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  1. Cancer, a disease with high morbidity and mortality rates, poses a significant threat to human health. Driver genes, which harbor mutations accountable for the initiation and progression of tumors, play a cruc...

    Authors: Xiaolu Xu, Zitong Qi, Lei Wang, Meiwei Zhang, Zhaohong Geng and Xiumei Han
    Citation: BMC Bioinformatics 2024 25:99
  2. Pathomics facilitates automated, reproducible and precise histopathology analysis and morphological phenotyping. Similar to molecular omics, pathomics datasets are high-dimensional, but also face large outlier...

    Authors: David L. Hölscher, Michael Goedertier, Barbara M. Klinkhammer, Patrick Droste, Ivan G. Costa, Peter Boor and Roman D. Bülow
    Citation: BMC Bioinformatics 2024 25:98
  3. Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across...

    Authors: Konstantin Yuditskiy, Igor Bezdvornykh, Anastasiya Kazantseva, Alexander Kanapin and Anastasia Samsonova
    Citation: BMC Bioinformatics 2024 25:96
  4. Dynamical compensation (DC) provides robustness to parameter fluctuations. As an example, DC enables control of the functional mass of endocrine or neuronal tissue essential for controlling blood glucose by in...

    Authors: Akram Ashyani, Yu-Heng Wu, Huan-Wei Hsu and Torbjörn E. M. Nordling
    Citation: BMC Bioinformatics 2024 25:95
  5. Analysis of time-resolved postprandial metabolomics data can improve the understanding of metabolic mechanisms, potentially revealing biomarkers for early diagnosis of metabolic diseases and advancing precisio...

    Authors: Lu Li, Shi Yan, Barbara M. Bakker, Huub Hoefsloot, Bo Chawes, David Horner, Morten A. Rasmussen, Age K. Smilde and Evrim Acar
    Citation: BMC Bioinformatics 2024 25:94
  6. An organism’s observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic ...

    Authors: Katharina Munk, Daria Ilina, Lisa Ziemba, Günter Brader and Eva M. Molin
    Citation: BMC Bioinformatics 2024 25:93
  7. In recent years, researchers have made significant strides in understanding the heterogeneity of breast cancer and its various subtypes. However, the wealth of genomic and proteomic data available today necess...

    Authors: Leandro Y. S. Okimoto, Rayol Mendonca-Neto, Fabíola G. Nakamura, Eduardo F. Nakamura, David Fenyö and Claudio T. Silva
    Citation: BMC Bioinformatics 2024 25:92
  8. Uncovering functional genetic variants from an allele-specific perspective is of paramount importance in advancing our understanding of gene regulation and genetic diseases. Recently, various allele-specific e...

    Authors: Qingru Xu, Xiaoqiong Bao, Zhuobin Lin, Lin Tang, Li-na He, Jian Ren, Zhixiang Zuo and Kunhua Hu
    Citation: BMC Bioinformatics 2024 25:91
  9. To explore the evolutionary history of sequences, a sequence alignment is a first and necessary step, and its quality is crucial. In the context of the study of the proximal origins of SARS-CoV-2 coronavirus, ...

    Authors: Jean-Noël Lorenzi, François Graner, Virginie Courtier-Orgogozo and Guillaume Achaz
    Citation: BMC Bioinformatics 2024 25:89
  10. Predicting outcome of breast cancer is important for selecting appropriate treatments and prolonging the survival periods of patients. Recently, different deep learning-based methods have been carefully design...

    Authors: Hua Chai, Siyin Lin, Junqi Lin, Minfan He, Yuedong Yang, Yongzhong OuYang and Huiying Zhao
    Citation: BMC Bioinformatics 2024 25:88
  11. Despite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called "twilight zone") remains a difficult problem. Many alignment algor...

    Authors: Benjamin Giovanni Iovino and Yuzhen Ye
    Citation: BMC Bioinformatics 2024 25:85
  12. Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) databa...

    Authors: K. M. Tahsin Hassan Rahit, Vladimir Avramovic, Jessica X. Chong and Maja Tarailo-Graovac
    Citation: BMC Bioinformatics 2024 25:84
  13. One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery se...

    Authors: Katelyn McNair, Peter Salamon, Robert A. Edwards and Anca M. Segall
    Citation: BMC Bioinformatics 2024 25:82
  14. 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
  15. With the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data a...

    Authors: Philippe Hauchamps, Babak Bayat, Simon Delandre, Mehdi Hamrouni, Marie Toussaint, Stephane Temmerman, Dan Lin and Laurent Gatto
    Citation: BMC Bioinformatics 2024 25:80
  16. 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
  17. 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
  18. Genetic ancestry, inferred from genomic data, is a quantifiable biological parameter. While much of the human genome is identical across populations, it is estimated that as much as 0.4% of the genome can diff...

    Authors: Audrey E. Bollas, Andrei Rajkovic, Defne Ceyhan, Jeffrey B. Gaither, Elaine R. Mardis and Peter White
    Citation: BMC Bioinformatics 2024 25:76
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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

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

  33. 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
  34. 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
  35. 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
  36. 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

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