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Page 23 of 249

  1. Recent studies on acute mountain sickness (AMS) have used fixed-location and fixed-time measurements of environmental and physiological variable to determine the influence of AMS-associated factors in the huma...

    Authors: Chih-Yuan Wei, Ping-Nan Chen, Shih-Sung Lin, Tsai-Wang Huang, Ling-Chun Sun, Chun-Wei Tseng and Ke-Feng Lin
    Citation: BMC Bioinformatics 2022 22(Suppl 5):628
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  3. In the context of biomedical and epidemiological research, gene-environment (G-E) interaction is of great significance to the etiology and progression of many complex diseases. In high-dimensional genetic data...

    Authors: Jie-Huei Wang, Kang-Hsin Wang and Yi-Hau Chen
    Citation: BMC Bioinformatics 2022 23:202
    Content type: Research Published on:

  4. A high-quality docking method tends to yield multifold gains with half pains for the new drug development. Over the past few decades, great efforts have been made for the development of novel docking programs ...

    Authors: Chao Li, Jinxing Li, Jun Sun, Li Mao, Vasile Palade and Bilal Ahmad
    Citation: BMC Bioinformatics 2022 23:201
    Content type: Research Published on:

  5. Cancer Immunoediting (CI) describes the cellular-level interaction between tumor cells and the Immune System (IS) that takes place in the Tumor Micro-Environment (TME). CI is a highly dynamic and complex proce...

    Authors: Alfonso Rojas-Domínguez, Renato Arroyo-Duarte, Fernando Rincón-Vieyra and Matías Alvarado-Mentado
    Citation: BMC Bioinformatics 2022 23:200
    Content type: Research Published on:

  6. The accurate characterization of protein functions is critical to understanding life at the molecular level and has a huge impact on biomedicine and pharmaceuticals. Computationally predicting protein function...

    Authors: Sai Hu, Zhihong Zhang, Huijun Xiong, Meiping Jiang, Yingchun Luo, Wei Yan and Bihai Zhao
    Citation: BMC Bioinformatics 2022 23:199
    Content type: Research Published on:

  7. FragGeneScan is currently the most accurate and popular tool for gene prediction in short and error-prone reads, but its execution speed is insufficient for use on larger data sets. The parallelization which s...

    Authors: Felix Van der Jeugt, Peter Dawyndt and Bart Mesuere
    Citation: BMC Bioinformatics 2022 23:198
    Content type: Software Published on:

  9. SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-Co...

    Authors: Ilya Plyusnin, Phuoc Thien Truong Nguyen, Tarja Sironen, Olli Vapalahti, Teemu Smura and Ravi Kant
    Citation: BMC Bioinformatics 2022 23:196
    Content type: Software Published on:

  10. Determining cell identity in volumetric images of tagged neuronal nuclei is an ongoing challenge in contemporary neuroscience. Frequently, cell identity is determined by aligning and matching tags to an “atlas...

    Authors: Michael Skuhersky, Tailin Wu, Eviatar Yemini, Amin Nejatbakhsh, Edward Boyden and Max Tegmark
    Citation: BMC Bioinformatics 2022 23:195
    Content type: Research Published on:

  11. Finding correlation patterns is an important goal of analyzing biological data. Currently available methods for correlation analysis mainly use non-direct associations, such as the Pearson correlation coeffici...

    Authors: Yi-Hua Jiang, Jie Long, Zhi-Bin Zhao, Liang Li, Zhe-Xiong Lian, Zhi Liang and Jia-Rui Wu
    Citation: BMC Bioinformatics 2022 23:194
    Content type: Research Published on:

  12. X chromosome inactivation (XCI) is an epigenetic phenomenon that one of two X chromosomes in females is transcriptionally silenced during early embryonic development. Skewed XCI has been reported to be associa...

    Authors: Wen-Yi Yu, Yu Zhang, Meng-Kai Li, Zi-Ying Yang, Wing Kam Fung, Pei-Zhen Zhao and Ji-Yuan Zhou
    Citation: BMC Bioinformatics 2022 23:193
    Content type: Research Published on:

  13. The effectiveness of biclustering, simultaneous clustering of rows and columns in a data matrix, was shown in gene expression data analysis. Several researchers recognize its potentialities in other research a...

    Authors: Eduardo N. Castanho, Helena Aidos and Sara C. Madeira
    Citation: BMC Bioinformatics 2022 23:192
    Content type: Research Published on:

  15. Interpretation of high-throughput gene expression data continues to require mathematical tools in data analysis that recognizes the shape of the data in high dimensions. Topological data analysis (TDA) has rec...

    Authors: Tamal K. Dey, Sayan Mandal and Soham Mukherjee
    Citation: BMC Bioinformatics 2022 22(Suppl 10):627
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  16. Gene expression is the result of the balance between transcription and degradation. Recent experimental findings have shown fine and specific regulation of RNA degradation and the presence of various molecular...

    Authors: Federica Conte, Federico Papa, Paola Paci and Lorenzo Farina
    Citation: BMC Bioinformatics 2022 23:190
    Content type: Research Published on:

  17. Nowadays, the inception of computer modeling and simulation in life science is a matter of fact. This is one of the reasons why regulatory authorities are open in considering in silico trials evidence for the ...

    Authors: Giulia Russo, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi and Francesco Pappalardo
    Citation: BMC Bioinformatics 2022 22(Suppl 14):626
    Content type: Software Published on:

    This article is part of a Supplement: Volume 22 Supplement 14

  18. Many long non-coding RNAs (lncRNAs) have key roles in different human biologic processes and are closely linked to numerous human diseases, according to cumulative evidence. Predicting potential lncRNA-disease...

    Authors: Ying Liang, Ze-Qun Zhang, Nian-Nian Liu, Ya-Nan Wu, Chang-Long Gu and Ying-Long Wang
    Citation: BMC Bioinformatics 2022 23:189
    Content type: Research Published on:

  19. Identifying associations among biological variables is a major challenge in modern quantitative biological research, particularly given the systemic and statistical noise endemic to biological systems. Drug se...

    Authors: Petr Smirnov, Ian Smith, Zhaleh Safikhani, Wail Ba-alawi, Farnoosh Khodakarami, Eva Lin, Yihong Yu, Scott Martin, Janosch Ortmann, Tero Aittokallio, Marc Hafner and Benjamin Haibe-Kains
    Citation: BMC Bioinformatics 2022 23:188
    Content type: Research Published on:

  22. Using DNA as a storage medium is appealing due to the information density and longevity of DNA, especially in the era of data explosion. A significant challenge in the DNA data storage area is to deal with the...

    Authors: Lekang Yuan, Zhen Xie, Ye Wang and Xiaowo Wang
    Citation: BMC Bioinformatics 2022 23:185
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2022 23:274

  26. Stomach adenocarcinoma (STAD) is a common malignant tumor in the world and its prognosis is poor, miRNA plays a role mainly by influencing the expression of mRNAs, and participates in the occurrence and develo...

    Authors: Hao Qian, Nanxue Cui, Qiao Zhou and Shihai Zhang
    Citation: BMC Bioinformatics 2022 23:181
    Content type: Research Published on:

  27. The Transmembrane Serine Protease 2 (TMPRSS2) of human cell plays a significant role in proteolytic cleavage of SARS-Cov-2 coronavirus spike protein and subsequent priming to the receptor ACE2. Approaching TMP...

    Authors: Reji Manjunathan, Vijayalakshmi Periyaswami, Kartik Mitra, Arokiaraj Sherlin Rosita, Medha Pandya, Jayaraman Selvaraj, Lokesh Ravi, Nalini Devarajan and Mukesh Doble
    Citation: BMC Bioinformatics 2022 23:180
    Content type: Research Published on:

  28. When analyzing large datasets from high-throughput technologies, researchers often encounter missing quantitative measurements, which are particularly frequent in metabolomics datasets. Metabolomics, the compr...

    Authors: Jonathan P. Dekermanjian, Elin Shaddox, Debmalya Nandy, Debashis Ghosh and Katerina Kechris
    Citation: BMC Bioinformatics 2022 23:179
    Content type: Research Published on:

  34. Boolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors–subsets of the state space towards which the BN...

    Authors: Nikola Beneš, Luboš Brim, Jakub Kadlecaj, Samuel Pastva and David Šafránek
    Citation: BMC Bioinformatics 2022 23:173
    Content type: Research Published on:

  35. Clustered regularly interspaced short palindromic repeats (CRISPR) and their spacers are important components of prokaryotic CRISPR-Cas systems. In order to analyze the CRISPR loci of multiple genomes more int...

    Authors: Lei Sun, Jinbiao Wang, Fu Yan, Gongming Wang, Yun Li and Jinlin Huang
    Citation: BMC Bioinformatics 2022 23(Suppl 3):172
    Content type: Software Published on:

    This article is part of a Supplement: Volume 23 Supplement 3

  36. Archaea are a vast and unexplored domain. Bioinformatic techniques might enlighten the path to a higher quality genome annotation in varied organisms. Promoter sequences of archaea have the action of a plethor...

    Authors: Gustavo Sganzerla Martinez, Ernesto Pérez-Rueda, Sharmilee Sarkar, Aditya Kumar and Scheila de Ávila e Silva
    Citation: BMC Bioinformatics 2022 23:171
    Content type: Research Published on:

  37. Gene co-expression networks (GCNs) can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarray...

    Authors: Junyao Kuang, Nicolas Buchon, Kristin Michel and Caterina Scoglio
    Citation: BMC Bioinformatics 2022 23:170
    Content type: Research Published on:

  40. De novo genome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is needed to resolve the complete structur...

    Authors: Riku Walve and Leena Salmela
    Citation: BMC Bioinformatics 2022 23:167
    Content type: Research Published on:

  44. To reduce drug side effects and enhance their therapeutic effect compared with single drugs, drug combination research, combining two or more drugs, is highly important. Conducting in-vivo and in-vitro experim...

    Authors: Yongsun Shim, Munhwan Lee, Pil-Jong Kim and Hong-Gee Kim
    Citation: BMC Bioinformatics 2022 23:163
    Content type: Research Published on:

  45. Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cu...

    Authors: Xiaodan Zhang, Jinxiang Xuan, Chensong Yao, Qijuan Gao, Lianglong Wang, Xiu Jin and Shaowen Li
    Citation: BMC Bioinformatics 2022 23:162
    Content type: Research Published on:

  49. Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq ex...

    Authors: John A. Hadish, Tyler D. Biggs, Benjamin T. Shealy, M. Reed Bender, Coleman B. McKnight, Connor Wytko, Melissa C. Smith, F. Alex Feltus, Loren Honaas and Stephen P. Ficklin
    Citation: BMC Bioinformatics 2022 23:156
    Content type: Software Published on:

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