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ORCIDBMC Bioinformatics, Volume 27
Volume 27, Number 1, December 2026
- Alexandre Chaussard
, Anna Bonnet, Sylvain Le Corff, Harry Sokol:
TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. 1 - Grigoriy Gogoshin, Andrei S. Rodin:
Correction: Minimum uncertainty as Bayesian network model selection principle. 2 - Jiadong Chu, Yu Wang, Na Sun, Qiang Han, Ziqing Sun, Mengtong Sun, Yuheng Yuan, Qida He, Yueping Shen:
A parametric survival model with bayesian structural equation based on multi-omics integration. 3 - Ramu Gautam, Yang Jiao, Yasong Pang, Mo Weng, Mei Yang:
ProTrack3D: a comprehensive tool for segmentation and tracking of proteins with split and fusion. 4 - Tazin Rahman, Ananth Kalyanaraman:
Density-reducing Jaccard estimators for sketch-based long read applications. 5 - Laura Aviñó-Esteban, Heura Cardona-Blaya, Marco Musy, Antoni Matyjaszkiewicz, James Sharpe, Giovanni Dalmasso:
Limblab: pipeline for 3D analysis and visualisation of limb bud gene expression. 6 - Binbin Wu, William W. Ja:
easyClock: a user-friendly desktop application for circadian rhythm analysis and visualization. 7 - Yaxin Fan, Yichao Mei, Shengbao Bao, Jianyong Wang, Junxiang Gao:
A DSSM network for inferring and prioritizing cell-type-specific regulons using single-cell RNA-seq data. 8 - Chun Hing She, Sophelia Hoi-Shan Chan, Wanling Yang:
SVhet: towards accurate detection of germline heterozygous deletions using short reads. 9 - Martin Engst, Martin Brokes, Tereza Calounová, Raman Samusevich, Roman Bushuiev, Anton Bushuiev, Ratthachat Chatpatanasiri, Adéla Tajovská, Safa Mert Akmese, Milana Perkovic, Matous Soldát, Josef Sivic, Tomás Pluskal:
MARTS-DB: a database of mechanisms and reactions of terpene synthases. 10 - Jiahui Sun, Shengli Wu, Xiangjun Shen, Chris D. Nugent, Hu Lu:
Subset selection based fusion for biomedical information retrieval tasks. 11 - Jie Kang, Melanie K. Hess, Ken G. Dodds, Rüdiger Bräuning, John C. McEwan, Barry J. Foote, Judy F. Foote, Agnieszka Konkolewska, Shannon M. Clarke, Andrew S. Hess:
SimGBS: a rapid method for simulating large-scale genotyping-by-sequencing data. 12 - Amr Mohamed, Kevin H. Lee:
Gradient boosting with knockoff filters: a biostatistical approach to variable selection. 13 - Annekathrin Silvia Nedwed, Arsenij Ustjanzew, Najla Abassi, Leon Dammer, Alicia Schulze, Sara Salome Helbich, Michael Delacher, Konstantin Strauch, Federico Marini:
GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor. 14 - Jacob Pfeil, Liqian Ma, Hin Ching Lo, Tolga Turan, R. Tyler McLaughlin, Xu Shi, Severiano Villarruel, Stephen Wilson, Xi Zhao, Josue Samayoa, Kyle Halliwill:
Pairwise ratio transformation of gene expression data leads to improved checkpoint response prediction in lung cancer patients. 15 - Jack Freeman, Robert J. Millikin, Leo Xu, Ishaan Sharma, Bethany Moore, Cannon Lock, Kevin Shine George, Aviral Bal, Chitrasen Mohanty, Ron M. Stewart:
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation. 16 - Violeta de Anca Prado, Fábio Pértille, Pedro Sá, Marta Gòdia, Joëlle Rüegg, Josep C. Jimenez-Chillaron, Carlos Guerrero-Bosagna:
Benchmarking of methods to analyse data derived from GBS-MeDIP. 17 - Istvan Szepesi-Nagy, Roberta Borosta, Zoltan Szabo, Gabor E. Tusnady, Lorinc S. Pongor, Gergely Rona:
Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments. 18 - Md. Masud Rana, Farjana Tasnim Mukta, Duc Duy Nguyen:
A geometric graph-based deep learning model for drug-target affinity prediction. 19 - Benjamin Lieser, Georgy Belousov, Johannes Söding:
Phylograd: fast column-specific calculation of substitution model gradients. 20 - Szabolcs Makai, Diána Makai, Erika Chonata-Jiménez, Ildikó Karsai, Péter Mikó, Adél Sepsi, András Cseh:
X-cross/over: a web tool for graph-based estimation of meiotic crossover events in plants. 21 - Chiara Schiller, Matthias Lemmer, Sonja Reitter, Janina A. Lehmann, Kai Fenzl, Johanna Schott:
QuAPPro: an R shiny app for quantification and alignment of polysome profiles. 22 - Jiaye Li, Zijian Sun, Shuo Chai, Hangming Li, Yijun Wang, Jingkui Tian:
AR-CDT NET: a deep deformable convolutional network for gut microbiome-based disease classification. 23 - Naafey Aamer, Muhammad Nabeel Asim, Andreas Dengel:
Comic: explainable drug repurposing via contrastive masking for interpretable connections. 24 - Fang Liu, Rui He, Tommy R. Sheeley, David A. Scheiblin, Stephen J. Lockett, Lisa A. Ridnour, David A. Wink, Mark Jensen, Janelle Cortner, George Zaki:
SPAC: a scalable and integrated enterprise platform for single-cell spatial analysis. 25 - He Li, Zander Gu, Said el Bouhaddani, Jeanine J. Houwing-Duistermaat:
Statistical modelling of an outcome variable with integrated multi-omics. 26 - Jinxin Li, Xinguo Lu, Zihao Li, Xing Liu, Hongrui Liu, Jingjing Ruan:
MGANSL: multi-network representation generating with generative adversarial network for synthetic lethality prediction. 27 - Lucas F. Jansen Klomp, Xinqi Yan, Rebecca R. Snabel, Gert Jan C. Veenstra, Hil G. E. Meijer, Janine N. Post:
DANSE: a pipeline for dynamic modelling of time-series multi-omics data. 28 - Tristan Cumer, Sotiria Milia, Alexander S. Leonard, Hubert Pausch:
PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers. 29 - Daniel Zyss, Amritansh Sharma, Susana A. Ribeiro, Claire E. Repellin, Oliver Lai, Mary J. C. Ludlam, Thomas Walter, Amin Fehri:
Contrastive learning for cell division detection and tracking in live cell imaging data. 30 - Xiao Han, Xiaochen Cen, Zhijin Li, Xiaobo Zhou, Zhiwei Ji:
DCPR: a deep learning framework for circadian phase reconstruction. 31 - Lei Chen, Jing Yang, Bo Zhou, Yu-Dong Cai:
PLysPTM-HGNN: predicting lysine PTM sites of proteins using hybrid graph neural networks. 32 - Sicheng He, Cheng Chen, Xianrun Pan, Gaogao Xue, Yu Yang, Juan Feng, Hasan Zulfiqar, Yang Zhang, Kejun Deng:
CMsiRNAdb: a database of chemically modified SiRNA silencing efficiency for nucleic acid drug design. 33 - Ponian Li, Guodong Xiao, Haihui Wang, Chunrui Xu, Yusen Zhang:
MODCAN: driver gene identification based on multi-omics features and differential co-association networks for tumor subtypes. 34 - Xiaowen Wang, Yanming Huang, Hongming Zhu, Dongsheng Mao, Xiaoli Zhu, Qin Liu:
Hgtsynergy: a transfer learning method for predicting anticancer synergistic drug combinations based on a drug-drug interaction heterogeneous graph. 35 - Erik D. Huckvale, Hunter N. B. Moseley:
Predicting the pathway involvement of metabolites annotated in the MetaCyc knowledgebase. 36 - David H. Rogers, Cullen Roth, Cameron Tauxe, Jeannie T. Lee, Christina R. Steadman, Karissa Y. Sanbonmatsu, Anna Lappala, Shawn R. Starkenburg:
From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture. 37 - Ivan Ferrari, Mattia Battistella, Francesca Vincenti, Andrea Gobbini, Federico Marini, Samuele Notarbartolo, Jole Costanza, Stefano Biffo, Renata M. Grifantini, Sergio Abrignani, Eugenia Galeota:
CIA: unveiling cellular identities with cluster-independent annotation in single-cell RNA sequencing data for comprehensive cell type characterization and exploration. 38 - Grazia Gargano, Flavia Esposito, Nicoletta Del Buono, Sabino Ciavarella, Maria Carmela Vegliante:
Identification of differentially expressed genes in RNA-seq data via semi-rigid orthogonal sparse KL-NMTF. 39 - Saman Zabihi, Sattar Hashemi, Eghbal Mansoori:
EDEN: multiscale expected density of nucleotide encoding for enhanced DNA sequence classification with hybrid deep learning. 40 - Nabil Rahiman, Michael A. Ochsenkühn, Shady A. Amin, Kristin C. Gunsalus:
MIMI: Molecular Isotope Mass Identifier for stable isotope-labeled Fourier transform ultra-high mass resolution data analysis. 41 - Mehmet Ali Balikci, Cyrille Mesue Njume, Ali Cakmak:
BioMark: biomarker analysis tool. 42 - Gilles Sireta, Gwendal Cueff, Vincent Darbot, Marie Lefebvre, Simon Amiard, Aline V. Probst, Christophe Tatout:
CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool. 43 - Sebastian Raubach, Miriam Schreiber, Ruth Hamilton, Gaynor McKenzie, Susan McCallum, Benjamin Kilian, Alan Humphries, Loi Huu Nguyen, Tin Huynh Quang, Akanksha Singh, Shivali Sharma, Sarah Trinder, Manuel Feser, Paul D. Shaw:
Beyond the clipboard: data collection with GridScore NEXT. 44 - Hyotae Kim, Nazema Y. Siddiqui, Lisa Karstens, Li Ma:
A negative binomial latent factor model for paired microbiome sequencing data. 45 - Artem Ershov, Renpeng Ding, Qian Fu, Ivan Kozlov, Ekaterina Fadeeva, Evgeniy Mozheiko, Ming Ni, Yong Hou, Yan Zhou:
zDUR: reference-free FASTQ compressor with high compression ratio and speed. 46 - Simone Montalbano, G. Bragi Walters, Gudbjorn F. Jonsson, Jesper R. Gådin, Thomas Werge, Daniel Fannar Gudbjartsson, Hreinn Stefansson, Andrés Ingason:
CNValidatron: accurate and efficient validation of PennCNV calls using computer vision. 47 - Blaz Brence, Josephine Brummer, Vincent J. Dercksen, Mehmet Neset Özel, Abhishek Kulkarni, Neele Wolterhoff, Steffen Prohaska, Peter Robin Hiesinger, Daniel Baum:
Semi-automatic geometrical reconstruction and analysis of filopodia dynamics in 4D two-photon microscopy images. 48 - Hamdiye Uzuner, Felix Wiegand, Sven Schrinner, David Laehnemann, Dirk Schadendorf, Johannes Köster:
Virus variant quantification with Orthanq. 49 - Abdulraheem Arome Musa, Norbert Reinsch:
PyMSQ: a Python package for fast Mendelian sampling (co)variance and haplotype-based similarity in genomic selection. 50 - Charlie Bayne, Brianna Hurysz, David J. Gonzalez, Anthony O'Donoghue:
mspms: an R package and GUI for multiplex substrate profiling by mass spectrometry. 51 - Thi Van Nguyen, Van Hoan Do, Vu-Linh Nguyen:
Srnc: semi-supervised learning for robust novel cell-type identification in single cell RNA sequencing data. 52 - Scott Silvey, Amy Olex, Shaojun Tang, Jinze Liu:
Sample size requirements for machine learning classification of binary outcomes in bulk RNA-Seq data. 53 - Dominik Robak, Guillem Ylla:
piRAT: piRNA Annotation Tool for annotating, analyzing, and visualizing piRNAs. 54 - Yongqing Zhang, Le Chen, Hong Luo, Tianhao Li, Shuwen Xiong, Zixuan Wang, Quan Zou, Wenqian Zhang:
Contrastive learning in both structure and function spaces improve drug-target interaction prediction. 55 - Simo Iisakki Inkala, Michele Fratello, Giusy del Giudice, Giorgia Migliaccio, Angela Serra, Dario Greco, Antonio Federico:
MUUMI: an R package for statistical and network-based meta-analysis for multi-omics data integration. 56 - John Stephen Malamon:
DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants. 57 - Guojing Cong, Robert M. Patton, Frank Chao, Daniel L. Svoboda, Jeremy N. Erickson, Michele R. Balik-Meisner, Deepak Mav, Dhiral P. Phadke, Elizabeth H. Scholl, Ruchir R. Shah, Scott S. Auerbach:
Transplatformer: translating toxicogenomic profiles between generations of platforms. 58 - Samuel Hamilton, Gaurav Gadhvi, Tyler Therron, Deborah R. Winter:
Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples. 59 - Niccolò Bianchi, Armel E. J. L. Lefebvre, Katherine J. Wolstencroft, Marco Spruit:
Design and evaluation of semantically-valid negative samples integration techniques for scalable semi-automated drug repurposing prediction pipelines in rare disease research. 60 - Muhaiminur Hossain, Anik Mojumder, S. M. Mahbubur Rashid, Abul Bashar Mir Md Khademul Islam:
ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species. 61 - Yi Zhao, Xuteng Ye, Jun Cheng, Li Yin, Danyu Shen, Daolong Dou, Jinding Liu:
YamOmics: a comprehensive data resource on yam multi-omics. 62 - Xuan Wang, Zhengao Mo, Fuwei Li, Fa Zhang, Xiaohua Wan:
Point cloud deformation modeling for particle selection following cryo-EM 2D classification. 63 - Gabriel Victor Pina Rodrigues, Lucas Yago Melo Ferreira, Eric Roberto Guimarães Rocha Aguiar:
ViralQuest: a user-friendly interactive pipeline for viral-sequences analysis and curation. 64 - Daehee Kim, Seongjun Byun, Jaehyun Park, Soo-Jin Jang, Yongku Kim, Seung Yeop Yang, Myungjin Kim, Semin Oh, Jieun Lee, Kee-Beom Kim, Dong Kyu Choi, Samuel Beck, Jun-Yeong Lee:
hStouffer: the enhanced meta-analysis method for the comprehensive analysis of large-scale RNA-seq data. 65 - Zeyu Chen, Yuqi Liu, Jia Meng, Jiaming Huang, Xuan Wang, Xiangyu Yin, Wei Zhong, Gang Tu, Yongshuang Xiao:
Domain-derived knowledge enabled machine learning and functional characterization of cancer-associated RNA methylation sites. 66 - Evelin Aasna, Simon Gottlieb, Marcel Ehrhardt, Knut Reinert:
DREAM-Stellar: parallel and space efficient exact local alignment. 67 - Ugochukwu O. Ugwu, Richard A. Slayden, Michael Kirby:
Transfer learning models for bacterial strain dissemination biomarkers using weighted non-parallel proximal support vector machines. 68 - Soumya Nayak, Dheemanth Reddy Regati, Murugavel Pavalam, Ramanathan Sowdhamini:
Cascade PSI-BLAST 2.0: a fast-searching parallelized remote homology detection tool and development of Cascade web server 2.0. 69 - Rui Geng, Benjamin L. Kidder:
ColonyQuant: automated quantification and morphometric analysis of pluripotent stem cell colonies. 70 - Awais Qureshi, Abdul Wahid, Shams Qazi, Muhammad K. Shahzad, Hashir Moheed Kiani, Muhammad Daud Abdullah Asif:
DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models. 71 - Nesma Lotfy:
Transformation to estimate the causal effect in Mendelian randomization study with binary risk factor and outcome. 72 - Kei Yoshida, Shoji Hisada, Ryoichi Takase, Atsushi Okuma, Yoshihito Ishida, Taketo Kawara, Takuya Miura-Yamashita, Daisuke Ito:
Enhancing CAR-T cell activity prediction via fine-tuning protein language models with generated CAR sequences. 73 - Mengke Guo, Xiucai Ye, Tetsuya Sakurai:
Robust graph structure learning to improve multi-omics cancer subtype classification. 74 - Reshma Rastogi, Mamta Bhattarai Lamsal:
Semisupervised approach for dominant gene selection and classification. 75 - Roberto Pagliarini, Francesco Nascimben, Alberto Policriti:
A two-phase clustering procedure based on allele specific expression. 76 - Bayu Brahmantio, Krzysztof Bartoszek, Etka Yapar:
Bayesian inference of mixed Gaussian phylogenetic models. 77 - Juan Kim, Doyeon Lee, Jina Park, Ick Hoon Jin, Min Jin Ha:
BDDN: bayesian dynamic differential network analysis in cancer proteomics. 78 - Akanksha Mishra, Wei Xia, Clint Pazhayidam George:
A weight-sharing Bayesian neural network for consistent feature selection with applications in cancer gene expression data. 79 - Georgina Fuentes-Páez, Nacho Molina, Mireia Ramos-Rodríguez, Lorenzo Pasquali:
SPICEY: an R package for quantifying tissue specificity from single cell multi-omics data. 80 - Alemu Tsega, Destaw Mullualem:
Machine learning for multi-omics data integration in crop improvement: a systematic review. 81 - Ruimeng Li, Ying Wang, Haozhou Li, Biyi Zhou, Qinke Peng:
Multimodal learning on heterogeneous subgraphs and LLMs representation for MHC-peptide binding affinity prediction. 82 - Akin Anarat, Jean Krutmann, Holger Schwender:
A nonparametric statistical method for deconvolving densities in the analysis of proteomic data. 83 - Saniya Gupta, A. Sherly Alphonse, Kavitha Dhanushkodi:
Uncertainty-aware hybrid deep generative framework for robust and explainable drug discovery. 84 - Moritz Stadler, Sabina Gansberger, Liliane Borik-Heil, Johannes Griss, Ichiro Okamoto, Wolfgang P. Weninger, Matthias Wielscher:
ACVI-Med, an open source variant interpretation tool for medical genomics. 85 - Lotfi Bouzeraa, Marc-André Sirard:
Bovine EpiMap explorer: an interactive web application for genome-wide DNA methylation analysis in dairy cattle. 86 - Samia Sultana, Hongmei Zhang, Yu Jiang, Mohammad Nahian Ferdous Abrar, Hasan Arshad, Lu Xie, Meredith Ray:
Impact of influential data on screening epigenome-wide data. 87 - Yannan Yuan, Liufang Sheng, Zhikang Chen, Yuejun Zhang, Qikang Li, Junping Chen, Ke Ding, Lei Shi, Qiaoxia Hu, Wenming He:
Design of a configurable SoC for Alzheimer's disease detection based on multimodal signals. 88 - Shanwen Zhang, Chuanlei Zhang, Dengwu Wang:
C2M-Mamba: drug-drug interaction prediction based on cross-modal cross-Mamba. 89 - Hao Zhu, Tong Liu, Bishal Shrestha, Zheng Wang:
SCW: building the whole-genome 3D structures based on extremely sparse single-cell Hi-C data. 90 - Xiao Gao, Jianhua Jia, Cong Hui, Yang Lin:
Mke-resnet: a lightweight and interpretable deep learning framework for efficient RNA m6A site identification. 91 - Long Tuan Vo, Van Vinh Le, Quoc Toan Ha, Anh Quoc Nguyen:
scZiva: imputation method for single-cell RNA-seq data with zero-inflated variational autoencoder. 92 - Bader F. Al-Anzi, Nasser B. Alkhalifah, Hesham A. Almansouri, Arwa AlSirhan:
Development of a comprehensive GWAS atlas for chicken breeds. 93 - Hailin Chen, Zirui Song:
SPGA: graph representation learning and attention fusion for enhanced disease-associated snoRNA prediction. 94 - Nan Zhou, Tong Yin, Huiran Sun, Qiqi Luo, Yuhong Zhang, Xiaolei Shi, Jinku Bao, Li Peng, Xiaoqing Yuan:
RCDRank: a web server to prioritize regulated cell death modalities. 95 - Tim Müller, Roman Hornung, Silke Szymczak, Hannes Buchner:
ShadowVIMP: permutation-based multiple testing-controlled variable selection. 96 - Xiujuan Guo, Ning Zhao, Guohua Wang, Chunlong Zhang:
MAGMDA: a multi-order adaptive graph-based miRNA-disease association prediction model. 97 - Tuna Alaygut, Emre Sefer:
A comparative analysis of topological domain callers over RNA-associated interactome. 98 - Tengfei Cui, Guanghao Qi:
DAESC + : high-performance, integrated software for single-cell allele-specific expression data. 99 - Yan Sun, Fanyu Zhang, Shijia Yan, Xiaotong Kong, Hanxiang Wang, Junliang Shang, Jin-Xing Liu:
DHGCMDA: a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction. 100 - Zhen Zhao, Rui Tang, Qifeng Liu:
Adaptive enhancement of chest X-ray images using tissue attenuation and local and global fusion. 101 - Wanqiu Cheng, Jintao Tang, Ting Wang, Shasha Li, Ting Deng:
AutoPrompt-SAM3D: integrated generation and selection for SAM2-based 3D medical segmentation. 102 - Joaquim Vertentes Rosa, João Andrade, Jorge Miguel Silva, José Luís Oliveira:
Biochef: a client-side WebAssembly-based workflow builder for genomic data analysis. 103 - Hong Wang, Xiaolong Ou, Wenshuai Zhang, Ben Niu:
Gradual spatial constraint feature selection for robust biomarker discovery in high-dimensional gene expression data. 104 - Euna Jeong, Seungyean Lee, Sumin Jeong, Hansaem Lee, Kyung-Chang Kim, Joo-Yeon Lee, Minwook Shin, Sukjoon Yoon:
QStrain: an interactive platform for viral genome analysis and nucleic acid therapeutic design. 105 - Alperen Dalkiran, Ahmet Süreyya Rifaioglu, Rengül Çetin-Atalay, Aybar C. Acar, Tunca Dogan, M. Volkan Atalay:
Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation. 106 - Zecheng Tang, Daohua Zhuang, Xinmin Duan, Qingqing Gong, Chen Tian, Peicheng Jiang, Jiangkun Yu, Fei Li, Fangfang Zhao, Guolin Shi, Hang Yang, Qinghang Du, Tong Li, Zhiqiang Ye, Zhigang Zhang:
MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels. 107 - Kareem Kabbani, Samir B. Belhaouari, Michaël Aupetit, Aisha Al-Qahtani, Ahmad Halabi, Sophia L. Haoudi, Halima Bensmail:
Efficient and interpretable DNA/RNA representation using Komlós-Hadamard transforms. 108 - Anjum Shahzad, Sheeraz Akram, Tahir Mehmood:
GGAR: gradient guided adaptive regularization enhances deep learning classification of brassica species using codon usage bias. 109 - Simon Witzke, Julian Zabbarov, Maximilian Kleissl, Pascal Iversen, Bernhard Y. Renard, Katharina Baum:
Selecting synthetic data for successful simulation-based transfer learning in dynamical biological systems. 110 - Kai-Yu Chen, Shang-Fu Chen, Raquel Dias, Ali Torkamani:
A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models. 111 - Zhihai Zhang, Weijia Jia, Joao Paulo Gomes Viana, Ping-Hung Hsieh, Yasuo Yoshikuni, Matthew Hudson:
pyFLANK, a graph neural network based null distribution inference model for FST outlier detection. 112 - Ben Bausch, Mina Naseh, Gonçalo Gaspar Alves, Andreas Husch, Thomas Gillet, Michael T. Heneka, Jorge M. Gonçalves, Sergio Castro-Gomez, Shekoufeh Gorgi Zadeh:
MOLT: multi-object and lineage tracking in 2D and 3D biomedical time-series imaging. 113 - Venkata Prasanna Nagari, Vinoth Subbiah:
A novel IVN-entropy based distance-driven MARCOS framework for evaluating and ranking global green hydrogen-producing countries. 114 - Salvatore Galgano:
Genomica: linear mixed model based, multiple hypothesis testing corrected, ortholog functional enrichment analysis. 115 - Li Qian, Lili Du, Mang Liang, Keanning Li, Jinbu Wang, Shiyuan Qiu, Meng Mao, Lupei Zhang, Xue Gao, Lingyang Xu, Caihong Zheng, Bo Zhu, Yan Chen, Zezhao Wang, Junya Li, Huijiang Gao:
Enhancing genomic prediction accuracy in Huaxi cattle through integration of transcriptomic data and a self-attention-based SNP selection strategy. 116 - Hu Xu, Yuanli Ni, Zixuan Chai, Xuan Cui, Xia Lei, Limei Liu, Juanjuan Shan, Cheng Qian:
TransBindpMHCI: a transformer-based model for pan-specific MHC-I peptide binding prediction. 117 - Xingyue Tan, Xiran Chen, Renjie Tian, Qinyu Cai, Miaoyuan Jiang, Dongqiu Yang, Lei Zhang:
Triad-LMF: a hierarchical low-rank multimodal fusion framework for robust cancer subtype classification using multi-omics data. 118 - Koyel Mandal, Sanghamitra Bandyopadhyay:
BKDRP: a biological knowledge-driven approach for drug response prediction using multi-omics data in cancer cell lines. 119 - Milad Rayka, S. Shahab Naghavi:
Reindeer: a protein-ligand feature generator software for machine learning algorithms. 120 - Lina Abou-Abbas, Khadidja Henni:
Protein and ligand novelty in drug-target interaction prediction: a dual-encoder fusion strategy for more interpretable and generalizable modeling. 121 - Jinyang Zhang, Xingyang Li, Bo Wei, Yuni Zeng:
DCI-SiteDTA: drug-target affinity prediction based on binding sites detection and site-aware dual cross-interaction block. 122 - Blaz Brence, Laura R. Wandelt, Sophie Walter, Stephan J. Sigrist, Astrid G. Petzoldt, Daniel Baum:
Semi-automatic 3D-quantification of in-vivo synapse formation. 123 - Josua Stadelmaier, Brandon Malone, Ralf Eggeling:
Transfer learning for T-cell response prediction. 124 - Zhanshan (Sam) Ma, Lianwei Li, Ya-Ping Zhang:
A new SNP comparison (SnpC) method for detecting unique/enriched gene-SNP variants and comparing population gene mutation diversity. 125 - Eleonora Meo, Veronica Lombardi, Veronica Venafra, Valerio Licursi, Francesca Sacco, Livia Perfetto:
MultiOmicsXplorer, a tool to browse, access and analyse multi-omics data. 126 - Amirhossein Akbarpour Arsanjani, Ziba Veisi Malekshahi, Bashir Mosayyebi, Babak Negahdari, Masoumeh Amirlou, Fatemeh Khavari, Davood Rabiei Faradonbeh:
A structural bioinformatics framework for prioritizing pH-sensitive proteins from 3D structural features. 127 - Zheng-Xiang Ye, Steven H. Wu:
A probabilistic approach for predicting indole-3-acetic acid synthesis in bacteria using genomic data. 128 - Paimon Goulart, Kieran Samuk:
vcfsim: flexible simulation of all-sites VCFs with missing data. 129 - Le Tong, Tao Shu, Xinru Zhuang, Jingrui Bai, Lun Hu, Feng Tan, Yu-An Huang, Zhuhong You, Pengwei Hu:
DeShiftNet: a deformable-shifted cross-attention network for lightweight and robust organoid image segmentation. 130 - Rira Matsuta, Hiroyuki Yamamoto, Atsushi Fukushima, Sho Tabata, Hideki Makinoshima, Tomoyoshi Soga, Rintaro Saito, Eisuke Hayakawa:
An enrichment-based approach to interpreting metabolomic data using differential metabolomic profiles within the iDMET framework. 131 - Haoran Liu, Xiaoli Lin, Jing Hu, Xiaolong Zhang:
A multi-target drug design method based on target feature fusion. 132 - Ping Xuan, Zhicheng Guo, Siyuan Lu, Hui Cui, Jian Ding, Tiangang Zhang:
Multi-granularity transformer contrastive learning and feature reconstruction for prediction of disease-related miRNAs. 133 - Daniel Pfeifer, Markus Graf, Clas Rurik:
Genestrip: exact and efficient read classification for selected groups of organisms. 134 - Emily Morgan, Shaylyn Govender, Prashant Singh, Ian Goodfellow, Stephen C. Graham, Nigel T. Bishop, Özlem Tastan Bishop:
Machine learning framework for cost effective deep mutational scanning through targeted substitution profiling. 135 - Rongqing Yuan, Jing Zhang, Qian Cong:
Reciprocal best matching: a new pipeline for scoring models with unknown stoichiometry in CASP experiments. 136 - Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt:
Accelign: a GPU-based library for accelerating pairwise sequence alignment. 137 - Jiyeon Min, Bernard R. Brooks, Muhamed Amin:
FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins. 138 - Jiahui Wu, Yiyu Lin, Peng Shen, Lun Zhu, Sen Yang:
UniPTMs: a unified multi-type PTM site prediction model via master-slave architecture-based multi-stage fusion strategy and hierarchical contrastive loss. 139 - Ronald Domi, Falko Noé, Peter Leary, Hubert Rehrauer:
GEO uploader: simplifying the data deposition in the GEO repository. 140 - Vito Paolo Pastore, Riccardo Rorato, Larbi Touijer, Roberto Di Via, Francesca Odone, Lisa M. Galli, Laura W. Burrus, Simone Bianco:
FiloAnalyzer: a deep learning approach for cell filopodia segmentation. 141 - Jinru Li, Sisi Ou, Shi Qiu, Yuxiang Ma, Songye Gao, Xiaohu Shi:
CMV-GLA: contrastive multi-view graph layer attention for predicting phosphorylation site-disease associations. 142 - Ahmad Rafi, Alimath Sambreena, Mahammad Nisar, Rajesh Raju, Poornima Ramesh:
M2Viz: a tool for visualizing genetic or proteomic modifications and variants. 143 - Chu Pan, Yanlin Chen, Tianwu Zhang:
Investigate synergistic and competitive regulation between miRNAs by using a multivariate information measurement. 144 - Shuaiyi Wang, Mengni Xu, Yuxin Tang, Kaixuan Wang, Jinbao Wen, Yu Cheng, Fangrong Yan, Tiantian Liu:
A multi-tissue mendelian randomization method based on eQTL data for mapping tissue-specific disease genes. 145 - Behrooz Darbani, Mogens Nicolaisen:
On the genetic origins of phenotypes in genome-wide association studies: the SAFE-h2 tool for exploring additive and non-additive allelic effects. 146 - John K. Pearman, Eva Aylagas, Susana Carvalho:
BIOWATCH: a R shiny application for the detection of species of interest in metabarcoding datasets. 147 - Alfonso Landeros, Dhwani Krishnan, Kenneth Lange, Mary E. Sehl:
mGEM: multigraph estimation models for pattern analysis. 148 - Hayat Ali Shah, Albash Khan:
Modeling and classifying neuronal activity with a fusion of mathematical and machine learning techniques. 149 - Lily He, Kaixin Pan, Youlin Shi, Kun Peter Li, Yuhua Ruan, Dan Li, Hengjian Cui:
Prediction of HIV-1 sensitivity to broadly neutralizing antibodies using statistical distribution sampling (SDS) technology. 150 - Mehmet Burak Koca, Fatih Erdogan Sevilgen:
Explainable graph learning for multimodal single-cell data integration. 151 - Sahil Thapa, Khushali Samderiya, Rohit Menon, Oluwatosin Oluwadare:
Spliceread: improving canonical and non-canonical splice site prediction with residual blocks and synthetic data augmentation. 152 - Natalia E. Jiménez, Mikael Espinoza, Sebastián Mejías, Sebastián Nelson Mendoza, Ignacia Segovia, J. Cristian Salgado, Carlos Conca, Ziomara P. Gerdtzen:
Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis. 153 - Guoqing Jiang, Jingming He, Xuemeng Fan, Xiaoya Gao, Ran Huang, Cong Wu, Bairong Shen:
Towards precision oncology: unsupervised manifold learning for spatial molecular profiling in cancer tissues. 154 - Soraya Mirzaei, Mojtaba Tefagh:
MOFA: microbial optimization without forced altruism. 155 - Qiang Gao, Zhijin Li, Yang Deng, Zhiwei Ji:
ProtSeqGen: a novel deep learning model for protein sequence design. 156 - Zohreh Piroozeh, Ildem Akerman, Olga V. Kalinina, Stefan Kesselheim, Alina Bazarova:
Interpretable prediction of DNA replication origins in S. cerevisiae using DNABERT and DNABERT-2. 157 - Qing Wu, Ailing Zhang, Zhibin Ning, Daniel Figeys:
MetaTree: an interactive web platform for aligned hierarchical data visualization and multi-group comparison. 158 - Nourhan Helmy, Huda Amin Maghawry, Nagwa L. Badr:
Mol2Image: an enhanced DDI prediction framework leveraging drug molecular descriptors. 159
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