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ORCIDBMC Bioinformatics, Volume 26
Volume 26, Number 1, December 2025
- Tongjun Xiang, Huibao Feng, Xin-hui Xing, Chong Zhang:
GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes. 1 - M. Eremeyeva, Y. Din, N. Shirokii, N. Serov:
SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes. 2 - Mohamed Elmanzalawi
, Takatomo Fujisawa, Hiroshi Mori, Yasukazu Nakamura, Yasuhiro Tanizawa:
DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes. 3 - James P. Long, Yumeng Yang, Shohei Shimizu, Thong Pham, Kim-Anh Do:
Causal models and prediction in cell line perturbation experiments. 4 - Xianfang Tang, Yawen Hou, Yajie Meng, Zhaojing Wang, Changcheng Lu, Juan Lv, Xinrong Hu, Junlin Xu, Jialiang Yang:
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction. 5 - Weijie Yang, Jingsi Ji, Gang Fang:
A metric and its derived protein network for evaluation of ortholog database inconsistency. 6 - Leonardo Campillos-Llanos, Ana Valverde-Mateos, Adrián Capllonch-Carrión:
Hybrid natural language processing tool for semantic annotation of medical texts in Spanish. 7 - Cristian Iperi, Álvaro Fernández-Ochoa, Guillermo Barturen, Jacques-Olivier Pers, Nathan Foulquier, Eléonore Bettacchioli, Marta E. Alarcón-Riquelme, Divi Cornec, Anne Bordron, Christophe Jamin:
BiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data. 8 - Olga Fourkioti, Matt De Vries, Reed Naidoo, Chris Bakal:
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology. 9 - Zixin Chen, Chengming Ji, Wenwen Xu, Jianfeng Gao, Ji Huang, Huanliang Xu, Guoliang Qian, Junxian Huang:
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides. 10 - Guang Yang, Yinbo Liu, Sijian Wen, Wenxi Chen, Xiaolei Zhu, Yongmei Wang:
DTI-MHAPR: optimized drug-target interaction prediction via PCA-enhanced features and heterogeneous graph attention networks. 11 - Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega-Sanz, Jacob L. Steenwyk, Samuel Sihvonen:
Solu: a cloud platform for real-time genomic pathogen surveillance. 12 - Jianwei Li, Xukun Zhang, Bing Li, Ziyu Li, Zhenzhen Chen:
MDFGNN-SMMA: prediction of potential small molecule-miRNA associations based on multi-source data fusion and graph neural networks. 13 - Gabriele Moro, Rossano Atzeni, Ali Al-Subhi, Maria Giovanna Marche:
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes. 14 - Lujun Luo, Tarikul I. Milon, Elijah K. Tandoh, Walter J. Galdamez, Andrei Y. Chistoserdov, Jianping Yu, Jan Kern, Yingchun Wang, Wu Xu:
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I. 15 - Leixia Tian, Qi Wang, Zhiheng Zhou, Xiya Liu, Ming Zhang, Guiying Yan:
Predicting drug combination side effects based on a metapath-based heterogeneous graph neural network. 16 - Minindu Weerakoon, Sangjin Lee, Emily Mitchell, Haynes Heaton:
TopoQual polishes circular consensus sequencing data and accurately predicts quality scores. 17 - Xiaomin Liu, Yi-Ju Li, Qiao Fan:
Zim4rv: an R package to modeling zero-inflated count phenotype on regional-based rare variants. 18 - Dhekra Saeed, Huanlai Xing, Barakat AlBadani, Li Feng, Raeed Al-Sabri, Monir Abdullah, Amir Rehman:
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction. 19 - Arash Shahbazpoor Shahbazi, Farzin Irandoost, Reza Mahdavian, Seyedehsamaneh Shojaeilangari, Abdollah Allahvardi, Hossein Naderi-manesh:
A multi-stage weakly supervised design for spheroid segmentation to explore mesenchymal stem cell differentiation dynamics. 20 - Thomas J. Booth, Simon Shaw, Pablo Cruz-Morales, Tilmann Weber:
getphylo: rapid and automatic generation of multi-locus phylogenetic trees. 21 - Jinming Cheng, Xinyi Jin, Gordon K. Smyth, Yunshun Chen:
Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data. 22 - Xiao Zhang, Qian Liu:
A graph neural network approach for hierarchical mapping of breast cancer protein communities. 23 - Stefan Pastore, Philipp Hillenbrand, Nils Molnar, Irina Kovlyagina, Monika Chanu Chongtham, Stanislav Sys, Beat Lutz, Margarita Tevosian, Susanne Gerber:
ClearFinder: a Python GUI for annotating cells in cleared mouse brain. 24 - Azam Shirali, Vitalii Stebliankin, Ukesh Karki, Jimeng Shi, Prem Chapagain, Giri Narasimhan:
A comprehensive survey of scoring functions for protein docking models. 25 - Clémence Réda, Jill-Jênn Vie, Olaf Wolkenhauer:
Joint embedding-classifier learning for interpretable collaborative filtering. 26 - Tatiana A. Semashko, Gleb Y. Fisunov, Georgiy Y. Shevelev, Vadim M. Govorun:
BAC-browser: the tool for synthetic biology. 27 - Jinchen Sun, Haoran Zheng:
HDN-DDI: a novel framework for predicting drug-drug interactions using hierarchical molecular graphs and enhanced dual-view representation learning. 28 - Qifeng Liu, Tao Zhou, Chi Cheng, Jin Ma, Marzia Hoque Tania:
Hybrid generative adversarial network based on frequency and spatial domain for histopathological image synthesis. 29 - Gregory Teicher, R. Madison Riffe, Wayne Barnaby, Gabrielle Martin, Benjamin E. Clayton, Josef G. Trapani, Gerald B. Downes:
Marigold: a machine learning-based web app for zebrafish pose tracking. 30 - Pere Palmer-Rodríguez, Ricardo Alberich, Mariana Reyes-Prieto, José A. Castro, Mercè Llabrés:
Metadag: a web tool to generate and analyse metabolic networks. 31 - Christopher Thron, Farhad Jafari:
Correcting scale distortion in RNA sequencing data. 32 - Xiaoxu Cui, Renkai Wu, Yinghao Liu, Peizhan Chen, Qing Chang, Pengchen Liang, Changyu He:
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder. 33 - Ram Chandra Bhushan, Rakesh Kumar Donthi, Yojitha Chilukuri, Ulligaddala Srinivasarao, Polisetty Swetha:
Biomedical named entity recognition using improved green anaconda-assisted Bi-GRU-based hierarchical ResNet model. 34 - Meng Zhang, Joel Parker, Lingling An, Yiwen Liu, Xiaoxiao Sun:
Flexible analysis of spatial transcriptomics data (FAST): a deconvolution approach. 35 - Jia Tian, Ziyu Gao, Minghao Li, Ergude Bao, Jin Zhao:
Accurate assembly of full-length consensus for viral quasispecies. 36 - Qiaowang Li, Yaser Gamallat, Jon G. Rokne, Tarek A. Bismar, Reda Alhajj:
BioLake: an RNA expression analysis framework for prostate cancer biomarker powered by data lakehouse. 37 - Antoine Allard, Maxime Liboz, Raphaël Crépin, Sid Labdi, Olek Maciejak, Michel Malo, Clément Campillo, Guillaume Lamour:
CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope. 38 - Samuel Boyd, Chad Slawson, Jeffrey A. Thompson:
AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs. 39 - Dimitrios Kioroglou:
Omilayers: a Python package for efficient data management to support multi-omic analysis. 40 - Francesco Caredda, Andrea Pagnani:
Direct coupling analysis and the attention mechanism. 41 - Bo Guan, Guangdi Chu, Ziying Wang, Jianmin Li, Bo Yi:
Instance-level semantic segmentation of nuclei based on multimodal structure encoding. 42 - Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha Bayer, Ingo Hein:
Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes. 43 - Masahiro Ono:
TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis. 44 - Chi-Jane Chen, Haidong Yi, Natalie Stanley:
Conditional similarity triplets enable covariate-informed representations of single-cell data. 45 - Yansong Wang, Yundong Sun, Baohui Lin, Haotian Zhang, Xiaoling Luo, Yumeng Liu, Xiaopeng Jin, Dongjie Zhu:
SEGT-GO: a graph transformer method based on PPI serialization and explanatory artificial intelligence for protein function prediction. 46 - Simon Schlumbohm, Julia E. Neumann, Philipp Neumann:
HarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation. 47 - Luke Kennedy, Jagdeep K. Sandhu, Mary-Ellen Harper, Miroslava Cuperlovic-Culf:
A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers. 48 - Yao Sun, Jing Gao:
HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer. 49 - Tianjiao Zhang, Liang Chen, Haibin Zhu, Garry Wong:
Mammalian piRNA target prediction using a hierarchical attention model. 50 - Diane M. Walker, Wendy A. Smith, Lia Gale, Jacob T. Wolff, Connor P. Healy, Hannah F. Van Hollebeke, Ashlie Stephenson, Marianne Kim:
CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity. 51 - Pia Keukeleire, Jonathan D. Rosen, Angelina Göbel-Knapp, Kilian Salomon, Max Schubach, Martin Kircher:
Using individual barcodes to increase quantification power of massively parallel reporter assays. 52 - Peng Sun, Yu Yang, Mengjie Yuan, Qin Tang:
CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes. 53 - Junheng Chen, Fangfang Han, Mingxiu He, Yiyang Shi, Yongming Cai:
A novel weighted pseudo-labeling framework based on matrix factorization for adverse drug reaction prediction. 54 - Jiashan Li, Xinqi Gong:
Harnessing pre-trained models for accurate prediction of protein-ligand binding affinity. 55 - Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya:
Identifying risk factors for Alzheimer's disease from multivariate longitudinal clinical data using temporal pattern mining. 56 - Na Quan, Shicheng Ma, Kai Zhao, Xuehua Bi, Linlin Zhang:
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism. 57 - Na Sun, Qiang Han, Yu Wang, Mengtong Sun, Ziqing Sun, Hongpeng Sun, Yueping Shen:
BHCox: Bayesian heredity-constrained Cox proportional hazards models for detecting gene-environment interactions. 58 - Lena Morrill Gavarró, Dominique-Laurent Couturier, Florian Markowetz:
A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures. 59 - Weiyin Zhou, Wen-Yi Huang, Neal D. Freedman, Mitchell J. Machiela:
Estimation of mosaic loss of Y chromosome cell fraction with genotyping arrays lacking coverage in the pseudoautosomal region. 60 - Sajid M. Hossain, Yiyun Rao, Jahid O. Hossain, Justin R. Pritchard, Boyang Zhao:
goloco: a web application to create genome scale information from surprisingly small experiments. 61 - Binhua Tang, Yiyao Chen:
scFTAT: a novel cell annotation method integrating FFT and transformer. 62 - Yu Wang, Hanghang Tong, Ziye Zhu, Fengzhen Hou, Yun Li:
Enhancing biomedical named entity recognition with parallel boundary detection and category classification. 63 - Shakeel Ahmed, Syed Muhammad Zaigham Abbas Naqvi, Muhammad Awais, Yongzhe Ren, Hao Zhang, Junfeng Wu, Linze Li, Vijaya Raghavan, Jiandong Hu:
Bacterial network for precise plant stress detection and enhanced crop resilience. 64 - Ahmed Miloudi, Aisha Al-Qahtani, Thamanna Hashir, Mohamed Chikri, Halima Bensmail:
Tisslet tissues-based learning estimation for transcriptomics. 65 - Matheus Henrique Pimenta-Zanon, André Yoshiaki Kashiwabara, André Luís Laforga Vanzela, Fabrício Martins Lopes:
GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs. 66 - Jaidip Gill, Abhijit Dasgupta, Brychan Manry, Natasha Markuzon:
Combining single-cell ATAC and RNA sequencing for supervised cell annotation. 67 - João Capela, Maria Zimmermann-Kogadeeva, Aalt D. J. van Dijk, Dick de Ridder, Oscar Días, Miguel Rocha:
Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction. 68 - Matthew D. Koslovsky:
Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model. 69 - Jianfeng Sun, Jinlong Ru, Adam P. Cribbs, Dapeng Xiong:
PyPropel: a Python-based tool for efficiently processing and characterising protein data. 70 - Petar Petrov, Valerio Izzi:
ProToDeviseR: an automated protein topology scheme generator. 71 - Joshua Chuah, Carmalena V. Cordi, Juergen Hahn, Jennifer M. Hurley:
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data. 72 - Yuyang Tao, Shufei Ge:
A distribution-guided Mapper algorithm. 73 - Daniel Agyapong, Jeffrey Ryan Propster, Jane Marks, Toby Dylan Hocking:
Cross-validation for training and testing co-occurrence network inference algorithms. 74 - Kangjin Kim, Sungho Won:
Robust phylogenetic tree-based microbiome association test using repeatedly measured data for composition bias. 75 - Austin Seamann, Maia Bennett-Boehm, Ryan Ehrlich, Anna Gil, Liisa K. Selin, Dario Ghersi:
TRain: T-cell receptor automated immunoinformatics. 76 - Tasfia Zahin, Md. Hasin Abrar, Mizanur Rahman Jewel, Tahrina Tasnim, Md. Shamsuzzoha Bayzid, Atif Rahman:
An alignment-free method for phylogeny estimation using maximum likelihood. 77 - Emily Zhang, Lauren Coombe, Johnathan Wong, René L. Warren, Inanç Birol:
GoldPolish-target: targeted long-read genome assembly polishing. 78 - Jordana Lindner, Bareket Dassa, Noa Wigoda, Gil Stelzer, Ester Feldmesser, Jaime Prilusky, Dena Leshkowitz:
UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline. 79 - He Zhao, Huan Xu, Tao Wang, Guixia Liu:
Constructing multilayer PPI networks based on homologous proteins and integrating multiple PageRank to identify essential proteins. 80 - Patrick Gohl, Baldo Oliva:
SNPeBoT: a tool for predicting transcription factor allele specific binding. 81 - Rohan Gnanaolivu, Gavin R. Oliver, W. Garrett Jenkinson, Emily Blake, Wenan Chen, Nicholas Chia, Eric W. Klee, Chen Wang:
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions. 82 - Yilin Feng, Zheyu Li, Gulsum Gudukbay Akbulut, Vijaykrishnan Narayanan, Mahmut Taylan Kandemir, Chita R. Das:
FPGA-based accelerator for adaptive banded event alignment in nanopore sequencing data analysis. 83 - Yan-Bo Pei, Zheng-Yang Yu, Jun-Shan Shen:
Transfer learning for accelerated failure time model with microarray data. 84 - Abigail Hui En Chan, Urusa Thaenkham, Tanaphum Wichaita, Sompob Saralamba:
Validating a web application's use of genetic distance to determine helminth species boundaries and aid in identification. 85 - Lei Chen, Yiwen Lu, Jing Xu, Bo Zhou:
Prediction of drug's anatomical therapeutic chemical (ATC) code by constructing biological profiles of ATC codes. 86 - Yasemin Bridges, Vinicius de Souza, Katherina G. Cortes, Melissa A. Haendel, Nomi L. Harris, Daniel R. Korn, Nikolaos M. Marinakis, Nicolas Matentzoglu, James A. McLaughlin, Christopher J. Mungall, Aaron Odell, David Osumi-Sutherland, Peter N. Robinson, Damian Smedley, Julius O. B. Jacobsen:
Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. 87 - Salman Khan, Sumaiya Noor, Hamid Hussain Awan, Shehryar Iqbal, Salman A. AlQahtani, Naqqash Dilshad, Nijad Ahmad:
Deep-ProBind: binding protein prediction with transformer-based deep learning model. 88 - Reinnier Padilla, Eric Bareke, Bo Hu, Jacek Majewski:
ChIPbinner: an R package for analyzing broad histone marks binned in uniform windows from ChIP-Seq or CUT&RUN/TAG data. 89 - Yuhang Huang, Fan Zhong, Lei Liu:
Uncovering latent biological function associations through gene set embeddings. 90 - Elise Coopman, Svenn D'Hert, Rosa Rademakers, Wouter De Coster:
Methylmap: visualization of modified nucleotides for large cohort sizes. 91 - Aissa Houdjedj, Yacine Marouf, Mekan Myradov, Süleyman Onur Dogan, Burak Onur Erten, Oznur Tastan, Cesim Erten, Hilal Kazan:
SCITUNA: single-cell data integration tool using network alignment. 92 - Qinghui Weng, Mingyi Hu, Guohao Peng, Jinlin Zhu:
DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts. 93 - Chia Yan Tan, Huey Fang Ong, Chern Hong Lim, Mei Sze Tan, Ean Hin Ooi, KokSheik Wong:
Amogel: a multi-omics classification framework using associative graph neural networks with prior knowledge for biomarker identification. 94 - Thomas M. Lange, Mehmet Gültas, Armin Otto Schmitt, Felix Heinrich:
optRF: Optimising random forest stability by determining the optimal number of trees. 95 - Junfeng Wang, Kuikui Cheng, Chaokun Yan, Huimin Luo, Junwei Luo:
DconnLoop: a deep learning model for predicting chromatin loops based on multi-source data integration. 96 - Carlos Uziel Pérez Malla, Jessica Kalla, Andreas Tiefenbacher, Gabriel Wasinger, Kilian Kluge, Gerda Egger, Raheleh Sheibani-Tezerji:
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences. 97 - Li Zhang, Xinyan Zhang, Justin M. Leach, A. K. M. F. Rahman, Carrie R. Howell, Nengjun Yi:
Bayesian compositional generalized linear mixed models for disease prediction using microbiome data. 98 - Yuyao Yan, Xinyi Chai, Jiajun Liu, Sijia Wang, Wenran Li, Tao Huang:
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations. 99 - Grigoriy Gogoshin, Andrei S. Rodin:
Minimum uncertainty as Bayesian network model selection principle. 100 - Daniel Henrique Ferreira Gomes, Inácio Gomes Medeiros, Tirzah Braz Petta, Beatriz Stransky, Jorge Estefano Santana de Souza:
DTreePred: an online viewer based on machine learning for pathogenicity prediction of genomic variants. 101
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