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  1. High-dimensional omics data are increasingly utilized in clinical and public health research for disease risk prediction. Many previous sparse methods have been proposed that using prior knowledge, e.g., biolo...

    Authors: Junjie Shen, Shuo Wang, Yongfei Dong, Hao Sun, Xichao Wang and Zaixiang Tang
    Citation: BMC Bioinformatics 2024 25:119
  2. Bacteria in the human body, particularly in the large intestine, are known to be associated with various diseases. To identify disease-associated bacteria (markers), a typical method is to statistically compar...

    Authors: Shota Nose, Hirotsugu Shiroma, Takuji Yamada and Yushi Uno
    Citation: BMC Bioinformatics 2024 25:118
  3. Neuroscience research in Drosophila is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. To exploit this knowledge base, r...

    Authors: Jody Clements, Cristian Goina, Philip M. Hubbard, Takashi Kawase, Donald J. Olbris, Hideo Otsuna, Robert Svirskas and Konrad Rokicki
    Citation: BMC Bioinformatics 2024 25:114
  4. The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the a...

    Authors: Simone Alessandri, Maria L. Ratto, Sergio Rabellino, Gabriele Piacenti, Sandro Gepiro Contaldo, Simone Pernice, Marco Beccuti, Raffaele A. Calogero and Luca Alessandri
    Citation: BMC Bioinformatics 2024 25:110
  5. RNA-protein interaction (RPI) is crucial to the life processes of diverse organisms. Various researchers have identified RPI through long-term and high-cost biological experiments. Although numerous machine le...

    Authors: Ying Liang, XingRui Yin, YangSen Zhang, You Guo and YingLong Wang
    Citation: BMC Bioinformatics 2024 25:108
  6. As noncommunicable diseases (NCDs) pose a significant global health burden, identifying effective diagnostic and predictive markers for these diseases is of paramount importance. Epigenetic modifications, such...

    Authors: Steven Gore, Bailey Meche, Danyang Shao, Benjamin Ginnett, Kelly Zhou and Rajeev K. Azad
    Citation: BMC Bioinformatics 2024 25:107
  7. Predicting protein–protein interactions (PPIs) from sequence data is a key challenge in computational biology. While various computational methods have been proposed, the utilization of sequence embeddings fro...

    Authors: Thanh Hai Dang and Tien Anh Vu
    Citation: BMC Bioinformatics 2024 25:106
  8. The prediction of cancer drug response is a challenging subject in modern personalized cancer therapy due to the uncertainty of drug efficacy and the heterogeneity of patients. It has been shown that the chara...

    Authors: Chuanqi Lao, Pengfei Zheng, Hongyang Chen, Qiao Liu, Feng An and Zhao Li
    Citation: BMC Bioinformatics 2024 25:105
  9. The identification of tumor-specific molecular dependencies is essential for the development of effective cancer therapies. Genetic and chemical perturbations are powerful tools for discovering these dependenc...

    Authors: Hanwen Xing and Christopher Yau
    Citation: BMC Bioinformatics 2024 25:104
  10. Blood test is extensively performed for screening, diagnoses and surveillance purposes. Although it is possible to automatically evaluate the raw blood test data with the advanced deep self-supervised machine ...

    Authors: Onder Tutsoy and Gizem Gul Koç
    Citation: BMC Bioinformatics 2024 25:103
  11. Viral infections have been the main health issue in the last decade. Antiviral peptides (AVPs) are a subclass of antimicrobial peptides (AMPs) with substantial potential to protect the human body against vario...

    Authors: Shahid Akbar, Ali Raza and Quan Zou
    Citation: BMC Bioinformatics 2024 25:102
  12. In the past decade, single nucleotide variants (SNVs) have been identified as having a significant relationship with the development and treatment of diseases. Among them, prioritizing missense variants for fu...

    Authors: Dong Wang, Jie Li, Edwin Wang and Yadong Wang
    Citation: BMC Bioinformatics 2024 25(Suppl 1):100

    This article is part of a Supplement: Volume 25 Supplement 1

  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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

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