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  1. Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source option...

    Authors: James M. Dolezal, Sara Kochanny, Emma Dyer, Siddhi Ramesh, Andrew Srisuwananukorn, Matteo Sacco, Frederick M. Howard, Anran Li, Prajval Mohan and Alexander T. Pearson
    Citation: BMC Bioinformatics 2024 25:134
  2. Cancer is one of the leading causes of deaths worldwide. Survival analysis and prediction of cancer patients is of great significance for their precision medicine. The robustness and interpretability of the su...

    Authors: Shuo Wang, Yuanning Liu, Hao Zhang and Zhen Liu
    Citation: BMC Bioinformatics 2024 25:133
  3. The global spread of the SARS-CoV-2 pandemic, originating in Wuhan, China, has had profound consequences on both health and the economy. Traditional alignment-based phylogenetic tree methods for tracking epide...

    Authors: Ahmed M. A. Elsherbini, Amr Hassan Elkholy, Youssef M. Fadel, Gleb Goussarov, Ahmed Mohamed Elshal, Mohamed El-Hadidi and Mohamed Mysara
    Citation: BMC Bioinformatics 2024 25:131
  4. Recent improvements in sequencing technologies enabled detailed profiling of genomic features. These technologies mostly rely on short reads which are merged and compared to reference genome for variant identi...

    Authors: Mehmet Arif Ergun, Omer Cinal, Berkant Bakışlı, Abdullah Asım Emül and Mehmet Baysan
    Citation: BMC Bioinformatics 2024 25:130
  5. The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions ar...

    Authors: Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone and Isaure Chauvot de Beauchene
    Citation: BMC Bioinformatics 2024 25:129
  6. Discovery biological motifs plays a fundamental role in understanding regulatory mechanisms. Computationally, they can be efficiently represented as kmers, making the counting of these elements a critical aspect ...

    Authors: Jader M. Caldonazzo Garbelini, Danilo S. Sanches and Aurora T. Ramirez Pozo
    Citation: BMC Bioinformatics 2024 25:128
  7. Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an importan...

    Authors: Jasper van Bemmelen, Davida S. Smyth and Jasmijn A. Baaijens
    Citation: BMC Bioinformatics 2024 25:126
  8. In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disea...

    Authors: Raquel L. Costa, Luiz Gadelha, Mirela D’arc, Marcelo Ribeiro-Alves, David L. Robertson, Jean-Marc Schwartz, Marcelo A. Soares and Fábio Porto
    Citation: BMC Bioinformatics 2024 25:125
  9. Next-generation sequencing (NGS) technologies offer fast and inexpensive identification of DNA sequences. Somatic sequencing is among the primary applications of NGS, where acquired (non-inherited) variants ar...

    Authors: Yunus Emre Cebeci, Rumeysa Aslihan Erturk, Mehmet Arif Ergun and Mehmet Baysan
    Citation: BMC Bioinformatics 2024 25:124
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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

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