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  1. 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
  2. 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
  3. 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
  4. 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

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

  5. 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
  6. 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
  7. 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
  8. 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

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

  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. The analysis of mass spectrometry-based quantitative proteomics data can be challenging given the variety of established analysis platforms, the differences in reporting formats, and a general lack of approach...

    Authors: Jeff Jones, Elliot J. MacKrell, Ting-Yu Wang, Brett Lomenick, Michael L. Roukes and Tsui-Fen Chou
    Citation: BMC Bioinformatics 2023 24:239
  16. Lung squamous cell carcinoma (LUSC) is associated with a worse prognosis than other histological subtypes of non-small cell lung cancer. Due to the vital role of CD8+ T cells in anti-tumor immunity, the character...

    Authors: Liang Chen, Yiming Weng, Xue Cui, Qian Li, Min Peng and Qibin Song
    Citation: BMC Bioinformatics 2023 24:238
  17. Stochastic optical reconstruction microscopy (STORM), a super-resolution microscopy technique based on single-molecule localizations, has become popular to characterize sub-diffraction limit targets. However, ...

    Authors: Øystein Øvrebø, Miina Ojansivu, Kimmo Kartasalo, Hanna M. G. Barriga, Petter Ranefall, Margaret N. Holme and Molly M. Stevens
    Citation: BMC Bioinformatics 2023 24:237
  18. Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. Th...

    Authors: Patrick Kunzmann, Tom David Müller, Maximilian Greil, Jan Hendrik Krumbach, Jacob Marcel Anter, Daniel Bauer, Faisal Islam and Kay Hamacher
    Citation: BMC Bioinformatics 2023 24:236
  19. Identifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying evolutionary processes. Given the exact locations of their genes, the...

    Authors: Lisa Fiedler, Matthias Bernt, Martin Middendorf and Peter F. Stadler
    Citation: BMC Bioinformatics 2023 24:235
  20. Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and und...

    Authors: Hua Zhong, Jing Luo, Lin Tang, Shicheng Liao, Zhonghao Lu, Guoliang Lin, Robert W. Murphy and Lin Liu
    Citation: BMC Bioinformatics 2023 24:234
  21. Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin and spread of pathogens. Laboratories arou...

    Authors: Chaoran Chen, Alexander Taepper, Fabian Engelniederhammer, Jonas Kellerer, Cornelius Roemer and Tanja Stadler
    Citation: BMC Bioinformatics 2023 24:232
  22. When it was first introduced in 2000, reverse vaccinology was defined as an in silico approach that begins with the pathogen's genomic sequence. It concludes with a list of potential proteins with a possible, ...

    Authors: Giulia Russo, Elena Crispino, Avisa Maleki, Valentina Di Salvatore, Filippo Stanco and Francesco Pappalardo
    Citation: BMC Bioinformatics 2023 24:231
  23. Clinical studies have shown that miRNAs are closely related to human health. The study of potential associations between miRNAs and diseases will contribute to a profound understanding of the mechanism of dise...

    Authors: Min Chen, Yingwei Deng, Zejun Li, Yifan Ye and Ziyi He
    Citation: BMC Bioinformatics 2023 24:229
  24. Comutation plot is a widely used visualization method to deliver a global view of the mutation landscape of large-scale genomic studies. Current tools for creating comutation plot are either offline packages t...

    Authors: Qiaonan Duan, Weiyi Wang, Feiling Feng, Xiaoqing Jiang, Hao Chen, Dadong Zhang and Tongyi Zhang
    Citation: BMC Bioinformatics 2023 24:226
  25. N6-methyladenosine (m6A) modification is involved in tumorigenesis and progression as well as closely correlated with stem cell differentiation and pluripotency. Moreover, tumor progression includes the acquis...

    Authors: Guihua Tang, Jianqiao Peng, Longwei Huo and Wen Yin
    Citation: BMC Bioinformatics 2023 24:225
  26. As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing th...

    Authors: Kyle A. O’Connell, Zelaikha B. Yosufzai, Ross A. Campbell, Collin J. Lobb, Haley T. Engelken, Laura M. Gorrell, Thad B. Carlson, Josh J. Catana, Dina Mikdadi, Vivien R. Bonazzi and Juergen A. Klenk
    Citation: BMC Bioinformatics 2023 24:221
  27. CRISPR/Cas is an efficient genome editing system that has been widely used for functional genetic studies and exhibits high potential in biomedical translational applications. Indel analysis has thus become on...

    Authors: Huancheng Fu, Ce Shan, Fanchen Kang, Ling Yu, Zhonghan Li and Yike Yin
    Citation: BMC Bioinformatics 2023 24:219
  28. Hepatocellular carcinoma (HCC) is the fifth most frequently diagnosed malignancy and the third leading cause of cancer death globally. T cells are significantly correlated with the progression, therapy and pro...

    Authors: Xu Chen, Chuang Peng, Yu Chen, Bai Ding, Sulai Liu, Yinghui Song, Yuhang Li, Bo Sun and Ranzhiqiang Yang
    Citation: BMC Bioinformatics 2023 24:216
  29. There is a pressing need for improved methods to identify effective therapeutics for diseases. Many computational approaches have been developed to repurpose existing drugs to meet this need. However, these to...

    Authors: Belinda B. Garana, James H. Joly, Alireza Delfarah, Hyunjun Hong and Nicholas A. Graham
    Citation: BMC Bioinformatics 2023 24:215
  30. Boolean Networks (BNs) are a popular dynamical model in biology where the state of each component is represented by a variable taking binary values that express, for instance, activation/deactivation or high/l...

    Authors: Georgios A. Argyris, Alberto Lluch Lafuente, Mirco Tribastone, Max Tschaikowski and Andrea Vandin
    Citation: BMC Bioinformatics 2023 24(Suppl 1):212

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

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