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1648 result(s) for 'natural language processing' within BMC Bioinformatics

Page 33 of 33

  2. With more T cell receptor sequence data becoming available, the need for bioinformatics approaches to predict T cell receptor specificity is even more pressing. Here we present SwarmTCR, a method that uses lab...

    Authors: Ryan Ehrlich, Larisa Kamga, Anna Gil, Katherine Luzuriaga, Liisa K. Selin and Dario Ghersi
    Citation: BMC Bioinformatics 2021 22:422
    Content type: Research Published on:

  3. A major current focus in the analysis of protein–protein interaction (PPI) data is how to identify essential proteins. As massive PPI data are available, this warrants the design of efficient computing methods...

    Authors: Peiqiang Liu, Chang Liu, Yanyan Mao, Junhong Guo, Fanshu Liu, Wangmin Cai and Feng Zhao
    Citation: BMC Bioinformatics 2023 24:203
    Content type: Research Published on:

  4. Non-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs...

    Authors: Qiu Xiao, Jiawei Luo, Cheng Liang, Jie Cai, Guanghui Li and Buwen Cao
    Citation: BMC Bioinformatics 2019 20:67
    Content type: Research article Published on:

  5. A microRNA (miRNA) sponge is an RNA molecule with multiple tandem miRNA response elements that can sequester miRNAs from their target mRNAs. Despite growing appreciation of the importance of miRNA sponges, our...

    Authors: Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li and Thuc Duy Le
    Citation: BMC Bioinformatics 2019 20:235
    Content type: Software Published on:

  6. Haplotyping reveals chromosome blocks inherited from parents to in vitro fertilized (IVF) embryos in preimplantation genetic diagnosis (PGD), enabling the observation of the transmission of disease alleles bet...

    Authors: Zhiqiang Yan, Xiaohui Zhu, Yuqian Wang, Yanli Nie, Shuo Guan, Ying Kuo, Di Chang, Rong Li, Jie Qiao and Liying Yan
    Citation: BMC Bioinformatics 2020 21:41
    Content type: Software Published on:

  8. Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have b...

    Authors: Ying Wang, Kun Wang, Yang Young Lu and Fengzhu Sun
    Citation: BMC Bioinformatics 2017 18:425
    Content type: Methodology Article Published on:

  9. The automated prediction of the enzymatic functions of uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most of these st...

    Authors: Alperen Dalkiran, Ahmet Sureyya Rifaioglu, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay and Tunca Doğan
    Citation: BMC Bioinformatics 2018 19:334
    Content type: Software Published on:

  11. Drug repositioning is a very important task that provides critical information for exploring the potential efficacy of drugs. Yet developing computational models that can effectively predict drug–disease assoc...

    Authors: Meng-Long Zhang, Bo-Wei Zhao, Xiao-Rui Su, Yi-Zhou He, Yue Yang and Lun Hu
    Citation: BMC Bioinformatics 2022 23:516
    Content type: Research Published on:

  12. 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:

  14. Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain rea...

    Authors: Kevin Vanneste, Linda Garlant, Sylvia Broeders, Steven Van Gucht and Nancy H. Roosens
    Citation: BMC Bioinformatics 2018 19:312
    Content type: Research article Published on:

  15. The identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homolog...

    Authors: Xiyin Wang, Xiaoli Shi, Zhe Li, Qihui Zhu, Lei Kong, Wen Tang, Song Ge and Jingchu Luo
    Citation: BMC Bioinformatics 2006 7:447
    Content type: Methodology article Published on:

  16. Several recent studies have used the Minimum Dominating Set (MDS) model to identify driver nodes, which provide the control of the underlying networks, in protein interaction networks. There may exist multiple...

    Authors: Xiao-Fei Zhang, Le Ou-Yang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu and Hong Yan
    Citation: BMC Bioinformatics 2016 17:358
    Content type: Research Article Published on:

  17. Running multiple-chain Markov Chain Monte Carlo (MCMC) provides an efficient parallel computing method for complex Bayesian models, although the efficiency of the approach critically depends on the length of t...

    Authors: Peng Guo, Bo Zhu, Hong Niu, Zezhao Wang, Yonghu Liang, Yan Chen, Lupei Zhang, Hemin Ni, Yong Guo, El Hamidi A. Hay, Xue Gao, Huijiang Gao, Xiaolin Wu, Lingyang Xu and Junya Li
    Citation: BMC Bioinformatics 2018 19:3
    Content type: Research article Published on:

  18. Drug combination that consists of distinctive agents is an attractive strategy to combat complex diseases and has been widely used clinically with improved therapeutic effects. However, the identification of e...

    Authors: Yin-Ying Wang, Ke-Jia Xu, Jiangning Song and Xing-Ming Zhao
    Citation: BMC Bioinformatics 2012 13(Suppl 7):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 7

  21. Feature selection in class-imbalance learning has gained increasing attention in recent years due to the massive growth of high-dimensional class-imbalanced data across many scientific fields. In addition to r...

    Authors: Guang-Hui Fu, Yuan-Jiao Wu, Min-Jie Zong and Jianxin Pan
    Citation: BMC Bioinformatics 2020 21:121
    Content type: Research Article Published on:

  23. Many content-based statistical features of secondary structural elements (CBF-PSSEs) have been proposed and achieved promising results in protein structural class prediction, but until now position distributio...

    Authors: Qi Dai, Yan Li, Xiaoqing Liu, Yuhua Yao, Yunjie Cao and Pingan He
    Citation: BMC Bioinformatics 2013 14:152
    Content type: Methodology article Published on:

  25. Transcription factors (TFs) are important regulatory proteins that govern transcriptional regulation. Today, it is known that in higher organisms different TFs have to cooperate rather than acting individually...

    Authors: Cornelia Meckbach, Rebecca Tacke, Xu Hua, Stephan Waack, Edgar Wingender and Mehmet Gültas
    Citation: BMC Bioinformatics 2015 16:400
    Content type: Methodology Article Published on:

  27. Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error ...

    Authors: Nathan LaPierre, Rob Egan, Wei Wang and Zhong Wang
    Citation: BMC Bioinformatics 2019 20:552
    Content type: Software Published on:

  34. Determining the association between tumor sample and the gene is demanding because it requires a high cost for conducting genetic experiments. Thus, the discovered association between tumor sample and gene fur...

    Authors: Mohan Timilsina, Haixuan Yang, Ratnesh Sahay and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2019 20:462
    Content type: Research Article Published on:

  35. Genotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because ge...

    Authors: Guilherme S. Pereira, Antonio Augusto F. Garcia and Gabriel R. A. Margarido
    Citation: BMC Bioinformatics 2018 19:398
    Content type: Software Published on:

  36. Relationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the li...

    Authors: Janet C. Siebert, Charles Preston Neff, Jennifer M. Schneider, Emilie H. Regner, Neha Ohri, Kristine A. Kuhn, Brent E. Palmer, Catherine A. Lozupone and Carsten Görg
    Citation: BMC Bioinformatics 2019 20:432
    Content type: Research article Published on:

  37. Studies exploring the potential of Chaos Game Representations (CGR) of genomic sequences to act as “genomic signatures” (to be species- and genome-specific) showed that CGR patterns of nuclear and organellar D...

    Authors: Rallis Karamichalis, Lila Kari, Stavros Konstantinidis, Steffen Kopecki and Stephen Solis-Reyes
    Citation: BMC Bioinformatics 2016 17:313
    Content type: Research Article Published on:

  38. Modern genomic and proteomic profiling methods produce large amounts of data from tissue and blood-based samples that are of potential utility for improving patient care. However, the design of precision medic...

    Authors: Joanna Roder, Carlos Oliveira, Lelia Net, Maxim Tsypin, Benjamin Linstid and Heinrich Roder
    Citation: BMC Bioinformatics 2019 20:325
    Content type: Methodology article Published on:

  39. Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each fami...

    Authors: P. K. Busk, B. Pilgaard, M. J. Lezyk, A. S. Meyer and L. Lange
    Citation: BMC Bioinformatics 2017 18:214
    Content type: Software Published on:

  42. Intra-tumor heterogeneity is known to contribute to cancer complexity and drug resistance. Understanding the number of distinct subclones and the evolutionary relationships between them is scientifically and c...

    Authors: Hosein Toosi, Ali Moeini and Iman Hajirasouliha
    Citation: BMC Bioinformatics 2019 20(Suppl 11):282
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  44. The interactions between non-coding RNAs (ncRNA) and proteins play an essential role in many biological processes. Several high-throughput experimental methods have been applied to detect ncRNA-protein interac...

    Authors: Hai-Cheng Yi, Zhu-Hong You, Mei-Neng Wang, Zhen-Hao Guo, Yan-Bin Wang and Ji-Ren Zhou
    Citation: BMC Bioinformatics 2020 21:60
    Content type: Methodology article Published on:

  46. Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patt...

    Authors: James E. Barrett, Andrew Feber, Javier Herrero, Miljana Tanic, Gareth A. Wilson, Charles Swanton and Stephan Beck
    Citation: BMC Bioinformatics 2017 18:354
    Content type: Methodology Article Published on:

  47. Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mappe...

    Authors: Hongfei Cui, Hailin Hu, Jianyang Zeng and Ting Chen
    Citation: BMC Bioinformatics 2019 20(Suppl 24):678
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 24

  48. Missense mutations in the first five exons of F9, which encodes factor FIX, represent 40% of all mutations that cause hemophilia B. To address the ongoing debate regarding in silico identification of disease-caus...

    Authors: Lennon Meléndez-Aranda, Ana Rebeca Jaloma-Cruz, Nina Pastor and Marina María de Jesús Romero-Prado
    Citation: BMC Bioinformatics 2019 20:363
    Content type: Research article Published on:

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