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  1. As one of the deadliest diseases in the world, cancer is driven by a few somatic mutations that disrupt the normal growth of cells, and leads to abnormal proliferation and tumor development. The vast majority ...

    Authors: Yun-Yun Tang, Pi-Jing Wei, Jian-ping Zhao, Junfeng Xia, Rui-Fen Cao and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2021 22(Suppl 3):457

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  2. The use of sound to represent sequence data—sonification—has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance m...

    Authors: Edward J. Martin, Thomas R. Meagher and Daniel Barker

    Citation: BMC Bioinformatics 2021 22:456

    Content type: Research

    Published on:

  3. With the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompts the development of precision medicine. Deep learning is a promising a...

    Authors: Victoria Bourgeais, Farida Zehraoui, Mohamed Ben Hamdoune and Blaise Hanczar

    Citation: BMC Bioinformatics 2021 22(Suppl 10):455

    Content type: Research

    Published on:

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

  4. Adenocarcinoma and squamous cell carcinoma are the two most prevalent lung cancer types, and their distinction requires different screenings, such as the visual inspection of histology slides by an expert path...

    Authors: Francisco Carrillo-Perez, Juan Carlos Morales, Daniel Castillo-Secilla, Yésica Molina-Castro, Alberto Guillén, Ignacio Rojas and Luis Javier Herrera

    Citation: BMC Bioinformatics 2021 22:454

    Content type: Research

    Published on:

  5. The liver plays a major role in the metabolic activation of xenobiotics (drugs, chemicals such as pollutants, pesticides, food additives...). Among environmental contaminants of concern, heterocyclic aromatic ...

    Authors: Mael Conan, Nathalie Théret, Sophie Langouet and Anne Siegel

    Citation: BMC Bioinformatics 2021 22:450

    Content type: Research

    Published on:

  6. This paper exploits recent developments in topological data analysis to present a pipeline for clustering based on Mapper, an algorithm that reduces complex data into a one-dimensional graph.

    Authors: Ewan Carr, Mathieu Carrière, Bertrand Michel, Frédéric Chazal and Raquel Iniesta

    Citation: BMC Bioinformatics 2021 22:449

    Content type: Software

    Published on:

  7. The growing researches of molecular biology reveal that complex life phenomena have the ability to demonstrating various types of interactions in the level of genomics. To establish the interactions between ge...

    Authors: Bin Yang, Wenzheng Bao, Wei Zhang, Haifeng Wang, Chuandong Song, Yuehui Chen and Xiuying Jiang

    Citation: BMC Bioinformatics 2021 22(Suppl 3):448

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  8. Protein kinases are among the largest druggable family of signaling proteins, involved in various human diseases, including cancers and neurodegenerative disorders. Despite their clinical relevance, nearly 30%...

    Authors: Liang-Chin Huang, Rahil Taujale, Nathan Gravel, Aarya Venkat, Wayland Yeung, Dominic P. Byrne, Patrick A. Eyers and Natarajan Kannan

    Citation: BMC Bioinformatics 2021 22:446

    Content type: Methodology article

    Published on:

  9. Proteins are integral part of all living beings, which are building blocks of many amino acids. To be functionally active, amino acids chain folds up in a complex way to give each protein a unique 3D shape, wh...

    Authors: Mohammad Shahedul Islam, Md. Abul Kashem Mia, Mohammad Shamsur Rahman, Mohammad Shamsul Arefin, Pranab Kumar Dhar and Takeshi Koshiba

    Citation: BMC Bioinformatics 2021 22:435

    Content type: Research

    Published on:

  10. One of the major challenges in precision medicine is accurate prediction of individual patient’s response to drugs. A great number of computational methods have been developed to predict compounds activity usi...

    Authors: Zhaorui Zuo, Penglei Wang, Xiaowei Chen, Li Tian, Hui Ge and Dahong Qian

    Citation: BMC Bioinformatics 2021 22:434

    Content type: Methodology article

    Published on:

  11. Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automa...

    Authors: David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini and Allen Goodman

    Citation: BMC Bioinformatics 2021 22:433

    Content type: Software

    Published on:

  12. Interactions of microbes and diseases are of great importance for biomedical research. However, large-scale of microbe–disease interactions are hidden in the biomedical literature. The structured databases for...

    Authors: Chengkun Wu, Xinyi Xiao, Canqun Yang, JinXiang Chen, Jiacai Yi and Yanlong Qiu

    Citation: BMC Bioinformatics 2021 22:432

    Content type: Research

    Published on:

  13. RNA secondary structure prediction is an important research content in the field of biological information. Predicting RNA secondary structure with pseudoknots has been proved to be an NP-hard problem. Traditi...

    Authors: Weizhong Lu, Yan Cao, Hongjie Wu, Yijie Ding, Zhengwei Song, Yu Zhang, Qiming Fu and Haiou Li

    Citation: BMC Bioinformatics 2021 22(Suppl 3):431

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  14. Essential proteins have great impacts on cell survival and development, and played important roles in disease analysis and new drug design. However, since it is inefficient and costly to identify essential pro...

    Authors: Shiyuan Li, Zhen Zhang, Xueyong Li, Yihong Tan, Lei Wang and Zhiping Chen

    Citation: BMC Bioinformatics 2021 22:430

    Content type: Research article

    Published on:

  15. With the broad application of high-throughput sequencing and its reduced cost, simple sequence repeat (SSR) genotyping by sequencing (SSR-GBS) has been widely used for interpreting genetic data across differen...

    Authors: Yongxue Huo, Yikun Zhao, Liwen Xu, Hongmei Yi, Yunlong Zhang, Xianqing Jia, Han Zhao, Jiuran Zhao and Fengge Wang

    Citation: BMC Bioinformatics 2021 22:429

    Content type: Software

    Published on:

  16. In mammalian cells the endoplasmic reticulum (ER) comprises a highly complex reticular morphology that is spread throughout the cytoplasm. This organelle is of particular interest to biologists, as its dysfunc...

    Authors: M. Elena Garcia-Pardo, Jeremy C. Simpson and Niamh C. O’Sullivan

    Citation: BMC Bioinformatics 2021 22:427

    Content type: Methodology article

    Published on:

  17. Interactions of single nucleotide polymorphisms (SNPs) and environmental factors play an important role in understanding complex diseases' pathogenesis. A growing number of SNP-environment studies have been co...

    Authors: Hui-Yi Lin, Po-Yu Huang, Tung-Sung Tseng and Jong Y. Park

    Citation: BMC Bioinformatics 2021 22:425

    Content type: Software

    Published on:

  18. In systems biology, it is important to reconstruct regulatory networks from quantitative molecular profiles. Gaussian graphical models (GGMs) are one of the most popular methods to this end. A GGM consists of ...

    Authors: Victor Bernal, Rainer Bischoff, Peter Horvatovich, Victor Guryev and Marco Grzegorczyk

    Citation: BMC Bioinformatics 2021 22:424

    Content type: Research article

    Published on:

  19. Assessing the reproducibility of measurements is an important first step for improving the reliability of downstream analyses of high-throughput metabolomics experiments. We define a metabolite to be reproduci...

    Authors: Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina Kechris and Debashis Ghosh

    Citation: BMC Bioinformatics 2021 22:423

    Content type: Research

    Published on:

  20. 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:

  21. Brain tumor segmentation is a challenging problem in medical image processing and analysis. It is a very time-consuming and error-prone task. In order to reduce the burden on physicians and improve the segment...

    Authors: Siyu Xiong, Guoqing Wu, Xitian Fan, Xuan Feng, Zhongcheng Huang, Wei Cao, Xuegong Zhou, Shijin Ding, Jinhua Yu, Lingli Wang and Zhifeng Shi

    Citation: BMC Bioinformatics 2021 22:421

    Content type: Research

    Published on:

  22. Glioblastoma multiforme (GBM) is the most common and aggressive primary malignant brain tumor with grim prognosis. Aberrant DNA methylation is an epigenetic mechanism that promotes GBM carcinogenesis, while th...

    Authors: Xiaoxiao Zhao, Jianghuai Ji, Shijia Wang, Rendong Wang, Qiuhong Yu and Dongguo Li

    Citation: BMC Bioinformatics 2021 22:420

    Content type: Research

    Published on:

  23. RNA velocity is a novel and powerful concept which enables the inference of dynamical cell state changes from seemingly static single-cell RNA sequencing (scRNA-seq) data. However, accurate estimation of RNA v...

    Authors: Xin Wang and Jie Zheng

    Citation: BMC Bioinformatics 2021 22(Suppl 10):419

    Content type: Methodology

    Published on:

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

  24. Variation in mitochondrial DNA (mtDNA) identified by genotyping microarrays or by sequencing only the hypervariable regions of the genome may be insufficient to reliably assign mitochondrial genomes to phyloge...

    Authors: Tim W. McInerney, Brian Fulton-Howard, Christopher Patterson, Devashi Paliwal, Lars S. Jermiin, Hardip R. Patel, Judy Pa, Russell H. Swerdlow, Alison Goate, Simon Easteal and Shea J. Andrews

    Citation: BMC Bioinformatics 2021 22:417

    Content type: Research

    Published on:

  25. Genetic heterogeneity of a cancer tumor that develops during clonal evolution is one of the reasons for cancer treatment failure, by increasing the chance of drug resistance. Clones are cell populations with d...

    Authors: Leila Baghaarabani, Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Seyed Peyman Shariatpanahi and Bahram Goliaei

    Citation: BMC Bioinformatics 2021 22:416

    Content type: Research

    Published on:

  26. Advances in the expression quantitative trait loci (eQTL) studies have provided valuable insights into the mechanism of diseases and traits-associated genetic variants. However, it remains challenging to evalu...

    Authors: Tao Wang, Yongzhuang Liu, Junpeng Ruan, Xianjun Dong, Yadong Wang and Jiajie Peng

    Citation: BMC Bioinformatics 2021 22(Suppl 9):403

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 9

  27. It is important to understand the composition of cell type and its proportion in intact tissues, as changes in certain cell types are the underlying cause of disease in humans. Although compositions of cell ty...

    Authors: Jiajie Peng, Lu Han and Xuequn Shang

    Citation: BMC Bioinformatics 2021 22(Suppl 9):281

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 9

  28. Gene prioritization (gene ranking) aims to obtain the centrality of genes, which is critical for cancer diagnosis and therapy since keys genes correspond to the biomarkers or targets of drugs. Great efforts ha...

    Authors: Yan Wang, Zuheng Xia, Jingjing Deng, Xianghua Xie, Maoguo Gong and Xiaoke Ma

    Citation: BMC Bioinformatics 2021 22(Suppl 9):274

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 9

  29. DNA sequence alignment is a common first step in most applications of high-throughput sequencing technologies. The accuracy of sequence alignments directly affects the accuracy of downstream analyses, such as ...

    Authors: Wei Quan, Bo Liu and Yadong Wang

    Citation: BMC Bioinformatics 2021 22(Suppl 9):172

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 9

  30. Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Que...

    Authors: Syed Ahmad Chan Bukhari, Shrikant Pawar, Jeff Mandell, Steven H. Kleinstein and Kei-Hoi Cheung

    Citation: BMC Bioinformatics 2021 22(Suppl 9):105

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 9

  31. Plant long non-coding RNAs (lncRNAs) play vital roles in many biological processes mainly through interactions with RNA-binding protein (RBP). To understand the function of lncRNAs, a fundamental method is to ...

    Authors: Haoran Zhou, Jael Sanyanda Wekesa, Yushi Luan and Jun Meng

    Citation: BMC Bioinformatics 2021 22(Suppl 3):415

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  32. The analyses of amplification and melting curves have been shown to provide valuable information on the quality of the individual reactions in quantitative PCR (qPCR) experiments and to result in more reliable...

    Authors: Andreas Untergasser, Jan M. Ruijter, Vladimir Benes and Maurice J. B. van den Hoff

    Citation: BMC Bioinformatics 2021 22:398

    Content type: Software

    Published on:

  33. Drug–drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive...

    Authors: Kyriakos Schwarz, Ahmed Allam, Nicolas Andres Perez Gonzalez and Michael Krauthammer

    Citation: BMC Bioinformatics 2021 22:412

    Content type: Research

    Published on:

  34. Once bulk RNA-seq data has been processed, i.e. aligned and then expression and differential tables generated, there remains the essential process where the biology is explored, visualized and interpreted. Wit...

    Authors: John J. Cole, Bekir A. Faydaci, David McGuinness, Robin Shaw, Rose A. Maciewicz, Neil A. Robertson and Carl S. Goodyear

    Citation: BMC Bioinformatics 2021 22:411

    Content type: Software

    Published on:

  35. With recent advances in microscopy, recordings of cell behaviour can result in terabyte-size datasets. The lattice light sheet microscope (LLSM) images cells at high speed and high 3D resolution, accumulating ...

    Authors: James G. Lefevre, Yvette W. H. Koh, Adam A. Wall, Nicholas D. Condon, Jennifer L. Stow and Nicholas A. Hamilton

    Citation: BMC Bioinformatics 2021 22:410

    Content type: Software

    Published on:

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