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  1.  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:

  2. 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:

  5. 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:

  6. 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:

  8. 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:

  10. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

    The Correction to this article has been published in BMC Bioinformatics 2024 25:7

  19. 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:

  22. 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:

  24. 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:

  25. 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:

  26. 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

  29. 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:

  30. 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:

  33. The prognosis and survival of lung adenocarcinoma (LUAD) patients are still not promising despite recent breakthroughs in treatment. Endoplasmic reticulum stress (ERS) is a self-protective mechanism resulting ...

    Authors: Yuqi Song, Jianzun Ma, Linan Fang, Mingbo Tang, Xinliang Gao, Dongshan Zhu and Wei Liu
    Citation: BMC Bioinformatics 2023 24:255
    Content type: Research Published on:

  34. In the field of neuroscience, neural modules and circuits that control biological functions have been found throughout entire neural networks. Correlations in neural activity can be used to identify such neura...

    Authors: Koki Tsuyuzaki, Kentaro Yamamoto, Yu Toyoshima, Hirofumi Sato, Manami Kanamori, Takayuki Teramoto, Takeshi Ishihara, Yuichi Iino and Itoshi Nikaido
    Citation: BMC Bioinformatics 2023 24:254
    Content type: Research Published on:

  35. The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as...

    Authors: Michela Quadrini, Luca Tesei and Emanuela Merelli
    Citation: BMC Bioinformatics 2023 23(Suppl 6):575
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 6

  37. Bioinformatics capability to analyze spatio–temporal dynamics of gene expression is essential in understanding animal development. Animal cells are spatially organized as functional tissues where cellular gene...

    Authors: Tomoya Mori, Toshiro Takase, Kuan-Chun Lan, Junko Yamane, Cantas Alev, Azuma Kimura, Kenji Osafune, Jun K. Yamashita, Tatsuya Akutsu, Hiroaki Kitano and Wataru Fujibuchi
    Citation: BMC Bioinformatics 2023 24:252
    Content type: Research Published on:

  38. Hennekam Lymphangiectasia–Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is characterized by lymphatic dysplasia, intestinal lymphangiectas...

    Authors: Khyber Shinwari, Yurong Wu, Hafiz Muzzammel Rehman, Ningkun Xiao, Mikhail Bolkov, Irina Tuzankina and Valery Chereshnev
    Citation: BMC Bioinformatics 2023 24:251
    Content type: Research Published on:

  39. Metabolomics is a dynamic tool for elucidating biochemical changes in human health and disease. Metabolic profiles provide a close insight into physiological states and are highly volatile to genetic and envir...

    Authors: Najeha R. Anwardeen, Ilhame Diboun, Younes Mokrab, Asma A. Althani and Mohamed A. Elrayess
    Citation: BMC Bioinformatics 2023 24:250
    Content type: Review Published on:

  40. All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being des...

    Authors: Roman Lukyanenko, Veda C. Storey and Oscar Pastor
    Citation: BMC Bioinformatics 2023 23(Suppl 11):574
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 11

  41. Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representatio...

    Authors: Shenghao Cao, Mengtian Li and Lei M. Li
    Citation: BMC Bioinformatics 2023 24:249
    Content type: Research Published on:

  43. Simulating DNA evolution has been done through coevolution-agnostic probabilistic frameworks for the past 3 decades. The most common implementation is by using the converse of the probabilistic approach used t...

    Authors: Carlos J. Rivera-Rivera and Djordje Grbic
    Citation: BMC Bioinformatics 2023 24:247
    Content type: Software Published on:

  44. Computational models of cell signaling networks are extremely useful tools for the exploration of underlying system behavior and prediction of response to various perturbations. By representing signaling casca...

    Authors: Willow Carretero Chavez, Marcus Krantz, Edda Klipp and Irina Kufareva
    Citation: BMC Bioinformatics 2023 24:246
    Content type: Software Published on:

  46. High throughput experiments in cancer and other areas of genomic research identify large numbers of sequence variants that need to be evaluated for phenotypic impact. While many tools exist to score the likely...

    Authors: Michael Sierk, Shashikala Ratnayake, Manoj M. Wagle, Ben Chen, Brian Park, Jiyao Wang, Philippe Youkharibache and Daoud Meerzaman
    Citation: BMC Bioinformatics 2023 24:244
    Content type: Software Published on:

  47. Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecti...

    Authors: Rohan S Mehta, Robert A Petit III, Timothy D Read and Daniel B Weissman
    Citation: BMC Bioinformatics 2023 24:243
    Content type: Research Published on:

  49. RNA sequencing (RNA-Seq) is a technique that utilises the capabilities of next-generation sequencing to study a cellular transcriptome i.e., to determine the amount of RNA at a given time for a given biologica...

    Authors: Girivinay Padegal, Murali Krishna Rao, Om Amitesh Boggaram Ravishankar, Sathwik Acharya, Prashanth Athri and Gowri Srinivasa
    Citation: BMC Bioinformatics 2023 24:241
    Content type: Research Published on:

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