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  1. Nanoscale connectomics, which aims to map the fine connections between neurons with synaptic-level detail, has attracted increasing attention in recent years. Currently, the automated reconstruction algorithms...

    Authors: Bei Hong, Jing Liu, Hao Zhai, Jiazheng Liu, Lijun Shen, Xi Chen, Qiwei Xie and Hua Han
    Citation: BMC Bioinformatics 2022 23:453
    Content type: Research Published on:

  4. Lysine succinylation is a newly discovered protein post-translational modifications. Predicting succinylation sites helps investigate the metabolic disease treatments. However, the biological experimental appr...

    Authors: Jianhua Jia, Genqiang Wu, Meifang Li and Wangren Qiu
    Citation: BMC Bioinformatics 2022 23:450
    Content type: Research Published on:

  5. Compositional systems, represented as parts of some whole, are ubiquitous. They encompass the abundances of proteins in a cell, the distribution of organisms in nature, and the stoichiometry of the most basic ...

    Authors: Corey Weistuch, Jiening Zhu, Joseph O. Deasy and Allen R. Tannenbaum
    Citation: BMC Bioinformatics 2022 23:449
    Content type: Research Published on:

  6. Internal tandem duplications in the FLT3 gene, termed FLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3-ITDs are increasingly screened thr...

    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 23:448
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2022 23:533

  7. The site information of substrates that can be cleaved by human immunodeficiency virus 1 proteases (HIV-1 PRs) is of great significance for designing effective inhibitors against HIV-1 viruses. A variety of ma...

    Authors: Lun Hu, Zhenfeng Li, Zehai Tang, Cheng Zhao, Xi Zhou and Pengwei Hu
    Citation: BMC Bioinformatics 2022 23:447
    Content type: Research Published on:

  9. Sophisticated methods to properly pre-process and analyze the increasing collection of single-cell RNA sequencing (scRNA-seq) data are increasingly being developed. On the contrary, the best practices to integ...

    Authors: Bruno G. Galuzzi, Marco Vanoni and Chiara Damiani
    Citation: BMC Bioinformatics 2022 23(Suppl 6):445
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 6

  11. Generating polygenic risk scores for diseases and complex traits requires high quality GWAS summary statistic files. Often, these files can be difficult to acquire either as a result of unshared or incomplete ...

    Authors: Mykyta Matushyn, Madhuchanda Bose, Abdallah Amr Mahmoud, Lewis Cuthbertson, Carlos Tello, Karatuğ Ozan Bircan, Andrew Terpolovsky, Varuna Bamunusinghe, Umar Khan, Biljana Novković, Manfred G. Grabherr and Puya G. Yazdi
    Citation: BMC Bioinformatics 2022 23:443
    Content type: Research Published on:

  13. Availability of next generation sequencing data, allows low-frequency and rare variants to be studied through strategies other than the commonly used genome-wide association studies (GWAS). Rare variants are i...

    Authors: Amrita Chattopadhyay, Ching-Yu Shih, Yu-Chen Hsu, Jyh-Ming Jimmy Juang, Eric Y. Chuang and Tzu-Pin Lu
    Citation: BMC Bioinformatics 2022 23:441
    Content type: Software Published on:

  14. High-content screening (HCS) experiments generate complex data from multiple object features for each cell within a treated population. Usually, these data are analyzed by using population-averaged values of t...

    Authors: Rajendra Kumar Gurumurthy, Klaus-Peter Pleissner, Cindrilla Chumduri, Thomas F. Meyer and André P. Mäurer
    Citation: BMC Bioinformatics 2022 23:440
    Content type: Research Published on:

  15. In fluorescence microscopy, co-localization refers to the spatial overlap between different fluorescent labels in cells. The degree of overlap between two or more channels in a microscope may reveal a physical...

    Authors: Alexia Akalestou-Clocher, Vivian Kalamara, Pantelis Topalis and George A. Garinis
    Citation: BMC Bioinformatics 2022 23:439
    Content type: Software Published on:

  16. Recently, Deep Learning based automatic generation of treatment recommendation has been attracting much attention. However, medical datasets are usually small, which may lead to over-fitting and inferior perfo...

    Authors: Chengkai Piao, Mengyue Lv, Shujie Wang, Rongyan Zhou, Yuchen Wang, Jinmao Wei and Jian Liu
    Citation: BMC Bioinformatics 2022 23:438
    Content type: Research Published on:

  18. In the context of a binary classification problem, the optimal linear combination of continuous predictors can be estimated by maximizing the area under the receiver operating characteristic curve. For ordinal...

    Authors: Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A. Hutcheson, Clifton D. Fuller, Bibhas Chakraborty and Christine B. Peterson
    Citation: BMC Bioinformatics 2022 23(Suppl 3):436
    Content type: Software Published on:

    This article is part of a Supplement: Volume 23 Supplement 3

  19. The aim of this study was to identify and screen long non-coding RNA (lncRNA) associated with immune genes in colon cancer, construct immune-related lncRNA pairs, establish a prognostic risk assessment model f...

    Authors: Zezhou Hao, Pengchen Liang, Changyu He, Shuang Sha, Ziyuan Yang, Yixin Liu, Junfeng Shi, Zhenggang Zhu and Qing Chang
    Citation: BMC Bioinformatics 2022 23:435
    Content type: Research Published on:

  20. Breast cancer is one of the most common cancers in women. It is necessary to classify breast cancer subtypes because different subtypes need specific treatment. Identifying biomarkers and classifying breast ca...

    Authors: Juntao Li, Hongmei Zhang and Fugen Gao
    Citation: BMC Bioinformatics 2022 23:434
    Content type: Research Published on:

  21. Increasing biomedical studies have shown that the dysfunction of miRNAs is closely related with many human diseases. Identifying disease-associated miRNAs would contribute to the understanding of pathological ...

    Authors: Ruiyu Guo, Hailin Chen, Wengang Wang, Guangsheng Wu and Fangliang Lv
    Citation: BMC Bioinformatics 2022 23:432
    Content type: Research Published on:

  22. Predicting morphological changes to anatomical structures from 3D shapes such as blood vessels or appearance of the face is a growing interest to clinicians. Machine learning (ML) has had great success driving...

    Authors: Joyce Zhanzi Wang, Jonathon Lillia, Ashnil Kumar, Paula Bray, Jinman Kim, Joshua Burns and Tegan L. Cheng
    Citation: BMC Bioinformatics 2022 23:431
    Content type: Research Published on:

  23. Studies have shown that classifying cancer subtypes can provide valuable information for a range of cancer research, from aetiology and tumour biology to prognosis and personalized treatment. Current methods u...

    Authors: Jiquan Shen, Jiawei Shi, Junwei Luo, Haixia Zhai, Xiaoyan Liu, Zhengjiang Wu, Chaokun Yan and Huimin Luo
    Citation: BMC Bioinformatics 2022 23:430
    Content type: Research Published on:

  24. Gene expression is regulated at different molecular levels, including chromatin accessibility, transcription, RNA maturation, and transport. These regulatory mechanisms have strong connections with cellular me...

    Authors: Surabhi Jagtap, Aurélie Pirayre, Frédérique Bidard, Laurent Duval and Fragkiskos D. Malliaros
    Citation: BMC Bioinformatics 2022 23:429
    Content type: Research Published on:

  26. Increasing evidence shows that circRNA plays an essential regulatory role in diseases through interactions with disease-related miRNAs. Identifying circRNA-disease associations is of great significance to prec...

    Authors: Lei Deng, Dayun Liu, Yizhan Li, Runqi Wang, Junyi Liu, Jiaxuan Zhang and Hui Liu
    Citation: BMC Bioinformatics 2022 23(Suppl 3):427
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 3

  27. Age estimation from panoramic radiographs is a fundamental task in forensic sciences. Previous age assessment studies mainly focused on juvenile rather than elderly populations (> 25 years old). Most proposed ...

    Authors: Xuedong Wang, Yanle Liu, Xinyao Miao, Yin Chen, Xiao Cao, Yuchen Zhang, Shuaicheng Li and Qin Zhou
    Citation: BMC Bioinformatics 2022 23(Suppl 3):426
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 23 Supplement 3

    The Correction to this article has been published in BMC Bioinformatics 2022 23:557

  28. Cardiovascular disease (CVD) is a serious disease that endangers human health and is one of the main causes of death. Therefore, using the patient’s electronic medical record (EMR) to predict CVD automatically...

    Authors: Yanlong Qiu, Wei Wang, Chengkun Wu and Zhichang Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 8):425
    Content type: Research Published on:

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

  29. RNA deleterious point mutation prediction was previously addressed with programs such as RNAmute and MultiRNAmute. The purpose of these programs is to predict a global conformational rearrangement of the secondar...

    Authors: Alexander Churkin, Yann Ponty and Danny Barash
    Citation: BMC Bioinformatics 2022 23(Suppl 8):424
    Content type: Methodology Published on:

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

  30. Accurate precision approaches have far not been developed for modeling mortality risk in intensive care unit (ICU) patients. Conventional mortality risk prediction methods can hardly extract the information in...

    Authors: Fan Yang, Jian Zhang, Wanyi Chen, Yongxuan Lai, Ying Wang and Quan Zou
    Citation: BMC Bioinformatics 2022 23:423
    Content type: Research Published on:

  32. Despite continuing technological advances, the cost for large-scale genotyping of a high number of samples can be prohibitive. The purpose of this study is to design a cost-saving strategy for SNP genotyping. ...

    Authors: Camille Clouard, Kristiina Ausmees and Carl Nettelblad
    Citation: BMC Bioinformatics 2022 23:421
    Content type: Research Published on:

  33. Observational studies and Mendelian randomization experiments have been used to identify many causal factors for complex traits in humans. Given a set of causal factors, it is important to understand the exten...

    Authors: Zhuoran Ding, Marylyn D. Ritchie, Benjamin F. Voight and Wei-Ting Hwang
    Citation: BMC Bioinformatics 2022 23:420
    Content type: Research Published on:

  34. With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving...

    Authors: Josh L. Espinoza and Chris L. Dupont
    Citation: BMC Bioinformatics 2022 23:419
    Content type: Research Published on:

  36. Gliomas are highly complex and heterogeneous tumors, rendering prognosis prediction challenging. The advent of deep learning algorithms and the accessibility of multi-omic data represent a new approach for the...

    Authors: Jing Tian, Mingzhen Zhu, Zijing Ren, Qiang Zhao, Puqing Wang, Colin K. He, Min Zhang, Xiaochun Peng, Beilei Wu, Rujia Feng and Minglong Fu
    Citation: BMC Bioinformatics 2022 23:417
    Content type: Research Published on:

  37. The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variatio...

    Authors: Joshua D. Harling-Lee, Jamie Gorzynski, Gonzalo Yebra, Tim Angus, J. Ross Fitzgerald and Tom C. Freeman
    Citation: BMC Bioinformatics 2022 23:416
    Content type: Research article Published on:

  38. Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, ...

    Authors: Yiru Sheng, R. Ayesha Ali and Andreas Heyland
    Citation: BMC Bioinformatics 2022 23:415
    Content type: Software Published on:

  39. Accurate identification of protein complexes in protein-protein interaction (PPI) networks is crucial for understanding the principles of cellular organization. Most computational methods ignore the fact that ...

    Authors: Rongquan Wang, Caixia Wang and Huimin Ma
    Citation: BMC Bioinformatics 2022 23:414
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2022 23:494

  42. Biological age (BA) has been recognized as a more accurate indicator of aging than chronological age (CA). However, the current limitations include: insufficient attention to the incompleteness of medical data...

    Authors: Qing Yang, Sunan Gao, Junfen Lin, Ke Lyu, Zexu Wu, Yuhao Chen, Yinwei Qiu, Yanrong Zhao, Wei Wang, Tianxiang Lin, Huiyun Pan and Ming Chen
    Citation: BMC Bioinformatics 2022 23:411
    Content type: Research Published on:

  43. We used a hybrid machine learning systems (HMLS) strategy that includes the extensive search for the discovery of the most optimal HMLSs, including feature selection algorithms, a feature extraction algorithm,...

    Authors: Eskandar Taghizadeh, Sahel Heydarheydari, Alihossein Saberi, Shabnam JafarpoorNesheli and Seyed Masoud Rezaeijo
    Citation: BMC Bioinformatics 2022 23:410
    Content type: Research Published on:

  45. Artificial intelligence (AI) and machine learning (ML) have resulted in significant enthusiasm for their promise in healthcare. Despite this, prospective randomized controlled trials and successful clinical im...

    Authors: Julian C. Hong, Neville C. W. Eclov, Sarah J. Stephens, Yvonne M. Mowery and Manisha Palta
    Citation: BMC Bioinformatics 2022 23(Suppl 12):408
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 12

  46. To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leverag...

    Authors: Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Larry Bu, Yuji Zhang, Yong Chen and Cui Tao
    Citation: BMC Bioinformatics 2022 23(Suppl 6):407
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 6

  47. Oxidative stress plays an important role in the progression of various types of tumors. However, its role in esophageal squamous cell carcinoma (ESCC) has seldom been explored. This study aimed to discover pro...

    Authors: Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng and Yi-Yan Lei
    Citation: BMC Bioinformatics 2022 23:406
    Content type: Research Published on:

  48. Identifying protein complexes from protein-protein interaction network is one of significant tasks in the postgenome era. Protein complexes, none of which exceeds 10 in size play an irreplaceable role in life ...

    Authors: Jiaqing Lyu, Zhen Yao, Bing Liang, Yiwei Liu and Yijia Zhang
    Citation: BMC Bioinformatics 2022 23:405
    Content type: Research Published on:

  49. Bioinformatics has gained much attention as a fast growing interdisciplinary field. Several attempts have been conducted to explore the field of bioinformatics by bibliometric analysis, however, such works did...

    Authors: Jiaqi Wang, Zeyu Li and Jiawan Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 8):404
    Content type: Research Published on:

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

  50. Population variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000 Genomes Project established a valuable reference for human genetic variat...

    Authors: Tommaso Alfonsi, Anna Bernasconi, Arif Canakoglu and Marco Masseroli
    Citation: BMC Bioinformatics 2022 23:401
    Content type: Software Published on:

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