| 0 | -- | 0 | Harshavardhan Khare, Nathaly Dongo Mendoza, Chiara Zurzolo. CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images |
| 0 | -- | 0 | Eszter Csibra, Guy-Bart Stan. Parsley: a web app for parsing data from plate readers |
| 0 | -- | 0 | Omar G. Younis, Matteo Turchetta, Daniel Ariza Suarez, Steven Yates, Bruno Studer, Ioannis N. Athanasiadis, Andreas Krause, Joachim M. Buhmann, Luca Corinzia. ChromaX: a fast and scalable breeding program simulator |
| 0 | -- | 0 | Nikolai Romashchenko, Benjamin Linard, Fabio Pardi, Eric Rivals. k-mers |
| 0 | -- | 0 | Cuifang Xu, Jiating Huang, Yongqiang Gao, Weixing Zhao, Yiqi Shen, Feihong Luo, Gang Yu, Feng Zhu, Yan Ni. OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases |
| 0 | -- | 0 | . Correction to: GIL: a python package for designing custom indexing primers |
| 0 | -- | 0 | William DeGroat, Dinesh Mendhe, Atharva Bhusari, Habiba Abdelhalim, Saman Zeeshan, Zeeshan Ahmed 0001. IntelliGenes: a novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles |
| 0 | -- | 0 | Zi Hao Liu, João M. C. Teixeira, Oufan Zhang, Thomas E. Tsangaris, Jie Li, Claudiu C. Gradinaru, Teresa Head-Gordon, Julie D. Forman-Kay. Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments |
| 0 | -- | 0 | Weihua Zheng, Wenwen Min, Shunfang Wang. TsImpute: an accurate two-step imputation method for single-cell RNA-seq data |
| 0 | -- | 0 | Herve Emissah, Bengt Ljungquist, Giorgio A. Ascoli. Bibliometric analysis of neuroscience publications quantifies the impact of data sharing |
| 0 | -- | 0 | Armin Rauschenberger, Zied Landoulsi, Mark A. van de Wiel, Enrico Glaab. Penalized regression with multiple sources of prior effects |
| 0 | -- | 0 | Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro. VSCode-Antimony: a source editor for building, analyzing, and translating antimony models |
| 0 | -- | 0 | Mikolaj Spytek, Mateusz Krzyzinski, Sophie Hanna Langbein, Hubert Baniecki, Marvin N. Wright, Przemyslaw Biecek. survex: an R package for explaining machine learning survival models |
| 0 | -- | 0 | Yang Li, Zihou Guo, Xin Gao, Guohua Wang. MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning |
| 0 | -- | 0 | Yitian Fang, Yi Jiang, Leyi Wei, Qin Ma, Zhixiang Ren, Qianmu Yuan, Dong-Qing Wei. DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model |
| 0 | -- | 0 | Hikmet Emre Kaya, Kevin J. Naidoo. CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform |
| 0 | -- | 0 | Rui Ren, Kuangnan Fang, Qingzhao Zhang, Shuangge Ma. FunctanSNP: an R package for functional analysis of dense SNP data (with interactions) |
| 0 | -- | 0 | Min Zeng, Yifan Wu, Yiming Li, Rui Yin, Chengqian Lu, Junwen Duan, Min Li 0007. LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism |
| 0 | -- | 0 | Bede Constantinides, Martin Hunt, Derrick W. Crook. Hostile: accurate decontamination of microbial host sequences |
| 0 | -- | 0 | Yu Huo, Hongpei Li, Xiao Wang, Xiaochen Du, Peter S. Swain. Nunchaku: optimally partitioning data into piece-wise contiguous segments |
| 0 | -- | 0 | Wunna Kyaw, Ryan C. Chai, Weng Hua Khoo, Leonard D. Goldstein, Peter I Croucher, John M. Murray, Tri Giang Phan. ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor-ligand interactions that specify cell fate |
| 0 | -- | 0 | Anisha Haldar, Vishal H. Oza, Nathaniel S. Devoss, Amanda D. Clark, Brittany N. Lasseigne. CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis |
| 0 | -- | 0 | Brendan S. McConnell, Matthew W. Parker. Protein intrinsically disordered regions have a non-random, modular architecture |
| 0 | -- | 0 | Marcos Díaz-Gay, Raviteja Vangara, Mark Barnes, Xi Wang, S. M. Ashiqul Islam, Ian Vermes, Stephen Duke, Nithish Bharadhwaj Narasimman, Ting Yang, Zichen Jiang, Sarah J. Moody, Sergey Senkin, Paul Brennan, Michael R. Stratton, Ludmil B. Alexandrov. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment |
| 0 | -- | 0 | Herui Liao, Jiayu Shang, Yanni Sun. GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data |
| 0 | -- | 0 | Ze-Gang Wei, Peng-Yu Bu, Xiao-dan Zhang, Fei Liu, Yu Qian, Fang-Xiang Wu. invMap: a sensitive mapping tool for long noisy reads with inversion structural variants |
| 0 | -- | 0 | Hongjing Xie, Xuewei Cao, Shuanglin Zhang, Qiuying Sha. Joint analysis of multiple phenotypes for extremely unbalanced case-control association studies using multi-layer network |
| 0 | -- | 0 | Jacob Morrison, Wanding Zhou, Benjamin K. Johnson, Hui Shen. Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing |
| 0 | -- | 0 | Gianluca Vozza, Emanuele Bonetti, Giulia Tini, Valentina Favalli, Gianmaria Frige, Gabriele Bucci, Simona De Summa, Mario Zanfardino, Francesco Zapelloni, Luca Mazzarella. Benchmarking and improving the performance of variant-calling pipelines with RecallME |
| 0 | -- | 0 | Mingzhi Yuan, Ao Shen, Kexue Fu, Jiaming Guan, Yingfan Ma, Qin Qiao, Manning Wang. ProteinMAE: masked autoencoder for protein surface self-supervised learning |
| 0 | -- | 0 | Duy T. Pham, Kenneth E. Westerman, Cong Pan, Ling Chen, Shylaja Srinivasan, Elvira Isganaitis, Mary Ellen Vajravelu, Fida Bacha, Steve Chernausek, Rose Gubitosi-Klug, Jasmin Divers, Catherine Pihoker, Santica M. Marcovina, Alisa K. Manning, Han Chen. Re-analysis and meta-analysis of summary statistics from gene-environment interaction studies |
| 0 | -- | 0 | Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar S. Deshpande, David Sehnal, Mihaly Varadi, Sameer Velankar. PDBImages: a command-line tool for automated macromolecular structure visualization |
| 0 | -- | 0 | Md. Abdullah-Al-Kamran Khan, Jian Wu, Yuhan Sun, Alexander D. Barrow, Anthony T. Papenfuss, Stefano Mangiola. cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling |
| 0 | -- | 0 | Kazim Kivanç Eren, Esra Çinar, Hamza Umut Karakurt, Arzucan Özgür. Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics |
| 0 | -- | 0 | Cristian Padron-Manrique, Aarón Vázquez-Jiménez, Diego Armando Esquivel-Hernandez, Yoscelina Estrella Martinez Lopez, Daniel Neri-Rosario, Jean Paul Sánchez-Castañeda, David Giron-Villalobos, Osbaldo Resendis-Antonio. mb-PHENIX: diffusion and supervised uniform manifold approximation for denoizing microbiota data |
| 0 | -- | 0 | Jae-Won Lee, Jong-Hyun Won, Seonggwang Jeon, Yujin Choo, Yubin Yeon, Jin-Seon Oh, Minsoo Kim, Seonhwa Kim, InSuk Joung, Cheongjae Jang, Sung-Jong Lee, Tae-Hyun Kim, Kyong Hwan Jin, Giltae Song, Eun-Sol Kim, Jejoong Yoo, Eunok Paek, Yung-Kyun Noh, Keehyoung Joo. DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function |
| 0 | -- | 0 | . Correction to: PEMT: a patent enrichment tool for drug discovery |
| 0 | -- | 0 | Jian Liu, Fubin Ma, Yongdi Zhu, Naiqian Zhang, Lingming Kong, Jia Mi, Haiyan Cong, Rui Gao, Mingyi Wang, Yusen Zhang. MaxCLK: discovery of cancer driver genes via maximal clique and information entropy of modules |
| 0 | -- | 0 | Daniel Stribling, Lauren A. Gay, Rolf Renne. Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods |
| 0 | -- | 0 | . Correction to: DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function |
| 0 | -- | 0 | Nima Nouri, Andre H. Kurlovs, Giorgio Gaglia, Emanuele de Rinaldis, Virginia Savova. Scaling up single-cell RNA-seq data analysis with CellBridge workflow |
| 0 | -- | 0 | Bassel Ghaddar, Subhajyoti De. Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census |
| 0 | -- | 0 | Susan L. Hoops, Dan Knights. LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients |
| 0 | -- | 0 | Tudor Groza, Honghan Wu, Marcel E. Dinger, Daniel Danis, Coleman Hilton, Anita Bagley, Jon R. Davids, Ling Luo 0001, Zhiyong Lu, Peter N. Robinson. Term-BLAST-like alignment tool for concept recognition in noisy clinical texts |
| 0 | -- | 0 | Xiaojing Wu, Mingfei Han, Xinyu Song, Song He, Xiaochen Bo, Yunping Zhu. COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods |
| 0 | -- | 0 | . Correction to: NeoFox: annotating neoantigen candidates with neoantigen features |
| 0 | -- | 0 | Kyriakos Soulios, Patrick Scheibe, Matthias Bernt, Jörg Hackermüller, Jana Schor. deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks |
| 0 | -- | 0 | Emil Hägglund, Siv G. E. Andersson, Lionel Guy. TADA: taxonomy-aware dataset aggregator |
| 0 | -- | 0 | Giovanni Visonà, Diane Duroux, Lucas Miranda, Emese Sükei, Yiran Li, Karsten M. Borgwardt, Carlos G. Oliver. Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information |
| 0 | -- | 0 | Nolan H. Hamilton, Terrence S. Furey. ROCCO: a robust method for detection of open chromatin via convex optimization |
| 0 | -- | 0 | . Correction to: Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads |
| 0 | -- | 0 | Kaspar Märtens, Michele Bortolomeazzi, Lucia Montorsi, Jo Spencer, Francesca D. Ciccarelli, Christopher Yau. Rarity: discovering rare cell populations from single-cell imaging data |
| 0 | -- | 0 | . Correction to: Prediction of gene co-expression from chromatin contacts with graph attention network |
| 0 | -- | 0 | Jaskaran Singh, Yingzhou Edward Pan, Shunmoogum A Patten. NMJ Analyser: a novel method to quantify neuromuscular junction morphology in zebrafish |
| 0 | -- | 0 | Quim Aguado-Puig, Max Doblas, Christos Matzoros, Antonio Espinosa, Juan Carlos Moure, Santiago Marco-Sola, Miquel Moretó. WFA-GPU: gap-affine pairwise read-alignment using GPUs |
| 0 | -- | 0 | Jose Espejo Valle-Inclán, Isidro Cortés-Ciriano. ReConPlot: an R package for the visualization and interpretation of genomic rearrangements |
| 0 | -- | 0 | Ying Zhang, Zhikang Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-jun Yu. Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues |
| 0 | -- | 0 | Dani Korpela, Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Satu Mustjoki, Harri Lähdesmäki. EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings |
| 0 | -- | 0 | . Correction to: KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality |