
262. **[Protein language models meet reduced amino acid alphabets ↗](https://doi.org/10.1093/bioinformatics/btae061)**Ioan Ieremie, Rob M. Ewing, Mahesan Niranjan*11 citations*
263. **[R2Dtool: integration and visualization of isoform-resolved RNA features ↗](https://doi.org/10.1093/bioinformatics/btae495)**Aditya J. Sethi, Pablo Acera Mateos, Rippei Hayashi et al.*11 citations*
264. **[Sitetack: a deep learning model that improves PTM prediction by using known PTMs ↗](https://doi.org/10.1093/bioinformatics/btae602)**Clair S. Gutierrez, Alia A. Kassim, Benjamin D. Gutierrez et al.*11 citations*
265. **[SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS ↗](https://doi.org/10.1093/bioinformatics/btae054)**Emese I. Végh, Katerina Douka*11 citations*
266. **[StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides ↗](https://doi.org/10.1093/bioinformatics/btae057)**Ding Wang, Junru Jin, Zhongshen Li et al.*11 citations*
267. **[SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models ↗](https://doi.org/10.1093/bioinformatics/btae340)**Ketrin Gjoni, Katherine S. Pollard*11 citations*
268. **[Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation ↗](https://doi.org/10.1093/bioinformatics/btae360)**Minzhu Xie, Yabin Kuang, Mengyun Song et al.*11 citations*
269. **[The Naïve Bayes classifier++ for metagenomic taxonomic classification—query evaluation ↗](https://doi.org/10.1093/bioinformatics/btae743)**Haozhe (Neil) Duan, Gavin Hearne, Robi Polikar A et al.*11 citations*
270. **[hictk: blazing fast toolkit to work with .hic and .cool files ↗](https://doi.org/10.1093/bioinformatics/btae408)**Roberto Rossini, Jonas Paulsen*11 citations*
271. **[iSeq: an integrated tool to fetch public sequencing data ↗](https://doi.org/10.1093/bioinformatics/btae641)**Haoyu Chao, Z Li, Dijun Chen et al.*11 citations*
272. **[mLiftOver: harmonizing data across Infinium DNA methylation platforms ↗](https://doi.org/10.1093/bioinformatics/btae423)**Brian H. Chen, Wanding Zhou*11 citations*
273. **[A survey of BWT variants for string collections ↗](https://doi.org/10.1093/bioinformatics/btae333)**Davide Cenzato, Zsuzsanna Lipták*10 citations*
274. **[BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities ↗](https://doi.org/10.1093/bioinformatics/btae266)**Telmo Blasco, Francesco Balzerani, Luis V. Valcárcel et al.*10 citations*
275. **[Flexible parsing, interpretation, and editing of technical sequences with splitcode ↗](https://doi.org/10.1093/bioinformatics/btae331)**Delaney K. Sullivan, Lior S. Pachter*10 citations*
276. **[For antibody sequence generative modeling, mixture models may be all you need ↗](https://doi.org/10.1093/bioinformatics/btae278)**Jonathan Parkinson, Wei Wang*10 citations*
277. **[GammaGateR: semi-automated marker gating for single-cell multiplexed imaging ↗](https://doi.org/10.1093/bioinformatics/btae356)**Jiangmei Xiong, Harsimran Kaur, Cody N. Heiser et al.*10 citations*
278. **[Improving dictionary-based named entity recognition with deep learning ↗](https://doi.org/10.1093/bioinformatics/btae402)**Katerina C. Nastou, Mikaela Koutrouli, Sampo Pyysalo et al.*10 citations*
279. **[LarvaTagger: manual and automatic tagging of Drosophila larval behaviour ↗](https://doi.org/10.1093/bioinformatics/btae441)**François Laurent, Alexandre Blanc, Lilly May et al.*10 citations*
280. **[MPH: fast REML for large-scale genome partitioning of quantitative genetic variation ↗](https://doi.org/10.1093/bioinformatics/btae298)**Jicai Jiang*10 citations*
281. **[MSDAFL: molecular substructure-based dual attention feature learning framework for predicting drug–drug interactions ↗](https://doi.org/10.1093/bioinformatics/btae596)**Chao Hou, Guihua Duan, Cheng Yan*10 citations*
282. **[Many-core algorithms for high-dimensional gradients on phylogenetic trees ↗](https://doi.org/10.1093/bioinformatics/btae030)**Karthik Gangavarapu, Xiang Ji, Guy Baele et al.*10 citations*
283. **[MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing ↗](https://doi.org/10.1093/bioinformatics/btae522)**Antoine Passemiers, Stefania Tuveri, Dhanya Sudhakaran et al.*10 citations*
284. **[MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data ↗](https://doi.org/10.1093/bioinformatics/btae459)**Ana Mendes, Jesper Foged Havelund, Jonas Lemvig et al.*10 citations*
285. **[MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability ↗](https://doi.org/10.1093/bioinformatics/btae473)**Yunxiang Yu, Mengyun Gu, Hai Yang Guo et al.*10 citations*
286. **[PanEffect: a pan-genome visualization tool for variant effects in maize ↗](https://doi.org/10.1093/bioinformatics/btae073)**Carson M. Andorf, Olivia C. Haley, Rita K. Hayford et al.*10 citations*
287. **[Pangenome graph layout by Path-Guided Stochastic Gradient Descent ↗](https://doi.org/10.1093/bioinformatics/btae363)**Simon Heumos, Andrea Guarracino, Jan-Niklas M. Schmelzle et al.*10 citations*
288. **[PhiHER2: phenotype-informed weakly supervised model for HER2 status prediction from pathological images ↗](https://doi.org/10.1093/bioinformatics/btae236)**Chaoyang Yan, Jialiang Sun, Yiming Guan et al.*10 citations*
289. **[Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies ↗](https://doi.org/10.1093/bioinformatics/btae498)**Hanbin Lee, Buhm Han*10 citations*
290. **[Reference-free structural variant detection in microbiomes via long-read co-assembly graphs ↗](https://doi.org/10.1093/bioinformatics/btae224)**Kristen D. Curry, Feiqiao Brian Yu, Summer E. Vance et al.*10 citations*
291. **[RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution ↗](https://doi.org/10.1093/bioinformatics/btae369)**Jonathan Chacko, Hakan Özadam, Can Cenik*10 citations*
292. **[Towards more accurate microbial source tracking via non-negative matrix factorization (NMF) ↗](https://doi.org/10.1093/bioinformatics/btae227)**Ziyi Huang, Dehan Cai, Yanni Sun*10 citations*
293. **[mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations ↗](https://doi.org/10.1093/bioinformatics/btae078)**Anna Sintsova, Hans‐Joachim Ruscheweyh, Christopher M. Field et al.*10 citations*
294. **[scToppR: a coding-friendly R interface to ToppGene ↗](https://doi.org/10.1093/bioinformatics/btae582)**Bryan Granger, Stefano Berto*10 citations*
295. **[A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data ↗](https://doi.org/10.1093/bioinformatics/btae425)**Sarah Samorodnitsky, Katie Marie Campbell, Antoni Ribas et al.*9 citations*
296. **[A deep learning architecture for metabolic pathway prediction ↗](https://doi.org/10.1093/bioinformatics/btae359)**Mayank Baranwal, Abram Magner, Paolo Elvati et al.*9 citations*
297. **[A dual-rule encoding DNA storage system using chaotic mapping to control GC content ↗](https://doi.org/10.1093/bioinformatics/btae113)**Xuncai Zhang, Baonan Qi, Ying Niu*9 citations*
298. **[A hybrid constrained continuous optimization approach for optimal causal discovery from biological data ↗](https://doi.org/10.1093/bioinformatics/btae411)**Yuehua Zhu, Panayiotis V. Benos, Maria D. Chikina*9 citations*
299. **[ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models ↗](https://doi.org/10.1093/bioinformatics/btae661)**Mukai Wang, Simon Fontaine, Hui Jiang et al.*9 citations*
300. **[AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions ↗](https://doi.org/10.1093/bioinformatics/btae268)**Zachary A. Rollins, Talal Widatalla, Andrew B. Waight et al.*9 citations*

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