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  1. The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is ...

    Authors: Jingchao Sun, Zhining Qiu, Rob Egan, Harrison Ho, Yue Li and Zhong Wang
    Citation: BMC Bioinformatics 2022 23:513
  2. Genome-scale metabolic reconstruction tools have been developed in the last decades. They have helped to reconstruct eukaryotic and prokaryotic metabolic models, which have contributed to fields, e.g., genetic...

    Authors: Gustavo Tamasco, Manish Kumar, Karsten Zengler, Rafael Silva-Rocha and Ricardo Roberto da Silva
    Citation: BMC Bioinformatics 2022 23:512
  3. Cancers are genetically heterogeneous, so anticancer drugs show varying degrees of effectiveness on patients due to their differing genetic profiles. Knowing patient’s responses to numerous cancer drugs are ne...

    Authors: Conghao Wang, Xintong Lye, Rama Kaalia, Parvin Kumar and Jagath C. Rajapakse
    Citation: BMC Bioinformatics 2022 22(Suppl 10):632

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

  4. Research on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental evolution to bioinformatics and theoretical models. Notwithstanding, a consens...

    Authors: Yuridia S. Posadas-García and Carlos Espinosa-Soto
    Citation: BMC Bioinformatics 2022 23:509
  5. Bacteria can exceptionally evolve and develop pathogenic features making it crucial to determine novel pathogenic proteins for specific therapeutic interventions. Therefore, we have developed a machine-learnin...

    Authors: Ankit Gupta, Aditya S. Malwe, Gopal N. Srivastava, Parikshit Thoudam, Keshav Hibare and Vineet K. Sharma
    Citation: BMC Bioinformatics 2022 23:507
  6. Histological feature representation is advantageous for computer aided diagnosis (CAD) and disease classification when using predictive techniques based on machine learning. Explicit feature representations in...

    Authors: Aravind Nair, Helena Arvidsson, Jorge E. Gatica V., Nikolce Tudzarovski, Karl Meinke and Rachael. V Sugars
    Citation: BMC Bioinformatics 2022 23:506
  7. Multiple processes impact the probability of retention of individual genes following whole genome duplication (WGD) events. In analyzing two consecutive whole genome duplication events that occurred in the lin...

    Authors: C. Nicholas Henry, Kathryn Piper, Amanda E. Wilson, John L. Miraszek, Claire S. Probst, Yuying Rong and David A. Liberles
    Citation: BMC Bioinformatics 2022 23:505
  8. Identifying polymorphism clades on phylogenetic trees could help detect punctual mutations that are associated with viral functions. With visualization tools coloring the tree, it is easy to visually find clad...

    Authors: Chengyang Ji, Na Han, Yexiao Cheng, Jingzhe Shang, Shenghui Weng, Rong Yang, Hang-Yu Zhou and Aiping Wu
    Citation: BMC Bioinformatics 2022 23:504
  9. Building biological networks with a certain function is a challenge in systems biology. For the functionality of small (less than ten nodes) biological networks, most methods are implemented by exhausting all ...

    Authors: Guo Mao, Ruigeng Zeng, Jintao Peng, Ke Zuo, Zhengbin Pang and Jie Liu
    Citation: BMC Bioinformatics 2022 23:503
  10. As genotype databases increase in size, so too do the number of detectable segments of identity by descent (IBD): segments of the genome where two individuals share an identical copy of one of their two parental ...

    Authors: Keith Noto and Luong Ruiz
    Citation: BMC Bioinformatics 2022 23:502
  11. Automatic and accurate recognition of various biomedical named entities from literature is an important task of biomedical text mining, which is the foundation of extracting biomedical knowledge from unstructu...

    Authors: Xiangwen Zheng, Haijian Du, Xiaowei Luo, Fan Tong, Wei Song and Dongsheng Zhao
    Citation: BMC Bioinformatics 2022 23:501
  12. Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and mo...

    Authors: Adrien Vidal, Franck Gauthier, Willy Rodrigez, Nadège Guiglielmoni, Damien Leroux, Nicolas Chevrolier, Sylvain Jasson, Elise Tourrette, Olivier C. Martin and Matthieu Falque
    Citation: BMC Bioinformatics 2022 23:499
  13. Genome-wide association studies (GWAS) are a powerful method to detect associations between variants and phenotypes. A GWAS requires several complex computations with large data sets, and many steps may need t...

    Authors: Jean-Tristan Brandenburg, Lindsay Clark, Gerrit Botha, Sumir Panji, Shakuntala Baichoo, Christopher Fields and Scott Hazelhurst
    Citation: BMC Bioinformatics 2022 23:498
  14. Classification of different cancer types is an essential step in designing a decision support model for early cancer predictions. Using various machine learning (ML) techniques with ensemble learning is one su...

    Authors: Abdu Rehaman Pasha Syed, Rahul Anbalagan, Anagha S. Setlur, Chandrashekar Karunakaran, Jyoti Shetty, Jitendra Kumar and Vidya Niranjan
    Citation: BMC Bioinformatics 2022 23:496
  15. Sequencing is the key method to study the impact of short RNAs, which include micro RNAs, tRNA-derived RNAs, and piwi-interacting RNA, among others. The first step to make use of these reads is to map them to ...

    Authors: Matthias Zytnicki and Christine Gaspin
    Citation: BMC Bioinformatics 2022 23:495
  16. Accurate annotation of protein function is the key to understanding life at the molecular level and has great implications for biomedicine and pharmaceuticals. The rapid developments of high-throughput technol...

    Authors: Sai Hu, Yingchun Luo, Zhihong Zhang, Huijun Xiong, Wei Yan, Meiping Jiang and Bihai Zhao
    Citation: BMC Bioinformatics 2022 23:493
  17. Clinical studies show that microorganisms are closely related to human health, and the discovery of potential associations between microbes and drugs will facilitate drug research and development. However, at ...

    Authors: Yaqin Tan, Juan Zou, Linai Kuang, Xiangyi Wang, Bin Zeng, Zhen Zhang and Lei Wang
    Citation: BMC Bioinformatics 2022 23:492
  18. Genomics and virology are unquestionably important, but complex, domains being investigated by a large number of scientists. The need to facilitate and support work within these domains requires sharing of dat...

    Authors: Anna Bernasconi, Giancarlo Guizzardi, Oscar Pastor and Veda C. Storey
    Citation: BMC Bioinformatics 2022 23(Suppl 11):491

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

  19. Decisions in healthcare usually rely on the goodness and completeness of data that could be coupled with heuristics to improve the decision process itself. However, this is often an incomplete process. Structu...

    Authors: Giuseppe Sgroi, Giulia Russo, Anna Maglia, Giuseppe Catanuto, Peter Barry, Andreas Karakatsanis, Nicola Rocco and Francesco Pappalardo
    Citation: BMC Bioinformatics 2022 22(Suppl 14):631

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

  20. Identification of deleterious genetic variants using DNA sequencing data relies on increasingly detailed filtering strategies to isolate the small subset of variants that are more likely to underlie a disease ...

    Authors: Thomas J. Nicholas, Michael J. Cormier and Aaron R. Quinlan
    Citation: BMC Bioinformatics 2022 23:490
  21. RNA-seq has become a standard technology to quantify mRNA. The measured values usually vary by several orders of magnitude, and while the detection of differences at high values is statistically well grounded,...

    Authors: Igor V. Deyneko, Orkhan N. Mustafaev, Alexander А. Tyurin, Ksenya V. Zhukova, Alexander Varzari and Irina V. Goldenkova-Pavlova
    Citation: BMC Bioinformatics 2022 23:488
  22. Cuproptosis, a newly discovered mode of cell death, has been less studied in hepatocellular carcinoma (HCC). Exploring the molecular characteristics of different subtypes of HCC based on cuproptosis-related ge...

    Authors: Li Zhang, Jingwei Xu, Xiufeng Chu, Hongqiao Zhang, Xueyuan Yao, Jian Zhang and Yanwei Guo
    Citation: BMC Bioinformatics 2022 23:485
  23. Mass screening programs for cervical cancer prevention in the Nordic countries have strongly reduced cancer incidence and mortality at the population level. An alternative to the current mass screening is a mo...

    Authors: Geir Severin R. E. Langberg, Mikal Stapnes, Jan F. Nygård, Mari Nygård, Markus Grasmair and Valeriya Naumova
    Citation: BMC Bioinformatics 2022 23(Suppl 12):484

    This article is part of a Supplement: Volume 23 Supplement 12

  24. Microorganisms in the human body have a great impact on human health. Therefore, mastering the potential relationship between microorganisms and diseases is helpful to understand the pathogenesis of diseases a...

    Authors: Jian Guan, Zhao Gong Zhang, Yong Liu and Meng Wang
    Citation: BMC Bioinformatics 2022 23:483
  25. Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is ident...

    Authors: Michael J. Cormier, Brent S. Pedersen, Pinar Bayrak-Toydemir and Aaron R. Quinlan
    Citation: BMC Bioinformatics 2022 23:482
  26. Enhancers are small regions of DNA that bind to proteins, which enhance the transcription of genes. The enhancer may be located upstream or downstream of the gene. It is not necessarily close to the gene to be...

    Authors: Meng Liao, Jian-ping Zhao, Jing Tian and Chun-Hou Zheng
    Citation: BMC Bioinformatics 2022 23:480
  27. A high recurrence rate has always been a serious problem for treatment of hepatocellular carcinoma (HCC). Exploring predictors of postoperative and posttransplantation recurrence in patients with HCC can guide...

    Authors: Xuanfeng Zhang, Dong Zhang, Xuefeng Bu, Xinhui Zhang and Long Cui
    Citation: BMC Bioinformatics 2022 23:479
  28. Variable selection is a common statistical approach to identifying genes associated with clinical outcomes of scientific interest. There are thousands of genes in genomic studies, while only a limited number o...

    Authors: Peixin Tian, Yiqian Hu, Zhonghua Liu and Yan Dora Zhang
    Citation: BMC Bioinformatics 2022 23:478
  29. The rapid evolution of image processing equipment and techniques ensures the development of novel picture analysis methodologies. One of the most powerful yet computationally possible algebraic techniques for ...

    Authors: Abbas Rammal, Rabih Assaf, Alban Goupil, Mohammad Kacim and Valeriu Vrabie
    Citation: BMC Bioinformatics 2022 23:476
  30. Single marker analysis (SMA) with linear mixed models for genome wide association studies has uncovered the contribution of genetic variants to many observed phenotypes. However, SMA has weak false discovery c...

    Authors: Jacob Williams, Marco A. R. Ferreira and Tieming Ji
    Citation: BMC Bioinformatics 2022 23:475
  31. Huge amounts of molecular interaction data are continuously produced and stored in public databases. Although many bioinformatics tools have been proposed in the literature for their analysis, based on their m...

    Authors: Lorenzo Di Rocco, Umberto Ferraro Petrillo and Simona E. Rombo
    Citation: BMC Bioinformatics 2022 23:474
  32. Personalized therapy has been at the forefront of cancer care, making cancer treatment more effective. Since cancer patients respond individually to drug therapy, predicting the sensitivity of each patient to ...

    Authors: Zhenlei Li, Ya Huang, Qingrun Li, Yidi Sun, Chen Li, Jiarui Wu, Haoran Zheng and Rong Zeng
    Citation: BMC Bioinformatics 2022 23:473
  33. Precision medicine is a promising approach that has revolutionized disease prevention and individualized treatment. The DELFOS oracle is a model-driven genomics platform that aids clinicians in identifying rel...

    Authors: Alberto García S., Mireia Costa, Ana Leon and Oscar Pastor
    Citation: BMC Bioinformatics 2022 23(Suppl 11):472

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

  34. Disseminated intravascular coagulation (DIC) is a complex, life-threatening syndrome associated with the end-stage of different coagulation disorders. Early prediction of the risk of DIC development is an urge...

    Authors: Hao Yang, Jiaxi Li, Siru Liu, Mengjiao Zhang and Jialin Liu
    Citation: BMC Bioinformatics 2022 23:471
  35. The expression changes of some proteins are associated with cancer progression, and can be used as biomarkers in cancer diagnosis. Automated systems have been frequently applied in the large-scale detection of...

    Authors: Zhen-Zhen Xue, Cheng Li, Zhuo-Ming Luo, Shan-Shan Wang and Ying-Ying Xu
    Citation: BMC Bioinformatics 2022 23:470
  36. Early detection of cancers has been much explored due to its paramount importance in biomedical fields. Among different types of data used to answer this biological question, studies based on T cell receptors ...

    Authors: Younghoon Kim, Tao Wang, Danyi Xiong, Xinlei Wang and Seongoh Park
    Citation: BMC Bioinformatics 2022 23:469
  37. In most parts of the world, especially in underdeveloped countries, acquired immunodeficiency syndrome (AIDS) still remains a major cause of death, disability, and unfavorable economic outcomes. This has neces...

    Authors: Emmanuel Onah, Philip F. Uzor, Ikenna Calvin Ugwoke, Jude Uche Eze, Sunday Tochukwu Ugwuanyi, Ifeanyi Richard Chukwudi and Akachukwu Ibezim
    Citation: BMC Bioinformatics 2022 23:466

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