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  1. The breakthrough high-throughput measurement of the cis-regulatory activity of millions of randomly generated promoters provides an unprecedented opportunity to systematically decode the cis-regulatory logic t...

    Authors: Il-Youp Kwak, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Daniel J. Garry, Jianyi Zhang and Wuming Gong
    Citation: BMC Bioinformatics 2024 25:81
    Content type: Research Published on:

  2. In recent years, the extensive use of drugs and antibiotics has led to increasing microbial resistance. Therefore, it becomes crucial to explore deep connections between drugs and microbes. However, traditiona...

    Authors: Haiyue Kuang, Zhen Zhang, Bin Zeng, Xin Liu, Hao Zuo, Xingye Xu and Lei Wang
    Citation: BMC Bioinformatics 2024 25:78
    Content type: Research Published on:

  3. Cryo-electron microscopy (Cryo-EM) plays an increasingly important role in the determination of the three-dimensional (3D) structure of macromolecules. In order to achieve 3D reconstruction results close to at...

    Authors: Huanrong Tang, Yaowu Wang, Jianquan Ouyang and Jinlin Wang
    Citation: BMC Bioinformatics 2024 25:77
    Content type: Research Published on:

  5. Graph coloring approach has emerged as a valuable problem-solving tool for both theoretical and practical aspects across various scientific disciplines, including biology. In this study, we demonstrate the gra...

    Authors: Arnab Kole, Arup Kumar Bag, Anindya Jyoti Pal and Debashis De
    Citation: BMC Bioinformatics 2024 25:74
    Content type: Research Published on:

  7. Copy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer progression by affecting gene expression and genomic stability. Comput...

    Authors: Valentina Crippa, Emanuela Fina, Daniele Ramazzotti and Rocco Piazza
    Citation: BMC Bioinformatics 2024 25:72
    Content type: Software Published on:

  8. Gene expression may be regulated by the DNA methylation of regulatory elements in cis, distal, and trans regions. One method to evaluate the relationship between DNA methylation and gene expression is the mapping...

    Authors: Kord M. Kober, Liam Berger, Ritu Roy and Adam Olshen
    Citation: BMC Bioinformatics 2024 25:71
    Content type: Software Published on:

  9. Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks...

    Authors: Anthony Baptista, Galadriel Brière and Anaïs Baudot
    Citation: BMC Bioinformatics 2024 25:70
    Content type: Research Published on:

  10. Technological advances have enabled the generation of unique and complementary types of data or views (e.g. genomics, proteomics, metabolomics) and opened up a new era in multiview learning research with the p...

    Authors: Hengkang Wang, Han Lu, Ju Sun and Sandra E. Safo
    Citation: BMC Bioinformatics 2024 25:69
    Content type: Research Published on:

  11. The advent of Next-Generation Sequencing (NGS) has catalyzed a paradigm shift in medical genetics, enabling the identification of disease-associated variants. However, the vast quantum of data produced by NGS ...

    Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini, Masoud Garshasbi and Javad Zahiri
    Citation: BMC Bioinformatics 2024 25:68
    Content type: Software Published on:

  13. DNA methylation is one of the most stable and well-characterized epigenetic alterations in humans. Accordingly, it has already found clinical utility as a molecular biomarker in a variety of disease contexts. ...

    Authors: Jesse R. Walsh, Guangchao Sun, Jagadheshwar Balan, Jayson Hardcastle, Jason Vollenweider, Calvin Jerde, Kandelaria Rumilla, Christy Koellner, Alaa Koleilat, Linda Hasadsri, Benjamin Kipp, Garrett Jenkinson and Eric Klee
    Citation: BMC Bioinformatics 2024 25:66
    Content type: Research Published on:

  14. Genetic variants can contribute differently to trait heritability by their functional categories, and recent studies have shown that incorporating functional annotation can improve the predictive performance o...

    Authors: Yongwen Zhuang, Na Yeon Kim, Lars G. Fritsche, Bhramar Mukherjee and Seunggeun Lee
    Citation: BMC Bioinformatics 2024 25:65
    Content type: Research Published on:

  15. Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upst...

    Authors: Dharmesh D. Bhuva, Chin Wee Tan, Ning Liu, Holly J. Whitfield, Nicholas Papachristos, Samuel C. Lee, Malvika Kharbanda, Ahmed Mohamed and Melissa J. Davis
    Citation: BMC Bioinformatics 2024 25:64
    Content type: Research Published on:

  17. Recent developments in the domain of biomedical knowledge bases (KBs) open up new ways to exploit biomedical knowledge that is available in the form of KBs. Significant work has been done in the direction of b...

    Authors: Ghanshyam Verma, Dietrich Rebholz-Schuhmann and Michael G. Madden
    Citation: BMC Bioinformatics 2024 25:62
    Content type: Research Published on:

  19. As a gold-standard quantitative technique based on mass spectrometry, multiple reaction monitoring (MRM) has been widely used in proteomics and metabolomics. In the analysis of MRM data, as no peak picking alg...

    Authors: Ruimin Wang, Hengxuan Jiang, Miaoshan Lu, Junjie Tong, Shaowei An, Jinyin Wang and Changbin Yu
    Citation: BMC Bioinformatics 2024 25:60
    Content type: Software Published on:

  20. The prediction of interactions between novel drugs and biological targets is a vital step in the early stage of the drug discovery pipeline. Many deep learning approaches have been proposed over the last decad...

    Authors: Dimitrios Iliadis, Bernard De Baets, Tapio Pahikkala and Willem Waegeman
    Citation: BMC Bioinformatics 2024 25:59
    Content type: Research Published on:

  21. Data from microbiomes from multiple niches is often collected, but methods to analyse these often ignore associations between niches. One interesting case is that of the oral microbiome. Its composition is rec...

    Authors: Vincent Y. Pappalardo, Leyla Azarang, Egija Zaura, Bernd W. Brandt and Renée X. de Menezes
    Citation: BMC Bioinformatics 2024 25:58
    Content type: Research Published on:

  22. Controlling the False Discovery Rate (FDR) in Multiple Comparison Procedures (MCPs) has widespread applications in many scientific fields. Previous studies show that the correlation structure between test stat...

    Authors: Sedighe Rastaghi, Azadeh Saki and Hamed Tabesh
    Citation: BMC Bioinformatics 2024 25:57
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2024 25:83

  23. Genome-wide association studies have successfully identified genetic variants associated with human disease. Various statistical approaches based on penalized and machine learning methods have recently been pr...

    Authors: Yongjun Choi, Junho Cha and Sungkyoung Choi
    Citation: BMC Bioinformatics 2024 25:56
    Content type: Research Published on:

  26. Non-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood....

    Authors: Rose-Marie Fraboulet, Yanis Si Ahmed, Marc Aubry, Sebastien Corre, Marie-Dominique Galibert and Yuna Blum
    Citation: BMC Bioinformatics 2024 25:53
    Content type: Software Published on:

  28. Strongly multicollinear covariates, such as those typically represented in metabolomics applications, represent a challenge for multivariate regression analysis. These challenges are commonly circumvented by r...

    Authors: Tim U. H. Baumeister, Eivind Aadland, Roger G. Linington and Olav M. Kvalheim
    Citation: BMC Bioinformatics 2024 25:51
    Content type: Software Published on:

  30. Genome streamlining, the process by which genomes become smaller and encode fewer genes over time, is a common phenomenon among pathogenic bacteria. This reduction is driven by selection for minimized energy e...

    Authors: Abigail Glascock, Eric Waltari, Gytis Dudas, Joan Wong and Vida Ahyong
    Citation: BMC Bioinformatics 2024 25:49
    Content type: Software Published on:

  31. The Drug–Target Interaction (DTI) prediction uses a drug molecule and a protein sequence as inputs to predict the binding affinity value. In recent years, deep learning-based models have gotten more attention....

    Authors: Alireza Dehghan, Karim Abbasi, Parvin Razzaghi, Hossein Banadkuki and Sajjad Gharaghani
    Citation: BMC Bioinformatics 2024 25:48
    Content type: Research Published on:

  32. Drug–drug interactions (DDI) are a critical concern in healthcare due to their potential to cause adverse effects and compromise patient safety. Supervised machine learning models for DDI prediction need to be...

    Authors: Rogia Kpanou, Patrick Dallaire, Elsa Rousseau and Jacques Corbeil
    Citation: BMC Bioinformatics 2024 25:47
    Content type: Research Published on:

  33. Many biological studies have shown that lncRNAs regulate the expression of epigenetically related genes. The study of lncRNAs has helped to deepen our understanding of the pathogenesis of complex diseases at t...

    Authors: Dengju Yao, Yuexiao Deng, Xiaojuan Zhan and Xiaorong Zhan
    Citation: BMC Bioinformatics 2024 25:46
    Content type: Research Published on:

  36. The computation of a similarity measure for genomic data is a standard tool in computational genetics. The principal components of such matrices are routinely used to correct for biases due to confounding by p...

    Authors: Georg Hahn, Sharon M. Lutz, Julian Hecker, Dmitry Prokopenko, Michael H. Cho, Edwin K. Silverman, Scott T. Weiss and Christoph Lange
    Citation: BMC Bioinformatics 2024 25:43
    Content type: Research Published on:

  37. The clustering of immune repertoire data is challenging due to the computational cost associated with a very large number of pairwise sequence comparisons. To overcome this limitation, we developed Anchor Clus...

    Authors: Haiyang Chang, Daniel A. Ashlock, Steffen P. Graether and Stefan M. Keller
    Citation: BMC Bioinformatics 2024 25:42
    Content type: Research Published on:

  38. With the development of single-cell technology, many cell traits can be measured. Furthermore, the multi-omics profiling technology could jointly measure two or more traits in a single cell simultaneously. In ...

    Authors: Lifei Wang, Rui Nie, Xuexia Miao, Yankai Cai, Anqi Wang, Hanwen Zhang, Jiang Zhang and Jun Cai
    Citation: BMC Bioinformatics 2024 25:41
    Content type: Research Published on:

  40. Drug–drug interactions (DDI) are prevalent in combination therapy, necessitating the importance of identifying and predicting potential DDI. While various artificial intelligence methods can predict and identi...

    Authors: Jing Zhu, Chao Che, Hao Jiang, Jian Xu, Jiajun Yin and Zhaoqian Zhong
    Citation: BMC Bioinformatics 2024 25:39
    Content type: Research Published on:

  41. Previously, many methods have been used to predict the incidence trends of infectious diseases. There are numerous methods for predicting the incidence trends of infectious diseases, and they have exhibited va...

    Authors: Tianhua Yao, Xicheng Chen, Haojia Wang, Chengcheng Gao, Jia Chen, Dali Yi, Zeliang Wei, Ning Yao, Yang Li, Dong Yi and Yazhou Wu
    Citation: BMC Bioinformatics 2024 25:38
    Content type: Research Published on:

  42. DNA methylation is a major epigenetic modification involved in many physiological processes. Normal methylation patterns are disrupted in many diseases and methylation-based biomarkers have shown promise in se...

    Authors: Naghme Nazer, Mohammad Hossein Sepehri, Hoda Mohammadzade and Mahya Mehrmohamadi
    Citation: BMC Bioinformatics 2024 25:37
    Content type: Research Published on:

  43. Given a genome-scale metabolic model (GEM) of a microorganism and criteria for optimization, flux balance analysis (FBA) predicts the optimal growth rate and its corresponding flux distribution for a specific ...

    Authors: Clémence Joseph, Haris Zafeiropoulos, Kristel Bernaerts and Karoline Faust
    Citation: BMC Bioinformatics 2024 25:36
    Content type: Research Published on:

  44. Natural proteins occupy a small portion of the protein sequence space, whereas artificial proteins can explore a wider range of possibilities within the sequence space. However, specific requirements may not b...

    Authors: Xiaoping Min, Chongzhou Yang, Jun Xie, Yang Huang, Nan Liu, Xiaocheng Jin, Tianshu Wang, Zhibo Kong, Xiaoli Lu, Shengxiang Ge, Jun Zhang and Ningshao Xia
    Citation: BMC Bioinformatics 2024 25:35
    Content type: Research Published on:

  45. Driver genes play a vital role in the development of cancer. Identifying driver genes is critical for diagnosing and understanding cancer. However, challenges remain in identifying personalized driver genes du...

    Authors: Yiran Huang, Fuhao Chen, Hongtao Sun and Cheng Zhong
    Citation: BMC Bioinformatics 2024 25:34
    Content type: Research Published on:

  46. Breast cancer remains a major public health challenge worldwide. The identification of accurate biomarkers is critical for the early detection and effective treatment of breast cancer. This study utilizes an i...

    Authors: Morteza Rakhshaninejad, Mohammad Fathian, Reza Shirkoohi, Farnaz Barzinpour and Amir H. Gandomi
    Citation: BMC Bioinformatics 2024 25:33
    Content type: Research Published on:

  47. Epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all RNA types. Precise recognition of RNA modifications is critical for understanding their functions and regulatory...

    Authors: Honglei Wang, Tao Huang, Dong Wang, Wenliang Zeng, Yanjing Sun and Lin Zhang
    Citation: BMC Bioinformatics 2024 25:32
    Content type: Research Published on:

  49. The impairment of sperm maturation is one of the major pathogenic factors in male subfertility, a serious medical and social problem affecting millions of global couples. Regrettably, the existing research on ...

    Authors: Yifan Li, Qianying Li, Lvying Wu, Haiyan Wang, Hui Shi, Chenhui Yang, Yiqun Gu, Jianyuan Li and Zhiliang Ji
    Citation: BMC Bioinformatics 2024 25:29
    Content type: Database Published on:

  50. COVID-19 is a disease that caused a contagious respiratory ailment that killed and infected hundreds of millions. It is necessary to develop a computer-based tool that is fast, precise, and inexpensive to dete...

    Authors: Rukundo Prince, Zhendong Niu, Zahid Younas Khan, Masabo Emmanuel and Niyishaka Patrick
    Citation: BMC Bioinformatics 2024 25:28
    Content type: Research Published on:

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