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  1. Since the introduction of next-generation sequencing (NGS) techniques, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have not only revolutionized research, but also diagnostics. The gradual sw...

    Authors: Fréderique Boeykens, Sofie F. M. Bhatti, Luc Peelman and Bart J. G. Broeckx
    Citation: BMC Bioinformatics 2023 24:305
    Content type: Software Published on:

  2. Integrating multi-omics data is fast becoming a powerful approach for predicting disease progression and treatment outcomes. In light of that, we introduce a modified version of the NetRank algorithm, a networ...

    Authors: Ali Al-Fatlawi, Eka Rusadze, Alexander Shmelkin, Negin Malekian, Cigdem Ozen, Christian Pilarsky and Michael Schroeder
    Citation: BMC Bioinformatics 2023 24:304
    Content type: Software Published on:

  3. The growing power and ever decreasing cost of RNA sequencing (RNA-Seq) technologies have resulted in an explosion of RNA-Seq data production. Comparing gene expression values within RNA-Seq datasets is relativ...

    Authors: Alvin Farrel, Peng Li, Sharon Veenbergen, Khushbu Patel, John M. Maris and Warren J. Leonard
    Citation: BMC Bioinformatics 2023 24:303
    Content type: Software Published on:

  4. Single-cell RNA sequencing (scRNA-seq) enables the high-throughput profiling of gene expression at the single-cell level. However, overwhelming dropouts within data may obscure meaningful biological signals. V...

    Authors: Yi Cheng, Xiuli Ma, Lang Yuan, Zhaoguo Sun and Pingzhang Wang
    Citation: BMC Bioinformatics 2023 24:302
    Content type: Research article Published on:

  5. The identification of tumor T cell antigens (TTCAs) is crucial for providing insights into their functional mechanisms and utilizing their potential in anticancer vaccines development. In this context, TTCAs a...

    Authors: Phasit Charoenkwan, Nalini Schaduangrat and Watshara Shoombuatong
    Citation: BMC Bioinformatics 2023 24:301
    Content type: Research Published on:

  6. Modern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions (e.g. genes) would yield new insights in genomic associations, such as ...

    Authors: Sven Berres, Jörg Gromoll, Marius Wöste, Sarah Sandmann and Sandra Laurentino
    Citation: BMC Bioinformatics 2023 24:300
    Content type: Software Published on:

  8. Protein biomarkers of cancer progression and response to therapy are increasingly important for improving personalized medicine. Advanced quantitative pathology platforms enable measurement of protein expressi...

    Authors: Misung Yi, Tingting Zhan, Amy R. Peck, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, Hai Hu, Yunguang Sun, Hallgeir Rui and Inna Chervoneva
    Citation: BMC Bioinformatics 2023 24:298
    Content type: Research Published on:

  10. Statistical correlation analysis is currently the most typically used approach for investigating the risk factors of type 2 diabetes mellitus (T2DM). However, this approach does not readily reveal the causal r...

    Authors: Xiu-E. Gao, Jian-Gang Hu, Bo Chen, Yun-Ming Wang and Sheng-Bin zhou
    Citation: BMC Bioinformatics 2023 24:296
    Content type: Research Published on:

  11. To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree ...

    Authors: Nuo Liu, Tonatiuh A. Gonzalez, Jacob Fischer, Chan Hong, Michelle Johnson, Ross Mawhorter, Fabrizia Mugnatto, Rachael Soh, Shifa Somji, Joseph S. Wirth, Ran Libeskind-Hadas and Eliot C. Bush
    Citation: BMC Bioinformatics 2023 24:295
    Content type: Software Published on:

  12. Identifying variants associated with diseases is a challenging task in medical genetics research. Current studies that prioritize variants within individual genomes generally rely on known variants, evidence f...

    Authors: Șenay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi, Malak Alghamdi and Robert Hoehndorf
    Citation: BMC Bioinformatics 2023 24:294
    Content type: Software Published on:

  14. The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract this information. This is especially challenging ...

    Authors: Adam J. H. Newton, David Chartash, Steven H. Kleinstein and Robert A. McDougal
    Citation: BMC Bioinformatics 2023 24:292
    Content type: Software Published on:

  15. The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the grow...

    Authors: Irene Ortega-Sanz, José A. Barbero-Aparicio, Antonio Canepa-Oneto, Jordi Rovira and Beatriz Melero
    Citation: BMC Bioinformatics 2023 24:291
    Content type: Research Published on:

  17. Cancer subtype classification is helpful for personalized cancer treatment. Although, some approaches have been developed to classifying caner subtype based on high dimensional gene expression data, it is diff...

    Authors: Junwei Luo, Yading Feng, Xuyang Wu, Ruimin Li, Jiawei Shi, Wenjing Chang and Junfeng Wang
    Citation: BMC Bioinformatics 2023 24:289
    Content type: Research Published on:

  18.  PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous...

    Authors: Marcela Uliano-Silva, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Giulio Formenti, Linelle Abueg, James Torrance, Eugene W. Myers, Richard Durbin, Mark Blaxter and Shane A. McCarthy
    Citation: BMC Bioinformatics 2023 24:288
    Content type: Software Published on:

  19. Next-generation sequencing technologies yield large numbers of genetic alterations, of which a subset are missense variants that alter an amino acid in the protein product. These variants can have a potentiall...

    Authors: Kobe Janssen, Ramon Duran-Romaña, Guy Bottu, Mainak Guharoy, Alexander Botzki, Frederic Rousseau and Joost Schymkowitz
    Citation: BMC Bioinformatics 2023 24:287
    Content type: Software Published on:

  20. Integration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based preclinical and clinical Gene Therapy (GT). A handful of groups have developed s...

    Authors: Aimin Yan, Cristina Baricordi, Quoc Nguyen, Luigi Barbarossa, Mariana Loperfido and Luca Biasco
    Citation: BMC Bioinformatics 2023 24:286
    Content type: Software Published on:

  23. Quantitative descriptions of multi-cellular structures from optical microscopy imaging are prime to understand the variety of three-dimensional (3D) shapes in living organisms. Experimental models of vertebrat...

    Authors: Marilyn Gatica, Carlos F. Navarro, Alejandro Lavado, German Reig, Eduardo Pulgar, Paula Llanos, Steffen Härtel, Andrea Ravasio, Cristina Bertocchi, Miguel L. Concha and Mauricio Cerda
    Citation: BMC Bioinformatics 2023 24:283
    Content type: Software Published on:

  24. Kernel methods have been proven to be a powerful tool for the integration and analysis of high-throughput technologies generated data. Kernels offer a nonlinear version of any linear algorithm solely based on ...

    Authors: Mitja Briscik, Marie-Agnès Dillies and Sébastien Déjean
    Citation: BMC Bioinformatics 2023 24:282
    Content type: Research Published on:

  26. Uveal melanoma arises from stromal melanocytes and is the most prevalent primary intraocular tumor in adults. It poses a significant diagnostic and therapeutic challenge due to its high malignancy and early on...

    Authors: Li Fu, Qun Huang, Yongfeng Wu and Diang Chen
    Citation: BMC Bioinformatics 2023 24:280
    Content type: Research Published on:

  28. Accurate identification of Drug-Target Interactions (DTIs) plays a crucial role in many stages of drug development and drug repurposing. (i) Traditional methods do not consider the use of multi-source data and...

    Authors: Yuanyuan Zhang, Yinfei Feng, Mengjie Wu, Zengqian Deng and Shudong Wang
    Citation: BMC Bioinformatics 2023 24:278
    Content type: Research Published on:

  31. P4 medicine (predict, prevent, personalize, and participate) is a new approach to diagnosing and predicting diseases on a patient-by-patient basis. For the prevention and treatment of diseases, prediction play...

    Authors: Roohallah Mahdi-Esferizi, Behnaz Haji Molla Hoseyni, Amir Mehrpanah, Yazdan Golzade, Ali Najafi, Fatemeh Elahian, Amin Zadeh Shirazi, Guillermo A. Gomez and Shahram Tahmasebian
    Citation: BMC Bioinformatics 2023 24:275
    Content type: Research Published on:

  32. N6-methyladenosine (m6A) and 5-methylcytosine (m5C) are the main RNA methylation modifications involved in the oncogenesis of cancer. However, it remains obscure whether m6A/m5C-related long non-coding RNAs (l...

    Authors: Ran Li, Haiyan Chen, Chaoxi Li, Yiwei Qi, Kai Zhao, Junwen Wang, Chao You and Haohao Huang
    Citation: BMC Bioinformatics 2023 24:274
    Content type: Research Published on:

  33. Pathogenic bacteria present a major threat to human health, causing various infections and illnesses, and in some cases, even death. The accurate identification of these bacteria is crucial, but it can be chal...

    Authors: Fareed Ahmad, Muhammad Usman Ghani Khan, Ahsen Tahir and Farhan Masud
    Citation: BMC Bioinformatics 2023 24:273
    Content type: Research Published on:

  34. This paper applies different link prediction methods on a knowledge graph generated from biomedical literature, with the aim to compare their ability to identify unknown drug-gene interactions and explain thei...

    Authors: Fotis Aisopos and Georgios Paliouras
    Citation: BMC Bioinformatics 2023 24:272
    Content type: Research Published on:

  35. Dealing with the high dimension of both neuroimaging data and genetic data is a difficult problem in the association of genetic data to neuroimaging. In this article, we tackle the latter problem with an eye t...

    Authors: Cédric Beaulac, Sidi Wu, Erin Gibson, Michelle F. Miranda, Jiguo Cao, Leno Rocha, Mirza Faisal Beg and Farouk S. Nathoo
    Citation: BMC Bioinformatics 2023 24:271
    Content type: Research Published on:

  36. Most Hepatocellular carcinoma (HCC) patients are in advanced or metastatic stage at the time of diagnosis. Prognosis for advanced HCC patients is dismal. This study was based on our previous microarray results...

    Authors: Xue-Qin Chen, Jie Ma, Di Xu and Zuo-Lin Xiang
    Citation: BMC Bioinformatics 2023 24:270
    Content type: Research Published on:

  37. This study aims to explore the predictive value of SLC25A17 in the prognosis and tumor microenvironment (TME) of patients with head and neck squamous cell carcinoma (HNSCC) and to provide ideas for individual ...

    Authors: Yunbin Shi, Juntao Huang, Yi Hu and Yi Shen
    Citation: BMC Bioinformatics 2023 24:269
    Content type: Research Published on:

  40. Pathway-level survival analysis offers the opportunity to examine molecular pathways and immune signatures that influence patient outcomes. However, available survival analysis algorithms are limited in pathwa...

    Authors: Alyssa N. Obermayer, Darwin Chang, Gabrielle Nobles, Mingxiang Teng, Aik-Choon Tan, Xuefeng Wang, Y. Ann Chen, Steven Eschrich, Paulo C. Rodriguez, G. Daniel Grass, Soheil Meshinchi, Ahmad Tarhini, Dung-tsa Chen and Timothy I. Shaw
    Citation: BMC Bioinformatics 2023 24:266
    Content type: Software Published on:

  42. A nonhomogeneous dynamic Bayesian network model, which combines the dynamic Bayesian network and the multi-change point process, solves the limitations of the dynamic Bayesian network in modeling non-stationar...

    Authors: Jiayao Zhang, Chunling Hu and Qianqian Zhang
    Citation: BMC Bioinformatics 2023 24:264
    Content type: Research Published on:

  43. Protein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. He...

    Authors: Aysam Guerler, Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz and Anton Nekrutenko
    Citation: BMC Bioinformatics 2023 24:263
    Content type: Software Published on:

  44. Microbial community simulations using genome scale metabolic networks (GSMs) are relevant for many application areas, such as the analysis of the human microbiome. Such simulations rely on assumptions about th...

    Authors: Axel Theorell and Jörg Stelling
    Citation: BMC Bioinformatics 2023 24(Suppl 1):262
    Content type: Research Published on:

    This article is part of a Supplement: Volume 24 Supplement 1

  47. Glycosylation is an important modification to proteins that plays a significant role in biological processes. Glycan structures are characterized by liquid chromatography (LC) combined with mass spectrometry (...

    Authors: Ashna Dhingra, Zayla Schaeffer, Natalia I. Majewska Nepomuceno, Jennifer Au and Joomi Ahn
    Citation: BMC Bioinformatics 2023 24:259
    Content type: Software Published on:

  48. Capturing the conditional covariances or correlations among the elements of a multivariate response vector based on covariates is important to various fields including neuroscience, epidemiology and biomedicin...

    Authors: Cansu Alakus, Denis Larocque and Aurélie Labbe
    Citation: BMC Bioinformatics 2023 24:258
    Content type: Research Published on:

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