SUBJECTS : Genome Analysis | Sequence Analysis | Phylogenetics | Gene Expression | Systems Biolog
Bioinformatics: 2023, vol: , issue:
- 1)- 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. Bioinformatics (Oxford, England). 2023, 39 (12):
Cited : 3Read More - 2)- 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 Moody, Sergey Senkin, Paul Brennan, Michael R Stratton, Ludmil B Alexandrov. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 18Read More
- 3)- Gianluca Vozza, Emanuele Bonetti, Giulia Tini, Valentina Favalli, Gianmaria Frigè, Gabriele Bucci, Simona De Summa, Mario Zanfardino, Francesco Zapelloni, Luca Mazzarella. Benchmarking and improving the performance of variant-calling pipelines with RecallME. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 4)- Kaspar Märtens, Michele Bortolomeazzi, Lucia Montorsi, Jo Spencer, Francesca Ciccarelli, Christopher Yau. Rarity: discovering rare cell populations from single-cell imaging data. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 5)- Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar Deshpande, David Sehnal, Mihaly Varadi, Sameer Velankar. PDBImages: a command-line tool for automated macromolecular structure visualization. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 6)- Herui Liao, Jiayu Shang, Yanni Sun. GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 7)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 8)- . Correction to: GIL: a python package for designing custom indexing primers. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 9)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 5Read More
- 10)- Hikmet Emre Kaya, Kevin J Naidoo. CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 1Read More
- 11)- Herve Emissah, Bengt Ljungquist, Giorgio A Ascoli. Bibliometric analysis of neuroscience publications quantifies the impact of data sharing. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 3Read More
- 12)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 13)- Jacob Morrison, Wanding Zhou, Benjamin K Johnson, Hui Shen. Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 1Read More
- 14)- Susan L Hoops, Dan Knights. LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 15)- Rui Ren, Kuangnan Fang, Qingzhao Zhang, Shuangge Ma. FunctanSNP: an R package for functional analysis of dense SNP data (with interactions). Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 16)- Harshavardhan Khare, Nathaly Dongo Mendoza, Chiara Zurzolo. CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 17)- Emil Hägglund, Siv G E Andersson, Lionel Guy. TADA: taxonomy-aware dataset aggregator. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 1Read More
- 18)- Jaskaran Singh, Yingzhou Edward Pan, Shunmoogum A Patten. NMJ Analyser: a novel method to quantify neuromuscular junction morphology in zebrafish. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 1Read More
- 19)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 20)- Jose Espejo Valle-Inclán, Isidro Cortés-Ciriano. ReConPlot: an R package for the visualization and interpretation of genomic rearrangements. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 2Read More
- 21)- Eszter Csibra, Guy-Bart Stan. Parsley: a web app for parsing data from plate readers. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 2Read More
- 22)- Brendan S McConnell, Matthew W Parker. Protein intrinsically disordered regions have a non-random, modular architecture. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 3Read More
- 23)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 24)- William DeGroat, Dinesh Mendhe, Atharva Bhusari, Habiba Abdelhalim, Saman Zeeshan, Zeeshan Ahmed. IntelliGenes: a novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 74Read More
- 25)- . Correction to: Prediction of gene co-expression from chromatin contacts with graph attention network. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 26)- . Correction to: Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 27)- . Correction to: KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 28)- . Correction to: NeoFox: annotating neoantigen candidates with neoantigen features. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 29)- . Correction to: DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 1Read More
- 30)- . Correction to: PEMT: a patent enrichment tool for drug discovery. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 31)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 1Read More
- 32)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 33)- Nima Nouri, Andre H Kurlovs, Giorgio Gaglia, Emanuele de Rinaldis, Virginia Savova. Scaling up single-cell RNA-seq data analysis with CellBridge workflow. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 1Read More
- 34)- 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. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 0Read More
- 35)- Min Zeng, Yifan Wu, Yiming Li, Rui Yin, Chengqian Lu, Junwen Duan, Min Li. LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism. Bioinformatics (Oxford, England). 2023, 39 (12): Cited : 9Read More
- 36)- Eric Lee, Dongkyu Lee, Wayne Fan, Andrew Lytle, Yuxiang Fu, , David W Scott, Christian Steidl, Samuel Aparicio, Andrew Roth. ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images. Bioinformatics (Oxford, England). 2023, : Cited : 0Read More
- 37)- Ting Liu, K Anton Feenstra, Jaap Heringa, Zhisheng Huang. Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph. Bioinformatics (Oxford, England). 2023, : Cited : 0Read More
- 38)- Xiran Liu, Naama M Kopelman, Noah A Rosenberg. Clumppling: cluster matching and permutation program with integer linear programming. Bioinformatics (Oxford, England). 2023, : Cited : 0Read More
- 39)- Patiphan Wongklaew, Sira Sriswasdi, Ekapol Chuangsuwanich. MHCSeqNet2 - Improved Peptide-Class I MHC Binding Prediction for Alleles with Low Data. Bioinformatics (Oxford, England). 2023, : Cited : 0Read More
- 40)- Zongquan Li, Pengxuan Ren, Hao Yang, Jie Zheng, Fang Bai. TEFDTA: A Transformer Encoder and Fingerprint Representation Combined Prediction Method for Bonded and Non-Bonded Drug-Target Affinities. Bioinformatics (Oxford, England). 2023, : Cited : 8Read More
- 41)- Chunyue Feng, Kokhaur Ong, David M Young, Bingxian Chen, Longjie Li, Xinmi Huo, Haoda Lu, Weizhong Gu, Fei Liu, Hongfeng Tang, Manli Zhao, Min Yang, Kun Zhu, Limin Huang, Qiang Wang, Gabriel Pik Liang Marini, Kun Gui, Hao Han, Stephan J Sanders, Lin Li, Weimiao Yu, Jianhua Mao. Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis. Bioinformatics (Oxford, England). 2023, : Cited : 1Read More
- 42)- Yan Zhou, Ying Zhang, Minjiao Peng, Yaru Zhang, Chenghao Li, Lianjie Shu, Yaohua Hu, Jianzhong Su, Jinfeng Xu. scDMV: A Zero-one Inflated Beta Mixture Model for DNA Methylation Variability with scBS-Seq Data. Bioinformatics (Oxford, England). 2023, : Cited : 0Read More
- 43)- Uxía Veleiro, Jesús de la Fuente, Guillermo Serrano, Marija Pizurica, Mikel Casals, Antonio Pineda-Lucena, Silve Vicent, Idoia Ochoa, Olivier Gevaert, Mikel Hernaez. GeNNius: An ultrafast drug-target interaction inference method based on graph neural networks. Bioinformatics (Oxford, England). 2023, : Cited : 4Read More
- 44)- Seungjun Ahn, Somnath Datta. SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation for Differential Network Analysis of Microbiome Data. Bioinformatics (Oxford, England). 2023, : Cited : 1Read More
- 45)- Robert W Gregg, Panayiotis V Benos. CellularPotts.jl: Simulating Multiscale Cellular Models in Julia. Bioinformatics (Oxford, England). 2023, : Cited : 0Read More
- 46)- Yang Li, Zihou Guo, Xin Gao, Guohua Wang. MMCL-CDR: Enhancing Cancer Drug Response Prediction with Multi-Omics and Morphology Images Contrastive Representation Learning. Bioinformatics (Oxford, England). 2023, : Cited : 2Read More
- 47)- Sebastian Staab, Anny Cardénas, Raquel S Peixoto, Falk Schreiber, Christian R Voolstra. Coracle-A Machine Learning Framework to Identify Bacteria Associated with Continuous Variables. Bioinformatics (Oxford, England). 2023, : Cited : 2Read More
- 48)- Yasin I Tepeli, Colm Seale, Joana P Gonçalves. ELISL: Early-Late Integrated Synthetic Lethality Prediction in Cancer. Bioinformatics (Oxford, England). 2023, : Cited : 1Read More
- 49)- Xinliang Sun, Xiao Jia, Zhangli Lu, Jing Tang, Min Li. Drug repositioning with adaptive graph convolutional networks. Bioinformatics (Oxford, England). 2023, : Cited : 4Read More
- 50)- Colin Brown, Anuradha Agarwal, Antoni Luque. pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells. Bioinformatics (Oxford, England). 2023, : Cited : 1Read More
