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  2. 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:

  4. 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:

  5. 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:

  6. 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

  9. 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:

  10. 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:

  13. 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:

  14. 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:

  15. 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

  17. 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:

  18. 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:

  19. 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:

  20. 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

  21. 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:

  23. 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:

  24. 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:

  26. 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:

  27. 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:

  29. 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:

  31. 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
    Content type: Software Published on:

  32. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  34. 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
    Content type: Software Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  38. 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
    Content type: Software Published on:

  39. 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
    Content type: Research Published on:

  41. 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
    Content type: Research Published on:

  45. 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
    Content type: Software Published on:

  46. 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
    Content type: Research Published on:

  50. 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
    Content type: Research Published on:

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