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  2. Compound–protein interaction site and binding affinity predictions are crucial for drug discovery and drug design. In recent years, many deep learning-based methods have been proposed for predications related ...

    Authors: Jialin Wu, Zhe Liu, Xiaofeng Yang and Zhanglin Lin
    Citation: BMC Bioinformatics 2022 23:543
    Content type: Research Published on:

  3. During atherosclerosis, the narrowing of the arterial lumen is observed through the accumulation of bio compounds and the formation of plaque within artery walls. A non-linear optical imaging modality (NLOM), ...

    Authors: Natasha N. Kunchur and Leila B. Mostaço-Guidolin
    Citation: BMC Bioinformatics 2022 23:542
    Content type: Research Published on:

  4. Brain tumor segmentation plays a significant role in clinical treatment and surgical planning. Recently, several deep convolutional networks have been proposed for brain tumor segmentation and have achieved im...

    Authors: Yuhu Wang, Yuzhen Cao, Jinqiu Li, Hongtao Wu, Shuo Wang, Xinming Dong and Hui Yu
    Citation: BMC Bioinformatics 2022 22(Suppl 5):636
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  5. Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics ana...

    Authors: Daniel M. Portik, C. Titus Brown and N. Tessa Pierce-Ward
    Citation: BMC Bioinformatics 2022 23:541
    Content type: Research Published on:

  7. With the rapid accumulation of scRNA-seq data, more and more automatic cell type identification methods have been developed, especially those based on deep learning. Although these methods have reached relativ...

    Authors: Lifei Wang, Rui Nie, Jiang Zhang and Jun Cai
    Citation: BMC Bioinformatics 2022 23:539
    Content type: Research article Published on:

  9. Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databas...

    Authors: Jero Schäfer, Ming Tang, Danny Luu, Anke Katharina Bergmann and Lena Wiese
    Citation: BMC Bioinformatics 2022 23:537
    Content type: Software Published on:

  11. Automatic functional annotation of proteins is an open research problem in bioinformatics. The growing number of protein entries in public databases, for example in UniProtKB, poses challenges in manual functi...

    Authors: Bishnu Sarker, Navya Khare, Marie-Dominique Devignes and Sabeur Aridhi
    Citation: BMC Bioinformatics 2022 23(Suppl 2):433
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 23 Supplement 2

  12. The widespread usage of Cap Analysis of Gene Expression (CAGE) has led to numerous breakthroughs in understanding the transcription mechanisms. Recent evidence in the literature, however, suggests that CAGE su...

    Authors: Dimitris Grigoriadis, Nikos Perdikopanis, Georgios K. Georgakilas and Artemis G. Hatzigeorgiou
    Citation: BMC Bioinformatics 2022 23(Suppl 2):395
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 23 Supplement 2

  13. Cis-regulatory regions (CRRs) are non-coding regions of the DNA that fine control the spatio-temporal pattern of transcription; they are involved in a wide range of pivotal processes such as the development of...

    Authors: Luca Cappelletti, Alessandro Petrini, Jessica Gliozzo, Elena Casiraghi, Max Schubach, Martin Kircher and Giorgio Valentini
    Citation: BMC Bioinformatics 2022 23(Suppl 2):154
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 2

  15. The central role of proteins in diseases has made them increasingly attractive as therapeutic targets and indicators of cellular processes. Protein microarrays are emerging as an important means of characteris...

    Authors: Metoboroghene Oluwaseyi Mowoe, Shaun Garnett, Katherine Lennard, Jade Talbot, Paul Townsend, Eduard Jonas and Jonathan Michael Blackburn
    Citation: BMC Bioinformatics 2022 23:534
    Content type: Research Published on:

  16. Authors: Augustin Boudry, Sasha Darmon, Nicolas Duployez, Martin Figeac, Sandrine Geffroy, Maxime Bucci, Karine Celli-Lebras, Matthieu Duchmann, Romane Joudinaud, Laurène Fenwarth, Olivier Nibourel, Laure Goursaud, Raphael Itzykson, Hervé Dombret, Mathilde Hunault, Claude Preudhomme…
    Citation: BMC Bioinformatics 2022 23:533
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2022 23:448

  17. Knowing the responses of a patient to drugs is essential to make personalized medicine practical. Since the current clinical drug response experiments are time-consuming and expensive, utilizing human genomic ...

    Authors: Minzhu Xie, Xiaowen Lei, Jianchen Zhong, Jianxing Ouyang and Guijing Li
    Citation: BMC Bioinformatics 2022 23(Suppl 8):532
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 23 Supplement 8

  18. Modern biomedical research is data-driven and relies heavily on the re-use and sharing of data. Biomedical data, however, is subject to strict data protection requirements. Due to the complexity of the data re...

    Authors: Felix Nikolaus Wirth, Tobias Kussel, Armin Müller, Kay Hamacher and Fabian Prasser
    Citation: BMC Bioinformatics 2022 23:531
    Content type: Software Published on:

  19. Researchers have tried to identify and count different blood cells in microscopic smear images by using deep learning methods of artificial intelligence to solve the highly time-consuming problem.

    Authors: Yao-Mei Chen, Jinn-Tsong Tsai and Wen-Hsien Ho
    Citation: BMC Bioinformatics 2022 22(Suppl 5):635
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  20. Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have bee...

    Authors: Jhen Yuan Yang and Jia-Ming Chang
    Citation: BMC Bioinformatics 2022 22(Suppl 10):634
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  21. Localization-based super-resolution microscopy resolves macromolecular structures down to a few nanometers by computationally reconstructing fluorescent emitter coordinates from diffraction-limited spots. The ...

    Authors: Sebastian Reinhard, Dominic A. Helmerich, Dominik Boras, Markus Sauer and Philip Kollmannsberger
    Citation: BMC Bioinformatics 2022 23:530
    Content type: Research Published on:

  23. The application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaff...

    Authors: Sen Wang, Hengchao Wang, Fan Jiang, Anqi Wang, Hangwei Liu, Hanbo Zhao, Boyuan Yang, Dong Xu, Yan Zhang and Wei Fan
    Citation: BMC Bioinformatics 2022 23:528
    Content type: Software Published on:

  24. Preeclampsia (PE) has an increasing incidence worldwide, and there is no gold standard for prediction. Recent progress has shown that abnormal decidualization and impaired vascular remodeling are essential to ...

    Authors: Hongya Zhang, Xuexiang Li, Tianying Zhang, Qianhui Zhou and Cong Zhang
    Citation: BMC Bioinformatics 2022 23:527
    Content type: Research Published on:

  25. Drug–drug interactions (DDIs) are preventable causes of medical injuries and often result in doctor and emergency room visits. Previous research demonstrates the effectiveness of using matrix completion approa...

    Authors: Guy Shtar, Asnat Greenstein-Messica, Eyal Mazuz, Lior Rokach and Bracha Shapira
    Citation: BMC Bioinformatics 2022 23:526
    Content type: Research Published on:

  26. The correct establishment of the barcode classification system for fish can facilitate biotaxonomists to distinguish fish species, and it can help the government to verify the authenticity of the ingredients o...

    Authors: Ting-Hui Wu, Cing-Han Yang, Tun-Wen Pai, Li-Ping Ho, Jen-Leih Wu and Hsin-Yiu Chou
    Citation: BMC Bioinformatics 2022 22(Suppl 10):633
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  27. Accurate estimate of relatedness is important for genetic data analyses, such as heritability estimation and association mapping based on data collected from genome-wide association studies. Inaccurate related...

    Authors: Wei Jiang, Xiangyu Zhang, Siting Li, Shuang Song and Hongyu Zhao
    Citation: BMC Bioinformatics 2022 23:525
    Content type: Research Published on:

  28. The roles of antibody and antigen are indispensable in targeted diagnosis, therapy, and biomedical discovery. On top of that, massive numbers of new scientific articles about antibodies and/or antigens are pub...

    Authors: Thuy Trang Dinh, Trang Phuong Vo-Chanh, Chau Nguyen, Viet Quoc Huynh, Nam Vo and Hoang Duc Nguyen
    Citation: BMC Bioinformatics 2022 23:524
    Content type: Research Published on:

  29. Glaucoma can cause irreversible blindness to people’s eyesight. Since there are no symptoms in its early stage, it is particularly important to accurately segment the optic disc (OD) and optic cup (OC) from fu...

    Authors: Yun Jiang, Zeqi Ma, Chao Wu, Zequn Zhang and Wei Yan
    Citation: BMC Bioinformatics 2022 23:523
    Content type: Research Published on:

  30. A deep understanding of carcinogenesis at the DNA level underpins many advances in cancer prevention and treatment. Mutational signatures provide a breakthrough conceptualisation, as well as an analysis framew...

    Authors: Dovydas Kičiatovas, Qingli Guo, Miika Kailas, Henri Pesonen, Jukka Corander, Samuel Kaski, Esa Pitkänen and Ville Mustonen
    Citation: BMC Bioinformatics 2022 23:522
    Content type: Research Published on:

  31. Protein–protein interactions are widespread in biological systems and play an important role in cell biology. Since traditional laboratory-based methods have some drawbacks, such as time-consuming, money-consu...

    Authors: Wen Zhong, Changxiang He, Chen Xiao, Yuru Liu, Xiaofei Qin and Zhensheng Yu
    Citation: BMC Bioinformatics 2022 23:521
    Content type: Research Published on:

  32. Monoclonal antibodies (mAbs) have been used as therapeutic agents, which must overcome many developability issues after the discovery from in vitro display libraries. Especially, polyreactive mAbs can strongly...

    Authors: Hocheol Lim and Kyoung Tai No
    Citation: BMC Bioinformatics 2022 23:520
    Content type: Research Published on:

  33. Independent Component Analysis (ICA) allows the dissection of omic datasets into modules that help to interpret global molecular signatures. The inherent randomness of this algorithm can be overcome by cluster...

    Authors: Miquel Anglada-Girotto, Samuel Miravet-Verde, Luis Serrano and Sarah A. Head
    Citation: BMC Bioinformatics 2022 23:519
    Content type: Software Published on:

  34. Self-interacting proteins (SIPs), two or more copies of the protein that can interact with each other expressed by one gene, play a central role in the regulation of most living cells and cellular functions. A...

    Authors: Yang Li, Xue-Gang Hu, Zhu-Hong You, Li-Ping Li, Pei-Pei Li, Yan-Bin Wang and Yu-An Huang
    Citation: BMC Bioinformatics 2022 23(Suppl 7):518
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 7

  35. This research aims to increase our knowledge of amyloidoses. These disorders cause incorrect protein folding, affecting protein functionality (on structure). Fibrillar deposits are the basis of some wellknown ...

    Authors: Alessia Auriemma Citarella, Luigi Di Biasi, Fabiola De Marco and Genoveffa Tortora
    Citation: BMC Bioinformatics 2022 23:517
    Content type: Research Published on:

  36. Drug repositioning is a very important task that provides critical information for exploring the potential efficacy of drugs. Yet developing computational models that can effectively predict drug–disease assoc...

    Authors: Meng-Long Zhang, Bo-Wei Zhao, Xiao-Rui Su, Yi-Zhou He, Yue Yang and Lun Hu
    Citation: BMC Bioinformatics 2022 23:516
    Content type: Research Published on:

  39. The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is ...

    Authors: Jingchao Sun, Zhining Qiu, Rob Egan, Harrison Ho, Yue Li and Zhong Wang
    Citation: BMC Bioinformatics 2022 23:513
    Content type: Research article Published on:

  40. Genome-scale metabolic reconstruction tools have been developed in the last decades. They have helped to reconstruct eukaryotic and prokaryotic metabolic models, which have contributed to fields, e.g., genetic...

    Authors: Gustavo Tamasco, Manish Kumar, Karsten Zengler, Rafael Silva-Rocha and Ricardo Roberto da Silva
    Citation: BMC Bioinformatics 2022 23:512
    Content type: Software Published on:

  42. Cancers are genetically heterogeneous, so anticancer drugs show varying degrees of effectiveness on patients due to their differing genetic profiles. Knowing patient’s responses to numerous cancer drugs are ne...

    Authors: Conghao Wang, Xintong Lye, Rama Kaalia, Parvin Kumar and Jagath C. Rajapakse
    Citation: BMC Bioinformatics 2022 22(Suppl 10):632
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  44. Research on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental evolution to bioinformatics and theoretical models. Notwithstanding, a consens...

    Authors: Yuridia S. Posadas-García and Carlos Espinosa-Soto
    Citation: BMC Bioinformatics 2022 23:509
    Content type: Research Published on:

  46. Bacteria can exceptionally evolve and develop pathogenic features making it crucial to determine novel pathogenic proteins for specific therapeutic interventions. Therefore, we have developed a machine-learnin...

    Authors: Ankit Gupta, Aditya S. Malwe, Gopal N. Srivastava, Parikshit Thoudam, Keshav Hibare and Vineet K. Sharma
    Citation: BMC Bioinformatics 2022 23:507
    Content type: Research Published on:

  47. Histological feature representation is advantageous for computer aided diagnosis (CAD) and disease classification when using predictive techniques based on machine learning. Explicit feature representations in...

    Authors: Aravind Nair, Helena Arvidsson, Jorge E. Gatica V., Nikolce Tudzarovski, Karl Meinke and Rachael. V Sugars
    Citation: BMC Bioinformatics 2022 23:506
    Content type: Research Published on:

  48. Multiple processes impact the probability of retention of individual genes following whole genome duplication (WGD) events. In analyzing two consecutive whole genome duplication events that occurred in the lin...

    Authors: C. Nicholas Henry, Kathryn Piper, Amanda E. Wilson, John L. Miraszek, Claire S. Probst, Yuying Rong and David A. Liberles
    Citation: BMC Bioinformatics 2022 23:505
    Content type: Software Published on:

  49. Identifying polymorphism clades on phylogenetic trees could help detect punctual mutations that are associated with viral functions. With visualization tools coloring the tree, it is easy to visually find clad...

    Authors: Chengyang Ji, Na Han, Yexiao Cheng, Jingzhe Shang, Shenghui Weng, Rong Yang, Hang-Yu Zhou and Aiping Wu
    Citation: BMC Bioinformatics 2022 23:504
    Content type: Software Published on:

  50. Building biological networks with a certain function is a challenge in systems biology. For the functionality of small (less than ten nodes) biological networks, most methods are implemented by exhausting all ...

    Authors: Guo Mao, Ruigeng Zeng, Jintao Peng, Ke Zuo, Zhengbin Pang and Jie Liu
    Citation: BMC Bioinformatics 2022 23:503
    Content type: Research Published on:

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