From Ontology to Semantic Similarity: Calculation of Ontology-Based Semantic Similarity by Mingxin Gan, Xue Dou, Rui Jiang

“…Ontologies, as abstract description systems for domain-specific knowledge composition, hence receive more and more attention in computational biology and bioinformatics. Particularly, many applications relying on domain ontologies require quantitative measures of relationships between terms in the ontologies, making it indispensable to develop computational methods for the derivation of ontology-based semantic similarity between terms. …”
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Raves, clubs and ecstasy: the impact of peer pressure by Baojun Song, Melissa Castillo-Garsow, Karen R. Ríos-Soto, Marcin Mejran, Leilani Henso, Carlos Castillo-Chavez

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An Efficient Approach to Mining Maximal Contiguous Frequent Patterns from Large DNA Sequence Databases by Md. Rezaul Karim, Md. Mamunur Rashid, Byeong-Soo Jeong, Ho-Jin Choi

“…Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. …”
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Validation of histopathology foundation models through whole slide image retrieval by Saghir Alfasly, Ghazal Alabtah, Sobhan Hemati, Krishna Rani Kalari, Joaquin J. Garcia, H. R. Tizhoosh

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Single-Cell Transcriptome Analysis of Human Adipose-Derived Stromal Cells Identifies a Contractile Cell Subpopulation by Elize Wolmarans, Juanita Mellet, Chrisna Durandt, Fourie Joubert, Michael S. Pepper

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PIPENN-EMB ensemble net and protein embeddings generalise protein interface prediction beyond homology by David P. G. Thomas, Carlos M. Garcia Fernandez, Reza Haydarlou, K. Anton Feenstra

“…Abstract Protein interactions are crucial for understanding biological functions and disease mechanisms, but predicting these remains a complex task in computational biology. Increasingly, Deep Learning models are having success in interface prediction. …”
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Machine learning of swimming data via wisdom of crowd and regression analysis by Jiang Xie, Junfu Xu, Celine Nie, Qing Nie

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Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut by Sophia Levy, Angela K. Jiang, Maggie R. Grant, Gabriela Arp, Glory Minabou Ndjite, Xiaofang Jiang, Brantley Hall

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Metabolomic and lipidomic pathways in aneurysmal subarachnoid hemorrhage by Bosco Seong Kyu Yang, Spiros L. Blackburn, Philip L. Lorenzi, Huimahn A. Choi, Aaron M. Gusdon

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An Exploration of Gene-Gene Interactions and Their Effects on Hypertension by Ying Meng, Susan Groth, Jill R. Quinn, John Bisognano, Tong Tong Wu

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Understanding metastasis mixed-treatment responses through genomic analyses by Susana Garcia-Recio, Paola Zagami, Brooke M. Felsheim, Amy Wheless, Kerry Thomas, Renato Trimarchi, Lisa A. Carey, Charles M. Perou

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From the Guest Editors by Fred Brauer, Carlos Castillo-Chavez, Thomas G. Hallam, Jia Li, Jianhong Wu, Yicang Zhou

“…His rapid rise to his current role as an international leader and premier mentor to 11 Ph.D. students has facilitated the placement of Chinese scientists and scholars at the forefront of research in the fields of mathematical, theoretical and computational biology.For the full paper, please click the 'Full Text' button above.…”
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Gastrointestinal Pathobionts in Pediatric Crohn’s Disease Patients by Rachel V. Purcell, Nadeem O. Kaakoush, Hazel M. Mitchell, John F. Pearson, Jacqueline I. Keenan

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Protocol for predicting the single-cell network-based gene activity landscape during human B cell development by Xin Huang, Xuetong Hou, Yizhen Li, Jun J. Yang, Jiyang Yu

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miRNA-Disease Association Prediction with Collaborative Matrix Factorization by Zhen Shen, You-Hua Zhang, Kyungsook Han, Asoke K. Nandi, Barry Honig, De-Shuang Huang

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Prevalence of Corneal Astigmatism in Patients before Cataract Surgery in Northern China by Xiaoyong Yuan, Hui Song, Gang Peng, Xia Hua, Xin Tang

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Correlating disordered activation domain ensembles with gene expression levels by Eduardo Flores, Aleah R. Camacho, Estefania Cuevas-Zepeda, Mary B. McCoy, Feng Yu, Max V. Staller, Shahar Sukenik

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G3DC: A Gene-Graph-Guided Selective Deep Clustering Method for Single Cell RNA-seq Data by Shuqing He, Jicong Fan, Tianwei Yu

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Identification and characteristics of distressed patients with coronary heart disease and insufficiently controlled medical risk factors: baseline findings and sex differences from... by Christoph Herrmann-Lingen, Christoph Herrmann-Lingen, Monika Sadlonova, Monika Sadlonova, Monika Sadlonova, Monika Sadlonova, Monika Sadlonova, Ingrid Becker, Kristina Bersch, Franziska Geiser, Martin Hellmich, Ingrid Kindermann, Matthias Michal, Mariel Nöhre, Astrid Petersmann, Astrid Petersmann, Rolf Wachter, Rolf Wachter, Rolf Wachter, Birgit Herbeck Belnap, Birgit Herbeck Belnap, Christian Albus

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EPIMR: Prediction of Enhancer-Promoter Interactions by Multi-Scale ResNet on Image Representation by Qiaozhen Meng, Yinuo Lyu, Xiaoqing Peng, Junhai Xu, Jijun Tang, Fei Guo

“…Due to limited resolution, biological experiments perform not as well as expected while precisely identifying specific interactions, giving rise to computational biology approaches. Many EPI predictors have been developed, but their prediction accuracy still needs to be enhanced. …”
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