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| 2 | -- | 0 | Madiha Shabbir, Aziz Mithani. Roast: a tool for reference-free optimization of supertranscriptome assemblies |
| 3 | -- | 0 | Pedro A. Saa, Sebastian Zapararte, Christopher C. Drovandi, Lars K. Nielsen. LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models |
| 4 | -- | 0 | Kimberly To, Judy Strickland, Emily Reinke, Alexandre Borrel, Jim Truax, Heather Maldonado, David G. Allen, Nicole C. Kleinstreuer. Computational application of internationally harmonized defined approaches to skin sensitization: DASS App |
| 5 | -- | 0 | Dengju Yao, Bailin Li, Xiaojuan Zhan, Xiaorong Zhan, Liyang Yu. GCNFORMER: graph convolutional network and transformer for predicting lncRNA-disease associations |
| 6 | -- | 0 | Yongjian Guan, Chang-qing Yu, Li-ping Li, Zhu-Hong You, Weixiao Meng 0001, Xin-Fei Wang, Chen Yang, Lu-Xiang Guo. MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules |
| 7 | -- | 0 | Xue-Qin Chen, Jie Ma, Di Xu, Zuo-Lin Xiang. Correction: Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma |
| 8 | -- | 0 | Qian Liu, Qiang Hu, Song Liu, Alan Hutson, Martin Morgan. ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management |
| 9 | -- | 0 | Lasse Meyer, Nils Eling, Bernd Bodenmiller. cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data |
| 10 | -- | 0 | Jiahao Wei, Linzhang Lu, Tie Shen. Predicting drug-protein interactions by preserving the graph information of multi source data |
| 11 | -- | 0 | Eli J. Draizen, John Readey, Cameron Mura, Philip E. Bourne. Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data |
| 12 | -- | 0 | Ali Hakem Alsaeedi, Haider Hameed R. Al-Mahmood, Zainab Fahad Alnaseri, Mohammad R. Aziz, Dhiah Al-Shammary, Ayman Ibaida, Khandakar Ahmed. Fractal feature selection model for enhancing high-dimensional biological problems |
| 13 | -- | 0 | Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori. DiCleave: a deep learning model for predicting human Dicer cleavage sites |
| 14 | -- | 0 | Xu Zhang, Ya Su, Andrew N. Lane, Arnold J. Stromberg, Teresa W.-M. Fan, Chi Wang 0003. Correction: Bayesian kinetic modeling for tracer-based metabolomic data |
| 15 | -- | 0 | Josip Maric, Kresimir Krizanovic, Sylvain Riondet, Niranjan Nagarajan, Mile Sikic. Comparative analysis of metagenomic classifiers for long-read sequencing datasets |
| 16 | -- | 0 | Eduardo N. Castanho, João Lobo, Rui Henriques, Sara C. Madeira. Correction: G-bic: generating synthetic benchmarks for biclustering |
| 17 | -- | 0 | Mahmoud Gamal, Marwa A. Ibrahim. 0% method: a reliable and accurate approach for qPCR analysis |
| 18 | -- | 0 | Sahar Mohseni-Takalloo, Hadis Mohseni, Hassan Mozaffari-Khosravi, Masoud Mirzaei, Mahdieh Hosseinzadeh. The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest |
| 19 | -- | 0 | Zachary L. Maas, Robin D. Dowell. Internal and external normalization of nascent RNA sequencing run-on experiments |
| 20 | -- | 0 | Joel Nulsen, Nosheen Hussain, Aws Al-Deka, Jason Yap, Khalil Uddin, Christopher Yau, Ahmed Ashour Ahmed. Correction: Completing a genomic characterisation of microscopic tumour samples with copy number |
| 21 | -- | 0 | Clayton Carter, Aaron Saporito, Stephen M. Douglass. MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots |
| 22 | -- | 0 | Yu Han, Qiong Zhou, Leibo Liu, Jianwei Li, Yuan Zhou. DNI-MDCAP: improvement of causal MiRNA-disease association prediction based on deep network imputation |
| 23 | -- | 0 | Tay Xin Hui, Shahreen Kasim, Izzatdin Abdul Aziz, Mohd Farhan Md Fudzee, Nazleeni Samiha Haron, Tole Sutikno, Rohayanti Hassan, Hairulnizam Mahdin, Seah Choon Sen. Robustness evaluations of pathway activity inference methods on gene expression data |
| 24 | -- | 0 | Emma E. Kim, Chloe Soohyun Jang, Hakin Kim, Buhm Han. PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects |
| 25 | -- | 0 | Jamshaid A. Shahir, Natalie Stanley, Jeremy E. Purvis. Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks |
| 25 | -- | 0 | Jamshaid A. Shahir, Natalie Stanley, Jeremy E. Purvis. Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks |
| 26 | -- | 0 | David Rojas-Velazquez, Sarah Kidwai, Aletta D. Kraneveld, Alberto Tonda, Daniel L. Oberski, Johan Garssen, Alejandro Lopez Rincon. Methodology for biomarker discovery with reproducibility in microbiome data using machine learning |
| 27 | -- | 0 | Bingjun Li, Sheida Nabavi. A multimodal graph neural network framework for cancer molecular subtype classification |
| 28 | -- | 0 | Rukundo Prince, Zhendong Niu, Zahid Younas Khan, Masabo Emmanuel, Niyishaka Patrick. COVID-19 detection from chest X-ray images using CLAHE-YCrCb, LBP, and machine learning algorithms |
| 29 | -- | 0 | Yifan Li, Qianying Li, Lvying Wu, Haiyan Wang, Hui Shi, Chenhui Yang, Yiqun Gu, Jianyuan Li, Zhiliang Ji. SperMD: the expression atlas of sperm maturation |
| 30 | -- | 0 | Benedikt Venn, Thomas Leifeld, Ping Zhang 0022, Timo Mühlhaus. Temporal classification of short time series data |
| 31 | -- | 0 | Thi Hau Nguyen, Ha-Nam Nguyen, Trung-Nghia Vu. CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs |
| 32 | -- | 0 | Honglei Wang, Tao Huang, Dong Wang, Wenliang Zeng, Yanjing Sun, Lin Zhang 0015. MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction |
| 33 | -- | 0 | Morteza Rakhshaninejad, Mohammad Fathian, Reza Shirkoohi, Farnaz Barzinpour, Amir H. Gandomi. Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach |
| 34 | -- | 0 | Yiran Huang, Fuhao Chen, Hongtao Sun, Cheng Zhong. Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation |
| 35 | -- | 0 | Xiaoping Min, Chongzhou Yang, Jun Xie, Yang Huang, Nan Liu, Xiaocheng Jin, Tianshu Wang, Zhibo Kong, Xiaoli Lu, Shengxiang Ge, Jun Zhang, Ningshao Xia. Tpgen: a language model for stable protein design with a specific topology structure |
| 36 | -- | 0 | Clémence Joseph, Haris Zafeiropoulos, Kristel Bernaerts, Karoline Faust. Predicting microbial interactions with approaches based on flux balance analysis: an evaluation |
| 37 | -- | 0 | Naghme Nazer, Mohammad Hossein Sepehri, Hoda Mohammadzade, Mahya Mehrmohamadi. A novel approach toward optimal workflow selection for DNA methylation biomarker discovery |
| 38 | -- | 0 | Tianhua Yao, Xicheng Chen, Haojia Wang, Chengcheng Gao, Jia Chen, Dali Yi, Zeliang Wei, Ning Yao, Yang Li, Dong Yi, Yazhou Wu. Deep evolutionary fusion neural network: a new prediction standard for infectious disease incidence rates |
| 39 | -- | 0 | Jing Zhu, Chao Che, Hao Jiang, Jian Xu, Jiajun Yin, Zhaoqian Zhong. SSF-DDI: a deep learning method utilizing drug sequence and substructure features for drug-drug interaction prediction |
| 40 | -- | 0 | Wei Han, Sanguo Zhang, Hailong Gao, Deliang Bu. Clustering on hierarchical heterogeneous data with prior pairwise relationships |
| 41 | -- | 0 | Lifei Wang, Rui Nie, Xuexia Miao, Yankai Cai, Anqi Wang, Hanwen Zhang, Jiang Zhang 0006, Jun Cai. InClust+: the deep generative framework with mask modules for multimodal data integration, imputation, and cross-modal generation |
| 42 | -- | 0 | Haiyang Chang, Daniel A. Ashlock, Steffen P. Graether, Stefan M. Keller. Anchor Clustering for million-scale immune repertoire sequencing data |
| 43 | -- | 0 | Georg Hahn, Sharon Marie Lutz, Julian Hecker, Dmitry Prokopenko, Michael H. Cho, Edwin K. Silverman, Scott T. Weiss, Christoph Lange 0003. Fast computation of the eigensystem of genomic similarity matrices |
| 44 | -- | 0 | Yuke Xie, Xueqing Peng, Peiluan Li. MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy |
| 45 | -- | 0 | Patrick E. Gelbach, Handan Cetin, Stacey D. Finley. Flux sampling in genome-scale metabolic modeling of microbial communities |
| 46 | -- | 0 | Dengju Yao, Yuexiao Deng, Xiaojuan Zhan, Xiaorong Zhan. Predicting lncRNA-disease associations using multiple metapaths in hierarchical graph attention networks |
| 47 | -- | 0 | Rogia Kpanou, Patrick Dallaire, Elsa Rousseau, Jacques Corbeil. Learning self-supervised molecular representations for drug-drug interaction prediction |
| 48 | -- | 0 | Alireza Dehghan, Karim Abbasi, Parvin Razzaghi, Hossein Banadkuki, Sajjad Gharaghani. CCL-DTI: contributing the contrastive loss in drug-target interaction prediction |
| 49 | -- | 0 | Abigail Glascock, Eric Waltari, Gytis Dudas, Joan Wong, Vida Ahyong. PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes |
| 50 | -- | 0 | Lei Chen 0002, Chenyu Zhang, Jing Xu. PredictEFC: a fast and efficient multi-label classifier for predicting enzyme family classes |
| 51 | -- | 0 | Tim U. H. Baumeister, Eivind Aadland, Roger G. Linington, Olav M. Kvalheim. Multivariate pattern analysis: a method and software to reveal, quantify, and visualize predictive association patterns in multicollinear data |
| 52 | -- | 0 | Hyunwhan Joe, Hong-Gee Kim. Multi-label classification with XGBoost for metabolic pathway prediction |
| 53 | -- | 0 | Rose-Marie Fraboulet, Yanis Si Ahmed, Marc Aubry, Sebastien Corre, Marie-Dominique Galibert, Yuna Blum. Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks |
| 54 | -- | 0 | Karl Johan Westrin, Warren Kretzschmar, Olof Emanuelsson. ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs |
| 54 | -- | 0 | Karl Johan Westrin, Warren Kretzschmar, Olof Emanuelsson. ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs |
| 55 | -- | 0 | Andrew D. McCall. Colocalization by cross-correlation, a new method of colocalization suited for super-resolution microscopy |
| 56 | -- | 0 | YongJun Choi, Junho Cha, Sungkyoung Choi. Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES) |
| 57 | -- | 0 | Sedighe Rastahi, Azadeh Saki, Hamed Tabesh. Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data |
| 58 | -- | 0 | Vincent Y. Pappalardo, Leyla Azarang, Egija Zaura, Bernd W. Brandt, Renée X. de Menezes. A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches |
| 59 | -- | 0 | Dimitrios Iliadis, Bernard De Baets, Tapio Pahikkala, Willem Waegeman. A comparison of embedding aggregation strategies in drug-target interaction prediction |
| 60 | -- | 0 | Ruimin Wang, Hengxuan Jiang, Miaoshan Lu, Junjie Tong, Shaowei An, Jinyin Wang, Changbin Yu. MRMPro: a web-based tool to improve the speed of manual calibration for multiple reaction monitoring data analysis by mass spectrometry |
| 61 | -- | 0 | Amira Sami, Sara El-Metwally, M. Z. Rashad. MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads |
| 62 | -- | 0 | Ghanshyam Verma, Dietrich Rebholz-Schuhmann, Michael G. Madden. Enabling personalised disease diagnosis by combining a patient's time-specific gene expression profile with a biomedical knowledge base |
| 63 | -- | 0 | Valeriia Sherina, Helene R. McMurray, Winslow Powers, Hartmut Land, Tanzy M. T. Love, Matthew N. McCall. Correction: Multiple imputation and direct estimation for qPCR data with non-detects |
| 64 | -- | 0 | Dharmesh D. Bhuva, Chin Wee Tan, Ning Liu, Holly J. Whitfield, Nicholas Papachristos, Samuel C. Lee, Malvika Kharbanda, Ahmed Mohamed, Melissa J. Davis. vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis |
| 65 | -- | 0 | Yongwen Zhuang, Na Yeon Kim, Lars G. Fritsche, Bhramar Mukherjee, SeungGeun Lee. Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction |
| 66 | -- | 0 | Jesse R. Walsh, Guangchao Sun, Jagadheshwar Balan, Jayson Hardcastle, Jason Vollenweider, Calvin Jerde, Kandelaria Rumilla, Christy Koellner, Alaa Koleilat, Linda Hasadsri, Benjamin Kipp, W. Garrett Jenkinson, Eric W. Klee. A supervised learning method for classifying methylation disorders |
| 67 | -- | 0 | Michael A. Reiter, Julia A. Vorholt. Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves |
| 68 | -- | 0 | Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini, Masoud Garshasbi, Javad Zahiri. 123VCF: an intuitive and efficient tool for filtering VCF files |
| 69 | -- | 0 | Hengkang Wang, Han Lu, Ju Sun, Sandra E. Safo. Interpretable deep learning methods for multiview learning |
| 70 | -- | 0 | Anthony Baptista, Galadriel Brière, Anaïs Baudot. Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond |
| 71 | -- | 0 | Kord M. Kober, Liam Berger, Ritu Roy, Adam B. Olshen. Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units |
| 72 | -- | 0 | Valentina Crippa, Emanuela Fina, Daniele Ramazzotti, Rocco Piazza. Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data |
| 73 | -- | 0 | Adam Bessa-Silva. Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format |
| 74 | -- | 0 | Arnab Kole, Arup Kumar Bag, Anindya Jyoti Pal, Debashis De. Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology |
| 75 | -- | 0 | Haiou Qi, Ting Yu, Wenwen Yu, Chenxi Liu. Drug-target affinity prediction with extended graph learning-convolutional networks |
| 76 | -- | 0 | Audrey E. Bollas, Andrei Rajkovic, Defne Ceyhan, Jeffrey B. Gaither, Elaine R. Mardis, Peter White. SNVstory: inferring genetic ancestry from genome sequencing data |
| 77 | -- | 0 | Huanrong Tang, Yaowu Wang, Jianquan Ouyang, Jinlin Wang. Simcryocluster: a semantic similarity clustering method of cryo-EM images by adopting contrastive learning |
| 78 | -- | 0 | Haiyue Kuang, Zhen Zhang, Bin Zeng, Xin Liu, Hao Zuo, Xingye Xu, Lei Wang. A novel microbe-drug association prediction model based on graph attention networks and bilayer random forest |
| 79 | -- | 0 | Shihui He, Lijun Yun, Haicheng Yi. Fusing graph transformer with multi-aggregate GCN for enhanced drug-disease associations prediction |
| 80 | -- | 0 | Philippe Hauchamps, Babak Bayat, Simon Delandre, Mehdi Hamrouni, Marie Toussaint, Stephane Temmerman, Dan Lin, Laurent Gatto. CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data |
| 81 | -- | 0 | Il-Youp Kwak, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Daniel J. Garry, Jianyi Zhang, Wuming Gong. Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences |
| 82 | -- | 0 | Katelyn McNair, Peter Salamon, Robert A. Edwards, Anca M. Segall. PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes |
| 83 | -- | 0 | Sedighe Rastaghi, Azadeh Saki, Hamed Tabesh. Correction: Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data |
| 84 | -- | 0 | K. M. Tahsin Hassan Rahit, Vladimir Avramovic, Jessica X. Chong, Maja Tarailo-Graovac. GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM |
| 85 | -- | 0 | Benjamin Giovanni Iovino, Yuzhen Ye. Protein embedding based alignment |
| 86 | -- | 0 | Louis J. M. Aslett, Ryan R. Christ. kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R |
| 87 | -- | 0 | Neda Emami, Reza Ferdousi. HormoNet: a deep learning approach for hormone-drug interaction prediction |
| 88 | -- | 0 | Hua Chai, Siyin Lin, Junqi Lin, Minfan He, Yuedong Yang, Yongzhong Ouyang, Huiying Zhao. An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome |
| 89 | -- | 0 | Jean-Noël Lorenzi, François Graner, Virginie Courtier-Orgogozo, Guillaume Achaz. CNCA aligns small annotated genomes |
| 90 | -- | 0 | Theresa Scharl, Bettina Grün. A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models |
| 91 | -- | 0 | Qingru Xu, Xiaoqiong Bao, Zhuobin Lin, Lin Tang, Li-na He, Jian Ren 0002, Zhixiang Zuo, Kunhua Hu. AStruct: detection of allele-specific RNA secondary structure in structuromic probing data |
| 92 | -- | 0 | Leandro Y. S. Okimoto, Rayol Mendonca-Neto, Fabíola G. Nakamura, Eduardo Freire Nakamura, David Fenyö, Cláudio Teixeira Silva. Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification |
| 93 | -- | 0 | Katharina Munk, Daria Ilina, Lisa Ziemba, Günter Brader, Eva M. Molin. Holomics - a user-friendly R shiny application for multi-omics data integration and analysis |
| 94 | -- | 0 | Lu Li, Shi Yan, Barbara M. Bakker, Huub C. J. Hoefsloot, Bo Chawes, David Horner, Morten A. Rasmussen, Age K. Smilde, Evrim Acar. Analyzing postprandial metabolomics data using multiway models: a simulation study |
| 95 | -- | 0 | Akram Ashyani, Yu-Heng Wu, Huan-Wei Hsu, Torbjörn E. M. Nordling. Ideal adaptive control in biological systems: an analysis of $\mathbb {P}$-invariance and dynamical compensation properties |
| 96 | -- | 0 | Konstantin Yuditskiy, Igor Bezdvornykh, Anastasiya Kazantseva, Alexander Kanapin, Anastasia Samsonova. BSXplorer: analytical framework for exploratory analysis of BS-seq data |
| 97 | -- | 0 | Chengzhou Wu, Xichen Mou, Hongmei Zhang. Gbdmr: identifying differentially methylated CpG regions in the human genome via generalized beta regressions |
| 98 | -- | 0 | David L. Hölscher, Michael Goedertier, Barbara Mara Klinkhammer, Patrick Droste, Ivan G. Costa, Peter Boor, Roman David Bülow. tRigon: an R package and Shiny App for integrative (path-)omics data analysis |
| 99 | -- | 0 | Xiaolu Xu, Zitong Qi, Lei Wang, Meiwei Zhang, Zhaohong Geng, Xiumei Han. Gsw-fi: a GLM model incorporating shrinkage and double-weighted strategies for identifying cancer driver genes with functional impact |
| 100 | -- | 0 | Dong Wang, Jie Li 0055, Edwin Wang, Yadong Wang. DVA: predicting the functional impact of single nucleotide missense variants |
| 101 | -- | 0 | Yeon-Ji Park, Geun-Je Yang, Chae-Bong Sohn, Soo-Jun Park. GPDminer: a tool for extracting named entities and analyzing relations in biological literature |
| 102 | -- | 0 | Shahid Akbar, Ali Raza, Quan Zou 0001. Deepstacked-AVPs: predicting antiviral peptides using tri-segment evolutionary profile and word embedding based multi-perspective features with deep stacking model |
| 103 | -- | 0 | Onder Tutsoy, Gizem Gul Koç. Deep self-supervised machine learning algorithms with a novel feature elimination and selection approaches for blood test-based multi-dimensional health risks classification |
| 104 | -- | 0 | Hanwen Xing, Christopher Yau. Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling |
| 105 | -- | 0 | Chuanqi Lao, Pengfei Zheng, Hongyang Chen, Qiao Liu, Feng An, Zhao Li. DeepAEG: a model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies |
| 106 | -- | 0 | Thanh Hai Dang, Tien Anh Vu. xCAPT5: protein-protein interaction prediction using deep and wide multi-kernel pooling convolutional neural networks with protein language model |
| 107 | -- | 0 | Steven Gore, Bailey Meche, Danyang Shao, Benjamin Ginnett, Kelly Zhou, Rajeev K. Azad. DiseaseNet: a transfer learning approach to noncommunicable disease classification |
| 108 | -- | 0 | Ying Liang, XingRui Yin, Yangsen Zhang, You Guo, Yinglong Wang. Predicting lncRNA-protein interactions through deep learning framework employing multiple features and random forest algorithm |
| 109 | -- | 0 | Jason R. Miller, Donald A. Adjeroh. Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq |
| 110 | -- | 0 | Simone Alessandri, Maria L. Ratto, Sergio Rabellino, Gabriele Piacenti, Sandro Gepiro Contaldo, Simone Pernice, Marco Beccuti, Raffaele A. Calogero, Luca Alessandrì. CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications |
| 111 | -- | 0 | Sheikh Hasib Ahmed, Dibyendu Brinto Bose, Rafi Khandoker, M. Saifur Rahman. StackDPP: a stacking ensemble based DNA-binding protein prediction model |
| 112 | -- | 0 | Ornella Irrera, Stefano Marchesin 0001, Gianmaria Silvello. MetaTron: advancing biomedical annotation empowering relation annotation and collaboration |
| 113 | -- | 0 | Kevin Z. Lin, Yixuan Qiu, Kathryn Roeder. eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings |
| 114 | -- | 0 | Jody Clements, Cristian Goina, Philip M. Hubbard, Takashi Kawase, Donald J. Olbris, Hideo Otsuna, Robert Svirskas, Konrad Rokicki. NeuronBridge: an intuitive web application for neuronal morphology search across large data sets |
| 115 | -- | 0 | Karen Sargsyan, Carmay Lim. Using protein language models for protein interaction hot spot prediction with limited data |
| 116 | -- | 0 | Renjing Liu, Kun Qian, Xinwei He, Hongwei Li. Integration of scRNA-seq data by disentangled representation learning with condition domain adaptation |
| 117 | -- | 0 | Seungjun Ahn, Somnath Datta. Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values |
| 118 | -- | 0 | Shota Nose, Hirotsugu Shiroma, Takuji Yamada, Yushi Uno. QNetDiff: a quantitative measurement of network rewiring |
| 119 | -- | 0 | Junjie Shen, Shuo Wang, Yongfei Dong, Hao Sun, Xichao Wang, Zaixiang Tang. A non-negative spike-and-slab lasso generalized linear stacking prediction modeling method for high-dimensional omics data |
| 120 | -- | 0 | Lin-Lin Gu, Run-Qing Yang, Zhi-Yong Wang, Dan Jiang, Ming Fang. Ensemble learning for integrative prediction of genetic values with genomic variants |
| 121 | -- | 0 | Donny Chan, Graham L. Cromar, Billy Taj, John Parkinson. Cell4D: a general purpose spatial stochastic simulator for cellular pathways |
| 122 | -- | 0 | Shangru Li, Xiangpeng Meng, Rui Li, Bingding Huang, Xin Wang. NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model |
| 123 | -- | 0 | H. M. A. Mohit Chowdhury, Terrance E. Boult, Oluwatosin Oluwadare. Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness |
| 124 | -- | 0 | Yunus Emre Cebeci, Rumeysa Aslihan Erturk, Mehmet Arif Ergun, Mehmet Baysan. Improving somatic exome sequencing performance by biological replicates |
| 125 | -- | 0 | Raquel Lopes Costa, Luiz M. R. Gadelha Jr., Mirela D'arc, Marcelo Ribeiro-Alves, David L. Robertson, Jean-Marc Schwartz, Marcelo A. Soares, Fábio Porto 0001. HIHISIV: a database of gene expression in HIV and SIV host immune response |
| 126 | -- | 0 | Jasper van Bemmelen, Davida S. Smyth, Jasmijn A. Baaijens. Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes |
| 127 | -- | 0 | Gang Tu, Xuan Wang, Rong Xia, Bowen Song. 6A sites using machine learning approach |
| 128 | -- | 0 | Jader M. Caldonazzo Garbelini, Danilo Sipoli Sanches, Aurora T. R. Pozo. biomapp::chip: large-scale motif analysis |
| 129 | -- | 0 | Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone, Isaure Chauvot de Beauchêne. HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses |
| 130 | -- | 0 | Mehmet Arif Ergun, Omer Cinal, Berkant Bakisli, Abdullah Asim Emül, Mehmet Baysan. COSAP: Comparative Sequencing Analysis Platform |
| 131 | -- | 0 | Ahmed M. A. Elsherbini, Amr Hassan Elkholy, Youssef M. Fadel, Gleb Goussarov, Ahmed Mohamed Elshal, Mohamed El-Hadidi, Mohamed Mysara. Utilizing genomic signatures to gain insights into the dynamics of SARS-CoV-2 through Machine and Deep Learning techniques |
| 132 | -- | 0 | Yiran Huang, Pingfan Zeng, Cheng Zhong. Classifying breast cancer subtypes on multi-omics data via sparse canonical correlation analysis and deep learning |
| 133 | -- | 0 | Shuo Wang, Yuanning Liu, Hao Zhang, Zhen Liu. SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images |
| 134 | -- | 0 | James M. Dolezal, Sara Kochanny, Emma C. Dyer, Siddhi Ramesh, Andrew Srisuwananukorn, Matteo Sacco, Frederick M. Howard, Anran Li, Prajval Mohan, Alexander T. Pearson. Slideflow: deep learning for digital histopathology with real-time whole-slide visualization |
| 135 | -- | 0 | Xiao He, Ming Yan. M prediction of wildtype and mutant enzymes |
| 136 | -- | 0 | Daniel Skubleny, Sunita Ghosh, Jennifer Spratlin, Daniel E. Schiller, Gina R. Rayat. Feature-specific quantile normalization and feature-specific mean-variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data |
| 137 | -- | 0 | Zhanshan (Sam) Ma. Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes |
| 138 | -- | 0 | Patrick Blumenkamp, Max Pfister, Sonja Diedrich, Karina Brinkrolf, Sebastian Jaenicke, Alexander Goesmann. Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data |
| 139 | -- | 0 | Yanling Liu, Ruiyan Zhang, Xiaojing Dong, Hong Yang, Jing Li, Hongyan Cao, Jing Tian, Yanbo Zhang. DAE-CFR: detecting microRNA-disease associations using deep autoencoder and combined feature representation |
| 140 | -- | 0 | Yunyun Dong, Yunqing Chang, Yuxiang Wang, Qixuan Han, Xiaoyuan Wen, Ziting Yang, Yan Zhang, Yan Qiang, Kun Wu, Xiaole Fan, Xiaoqiang Ren. MFSynDCP: multi-source feature collaborative interactive learning for drug combination synergy prediction |
| 141 | -- | 0 | Xiaoting Zeng, Weilin Chen, Baiying Lei. CAT-DTI: cross-attention and Transformer network with domain adaptation for drug-target interaction prediction |
| 142 | -- | 0 | 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. CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny |
| 143 | -- | 0 | Ka Yin Chin, Shoichi Ishida, Yukio Sasaki, Kei Terayama. Predicting condensate formation of protein and RNA under various environmental conditions |
| 145 | -- | 0 | Muhammad Arif 0012, Ge Fang, Ali Ghulam, Saleh Musleh, Tanvir Alam. DPI_CDF: druggable protein identifier using cascade deep forest |
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| 159 | -- | 0 | Tingpeng Yang, Yu Wang, Yonghong He. TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences |
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| 162 | -- | 0 | Terrence R. Ernst, John D. Blischak, Paul Nordlund, Joe Dalen, Justin Moore, Akshay Bhamidipati, Pankaj Dwivedi, Joe LoGrasso, Marco Rocha Curado, Brett Warren Engelmann. OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies |
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| 164 | -- | 0 | Yufang Liu, Yongkai Chen, Haoran Lu, Wenxuan Zhong, Guo-Cheng Yuan, Ping Ma. Orthogonal multimodality integration and clustering in single-cell data |
| 165 | -- | 0 | William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber, Mahdi Belcaid. Improvements in viral gene annotation using large language models and soft alignments |
| 166 | -- | 0 | Leonardo Giannantoni, Roberta Bardini, Alessandro Savino, Stefano Di Carlo. Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems |
| 167 | -- | 0 | S. R. Oshternian, S. Loipfinger, A. Bhattacharya, Rudolf S. N. Fehrmann. Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data |
| 168 | -- | 0 | Adusei Bofa, Temesgen Zewotir. Optimizing spatio-temporal correlation structures for modeling food security in Africa: a simulation-based investigation |
| 169 | -- | 0 | Gao-Fei Wang, Longying Shen. Cauchy hyper-graph Laplacian nonnegative matrix factorization for single-cell RNA-sequencing data analysis |
| 170 | -- | 0 | Hyun Jung Lee, Utku Ozbulak, Homin Park, Stephen Depuydt, Wesley De Neve, Joris Vankerschaver. Assessing the reliability of point mutation as data augmentation for deep learning with genomic data |
| 171 | -- | 0 | Youngjun Park, Anne-Christin Hauschild. The effect of data transformation on low-dimensional integration of single-cell RNA-seq |
| 172 | -- | 0 | Sagara N. S. Gurusinghe, Julia M. Shifman. Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces |
| 173 | -- | 0 | Weiming He, Lian Xu, Jingxian Wang, Zhen Yue, Yi Jing, Shuaishuai Tai, Jian Yang, Xiaodong Fang. VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs |
| 174 | -- | 0 | Robert Ebo Armah-Sekum, Sándor Szedmák, Juho Rousu. Protein function prediction through multi-view multi-label latent tensor reconstruction |
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| 183 | -- | 0 | Qi Guan, Xianzhong Yan, Yida Wu, Da Zhou, Jie Hu. Biclustering analysis on tree-shaped time-series single cell gene expression data of Caenorhabditis elegans |
| 184 | -- | 0 | Samuel Piquer-Esteban, Vicente Arnau, Wladimiro Díaz, Andrés Moya. OMD Curation Toolkit: a workflow for in-house curation of public omics datasets |
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| 187 | -- | 0 | Mariella Bonomo, Simona E. Rombo. Neighborhood based computational approaches for the prediction of lncRNA-disease associations |
| 188 | -- | 0 | Andrea Simeon, Milos Radovanovic, Tatjana Loncar-Turukalo, Michelangelo Ceci, Sanja Brdar, Gianvito Pio. Multi-class boosting for the analysis of multiple incomplete views on microbiome data |
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| 191 | -- | 0 | Ryan Kuster, Margaret Staton. Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches |
| 192 | -- | 0 | Wonseok Oh, Junghyun Jung, Jong Wha J. Joo. MR-GGI: accurate inference of gene-gene interactions using Mendelian randomization |
| 193 | -- | 0 | Duc Quang Le, Son Hoang Nguyen, Tam Thi Nguyen, Canh Hao Nguyen, Tho Huu Ho, Nam S. Vo, Trang Nguyen, Hoang Anh Nguyen, Minh Duc Cao. AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance |
| 194 | -- | 0 | Zachary Stephens, Jean-Pierre A. Kocher. Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation |
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| 196 | -- | 0 | Wuyong Liu, Jingyu Zhang, Guanyu Qiao, Jilong Bian, BenZhi Dong, Yang Li. HMMF: a hybrid multi-modal fusion framework for predicting drug side effect frequencies |
| 197 | -- | 0 | Zhenyu Wei, Chengkui Zhao, Min Zhang, Jiayu Xu, Nan Xu, Shiwei Wu, Xiaohui Xin, Lei Yu, Weixing Feng. PrCRS: a prediction model of severe CRS in CAR-T therapy based on transfer learning |
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| 200 | -- | 0 | Miguel Reboiro-Jato, Daniel Pérez-Rodríguez, Miguel José Da Silva, David Vila-Fernández, Cristina P. Vieira, Jorge Vieira, Hugo López-Fernández. SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines |
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| 202 | -- | 0 | Georgios Bartzis, Carel F. W. Peeters, Wilco Ligterink, Fred A. van Eeuwijk. A guided network estimation approach using multi-omic information |
| 203 | -- | 0 | Hao Zhang, Yang Liu, Xiaoyan Liu, Cheng Wang, Maozu Guo 0001. Equivariant score-based generative diffusion framework for 3D molecules |
| 204 | -- | 0 | Bin Li, Dengming Ming. GATSol, an enhanced predictor of protein solubility through the synergy of 3D structure graph and large language modeling |
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| 206 | -- | 0 | Yance Feng, Fei Gao. bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data |
| 207 | -- | 0 | Laila Viana Almeida, João Luís Reis-Cunha, Daniella C. Bartholomeu. dgfr: an R package to assess sequence diversity of gene families |
| 208 | -- | 0 | Nicholas Aksamit, Jinqiang Hou, Yifeng Li, Beatrice M. Ombuki-Berman. Integrating transformers and many-objective optimization for drug design |
| 209 | -- | 0 | Khong-Loon Tiong, Dmytro Luzhbin, Chen-Hsiang Yeang. Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data |
| 210 | -- | 0 | Tanguy Pace-Loscos, Jocelyn Gal, Sara Contu, Renaud Schiappa, Emmanuel Chamorey, Dorian Culié. StatiCAL: an interactive tool for statistical analysis of biomedical data and scientific valorization |
| 211 | -- | 0 | Pietro Cinaglia. PyMulSim: a method for computing node similarities between multilayer networks via graph isomorphism networks |
| 212 | -- | 0 | Courtney Schiebout, H. Robert Frost. CAraCAl: CAMML with the integration of chromatin accessibility |
| 213 | -- | 0 | Ilya Tyagin, Ilya Safro. Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique |
| 214 | -- | 0 | Xianghu Jia, Weiwen Luo, Jiaqi Li, Jieqi Xing, Hongjie Sun, Shunyao Wu, Xiaoquan Su. A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation |
| 215 | -- | 0 | Jing Ren, Peiluan Li, Jinling Yan. CPMI: comprehensive neighborhood-based perturbed mutual information for identifying critical states of complex biological processes |
| 216 | -- | 0 | Fatma S. Ahmed, Saleh Aly, Xiangrong Liu. EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction |
| 217 | -- | 0 | Carlos Willian Dias Dantas, Sebastião Rodrigues da Costa Neto, Sandy Ingrid Aguiar Alves, Kenny da Costa Pinheiro, Edian Franklin Franco de Los Santos, Rommel Thiago Juca Ramos. SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions |
| 218 | -- | 0 | Shiwei Xu, Margaret E. Ackerman. Leveraging permutation testing to assess confidence in positive-unlabeled learning applied to high-dimensional biological datasets |
| 219 | -- | 0 | Yangyang Li, Rendong Yang. PxBLAT: an efficient python binding library for BLAT |
| 220 | -- | 0 | Sanghoon Lee, Min Sun, Yiheng Hu, Yue Wang, Md N. Islam, David Goerlitz, Peter C. Lucas, Adrian V. Lee, Sandra M. Swain, Gong Tang, Xiao-Song Wang. iGenSig-Rx: an integral genomic signature based white-box tool for modeling cancer therapeutic responses using multi-omics data |
| 221 | -- | 0 | Yuto Takemoto, Daisuke Ito, Shota Komori, Yoshiyuki Kishimoto, Shinichiro Yamada, Atsushi Hashizume, Masahisa Katsuno, Masahiro Nakatochi. Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs |
| 222 | -- | 0 | Worakorn Phumiphanjarphak, Pakorn Aiewsakun. Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling |
| 223 | -- | 0 | Yunus Emre Cebeci, Rumeysa Aslihan Erturk, Mehmet Arif Ergun, Mehmet Baysan. Correction: Improving somatic exome sequencing performance by biological replicates |
| 224 | -- | 0 | Binchao Peng, Guicong Sun, Yongxian Fan. iProL: identifying DNA promoters from sequence information based on Longformer pre-trained model |
| 225 | -- | 0 | Seyedeh Shaghayegh Sadeghi, Alan Bui, Ali Forooghi, Jianguo Lu, Alioune Ngom. Can large language models understand molecules? |
| 226 | -- | 0 | Vera Djordjilovic, Erica Ponzi, Therese Haugdahl Nøst, Magne Thoresen. penalizedclr: an R package for penalized conditional logistic regression for integration of multiple omics layers |
| 228 | -- | 0 | Fábio Malcher Miranda, Vasco Ariston de Carvalho Azevedo, Rommel Thiago Juca Ramos, Bernhard Y. Renard, Vitor Piro. Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2 |
| 229 | -- | 0 | Matteo De Leonardis, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni, Andrea Pagnani. Unsupervised modeling of mutational landscapes of adeno-associated viruses viability |
| 230 | -- | 0 | Niloofar Aghaieabiane, Ioannis Koutis. SGCP: a spectral self-learning method for clustering genes in co-expression networks |
| 236 | -- | 0 | Jae Jun Lee, Hyun Ju Kang, Donghyo Kim, Si On Lim, Stephanie S. Kim, Gahyun Kim, Sanguk Kim, Jin-Ku Lee, Jinho Kim. expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer |
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| 239 | -- | 0 | Emrulla Spahiu, Esra Kastrati, Mamta Amrute-Nayak. PyChelator: a Python-based Colab and web application for metal chelator calculations |
| 240 | -- | 0 | Hamdiye Uzuner, Annette Paschen, Dirk Schadendorf, Johannes Köster. Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing |
| 241 | -- | 0 | Amin Darabi, Sayeh Sobhani, Rosa Aghdam, Changiz Eslahchi. AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides |
| 242 | -- | 0 | Jingchen Liu, Yan Wang, Jiali Men, Haohua Wang. Identifying vital nodes for yeast network by dynamic network entropy |
| 243 | -- | 0 | Richard James Sugden, Ingrid Campbell, Viet-Linh Luke Pham-Kim-Nghiem-Phu, Randa Higazy, Eliza Dent, Kim Edelstein, Alberto Leon, Phedias Diamandis. HEROIC: a platform for remote collection of electroencephalographic data using consumer-grade brain wearables |
| 244 | -- | 0 | Nicholas S. McCloskey, Ayna Mammedova, David A. Liberles. PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways |
| 248 | -- | 0 | Amartya Singh, Hossein Khiabanian. Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis |
| 249 | -- | 0 | Helen Xie, Lorin Crawford, Ashley Mae Conard. Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks |
| 250 | -- | 0 | Yi-Ching Tang, Rongbin Li, Jing Tang 0002, W. Jim Zheng, Xiaoqian Jiang. SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations |
| 251 | -- | 0 | Anran Hao, Haohan Yuan, Siu Cheung Hui, Jian Su. Effective type label-based synergistic representation learning for biomedical event trigger detection |
| 252 | -- | 0 | Zijian Feng, Weihong Huang, Haohao Li, Hancan Zhu, Yanlei Kang, Zhong Li. DGCPPISP: a PPI site prediction model based on dynamic graph convolutional network and two-stage transfer learning |
| 253 | -- | 0 | Gunther Schauberger, Stefanie J. Klug, Moritz Berger. Random forests for the analysis of matched case-control studies |
| 254 | -- | 0 | Eileen Marie Hanna, Ghadi El Hasbani, Danielle Azar. Ant colony optimization for the identification of dysregulated gene subnetworks from expression data |
| 256 | -- | 0 | Gul Rukh, Shahid Akbar, Gauhar Rehman, Fawaz Khaled Alarfaj, Quan Zou 0001. StackedEnC-AOP: prediction of antioxidant proteins using transform evolutionary and sequential features based multi-scale vector with stacked ensemble learning |
| 257 | -- | 0 | Yunhee Jeong, Jonathan Ronen, Wolfgang Kopp, Pavlo Lutsik, Altuna Akalin. scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data |
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| 259 | -- | 0 | Jing Yan, Qiuhong Zeng, Xianlong Wang. RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics |
| 260 | -- | 0 | Xing Zhao, Zigui Chen, Huating Wang, Hao Sun 0001. Occlusion enhanced pan-cancer classification via deep learning |
| 261 | -- | 0 | Guanghui Li 0003, Shuwen Li, Cheng Liang, Qiu Xiao, Jiawei Luo 0001. Drug repositioning based on residual attention network and free multiscale adversarial training |
| 262 | -- | 0 | Jie Yang, Jiya Tian, Jinchao Miao, Yunsheng Chen. Adaptive loss-guided multi-stage residual ASPP for lesion segmentation and disease detection in cucumber under complex backgrounds |
| 263 | -- | 0 | Oieswarya Bhowmik, Tazin Rahman, Ananth Kalyanaraman. Maptcha: an efficient parallel workflow for hybrid genome scaffolding |
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| 265 | -- | 0 | Li-Pang Chen, Hsiao-Ting Huang. AFFECT: an R package for accelerated functional failure time model with error-contaminated survival times and applications to gene expression data |
| 266 | -- | 0 | Dallace Francis, Fengzhu Sun. A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data |
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| 269 | -- | 0 | Liqun Zhong, Lingrui Li, Ge Yang 0002. Benchmarking robustness of deep neural networks in semantic segmentation of fluorescence microscopy images |
| 270 | -- | 0 | Maxime Estavoyer, Marion Dufeu, Grégoire Ranson, Sylvain Lefort, Thibault Voeltzel, Véronique Maguer-Satta, Olivier Gandrillon, Thomas Lepoutre. Modeling relaxation experiments with a mechanistic model of gene expression |
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| 279 | -- | 0 | O. J. Charles, C. Venturini, R. A. Goldstein, J. Breuer. HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping |
| 281 | -- | 0 | Wasim Aftab, Zivkos Apostolou, Karim Bouazoune, Tobias Straub. Optimizing biomedical information retrieval with a keyword frequency-driven prompt enhancement strategy |
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| 285 | -- | 0 | Sergey Dolgov, Dmitry V. Savostyanov. Tensor product algorithms for inference of contact network from epidemiological data |
| 286 | -- | 0 | Giovanni Marturano, Diego Carli, Claudio Cucini, Antonio Carapelli, Federico Plazzi, Francesco Frati, Marco Passamonti, Francesco Nardi. SmithHunter: a workflow for the identification of candidate smithRNAs and their targets |
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| 292 | -- | 0 | Lan-Yun Chang, Ting-Yi Hao, Wei-Jie Wang, Chun-Yu Lin 0003. Inference of single-cell network using mutual information for scRNA-seq data analysis |
| 293 | -- | 0 | Stephan Weißbach, Jonas Milkovits, Stefan Pastore, Martin Heine, Susanne Gerber, Hristo Todorov. Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain |
| 294 | -- | 0 | Sarah E. Fumagalli, Sean Smith, Tigran Ghazanchyan, Douglas Meyer, Rahul Paul, Collin Campbell, Luis V. Santana-Quintero, Anton Golikov, Juan Ibla, Haim Bar, Anton A. Komar, Ryan Hunt, Brian Lin, Michael DiCuccio, Chava Kimchi-Sarfaty. Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages |
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| 297 | -- | 0 | Shion Hosoda, Hisashi Iwata, Takuya Miura, Maiko Tanabe, Takashi Okada, Atsushi Mochizuki, Miwa Sato. BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks |
| 298 | -- | 0 | Mohamed Elshrif, Keivin Isufaj, Khalid Kunji, Mohamad Saad 0001. PopMLvis: a tool for analysis and visualization of population structure using genotype data from genome-wide association studies |
| 299 | -- | 0 | Maximilian Radtke, Johanna Moch, Julia Hentschel, Isabell Schumann. altAFplotter: a web app for reliable UPD detection in NGS diagnostics |
| 300 | -- | 0 | Bo Lin, Kaipeng Wang, Yuan Yuan, Yueguo Wang, Qingyuan Liu, Yulan Wang, Jian Sun, Wenwen Wang, Huanli Wang, Shusheng Zhou, Kui Jin, Mengping Zhang, Yinglei Lai. A novel approach to the analysis of Overall Survival (OS) as response with Progression-Free Interval (PFI) as condition based on the RNA-seq expression data in The Cancer Genome Atlas (TCGA) |
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| 302 | -- | 0 | Simo Kitanovski, Yingying Cao, Dimitris Ttoouli, Farnoush Farahpour, Jun Wang, Daniel Hoffmann. scBubbletree: computational approach for visualization of single cell RNA-seq data |
| 303 | -- | 0 | Erwan Moreau, Orla Hardiman, Mark Heverin, Declan O'Sullivan. Mining impactful discoveries from the biomedical literature |
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| 305 | -- | 0 | Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott Atwood, Qing Nie, Arthur D. Lander. Leveraging gene correlations in single cell transcriptomic data |
| 307 | -- | 0 | Chenchen Xiong, Mingfang Zhang, Haolin Yang, Xuemei Wei, Chunwen Zhao, Junpeng Zhang 0001. Modelling cell type-specific lncRNA regulatory network in autism with Cycle |
| 308 | -- | 0 | Teng Li, Yiran Zou, Xianghan Li, Thomas K. F. Wong, Allen G. Rodrigo. Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data |
| 309 | -- | 0 | Kunjie Fan, Yuanyuan Li, Zhiwei Chen, Long Fan. GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes |
| 310 | -- | 0 | C. Mahncke, F. Schmiedeke, S. Simm, L. Kaderali, B. M. Bröker, U. Seifert, C. Cammann. DiscovEpi: automated whole proteome MHC-I-epitope prediction and visualization |
| 311 | -- | 0 | Tung Tho Nguyen, Korey J. Brownstein. Utilization of a natural language processing-based approach to determine the composition of artifact residues |
| 312 | -- | 0 | Harley Edwards, Joseph Zavorskas, Walker Huso, Alexander G. Doan, Caton Silbiger, Steven Harris, Ranjan Srivastava, Mark R. Marten. Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP |
| 313 | -- | 0 | Johanna B. Holm, Pawel Gajer, Jacques Ravel. SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota |
| 314 | -- | 0 | George Luo, Toby Chen, John J. Letterio. LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example |
| 315 | -- | 0 | Yan Zheng, Xuequn Shang. FindCSV: a long-read based method for detecting complex structural variations |
| 316 | -- | 0 | You Zhou, Giulia Pedrielli, Fei Zhang, Teresa Wu. Predicting RNA sequence-structure likelihood via structure-aware deep learning |
| 317 | -- | 0 | Liang Bai, Boya Ji, Shulin Wang. SAE-Impute: imputation for single-cell data via subspace regression and auto-encoders |
| 318 | -- | 0 | Sushma Koirala, Harman Sharma, Yee Lian Chew, Anna Konopka. SimplySmart_v1, a new tool for the analysis of DNA damage optimized in primary neuronal cultures |
| 319 | -- | 0 | Rhalena A. Thomas, Michael R. Fiorini, Saeid Amiri, Edward A. Fon, Sali M. K. Farhan. ScRNAbox: empowering single-cell RNA sequencing on high performance computing systems |
| 320 | -- | 0 | Yunfei Gao, Albert No. Efficient and low-complexity variable-to-variable length coding for DNA storage |
| 321 | -- | 0 | Pratima Chatterjee, Prasun Ghosal, Sahadeb Shit, Arindam Biswas 0007, Saurav Mallik, Sarah Allabun, Manal Othman, Almubarak Hassan Ali, E. Elshiekh, Ben Othman Soufiene. Ribosomal computing: implementation of the computational method |
| 322 | -- | 0 | Yuhua Fan, Patrik Waldmann. Tabular deep learning: a comparative study applied to multi-task genome-wide prediction |
| 323 | -- | 0 | Daniel Chafamo, Vignesh Shanmugam, Neriman Tokcan. C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data |
| 324 | -- | 0 | Bin Baek, Hyunju Lee. Crossfeat: a transformer-based cross-feature learning model for predicting drug side effect frequency |
| 325 | -- | 0 | Xavier Bledsoe, Eric R. Gamazon. NeuroimaGene: an R package for assessing the neurological correlates of genetically regulated gene expression |
| 327 | -- | 0 | Samar Monem, Aboul Ella Hassanien, Alaa H. Abdel-Hamid. A multi-task graph deep learning model to predict drugs combination of synergy and sensitivity scores |
| 333 | -- | 0 | Yaxun Jia, Haoyang Wang, Zhu Yuan, Lian Zhu, Zuo-Lin Xiang. Biomedical relation extraction method based on ensemble learning and attention mechanism |
| 334 | -- | 0 | Cezary Turek, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, Eszter Ari. mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate |
| 336 | -- | 0 | Anhui Yin, Lei Chen, Bo Zhou, Yu-Dong Cai. CMAGN: circRNA-miRNA association prediction based on graph attention auto-encoder and network consistency projection |
| 337 | -- | 0 | Yorgos M. Psarellis, Seungjoon Lee, Tapomoy Bhattacharjee, Sujit S. Datta, Juan M. Bello-Rivas, Ioannis G. Kevrekidis. Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning |
| 338 | -- | 0 | Elisabeth Hellec, Flavia Nunes, Charlotte Corporeau, Alexandre Cormier. KiNext: a portable and scalable workflow for the identification and classification of protein kinases |
| 339 | -- | 0 | Duong H. T. Vo, Thomas Thorne. Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data |
| 340 | -- | 0 | Hyojin Son, Sechan Lee, Jaeuk Kim, Haangik Park, Myeong-Ha Hwang, Gwan-Su Yi. BASE: a web service for providing compound-protein binding affinity prediction datasets with reduced similarity bias |
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| 342 | -- | 0 | Bertil Schmidt, Felix Kallenborn, Alejandro Chacón, Christian Hundt 0002. CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search |
| 343 | -- | 0 | Fan Liu, Han Zhou, Xiaonong Li, Liangliang Zhou, Chungong Yu, Haicang Zhang, Dongbo Bu, Xinmiao Liang. GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states |
| 344 | -- | 0 | Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti. PangeBlocks: customized construction of pangenome graphs via maximal blocks |
| 345 | -- | 0 | Shuang Wang, Kaiyu Dong, Dingming Liang, Yunjing Zhang, Xue Li, Tao Song 0001. MIPPIS: protein-protein interaction site prediction network with multi-information fusion |
| 346 | -- | 0 | Chun-Chi Chen, Yi-Ming Chan, Hyundoo Jeong. REDalign: accurate RNA structural alignment using residual encoder-decoder network |
| 347 | -- | 0 | Bowen Yan, Lin Zeng, Yanyi Lu, Min Li, Weiping Lu, Bangfu Zhou, Qinghua He. Rapid bacterial identification through volatile organic compound analysis and deep learning |
| 348 | -- | 0 | Miao Gu, Weiyang Yang, Min Liu. Prediction of antibody-antigen interaction based on backbone aware with invariant point attention |
| 349 | -- | 0 | Hajer Akid, Kirsley Chennen, Gabriel Frey, Julie Dawn Thompson, Mounir Ben Ayed, Nicolas Lachiche. Graph-based machine learning model for weight prediction in protein-protein networks |
| 350 | -- | 0 | Martin Helfrich, Roman Andriushchenko, Milan Ceska 0002, Jan Kretínský, Stefan Marticek, David Safránek. Abstraction-based segmental simulation of reaction networks using adaptive memoization |
| 351 | -- | 0 | Jorge Beltrán, Lisandra Herrera Belén, Alejandro J. Yáñez, Luis Jimenez. Predicting viral proteins that evade the innate immune system: a machine learning-based immunoinformatics tool |
| 352 | -- | 0 | Ming Zhang, Jianren Zhou, Xiaohua Wang, Xun Wang, Fang Ge. DeepBP: Ensemble deep learning strategy for bioactive peptide prediction |
| 352 | -- | 0 | Ming Zhang, Jianren Zhou, Xiaohua Wang, Xun Wang, Fang Ge. DeepBP: Ensemble deep learning strategy for bioactive peptide prediction |
| 353 | -- | 0 | Gunhwan Ko, Pan-Gyu Kim, Byung-Ha Yoon, Jaehee Kim, Wangho Song, Iksu Byeon, Jongcheol Yoon, Byungwook Lee, Young-Kuk Kim. Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure |
| 354 | -- | 0 | Tomasz Strzoda, Lourdes Cruz-Garcia, Mustafa Najim, Christophe Badie, Joanna Polanska. A mapping-free natural language processing-based technique for sequence search in nanopore long-reads |
| 355 | -- | 0 | Xuqing Wang, Yahang Liu, Guoyou Qin, Yongfu Yu. Robust double machine learning model with application to omics data |
| 356 | -- | 0 | Riyad Hakim, Saeed Salem. Mining contextually meaningful subgraphs from a vertex-attributed graph |
| 357 | -- | 0 | Haydee Artaza, Ksenia Lavrichenko, Anette S. B. Wolff, Ellen C. Røyrvik, Marc Vaudel, Stefan Johansson. Rare copy number variant analysis in case-control studies using snp array data: a scalable and automated data analysis pipeline |
| 358 | -- | 0 | Ariane Marandon, Tabea Rebafka, Nataliya Sokolovska, Hédi Soula. Conformal novelty detection for multiple metabolic networks |
| 359 | -- | 0 | Pietro Hiram Guzzi, Arkaprava Roy, Marianna Milano, Pierangelo Veltri. Non parametric differential network analysis: a tool for unveiling specific molecular signatures |
| 360 | -- | 0 | Sumaiya Noor, Afshan Naseem, Hamid Hussain Awan, Wasiq Aslam, Salman Khan 0005, Salman A. AlQahtani, Nijad Ahmad. Deep-m5U: a deep learning-based approach for RNA 5-methyluridine modification prediction using optimized feature integration |
| 361 | -- | 0 | Yuanyuan Zhang, Yingdong Wang, Chaoyong Wu, Lingmin Zhan, Aoyi Wang, Caiping Cheng, Jinzhong Zhao, Wuxia Zhang, Jianxin Chen, Peng Li 0004. Drug-target interaction prediction by integrating heterogeneous information with mutual attention network |
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| 363 | -- | 0 | Quinlan Furumo, Michelle M. Meyer. PIPETS: a statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3′-end sequencing |
| 364 | -- | 0 | Lei Cheng, Qian Huang, Zhengqun Zhu, Yanan Li, Shuguang Ge, Longzhen Zhang, Ping Gong. MoAGL-SA: a multi-omics adaptive integration method with graph learning and self attention for cancer subtype classification |
| 365 | -- | 0 | Aniket C. Mane, Haley Sanderson, Aaron P. White, Rahat Zaheer, Robert Beiko, Cédric Chauve. Plaseval: a framework for comparing and evaluating plasmid detection tools |
| 366 | -- | 0 | Rosa Aghdam, Xudong Tang, Shan Shan, Richard Lankau, Claudia R. Solís-Lemus. Human limits in machine learning: prediction of potato yield and disease using soil microbiome data |
| 367 | -- | 0 | Nasma Boumajdi, Houda Bendani, Lahcen Belyamani, Azeddine Ibrahimi. TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing |
| 368 | -- | 0 | Ibrahim Abdelbaky, Mohamed Elhakeem, Hilal Tayara, Elsayed M. Badr, Mustafa Abdul Salam. Enhanced prediction of hemolytic activity in antimicrobial peptides using deep learning-based sequence analysis |
| 369 | -- | 0 | Jianjun Zhang, Jane Zizhen Zhao, Samantha Gonzales, Xuexia Wang, Qiuying Sha. A novel phenotype imputation method with copula model |
| 370 | -- | 0 | Gholamhossein Jowkar, Julija Pecerska, Manuel Gil, Maria Anisimova. Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction |
| 371 | -- | 0 | Dinithi V. Wanniarachchi, Sameera Viswakula, Anushka M. Wickramasuriya. The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes |
| 372 | -- | 0 | Lauren M. Bradford, Catherine Carrillo, Alex Wong. Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets |
| 373 | -- | 0 | Ivo C. Leist, María Rivas-Torrubia, Marta E. Alarcón-Riquelme, Guillermo Barturen, Ivo Glynne Gut, Manuel Rueda. Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond |
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| 375 | -- | 0 | Jinghong Sun, Han Wang, Jia Mi, Jing Wan, Jingyang Gao. MTAF-DTA: multi-type attention fusion network for drug-target affinity prediction |
| 376 | -- | 0 | Jeremias Krause, Carlos Classen, Daniela Dey, Eva Lausberg, Luise Kessler, Thomas Eggermann, Ingo Kurth, Matthias Begemann, Florian Kraft. CNVizard - a lightweight streamlit application for an interactive analysis of copy number variants |
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| 378 | -- | 0 | Andrea Conte, Nicola Gulmini, Francesco Costa, Matteo Cartura, Felix Bröhl, Francesco Patane, Francesco Filippini. NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface |
| 379 | -- | 0 | Zhongning Jiang, Wei Huang, Raymond H. W. Lam, Wei Zhang. Spall: accurate and robust unveiling cellular landscapes from spatially resolved transcriptomics data using a decomposition network |
| 380 | -- | 0 | Jon Bohlin, Siri E. Håberg, Per Magnus, Håkon K. Gjessing. MinLinMo: a minimalist approach to variable selection and linear model prediction |
| 381 | -- | 0 | sasan azizian, Juan Cui. DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity |
| 382 | -- | 0 | Chu Pan, Yanlin Chen. Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective |
| 383 | -- | 0 | Christopher Patsalis, Gayatri Iyer, Marci Brandenburg, Alla Karnovsky, George Michailidis. DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data |
| 384 | -- | 0 | Daniel Antonio Negrón, Shipra Trivedi, Nicholas Tolli, David Ashford, Gabrielle Melton, Stephanie Guertin, Katharine Jennings, Bryan D. Necciai, Shanmuga Sozhamannan, Bradley W. Abramson. Loop-mediated isothermal amplification assays for the detection of antimicrobial resistance elements in Vibrio cholera |
| 385 | -- | 0 | Jeet Sukumaran, Marina Meila. Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space |
| 386 | -- | 0 | Chuanlei Zhang, Yubo Li, Yinglun Dong, Wei Chen, Changqing Yu. Prediction of miRNA-disease associations based on PCA and cascade forest |
| 387 | -- | 0 | Shengrong Zhu, Ruijia Yang, Zifeng Pan, Xuan Tian, Hong Ji. MISDP: multi-task fusion visit interval for sequential diagnosis prediction |
| 388 | -- | 0 | Toshiaki Yachimura, Hanbo Wang, Yusuke Imoto, Momoko Yoshida, Sohei Tasaki, Yoji Kojima, Yukihiro Yabuta, Mitinori Saitou, Yasuaki Hiraoka. scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport |
| 389 | -- | 0 | Zoltán Maróti, Peter Juma Ochieng, József Dombi 0001, Miklós Krész, Tibor Kalmár. Optimizing sequence data analysis using convolution neural network for the prediction of CNV bait positions |
| 390 | -- | 0 | Hyunseok Shin, Sejong Oh. An effective heuristic for developing hybrid feature selection in high dimensional and low sample size datasets |
| 391 | -- | 0 | Liqiang Sun, Xiaojing Fan, Yunwei Zhao, Qi Zhang, Mingyang Jiang. Deep learning-based metabolomics data study of prostate cancer |
| 392 | -- | 0 | Qiaosheng Zhang, Yalong Wei, Jie Hou, Hongpeng Li, Zhaoman Zhong. AEGAN-Pathifier: a data augmentation method to improve cancer classification for imbalanced gene expression data |
| 393 | -- | 0 | Shuang Liang, Linzhe Li, Wei Zu, Wei Feng, Wenlong Hang. Adaptive deep feature representation learning for cross-subject EEG decoding |