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Bioinformatics Advances

IF2.8
Papers131
Citations
Journal Papers 131
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memod-s: a standardised workflow to explore and analyse prokaryotic methylation patterns for Nanopore sequencing data
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IF2.8
delete2026-01-01
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deleteMarotta, Alessia; Doni, Lapo; Avesani, Alessia; Passeri, Iacopo; Fagorzi, Camilla; Mengoni, Alessio; Martinez-Urtaza, Jaime; Batista, Frederico M.; Vezzulli, Luigi; Bosi, Emanuele
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Sketchbook: logical model inference from Boolean network sketches
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IF2.8
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deleteHuvar, Ondrej; Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safranek, David
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CanDrivR-CS: a cancer-specific machine learning framework for distinguishing recurrent and rare variants
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IF2.8
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deleteFrancis, Amy; Campbell, Colin; Gaunt, Tom R.
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Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant
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IF2.8
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deleteDavis, Jade M.; Gagalova, Kristina K.; Sanglard, Lilian M. V. P.; Cuellar, Sabrina; Gibberd, Mark R.; Naim, Fatima
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Cell type annotation using large language models (LLMs) and CytoAnalyst
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deleteNguyen, Khoi; Tran, Duy; Nguyen, Phuong; Ro, Seungil; Bya, Phi; Nguyen, Tin
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Sigscores: summary scores for molecular signatures in R
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IF2.8
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deleteBarberis, Alessandro; Buffa, Francesca M.
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Vector semantics of multidomain protein architectures
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IF2.8
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deleteCui, Xiaoyue; Xiao, Yuting; Stolzer, Maureen; Durand, Dannie
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Integrative analysis and imputation of multiple data streams via deep Gaussian processes
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IF2.8
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deleteSeptiandri, Ali A.; Ming, Deyu; DiazDelao, Francisco Alejandro; Jendoubi, Takoua; Ray, Samiran
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DCGAT-DTI: dynamic cross-graph attention network for drug-target interaction prediction
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deleteAbir, Abrar Rahman; Alif, Muhtasim Noor; Zhang, Wencai; Ahmed, Khandakar Tanvir; Zhang, Wei
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Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation
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IF2.8
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deleteWood, Valerie; Jeffryes, Matt; Green, Andrew F.; Blum, Matthias; Orchard, Sandra; Panni, Simona; Quaglia, Federica; Rodriguez-Esteban, Raul; Seager, James; Tosatto, Silvio C. E.; Wittig, Ulrike; Harrison, Melissa
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Graph convolutional networks for inferring cell-cell communication from spatial transcriptomics data
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IF2.8
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deleteKouznetsov, Roman; Loper, Jackson; Regier, Jeffrey
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m6AnetAnalyzer: an R toolkit for post-processing of m6A sites detected by m6Anet
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deleteLee, Hanna; Gashi, Denalda; Batool, Syeda Maheen; Escobedo, Ana K.; Petti, Allegra A.; Carter, Bob S.; Balaj, Leonora
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OMAnnotator: a novel approach to building an annotated consensus genome sequence
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IF2.8
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deleteBates, Sade; Dessimoz, Christophe; Nevers, Yannis
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DeepCE: a deep learning framework for correlation-enhanced gene regulatory network inference in single-cell RNA sequencing data
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deleteWu, Qianqian; Dai, Xingmiao; Lou, Shiyi; Wu, Siyuan; Tian, Tianhai
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GenomeDepot: data management system for microbial comparative genomics
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IF2.8
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deleteKazakov, Alexey; Deutschbauer, Adam M.
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GeneSNAKE: a Python package for simulation of gene regulatory networks and perturbation-induced expression data
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deleteHillerton, Thomas; Bjork, Anton; Lundqvist, Nils; Zhivkoplias, Erik K.; Garbulowski, Mateusz; Sonnhammer, Erik L. L.
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parsomics: a data-driven framework for metagenomics data integration powered by a local relational database
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deletede Azevedo, Pedro Sader; Vedovatto, Meiski Maria; de Freitas, Pedro Coelho Gimenes; Luz, Rafaela Beatriz Silva; Streit, Rodrigo Silva Araujo; Persinoti, Gabriela Felix
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A network-guided penalized regression with application to proteomics data
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deleteAhn, Seungjun; Oh, Eun Jeong
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Sparse dimensionality reduction for analyzing single-cell-resolved interactions (vol 6, vbag047, 2026)
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deleteBrunn, Niklas; Hackenberg, Maren; Fullio, Camila L.; Vogel, Tanja; Binder, Harald
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Advancing understanding of long COVID pathophysiology through quantum walk-based network analysis
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IF2.8
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deletePark, Jaesub; Hwang, Woochang; Lee, Seokjun; Lee, Hyun Chang; Macmahon, Meabh; Zilbauer, Matthias; Han, Namshik
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