default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
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 Dias, 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 - Mahsa Sheikholeslami, Mohammad Hasan Nazari, Afshin Fassihi:
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures. 102 - Yasir Rahmatallah, Galina V. Glazko:
Improving data interpretability with new differential sample variance gene set tests. 103 - Yue Xie, Zehua Jing, Hailin Pan, Xun Xu, Qi Fang:
Redefining the high variable genes by optimized LOESS regression with positive ratio. 104 - Camille Guilmineau, Marie Tremblay-Franco, Nathalie Vialaneix, Rémi Servien:
Phoenics: a novel statistical approach for longitudinal metabolomic pathway analysis. 105 - Daniel Ortiz-Martínez:
DeBasher: a flow-based programming bash extension for the implementation of complex and interactive workflows with stateful processes. 106 - Georgios A. Manios, Aikaterini Michailidi, Panagiota I. Kontou, Pantelis G. Bagos:
PRED-LD: efficient imputation of GWAS summary statistics. 107 - Kai Wang, Yulong Li, Fei Liu, Xiaoli Luan, Xinglong Wang, Jingwen Zhou:
GRLGRN: graph representation-based learning to infer gene regulatory networks from single-cell RNA-seq data. 108 - Evgenia K. Nikolitsa, Panagiota I. Kontou, Pantelis G. Bagos:
metacp: a versatile software package for combining dependent or independent p-values. 109 - Kai Zhao, Zhuocheng Ji, Linlin Zhang, Na Quan, Yuheng Li, Guanglei Yu, Xuehua Bi:
HPOseq: a deep ensemble model for predicting the protein-phenotype relationships based on protein sequences. 110 - Limuxuan He, Quan Zou, Yansu Wang:
metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows. 111 - Xingjian Gao, Jiarui Li, Xinxuan Liu, Qianqian Peng, Han Jing, Sibte Hadi, Andrew E. Teschendorff, Sijia Wang, Fan Liu:
FastQTLmapping: an ultra-fast and memory efficient package for mQTL-like analysis. 112 - Franco Liberati, Taiel Maximiliano Pose Marino, Paolo Bottoni, Daniele Canestrelli, Tiziana Castrignanò:
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets. 113 - Kazuki Nakamae, Saya Ide, Nagaki Ohnuki, Yoshiko Nakagawa, Keisuke Okuhara, Hidemasa Bono:
PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing. 114 - Javier Munoz Briones, Douglas K. Brubaker:
A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling. 115 - Jun Xie, Youli Zhang, Ziyang Wang, Xiaocheng Jin, Xiaoli Lu, Shengxiang Ge, Xiaoping Min:
PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models. 116 - Nalini Schaduangrat, Hathaichanok Chuntakaruk, Thanyada Rungrotmongkol, Pakpoom Mookdarsanit, Watshara Shoombuatong:
M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy. 117 - Zeyu Xia, Canqun Yang, Chenchen Peng, Yifei Guo, Yufei Guo, Tao Tang, Yingbo Cui:
Fast noisy long read alignment with multi-level parallelism. 118 - Dohee Lee, Jaegyoon Ahn, Jonghwan Choi:
PathNetDRP: a novel biomarker discovery framework using pathway and protein-protein interaction networks for immune checkpoint inhibitor response prediction. 119 - Xinyue Cui, Yuhao Xia, Minghua Hou, Xuanfeng Zhao, Suhui Wang, Guijun Zhang:
M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling. 120 - Rémi-Vinh Coudert, Jean-Philippe Charrier, Frédéric Jauffrit, Jean-Pierre Flandrois, Céline Brochier-Armanet:
Multi-proteins similarity-based sampling to select representative genomes from large databases. 121 - Miguel Guardado, Cynthia Perez, Sthen Campana, Berenice Chavez Rojas, Joaquín Magaña, Shalom Jackson, Emily Samperio, Selena Hernandez, Kaela Syas, Ryan D. Hernandez, Elena I. Zavala, Rori Rohlfs:
py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis. 122 - Kaiwei Zhang, Yange Lin, Guangcheng Wu, Yuxiang Ren, Xuecang Zhang, Bo Wang, Xiao-Yu Zhang, Weitao Du:
Sculpting molecules in text-3D space: a flexible substructure aware framework for text-oriented molecular optimization. 123 - Alessandro Dipalma, Michele Fontanesi, Alessio Micheli, Paolo Milazzo, Marco Podda:
Sensitivity analysis on protein-protein interaction networks through deep graph networks. 124 - Jiarui Zhou, Hui Wu, Kang Du, Wengang Zhou, Cong-Zhao Zhou, Houqiang Li:
PCVR: a pre-trained contextualized visual representation for DNA sequence classification. 125 - Kenny Liou, Ji-Ping Wang:
Integrating genetic and gene expression data in network-based stratification analysis of cancers. 126 - Samyabrata Sen, Indraneel Vairagare, Jitendrapuri Gosai, Abhishek Shrivastava:
RABiTPy: an open-source Python software for rapid, AI-powered bacterial tracking and analysis. 127 - Yin-Chen Hsieh, Mathias Bockwoldt, Ines Heiland:
ProTaxoVis - protein taxonomic visualisation of presence. 128 - Yue Cui, Yi Qiao, Rongming An, Xuan Pan, Jing Tu:
The application of compressed sensing on tumor mutation burden calculation from overlapped pooling sequencing data. 129 - You Wu, Li Xu, Xiaohong Cong, Hanxiao Li, Yanli Li:
Scmaskgan: masked multi-scale CNN and attention-enhanced GAN for scRNA-seq dropout imputation. 130 - Shani Cohen, Lior Rokach, Isana Veksler-Lublinsky:
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions. 131 - Qing Xie, Wang Meng, Shili Lin:
scHiCSRS: a self-representation smoothing method with Gaussian mixture model for imputing single cell Hi-C data. 132 - Dongin Kim, Ji Yeon Sohn, Jin Hee Cho, Ji-Hye Choi, Gwi-young Oh, Hyun Goo Woo:
KF-NIPT: K-mer and fetal fraction-based estimation of chromosomal anomaly from NIPT data. 133 - Xin Zeng, Shu Liu, Bowen Liu, Weihang Zhang, Wanzhe Xu, Fujio Toriumi, Kenta Nakai:
Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks. 134 - Jennifer K. Briggs, Erli Jin, Matthew J. Merrins, Richard K. P. Benninger:
CRISP: correlation-refined image segmentation process. 135 - Qingrong Shen, Xiaoqian Fan, Yangyang Sun, Hao Gao, Xiaoquan Su:
TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data. 136 - Fernando M. Delgado-Chaves, Ferdinand Spurny, Tanja Laske, Mhaned Oubounyt, Jan Baumbach:
DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics. 137 - Julien Charest, Paul Loebenstein, Robert L. Mach, Astrid R. Mach-Aigner:
FunFEA: an R package for fungal functional enrichment analysis. 138 - Alikhan Anuarbekov, Jirí Kléma:
Utilizing RNA-seq data in monotone iterative generalized linear model to elevate prior knowledge quality of the circRNA-miRNA-mRNA regulatory axis. 139 - Brice Edelman, Jeffrey Skolnick:
Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models. 140 - Mateusz Mazdziarz, Sebastian Zajac, Lukasz Paukszto, Jakub Sawicki:
RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU). 141 - Michail Patsakis, Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos, Ioannis Mouratidis, Ilias Georgakopoulos-Soares:
MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files. 142 - Christelle Kemda Ngueda, Julia Palm, Flavia Remo, André Scherag, Lutz Leistritz:
One-sample missing DNA-methylation value imputation. 143 - Jes Hui Min Kwek, Melissa Jane Fullwood:
MultiVis.js: a software tool for the visualization of multiway chromatin interactions and SPRITE data. 144 - Osamu Maruyama, Tsukasa Koga:
Class-balanced negative training sets for improving classifier model predictions of enhancer-promoter interactions. 145 - Miki Okuno, Takeshi Yamamoto, Yoshitoshi Ogura:
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons. 146 - Maryam Yousefian, Anna-Simone Frank, Marcus Weber, Susanna Röblitz:
Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition. 147 - Linbu Liao, Esha Madan, António M. Palma, Hyobin Kim, Amit Kumar, Praveen Bhoopathi, Robert Winn, Jose Trevino, Paul Fisher, Cord Herbert Brakebusch, Gahyun Kim, Junil Kim, Rajan Gogna, Kyoung-Jae Won:
SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution. 148 - Léo Pio-Lopez, Michael Levin:
Universal multilayer network embedding reveals a causal link between GABA neurotransmitter and cancer. 149 - Dániel Sándor, Péter Antal:
Efficient structure learning of gene regulatory networks with Bayesian active learning. 150 - Lianming Du, Dalin Sun, Jiahao Chen, Xinyi Zhou, Kelei Zhao, Qiang-Lin Zeng, Nan Yang:
Pytrf: a python package for finding tandem repeats from genomic sequences. 151 - Yue Luo, Lei Deng, Zhijian Huang:
HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction. 152 - Nuriye Özlem Özcan Simsek, Arzucan Özgür, Fikret Gürgen:
GNNMutation: a heterogeneous graph-based framework for cancer detection. 153 - Cristina Galisteo, Rafael R. de la Haba:
'gitana' (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures. 154 - Vladyslav Oles, Sajal Dash, Ramu Anandakrishnan:
Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data. 155 - Joy Ramielle L. Santos, Weijie Sun, A. Dean Befus, Marcelo Marcet-Palacios:
SEQSIM: A novel bioinformatics tool for comparisons of promoter regions - a case study of calcium binding protein spermatid associated 1 (CABS1). 156 - Shanwen Zhang, Changqing Yu, Chuanlei Zhang:
SCATrans: semantic cross-attention transformer for drug-drug interaction predication through multimodal biomedical data. 157 - Riccardo Smeriglio, Roberta Bardini, Alessandro Savino, Stefano Di Carlo:
Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control. 158 - Amin Khodaei, Sania Eskandari, Hadi Sharifi, Behzad Mozaffari Tazehkand:
PRCFX-DT: a new graph-based approach for feature selection and classification of genomic sequences. 159 - Maximilien Colange, Guillaume Appé, Léa Meunier, Solène Weill, Akpéli Nordor, Abdelkader Behdenna:
Differential expression analysis with inmoose, the integrated multi-omic open-source environment in Python. 160 - Vitalii Kapitan, Michael Choi:
Adaptive gradient scaling: integrating Adam and landscape modification for protein structure prediction. 161 - Shauvik Paul, Rahul Pramanick, Nirmal Das, Ewa Baczynska, Zeinab Bedrood, Tapabrata Chakraborti, Subhadip Basu, Jakub Wlodarczyk:
2dSpAn-Auto: an automated tool for analysis of two-dimensional dendritic spine images. 162 - Yan Li, Yanmei Li, Han Ma, Zitong Yue, Xin Zhang:
Coconut: covariate-assisted composite null hypothesis testing with applications to replicability analysis of high-throughput experimental data. 163 - Kyle C. McGovern, Justin D. Silverman:
Replacing normalizations with interval assumptions enhances differential expression and differential abundance analyses. 164 - FuDong Wen, Yue Su, Dan Liu, YuPeng Wang, MeiNa Liu:
Automated sparse feature selection in high-dimensional proteomics data via 1-bit compressed sensing and K-Medoids clustering. 165 - Osama Elnahas, Waleed M. Ead, Yushan Qiu, Jian Lu:
Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer. 166 - Yuhua Fan, Patrik Waldmann:
Multi-task genomic prediction using gated residual variable selection neural networks. 167 - Thoai Dotrang, Brad T. Sherman, Lisheng Dai, Muhammad Ayub Khan, Helene C. Highbarger, Whitney Bruchey, Sylvain Laverdure, Michael W. Baseler, Tomozumi Imamichi, Robin L. Dewar, Weizhong Chang:
HIVGenoPipe: a nextflow pipeline for the detection of HIV-1 drug resistance using a real-time sample-specific reference sequence. 168 - Agorakis Bompotas, Nikitas-Rigas Kalogeropoulos, Maria Giachali, Ioly Kotta-Loizou, Christos Makris:
DiscMycoVir: a user-friendly platform for discovering mycoviruses in fungal transcriptomes. 169 - Lily He, Mochao Huang, Gulinisha Yiming, Yi Zhu, Ruowei Liu, Jinghan Chen, Stephen S.-T. Yau:
A new alignment-free method: K-mer Subsequence Natural Vector (K-mer SNV) for classification of fungi. 170 - Yichuan Zhang, Wen Zhang:
Rprot-Vec: a deep learning approach for fast protein structure similarity calculation. 171 - Jiajia Wang, Bo Zhang, Linglu Zheng, Yan Chen, Chunyang Zhang, Guojiao Lin, Zhen Meng, Xuezhi Wang, Yuanchun Zhou:
PhyloScape: interactive and scalable visualization platform for phylogenetic trees. 172 - Feiyan Liu, Wenhao Wang, Jiawei Zheng, Yibo Xie, Xiaoli Wang, Dongxiang Zhang:
EDRMM: enhancing drug recommendation via multi-granularity and multi-attribute representation. 173 - Michael Strobel, Alberto Gil-de-la-Fuente, Mohammad Reza Shahneh, Yasin El Abiead, Roman Bushuiev, Anton Bushuiev, Tomás Pluskal, Mingxun Wang:
An evaluation methodology for machine learning-based tandem mass spectra similarity prediction. 174 - Koki Chigira, Masanori Yamasaki, Taiichiro Ookawa:
MKDESIGNER and TASEQ: a set of tools for plant genotyping by targeted amplicon sequencing. 175 - Jiangbo Zhang, Yunhui Peng, Feifei Cui, Zilong Zhang, Shankai Yan, Qingchen Zhang:
RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein binding sites prediction. 176 - Qiaosheng Zhang, Zhenyu Sun, Zhaoman Zhong, Huihui Yang, Yalong Wei, Junjie Xu:
SaeGraphDTI: drug-target interaction prediction based on sequence attribute extraction and graph neural network. 177 - Luna Xingyu Li, Boris Aguilar, John H. Gennari, Guangrong Qin:
LM-Merger: a workflow for merging logical models with an application to gene regulatory network models. 178 - Jiaqi Xiong, Nan Yin, Shiyang Liang, Haoyang Li, Yingxu Wang, Duo Ai, Jingjie Wang:
Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution. 179 - Bassel Hammoud, Aline Semaan, Lenka Benová, Imad H. Elhajj:
A novel machine learning architecture to improve classification of intermediate cases in health: workflow and case study for public health. 180 - Mario Blázquez-Sánchez, Alejandro Guerrero-López, Ana Candela, Albert Belenguer-Llorens, José Miguel Moreno, Carlos Sevilla-Salcedo, María Sánchez-Cueto, Manuel J. Arroyo, Mark Gutiérrez-Pareja, Vanessa Gómez-Verdejo, Pablo M. Olmos, Luis Mancera, Patricia Muñoz, Mercedes Marín, Luis Alcalá, David Rodríguez-Temporal, Belén Rodríguez-Sánchez:
Automated web-based typing of Clostridioides difficile ribotypes via MALDI-TOF MS. 181 - Wynand S. Verwoerd, Longfei Mao:
The FBA solution space kernel: introduction and illustrative examples. 182 - Yu Li, Denggao Zheng, Kaijie Sun, Chi Qin, Yuchen Duan, Qingqing Zhou, Yunxia Yin, Hongxing Kan, Jili Hu:
A densely connected framework for cancer subtype classification. 183 - Jianbo Qing, Jialu Wu, Yafeng Li, Junnan Wu:
SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics. 184 - Kavipriya Gananathan, D. Manjula, Vijayan Sugumaran:
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit. 185 - Keith Mitchell, Samuel Hunter, Lutz Froenicke, Karl Murray, Matthew Settles, James S. Trimmer:
clonevdjseq: A workflow and bioinformatics management system for sequencing, archiving, and analysis of VDJ sequences from clonal libraries. 186 - Lun Zhu, Hao Sun, Sen Yang:
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information. 187 - Hassan Nikaein, Ali Sharifi-Zarchi, Afsoon Afzal, Saeedeh Ezzati, Farzane Rasti, Hamidreza Chitsaz, Kunde Ramamoorthy Govindarajan:
Aryana-bs: context-aware alignment of bisulfite-sequencing reads. 188 - Ahmed Abdelkader, Nur A. Ferdous, Mohamed El-Hadidi, Tomasz Burzykowski, Mohamed Mysara:
metaGEENOME: an integrated framework for differential abundance analysis of microbiome data in cross-sectional and longitudinal studies. 189 - Chengqiu Dai, Linna Wang, Yingwei Deng, Xuzhu Gao, Jingyu Zhang:
LDA-SCGB: inferring lncRNA-disease associations based on condensed gradient boosting. 190 - Anirban Chakraborty, Erin K. Purcell, Michael G. Moore:
DiffCoRank: a comprehensive framework for discovering hub genes and differential gene co-expression in brain implant-associated tissue responses. 191 - Elior Avraham, Noam Shental:
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens. 192 - Mai T. Pham, Michael J. G. Milevskiy, Jane E. Visvader, Yunshun Chen:
Incorporating exon-exon junction reads enhances differential splicing detection. 193 - Andrew Carroll, Alexey Kolesnikov, Daniel E. Cook, Lucas Brambrink, Kelly N. Wiseman, Sophie M. Billings, Semyon Kruglyak, Bryan R. Lajoie, Junhua Zhao, Shawn E. Levy, Cory Y. McLean, Kishwar Shafin, Maria Nattestad, Pi-Chuan Chang:
Accurate human genome analysis with element avidity sequencing. 194 - Ping Xu, Pengfei Wang, Zhiyuan Ning, Meng Xiao, Min Wu, Yuanchun Zhou:
Soft graph clustering for single-cell RNA sequencing data. 195 - Dylan Clark-Boucher, Brent A. Coull, Harrison T. Reeder, Fenglei Wang, Qi Sun, Jacqueline R. Starr, Kyu Ha Lee:
Group-wise normalization in differential abundance analysis of microbiome samples. 196 - Sriram Vijendran, Tavis K. Anderson, Alexey Markin, Oliver Eulenstein:
Phylo-rs: an extensible phylogenetic analysis library in rust. 197 - Valentine Rech de Laval, Benjamin Dainat, Philippe Engel, Marc Robinson-Rechavi:
The BeeBiome data portal provides easy access to bee microbiome information. 198 - Shuyi Yang, Anderson Bussing, Giampiero Marra, Michelle L. Brinkmeier, Sally A. Camper, Shannon W. Davis, Yen-Yi Ho:
Time-coexpress: temporal trajectory modeling of dynamic gene co-expression patterns using single-cell transcriptomics data. 199 - Ming Zeng, Min Wang, Fuqiang Xie, Zhiwei Ji:
Drug-target interaction prediction based on graph convolutional autoencoder with dynamic weighting residual GCN. 200 - Lucas Bickmann, Sarah Sandmann, Carolin Walter, Julian Varghese:
PuMA: PubMed gene/cell type-relation Atlas. 201 - Han Ji, Xinwei He, Hongwei Li:
CYCLONE: recycle contrastive learning for integrating single-cell gene expression data. 202 - Xianglong Liang, Xin Jiang, Yifang Ma:
Literature data-based de novo candidates for drug repurposing. 203 - Gadi Chaykin, Omer Sabary, Nili Furman, Dvir Ben Shabat, Eitan Yaakobi:
Dna-storalator: a computational simulator for DNA data storage. 204 - Dave T. Gerrard:
GenomicLayers: sequence-based simulation of epi-genomes. 205 - Zihao Wang, Zeyu Wu, Minghua Deng:
Semi-supervised contrastive learning variational autoencoder Integrating single-cell multimodal mosaic datasets. 206 - Chen Sun, Haiyan Chen, Jing Xu, Siyu Wei, Junxian Tao, Jiacheng Wang, Yuping Zou, Wei She, Ruilin Li, Linna Yuan, Fanwu Kong, Guoping Tang, Zhenwei Shang, Wenhua Lyu, Mingming Zhang, Hongchao Lyu, Yongshuai Jiang:
Individualized co-expression-like index (iCKI) enables gene-gene interactions as individual biomarkers for complex disease. 207 - Wei Zhang, Zeqi Xu, Ruochen Yu, Mingfeng Jiang, Qi Dai:
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson's disease subtypes. 208 - Yuyang Zhang, Qihuang Zhang:
Winnow-KAN: single-cell RNA-seq location recovery with small-gene-set spatial transcriptomics. 209 - Tobias Olenyi, Constantin Carl, Tobias Senoner, Ivan Koludarov, Burkhard Rost:
FlatProt: 2D visualization eases protein structure comparison. 210 - Jing Zhai, Nelly Pitteloud, Federico A. Santoni:
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants. 211 - Tanya Golubchik, Lucie Abeler-Dörner, Matthew Hall, Chris Wymant, David G. Bonsall, George Macintyre-Cockett, Laura Thomson, Jared M. Baeten, Connie L. Celum, Ronald Galiwango, Barry Kosloff, Mohammed Limbada, Andrew Mujugira, Nelly R. Mugo, Astrid Gall, François Blanquart, Margreet Bakker, Daniela Bezemer, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, Barbara Gunsenheimer-Bartmeyer, Huldrych F. Günthard, Pia Kivelä, Roger D. Kouyos, Laurence Meyer, Kholoud Porter, Ard van Sighem, Mark van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Helen Ayles, David N. Burns, Sarah Fidler, Mary Kate Grabowski, Richard J. Hayes, Joshua T. Herbeck, Joseph Kagaayi, Pontiano Kaleebu, Jairam R. Lingappa, Deogratius Ssemwanga, Susan H. Eshleman, Myron S. Cohen, Oliver Ratmann, Oliver Laeyendecker, Christophe Fraser:
HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data. 212 - Amrit Sudershan, Kuljeet Singh, Parvinder Kumar:
GeneRiskCalc: a web-based tool for genetic risk association analysis in case-control studies. 213 - Chao Wang, Michael J. O'Connell:
Autoencoders with shared and specific embeddings for multi-omics data integration. 214 - Rachel Bowen-James, Weilin Wu, Marie Wong-Erasmus, Julian M. W. Quinn, Chelsea Mayoh, Mark J. Cowley:
consHLA: a next generation sequencing consensus-based HLA typing workflow. 215 - Line Sandvad Nielsen, Anders Gorm Pedersen, Ole Winther, Henrik Nielsen:
NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model. 216 - Xiangxing Lai, Minguang Xiao, Lingling Weng, Zhiguang Chen:
Learning-based parallel acceleration for HaplotypeCaller. 217 - Rudel Christian Nkouamedjo-Fankep, Arda Söylev, Anna-Lena Kobiela, Jochen Blom, Corinna Ernst, Susanne Motameny:
SV-MeCa: an XGBoost-based meta-caller approach for structural variant calling from short-read data. 218 - Asier Ortega-Legarreta, Alberto Maillo, Daniel Mouzo, Ana Rosa López-Pérez, Lara Kular, Majid Pahlevan Kakhki, Maja Jagodic, Jesper Tegnér, Vincenzo Lagani, Ewoud Ewing, David Gomez-Cabrero:
GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis. 219 - Simone Lenci, Dirk Sieger:
Calciumnetexplorer: an R package for network analysis of calcium imaging data. 220 - Césaire J. K. Fouodo, Marina Bleskina, Silke Szymczak:
fuseMLR: an R package for integrative prediction modeling of multi-omics data. 221 - Hideyuki Miyazawa, Toshiyuki Oda:
Dotplotic: a lightweight visualization tool for BLAST + alignments and genomic annotations. 222 - Burak Demiralay, Tolga Can:
Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets. 223 - Tiago Cabral Borelli, Alexandre Rossi Paschoal, Ricardo Roberto da Silva:
DeepSEA: an alignment-free explainable approach to annotate antimicrobial resistance proteins. 224 - Christos Theodoropoulos, Andrei Catalin Coman, James Henderson, Marie-Francine Moens:
Reduction of supervision for biomedical knowledge discovery. 225 - Fabian Kolesch, Marco Sohn, Andreas Rempel, Pia Hippel, Roland Wittler:
SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences. 227 - Océane Fourquet, Martin S. Krejca, Carola Doerr, Benno Schwikowski:
Towards the genome-scale discovery of bivariate monotonic classifiers. 228 - Dan Huang, Geunsu Jo, Kipoong Kim, Hokeun Sun:
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis. 226 - Antonia Gocke, Yannis Schumann, Jelena Navolic, Shweta Godbole, Melanie Schoof, Matthias Dottermusch, Julia E. Neumann:
CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data. 229 - Pablo Peiro-Corbacho, Francisco J. Lara-Abelenda, David Chushig-Muzo, Ana M. Wägner, Conceição Granja, Cristina Soguero-Ruíz:
Glucostats: an efficient Python library for glucose time series feature extraction and visual analysis. 230 - Ping Xuan, Rui Wang, Jing Gu, Hui Cui, Tiangang Zhang:
Structure-sensitive transformer and multi-view graph contrastive learning enhanced prediction of drug-related microbes. 231 - Mohammad Sadegh Loeloe, Seyyed Mohammad Tabatabaei, Reyhane Sefidkar, Amir Houshang Mehrparvar, Sara Jambarsang:
Boosting K-nearest neighbor regression performance for longitudinal data through a novel learning approach. 232 - Pi-Jing Wei, Jingxin Zhou, Rui-Fen Cao, Yun Ding, Zhenyu Yue, Chun-Hou Zheng:
MLGCN-Driver: a cancer driver gene identification method based on multi-layer graph convolutional neural network. 233 - Sih-Han Chen, Jen-Chieh Yu, Yi-Hsiang Lin, Shao-Chun Kuo, Kuan Ni, Ching-Tai Chen:
HEPAD: enhancing hemolytic peptide prediction with adaptive feature engineering and diverse sequence descriptors. 234 - Abdolrahman Khezri, Sverre Branders, Anurag Basavaraj Bellankimath, Jawad Ali, Crystal Chapagain, Fatemeh Asadi, Manfred G. Grabherr, Rafi Ahmad:
MysteryMaster: scraping the bottom of the barrel of barcoded Oxford nanopore reads. 235 - Jennifer Jessica Bruscadin, Tainã Figueiredo Cardoso, Liliane Costa Conteville, Juliana Virginio da Silva, Adriana Mércia Guaratini Ibelli, Gabriel Alexander Colmenarez Pena, Thanny Porto, Priscila Silva Neubern de Oliveira, Bruno Gabriel Nascimento Andrade, Adhemar Zerlotini, Luciana Correia de Almeida Regitano:
HolomiRA: a reproducible pipeline for miRNA binding site prediction in microbial genomes. 236 - Svetlana Poznanovic, Owen Cardwell, Christine E. Heitsch:
Can geometric combinatorics improve RNA branching predictions? 237 - Emmanuel P. Dollinger, Kai Silkwood, Scott Atwood, Qing Nie, Arthur D. Lander:
Statistically principled feature selection for single cell transcriptomics. 238 - Alessia Petescia, Gerardo Benevento, Anna Falanga, Alessandro Macaro, Delfina Malandrino, Alberto Montefusco, Rosalinda Sorrentino, Rocco Zaccagnino:
Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis. 239 - Mario Sänger, Ulf Leser:
Knowledge-augmented pre-trained language models for biomedical relation extraction. 240 - Maurizio Patrignani, Giordano Dionisi, Blerina Sinaimeri, Tiziana Calamoneri:
VIRI: a visualization tool for tree reconciliations. 241 - Qihan Guo, Dan Lv, Bo Lan, Haili Qian, Fei Ma, Ting Chen:
MyClone: rapid and precise reconstruction of clonal population structures for tumors. 242 - Hyeon Ho Heo, Soo-Jong Um:
H3NGST: a fully automated, web-based platform for end-to-end ChIP-seq analysis. 243 - Garth L. Kong, Thai T. Nguyen, Wesley K. Rosales, Anjali D. Panikar, John H. W. Cheney, Theresa A. Lusardi, William M. Yashar, Brittany M. Curtiss, Sarah A. Carratt, Theodore P. Braun, Julia E. Maxson:
Correction: CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny. 244 - Patrick Pflughaupt, Aleksandr B. Sahakyan:
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms. 245 - Jinpeng Wang, Shuo Sun, Yaran Zhang, Ning Huang, Chunhong Yang, Yaping Gao, Xiuge Wang, Zhihua Ju, Qiang Jiang, Yao Xiao, Xiaochao Wei, Wenhao Liu, Jinming Huang:
SAGPEK: fast and flexible approach to identify genotypes of Sanger sequencing data. 246 - Siqi Chen, Anhong Zheng, Weichi Yu, Chao Zhan:
DCMF-PPI: a protein-protein interaction predictor based on dynamic condition and multi-feature fusion. 247 - Giada Lalli, James Collier, Yves Moreau, Daniele Raimondi:
JINet: easy and secure private data analysis for everyone. 248 - Tianjian Yang, Wei Vivian Li:
Generalized probabilistic canonical correlation analysis for multi-modal data integration with full or partial observations. 249 - Pradyumna Harlapur, Harshavardhan BV, Mohit Kumar Jolly:
GRiNS: a python library for simulating gene regulatory network dynamics. 250 - Alexis L. Tang, David A. Liberles:
SMILES alignment: a dynamic programming approach for the alignment of metabolites and other small organic molecules. 251 - Simon Van de Vyver, Tibo Vande Moortele, Peter Dawyndt, Bart Mesuere, Pieter Verschaffelt:
Direct construction of sparse suffix arrays with Libsais. 252 - Marc Pereyra, Mariia Golden, Zoë Lange, Artemiy Golden, Frederic Strobl, Ernst H. K. Stelzer, Franziska Matthäus:
Spatiotemporal segmentation of contraction waves in the extra-embryonic membranes of the red flour beetle. 253 - Magdalena Schüttler, Leyla Dogan, Jana Kirchner, Süleyman Ergün, Philipp Wörsdörfer, Sabine C. Fischer:
VESNA: an open-source tool for automated 3D vessel segmentation and network analysis. 254 - Peng Wang:
Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation. 255 - Onder Tutsoy, Huseyin Ali Ozturk, Hilmi Erdem Sumbul:
Big data dimensionality reduction-based supervised machine learning algorithms for NASH diagnosis. 256 - Weisheng Wu, Kerby Shedden, Claudius Vincenz, Chris Gates, Beverly Strassmann:
ASET: an end-to-end pipeline for quantification and visualization of allele specific expression. 257 - Zihe Wang, Zilun Mei, Xiaogang Wang, Jinpeng Zhang, Zhenghong Xu, Fei Liu, Xiaojuan Zhang:
Dual-channel heterogeneous feature fusion neural network for the prediction of post-transcriptional gene expression in Escherichia coli. 258 - Foziya Ahmed Mohammed, El Hadj Malick Fall, Kula Kekeba Tune, Rasha Hammamieh, Marti Jett, Seid Y. Muhie:
MultiModalGraphics: an R package for graphical integration of multi-omics datasets. 259 - Yan Zhang, Ju Xiang, Jianming Li:
Denoising self-supervised learning for disease-gene association prediction. 260 - Salvatore Contino, Paolo Sortino, Maria Rita Gulotta, Ugo Perricone, Roberto Pirrone:
Unveiling molecular moieties through hierarchical Grad-CAM graph explainability. 261 - Philip Rutten, Tim R. Mocking, Jacqueline Cloos, Wessel N. van Wieringen, Costa Bachas:
Computationally efficient multi-sample flow cytometry data analysis using Gaussian mixture models. 262 - Stephen P. G. Moore, Anqi Zou, Xinyu Zhang, Olivia Chika Jonathan, Deborah Lang, Chao Zhang:
VaMiAnalyzer: an open source, Python-based application for analysis of 3D in vitro vasculogenic mimicry assays. 263 - Ylenia Galluzzo, Raffaele Giancarlo, Simona E. Rombo, Filippo Utro:
BioSet2Vec: extraction of k-mer dictionaries from multiple sets of biological sequences via big data technologies. 264 - Konstantinos G. Alexiou, Iban Eduardo, Pere Arús:
ResynPy: a software for selecting pairs of complementary inbred lines to resynthesize valuable heterozygous genotypes. 265 - Nicolas Handke, Thomas Gatter, Franziska Reinhardt, Peter F. Stadler:
TRAMbio: a flexible python package for graph rigidity analysis of macromolecules. 266 - Mpho Mokoatle, Vukosi Marivate, Darlington S. Mapiye, Riana Bornman, Vanessa M. Hayes:
Fine-tuning a sentence transformer for DNA. 267 - Wenjun Li, Yiting Zhou, Wanjun Ma, Weijun Liang, Xiwei Tang:
MDG-DDI: multi-feature drug graph for drug-drug interaction prediction. 268 - Namgil Lee, Hojin Yoo, Juhyoung Kim, Heejung Yang:
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics. 269 - Xinqing Jiang, Xiaojun Chen, Lifeng Xu, Feng Zhang, Jiawei Chen, Wenqian Zhang:
ESAE-SDA: ensemble sparse autoencoder framework for epigenomics-informed snoRNA-disease associations prediction. 270 - Duoyi Zhang, Md. Abul Bashar, Richi Nayak, Leila Cuttle:
A novel modality contribution confidence-enhanced multimodal deep learning framework for multiomics data. 271 - Nilesh Subramanian, Philge Philip, Anuradha Rajamanickam, Nathella Pavan Kumar, Subash Babu, Manikandan Narayanan:
Delineating markers of disease-disease interaction: a systematic methodology and its application to multiple diabetes-helminth cohorts. 272 - Jianqiang Hu, Mingyi Hu, Yangxiang Wu, Songyao Mu, Dahao Huang, Baolong Wang, Yuchen Gao, Shixin Gu, Jinlin Zhu:
A lightweight single-view contrastive learning hypergraph neural network for food-microbe-disease association prediction. 273 - Shuo Shuo Liu, Shikun Wang, Yuxuan Chen, Anil K. Rustgi, Ming Yuan, Jianhua Hu:
TransST: transfer learning embedded spatial factor modeling of spatial transcriptomics data. 274 - Shujuan Cao, Binying Cai, Zhejian Qiu, Tiantian Chang, Qiqige Wuyun, Fang-Xiang Wu:
Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction. 275 - Lilija Wehling, Gurdeep Singh, Ahmad Wisnu Mulyadi, Rakesh Hadne Sreenath, Henning Hermjakob, Tung V. N. Nguyen, Thomas Rückle, Mohammed H. Mosa, Henrik Cordes, Tommaso Andreani, Thomas Klabunde, Rahuman S. Malik-Sheriff, Douglas McCloskey:
Talk2Biomodels: AI agent-based open-source LLM initiative for kinetic biological models. 276 - Nan Sun, Yu Wang, Xiang Shi, Dengcheng Yang, Rongling Wu, Stephen S.-T. Yau:
scMFF: a machine learning framework with multiple feature fusion strategies for cell type identification. 277 - Ze Chen, Julie Blommaert, Yi Mei, Linley Jesson, Maren Wellenreuther, Mengjie Zhang:
Machine learning for genomic prediction of growth traits in aquaculture: a case study of the Australasian snapper (Chrysophrys auratus). 278 - Jiajia Liu, Surendra S. Negi, Chengyuan Yang, Xiaobo Zhou, Catherine H. Schein, Werner Braun, Pora Kim:
AllergenAI: a deep learning model predicting allergenicity based on protein sequence. 279 - Elijah R. Bring Horvath, Jaclyn M. Winter:
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets. 280 - Honglei Wang, Xuesong Zhang, Yanjing Sun, Zhaoyang Liu, Lin Zhang:
MCLCBA: multi-view contrastive learning network for RNA methylation site prediction. 281 - Qinhuan Luo, Yongzhen Yu, Tianying Wang:
Denoising single-cell RNA-seq data with a deep learning-embedded statistical framework. 282 - Maryam Mehrabani, Amir Lakizadeh, Alireza Fotuhi Siahpirani, Ali Masoudi-Nejad:
SynergyImage: image-based model for drug combinations synergy score prediction. 283 - Minindu Weerakoon, Christopher T. Saunders, Haynes Heaton:
LCSkPOA: enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended LCSk++. 284 - Kumar Thurimella, Ahmed M. T. Mohamed, Chenhao Li, Tommi Vatanen, Daniel B. Graham, Roisin M. Owens, Sabina Leanti La Rosa, Damian R. Plichta, Sergio Bacallado, Ramnik J. Xavier:
Protein language models uncover carbohydrate-active enzyme function in metagenomics. 285 - Jinxiong Zhang, Yunjv Zeng, Chunyan Tang, Cheng Zhong, Hao Wen, Yang Liu:
Contrastive learning-based multi-mechanism disentangled assessment for drug-drug interaction. 286 - Francesca Longhin, Giacomo Baruzzo, Enidia Hazizaj, Diego Boscarino, Dino Paladin, Barbara Di Camillo:
MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation. 287 - Espoir K. Kabanga, Seonil Jee, Soeun Yun, Stephen Depuydt, Arnout Van Messem, Wesley De Neve:
Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning. 288 - Philipp Georg Heilmann, Emanuel Grosch, Matthias Frisch, Matthias Herrmann, Steffen Beuch, Vivek Kurra, Martin Mascher, Raz Avni, Klaus Oldach, Ina Röhrs, Anja Hanemann, Raja Ram Mehta, Carsten Reinbrecht, Albrecht Serfling, Andreas Stahl, Marco Stucke, Amine Abbadi, Tobias Kox, Carola Zenke-Philippi:
Haplotype-based autoencoders can reduce the dataset dimension and estimate haplotype block effects in different crop species. 289 - Hao Luo, Yunhao Yang, Zhipeng Gong, Lunxu Liu, Yaohui Chen:
LOSTdb: a manually curated multi-omics database for lung cancer research. 290 - Muhammad Ali Nayeem, Shehab Sarar Ahmed, Suliman Aladhadh, M. Sohel Rahman:
Revisiting motif finding: do bi-objective metaheuristics surpass single-objective metaheuristics? 291 - Jian Zhang, Jingjing Yang, Changlong Wen:
EasyKASP: a simple and fast tool for KASP primer design. 292 - Xingxin Chen, Zhuo Wang, Zhen Miao, Bin Nie:
Research on drug-drug interaction prediction using capsule neural network based on self-attention mechanism. 293 - Mengdi Nan, Qing Ren, Yuhan Fu, Xiang Chen, Guanpeng Qi, Liugen Wang, Jie Gao:
LONMF: a non-negative matrix factorization model based on graph Laplacian and optimal transmission for paired single-cell multi-omics data integration. 294 - Xianyong Zhou, Xindian Wei, Cheng Liu, Wenjun Shen, Ping Xuan, Si Wu, Hau-San Wong:
Robust subspace structure discovery for cell type identification in scRNA-seq data. 295 - Alisson Silva, Carlos Marquez, Iury Godoy, Lucas Silva, Matheus Prado, Murilo Beppler, Natanael Avila, Bruno Travençolo, Anderson R. Santos:
Improving protein interaction prediction in GenPPi: a novel interaction sampling approach preserving network topology. 296 - Junrong Song, Yuanli Gong, Zhiming Song, Xinggui Xu, Kun Qian, Yingbo Liu:
DriverSub-SVM: a machine learning approach for cancer subtype classification by integrating patient-specific and global driver genes. 297 - Matthew Massett, Adrian Carr:
Prodigy protein: Python package for zero-shot protein engineering using protein language models. 298 - Shen Xiao, Yuhang Li, Jinwei Bai, Zhenhua Shen, Can Huang, Rongwu Xiang, Yuxuan Zhai, Xiwei Jiang:
A directed weighted network-based method for drug combinations identification using drug-target and inter-target regulation. 299 - Yiming Ma:
Batch optimization for balanced binary sequences and DNA sequences. 300 - Shengyang Chen, Xinyue Gao, Congmin Zhu, Honglei Liu, Yuqing Yang:
Hierarchical clustering-based coarse-to-fine classification framework for microbial protein function prediction. 301 - El Hacene Djaout, Nicolas Cluzel, Vincent Maréchal, Grégory Nuel, Marie Courbariaux:
Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160). 302 - Guicong Sun, Yongxian Fan, Yangfeng Zhu, Mengxin Zheng:
EGCPPIS: learning hierarchical equivariant graph representations with contrastive integration for protein-protein interaction site identification. 303 - Peng Shen, Yiyu Lin, Sen Yang, Ziding Zhang:
OMetaNet: an efficient hybrid deep learning model based on multimodal data fusion and contrastive learning for predicting 2'-O-methylation sites in human RNA. 304 - Niharika Saraf, Vishvesh Karthik, Gaurav Sharma:
AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions. 305 - Xiaoyan Li, Shixin Xu, Faisal Habib, Neda Aminnejad, Arvind Gupta, Huaxiong Huang:
CLEP-GAN: an innovative approach to subject-independent ECG reconstruction from PPG signals. 306 - Christopher T. Boughter, Budha Chatterjee, Yuko Ohta, Katrina Gorga, Carly Blair, Elizabeth M. Hill, Zachary Fasana, Adedola O. Adebamowo, Farah Ammar, Ivan Kosik, Vel Murugan, Wilbur H. Chen, Nevil J. Singh, Martin Meier-Schellersheim:
CountASAP: a lightweight, easy to use python package for processing ASAPseq data. 307 - William Wheeler, Difei Wang, Isaac Zhao, Filipa F. Vale, Yumi Jin, Charles S. Rabkin:
GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes. 308
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2026-01-24 01:53 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
