BMC Bioinformatics, Volume 23 - Supplements

Volume 23-S, Number 1, January 2022

Selected articles from the Biological Ontologies and Knowledge bases workshop 2020

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  Zhen Tian, Haichuan Fang, Yangdong Ye, Zhenfeng Zhu:
  A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. 47
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  Ying Wang, Qinke Peng, Xu Mou, Xinyuan Wang, Haozhou Li, Tian Han, Zhao Sun, Xiao Wang:
  A successful hybrid deep learning model aiming at promoter identification. 206

Volume 23-S, Number 2, December 2022

Selected articles from the 8th International Work-Conference on Bioinformatics and Biomedical Engineering

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  Luca Cappelletti, Alessandro Petrini, Jessica Gliozzo, Elena Casiraghi, Max Schubach, Martin Kircher, Giorgio Valentini:
  Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques. 154
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  Dimitris Grigoriadis, Nikos Perdikopanis, Georgios K. Georgakilas, Artemis G. Hatzigeorgiou:
  DeepTSS: multi-branch convolutional neural network for transcription start site identification from CAGE data. 395
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  Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi:
  Improving automatic GO annotation with semantic similarity. 433

Volume 23-S, Number 3, March 2022

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2021): bioinformatics

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  Jeerthi Kannan, Liza Mathews, Zhijie Wu, Neal S. Young, Shouguo Gao:
  CAISC: A software to integrate copy number variations and single nucleotide mutations for genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing. 98
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  Wei Shao, Xiao Luo, Zuoyi Zhang, Zhi Han, Vasu Chandrasekaran, Vladimir Turzhitsky, Vishal Bali, Anna R. Roberts, Megan Metzger, Jarod Baker, Carmen La Rosa, Jessica Weaver, Paul R. Dexter, Kun Huang:
  Application of unsupervised deep learning algorithms for identification of specific clusters of chronic cough patients from EMR data. 140
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  Xiao Chen, Jianlin Cheng:
  DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network. 141
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  Inyoung Sung, Sangseon Lee, Minwoo Pak, Yunyol Shin, Sun Kim:
  AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning. 149
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  Tapas Bhadra, Saurav Mallik, Neaj Hasan, Zhongming Zhao:
  Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer. 153
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  Yang Liu, Hansaim Lim, Lei Xie:
  Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. 158
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  Lei Sun, Jinbiao Wang, Fu Yan, Gongming Wang, Yun Li, Jinlin Huang:
  CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes. 172
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  Naima Ahmed Fahmi, Khandakar Tanvir Ahmed, Jae-Woong Chang, Heba Nassereddeen, Deliang Fan, Jeongsik Yong, Wei Zhang:
  APA-Scan: detection and visualization of 3′-UTR alternative polyadenylation with RNA-seq and 3′-end-seq data. 396
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  Nathan Ranno, Dong Si:
  Neural representations of cryo-EM maps and a graph-based interpretation. 397
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  Hung Mai, Jingxuan Bao, Paul M. Thompson, Dokyoon Kim, Li Shen:
  Identifying genes associated with brain volumetric differences through tissue specific transcriptomic inference from GWAS summary data. 398
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  Jian Zhao, Minhui Zhuang, Jingjing Liu, Meng Zhang, Cong Zeng, Bin Jiang, Jing Wu, Xiaofeng Song:
  pHisPred: a tool for the identification of histidine phosphorylation sites by integrating amino acid patterns and properties. 399
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  Yixue Feng, Mansu Kim, Xiaohui Yao, Kefei Liu, Qi Long, Li Shen:
  Deep multiview learning to identify imaging-driven subtypes in mild cognitive impairment. 402
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  Qiao Liu, Bohyun Lee, Lei Xie:
  Small molecule modulation of microbiota: a systems pharmacology perspective. 403
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  Xuedong Wang, Yanle Liu, Xinyao Miao, Yin Chen, Xiao Cao, Yuchen Zhang, Shuaicheng Li, Qin Zhou:
  DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs. 426
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  Lei Deng, Dayun Liu, Yizhan Li, Runqi Wang, Junyi Liu, Jiaxuan Zhang, Hui Liu:
  MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network. 427
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  Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A. Hutcheson, Clifton D. Fuller, Bibhas Chakraborty, Christine B. Peterson:
  Estimating the optimal linear combination of predictors using spherically constrained optimization. 436
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  Jianan Lin, Yang Chen, Yuping Zhang, Haifan Lin, Zhengqing Ouyang:
  Deciphering the role of RNA structure in translation efficiency. 559
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  Jin Zhang, Huiai Wang, Ying Zhao, Lei Guo, Lei Du:
  Identification of multimodal brain imaging association via a parameter decomposition based sparse multi-view canonical correlation analysis method. 128
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  Jiaxing Chen, Yen Kaow Ng, Lu Lin, Xianglilan Zhang, Shuaicheng Li:
  Correction: On triangle inequalities of correlation-based distances for gene expression profiles. 571
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  Zilin Ren, Quan Li, Kajia Cao, Marilyn M. Li, Yunyun Zhou, Kai Wang:
  Correction: Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data. 572

Volume 23-S, Number 4, April 2022

The 20th International Conference on Bioinformatics (InCoB 2021)

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  Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang:
  DualGCN: a dual graph convolutional network model to predict cancer drug response. 129
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  Yu-Wei Huang, Yen-Chao Hsu, Yi-Hsuan Chuang, Yun-Ti Chen, Xiang-Yu Lin, You-Wei Fan, Nikhil Pathak, Jinn-Moon Yang:
  Discovery of moiety preference by Shapley value in protein kinase family using random forest models. 130
• 
  Ming-Ren Yang, Yu-Wei Wu:
  Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach. 131
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  Hamid Hadipour, Chengyou Liu, Rebecca L. Davis, Silvia T. Cardona, Pingzhao Hu:
  Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means. 132
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  You-Wei Fan, Wan-Hsin Liu, Yun-Ti Chen, Yen-Chao Hsu, Nikhil Pathak, Yu-Wei Huang, Jinn-Moon Yang:
  Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations. 242
• 
  Xiujin Wu, Wenhua Zeng, Fan Lin:
  GCNCPR-ACPs: a novel graph convolution network method for ACPs prediction. 560
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  Xiang-Yu Lin, Yu-Wei Huang, You-Wei Fan, Yun-Ti Chen, Nikhil Pathak, Yen-Chao Hsu, Jinn-Moon Yang:
  Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties. 247

Volume 23-S, Number 5, December 2022

Selected articles from the 2020 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2020): bioinformatics

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  Hongzhe Guo, Zhongbo Yang, Tao Jiang, Shiqi Liu, Yadong Wang, Zhe Cui:
  Evaluation of classification in single cell atac-seq data with machine learning methods. 249
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  Zhihui Yang, Juan Liu, Hayat Ali Shah, Jing Feng:
  A novel hybrid framework for metabolic pathways prediction based on the graph attention network. 329

Volume 23-S, Number 6, July 2022

Selected articles from the 17th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2021)

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  Daniele Marchei, Emanuela Merelli:
  RNA secondary structure factorization in prime tangles. 345
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  Giuseppe Agapito, Marianna Milano, Mario Cannataro:
  A statistical network pre-processing method to improve relevance and significance of gene lists in microarray gene expression studies. 393
• 
  Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Larry Bu, Yuji Zhang, Yong Chen, Cui Tao:
  Mining on Alzheimer's diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing. 407
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  Bruno G. Galuzzi, Marco Vanoni, Chiara Damiani:
  Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells. 445
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  Angelo Ciaramella, Emanuel Di Nardo, Daniela Terracciano, Lia Conte, Ferdinando Febbraio, Amelia Cimmino:
  A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology. 569
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  Michela Quadrini, Luca Tesei, Emanuela Merelli:
  Automatic generation of pseudoknotted RNAs taxonomy. 575

Volume 23-S, Number 7, December 2022

Selected articles from the 20th Asia Pacific Bioinformatics Conference (APBC 2022): bioinformatics

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  Biao Duan, Jing Peng, Yi Zhang:
  IMSE: interaction information attention and molecular structure based drug drug interaction extraction. 338
• 
  Yang Li, Xuegang Hu, Zhu-Hong You, Li-Ping Li, Pei-Pei Li, Yan-Bin Wang, Yu-An Huang:
  Robust and accurate prediction of self-interacting proteins from protein sequence information by exploiting weighted sparse representation based classifier. 518

Volume 23-S, Number 8, December 2022

Selected articles from the 16th International Symposium on Bioinformatics Research and Applications (ISBRA-20): bioinformatics

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  Weixia Xu, Yunfeng Dong, Jihong Guan, Shuigeng Zhou:
  Identifying essential proteins from protein-protein interaction networks based on influence maximization. 339
• 
  Lovemore Tenha, Mingzhou Song:
  Statistical evidence for the presence of trajectory in single-cell data. 340
• 
  Jiaqi Wang, Zeyu Li, Jiawan Zhang:
  Visualizing the knowledge structure and evolution of bioinformatics. 404
• 
  Alexander Churkin, Yann Ponty, Danny Barash:
  IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. 424
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  Minzhu Xie, Xiaowen Lei, Jiancheng Zhong, Jianxing Ouyang, Guijing Li:
  Drug response prediction using graph representation learning and Laplacian feature selection. 532
• 
  Yan-Long Qiu, Wei Wang, Chengkun Wu, Zhichang Zhang:
  A risk factor attention-based model for cardiovascular disease prediction. 425
• 
  Xin Li, Yufeng Wu:
  Detecting genomic deletions from high-throughput sequence data with unsupervised learning. 568

Volume 23-S, Number 9, August 2022

Proceedings of the 15th International Conference on Data and Text Mining in Biomedical Informatics (DTMBIO 2021)

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  Joo-Seong Oh, Hyithaek Ceong, Dokyun Na, Chungoo Park:
  A machine learning model for classifying G-protein-coupled receptors as agonists or antagonists. 346
• 
  Judita Preiss:
  Avoiding background knowledge: literature based discovery from important information. 570
• 
  Seungwon Oh, Sae-Ryung Kang, In-Jae Oh, Min-Soo Kim:
  Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients. 573

Volume 23-S, Number 10, August 2022

Application of Bioinformatics in Medical Science

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  Shuchun Yu, Li Xianxiang, Tian Xue, Ming Pang:
  Protein structure prediction based on particle swarm optimization and tabu search strategy. 352
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  Hai-Hui Huang, Hao Rao, Rui Miao, Yong Liang:
  A novel meta-analysis based on data augmentation and elastic data shared lasso regularization for gene expression. 353

Volume 23-S, Number 11, November 2022

Selected articles on Conceptual Modeling for Life Sciences (CMLS 2021 workshop and ER 2021 conference)

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  Anna Bernasconi, Giancarlo Guizzardi, Oscar Pastor, Veda C. Storey:
  Semantic interoperability: ontological unpacking of a viral conceptual model. 491
• 
  Roman Lukyanenko, Veda C. Storey, Oscar Pastor:
  Conceptual modelling for life sciences based on systemist foundations. 574
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  Alberto García S., Mireia Costa, Ana León, Oscar Pastor:
  The challenge of managing the evolution of genomics data over time: a conceptual model-based approach. 472

Volume 23-S, Number 12, December 2022

Fifth and Sixth Computational Approaches for Cancer Workshop

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  Julian C. Hong, Neville C. W. Eclov, Sarah J. Stephens, Yvonne M. Mowery, Manisha Palta:
  Implementation of machine learning in the clinic: challenges and lessons in prospective deployment from the System for High Intensity EvaLuation During Radiation Therapy (SHIELD-RT) randomized controlled study. 408
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  Geir Severin R. E. Langberg, Mikal Stapnes, Jan F. Nygård, Mari Nygård, Markus Grasmair, Valeriya Naumova:
  Matrix factorization for the reconstruction of cervical cancer screening histories and prediction of future screening results. 484
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  Jong Cheol Jeong, Isaac Hands, Jill M. Kolesar, Mahadev Rao, Bront Davis, York H. Dobyns, Joseph Hurt-Mueller, Justin Levens, Jenny Gregory, John Williams, Lisa Witt, Eun Mi Kim, Carlee Burton, Amir A. Elbiheary, Mingguang Chang, Eric B. Durbin:
  Local data commons: the sleeping beauty in the community of data commons. 368