PyBootNet: a python package for bootstrapping and network construction by Shayan R. Akhavan, Scott T. Kelley

“…PyBootNet provides a powerful and extendible Python bioinformatics solution for bootstrapping analysis and network construction that can be applied to microbes, genes, metabolites and other biological data appropriate for network correlation comparison and analysis.…”
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Using DIMet for Differential Analysis of Labeled Metabolomics Data: A Step-by-step Guide Showcasing the Glioblastoma Metabolism by Johanna Galvis, Joris Guyon, Thomas Daubon, Macha Nikolski

“…Integrating metabolomics data with gene expression profiles further enriches the analysis, as we demonstrated in our prior study on glioblastoma metabolic symbiosis. However, the bioinformatics tools for analyzing tracer metabolomics data have been limited. …”
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Exome sequencing in Nigerian children with early‐onset epilepsy syndromes by Ibitayo Abigail Ademuwagun, Yagoub Adam, Solomon Oladapo Rotimi, Steffen Syrbe, Maximilian Radtke, Julia Hentschel, Johannes R. Lemke, Ezekiel Adebiyi

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IL-23 tunes inflammatory functions of human mucosal-associated invariant T cells by Laetitia Camard, Tharshana Stephen, Hanane Yahia-Cherbal, Vincent Guillemot, Sébastien Mella, Victoire Baillet, Hélène Lopez-Maestre, Daniele Capocefalo, Laura Cantini, Claire Leloup, Julie Marsande, Katherine Garro, Juan Sienes Bailo, Ambre Dangien, Natalia Pietrosemoli, Milena Hasan, Huimeng Wang, Sidonia B.G. Eckle, Anne M. Fourie, Carrie Greving, Barbara Joyce-Shaikh, Raphaelle Parker, Daniel J. Cua, Elisabetta Bianchi, Lars Rogge

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The effects of Thymus capitatus essential oil topical application on milk quality: a systems biology approach by Ralph Nehme, Chiara Gini, Elise Vanbergue, Sergine Even, Filippo Biscarini, Sonia Andrés, Lucie Rault, Faustine Noel, Valerie Hardit, Said Bouhallab, David M. Pereira, Riadh Ksouri, Philippe Roussel, Secundino López, Paola Cremonesi, Bianca Castiglioni, Donatella Caruso, Fiorenza Faré, Manuela Fontana, Fabrizio Ceciliani, Latifa Abdennebi-Najar

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Target miRNA identification for the LPL gene in large yellow croaker (Larimichthys crocea) by Kalim Ullah, Aslam Hossain, Mingyue Cao, Liangyi Xue, Yajun Wang

“…The bioinformatics analysis facilitated the compilation and examination of miRNA datasets specific to these tissues. …”
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AI-enhanced 3D-QSAR screening of fragment-based novel designed molecules targeting Phalaris minor ACCase by Bikash Kumar Rajak, Priyanka Rani, Durg Vijay Singh, Nitesh Singh

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PhyIndBC: Development of a machine learning tool for screening of potential breast cancer inhibitors from phytochemicalsGitHub by Agneesh Pratim Das, Subhash M. Agarwal

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Massively parallel variant-to-function mapping determines functional regulatory variants of non-small cell lung cancer by Congcong Chen, Yang Li, Yayun Gu, Qiqi Zhai, Songwei Guo, Jun Xiang, Yuan Xie, Mingxing An, Chenmeijie Li, Na Qin, Yanan Shi, Liu Yang, Jun Zhou, Xianfeng Xu, Ziye Xu, Kai Wang, Meng Zhu, Yue Jiang, Yuanlin He, Jing Xu, Rong Yin, Liang Chen, Lin Xu, Juncheng Dai, Guangfu Jin, Zhibin Hu, Cheng Wang, Hongxia Ma, Hongbing Shen

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In Vitro Acid Resistance of Pathogenic Candida Species in Simulated Gastric Fluid by Eri Ikeda, Masaya Yamaguchi, Masayuki Ono, Shigetada Kawabata

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An optimized deep-forest algorithm using a modified differential evolution optimization algorithm: A case of host-pathogen protein-protein interaction prediction by Jerry Emmanuel, Itunuoluwa Isewon, Jelili Oyelade

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High-sensitivity colorimetric sensor based on oxidase-like Mn3O4 nanozyme for Cys detection by Junting Liang, Dihan Duan, Lubing Sun, Jinming Li, Mengke Wang, Ziyi Chang, Rick F. Thorne, Chuanliang Chen, Demin Duan

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Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins by Maria Angelica Freitas-Cortez, Fatemeh Masrorpour, Hong Jiang, Iqbal Mahmud, Yue Lu, Ailing Huang, Lisa K. Duong, Qi Wang, Tiffany A. Voss, Claudia S. Kettlun Leyton, Bo Wei, Wai-Kin Chan, Kevin Lin, Jie Zhang, Efrosini Tsouko, Shonik Ganjoo, Hampartsoum B. Barsoumian, Thomas S. Riad, Yun Hu, Carola Leuschner, Nahum Puebla-Osorio, Jing Wang, Jian Hu, Michael A. Davies, Vinay K. Puduvalli, Cyrielle Billon, Thomas P. Burris, Philip L. Lorenzi, Boyi Gan, James W. Welsh

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EpigenomeViewer: A Shiny Web Application for Visualizing Methylation Patterns Across Biological Samples by Nurul Syakima Ab Mutalib

“…This application is an invaluable tool for both experienced researchers and educators in bioinformatics and epigenetics, supporting a wide range of studies from academic research to clinical applications. …”
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Implementation of a genotyped African population cohort, with virtual follow-up: A feasibility study in the Western Cape Province, South Africa [version 2; peer review: 2 approved,... by Robert J Wilkinson, Francisco Lakay, Nicki Tiffin, Joel A Dave, Catherine Riou, Peter Raubenheimer, Anna K Coussens, Tsaone Tamuhla, Melissa J Blumenthal, Maleeka Abrahams

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Apoptosis-inducing proteins with reduced expression in breast cancer: A review article by Mohammad Mehdi Khaleghi, Faezeh Rouhi, Kourosh Eslami, Fatemeh Shafiee

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Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing by Ting-Yu Yen, Ching Hsu, Ni-Chung Lee, Chao-Szu Wu, Hsin Wang, Kuan-Yi Lee, Chia-Ray Lin, Chun-Yi Lu, Mo-Li Tsai, Tzu-Yu Liu, Che Lin, Chien-Yu Chen, Luan-Yin Chang, Feipei Lai, Li-Min Huang

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Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data by Ísak Valsson, Matthew T. Warren, Charlotte M. Deane, Aniket Magarkar, Garrett M. Morris, Philip C. Biggin

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The data-intensive research paradigm: challenges and responses in clinical professional graduate education by Chunhong Yang, Yijing Chen, Changshun Qian, Fangmin Shi, Fangmin Shi, You Guo, You Guo, You Guo, You Guo, You Guo

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Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods by Rué, Olivier, Coton, Monika, Dugat-Bony, Eric, Howell, Kate, Irlinger, Françoise, Legras, Jean-Luc, Loux, Valentin, Michel, Elisa, Mounier, Jérôme, Neuvéglise, Cécile, Sicard, Delphine

“…We created a database, including all mock species sequences for each barcode to compensate for the lack of curated data in available databases. Four bioinformatics tools (DADA2, QIIME, FROGS and a combination of DADA2 and FROGS) were compared. …”
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