Skip to main content


Page 4 of 237

  1. The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAS...

    Authors: Trinity Cheng, Pei-Ju Chin, Kenny Cha, Nicholas Petrick and Mike Mikailov
    Citation: BMC Bioinformatics 2022 23:544
  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
  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
  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

    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
  6. 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
  7. 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
  8. 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

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

  9. 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

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

  10. 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

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

  11. 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
  12. 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

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

  13. 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

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

  14. 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
  15. 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

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

  16. 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

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

  17. 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
  18. 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
  19. 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
  20. 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
  21. 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

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

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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

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

  30. 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
  31. 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
  32. 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
  33. 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
  34. 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

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

  35. 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
  36. 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
  37. 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
  38. 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
  39. 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

Featured videos

View featured videos from across the BMC-series journals

Annual Journal Metrics

  • Citation Impact
    3.328 - 2-year Impact Factor (2021)
    4.341 - 5-year Impact Factor (2021)
    1.105 - SNIP (Source Normalized Impact per Paper)
    1.246 - SJR (SCImago Journal Rank)

    15 days to first decision for all manuscripts (Median)
    56 days to first decision for reviewed manuscripts only (Median)

    6,337,109 Downloads (2021)
    8,344 Altmetric mentions (2021)

Sign up for article alerts and news from this journal