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  1. 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
    Content type: Research Published on:

  2. 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
    Content type: Research Published on:

  3. 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
    Content type: Research Published on:

  5. 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
    Content type: Software Published on:

  6. 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
    Content type: Software Published on:

  8. 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
    Content type: Research Published on:

  9. 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
    Content type: Research Published on:

  11. 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
    Content type: Research Published on:

  12. 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
    Content type: Research Published on:

  13. 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
    Content type: Research Published on:

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

  14. 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
    Content type: Research Published on:

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

  15. 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
    Content type: Software Published on:

  17. 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
    Content type: Software Published on:

  20. 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
    Content type: Research Published on:

  21. 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
    Content type: Methodology Published on:

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

  22. 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
    Content type: Research Published on:

  23. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  26. 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
    Content type: Research Published on:

  27. 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
    Content type: Research Published on:

  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
    Content type: Research Published on:

  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
    Content type: Research Published on:

  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
    Content type: Software Published on:

  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
    Content type: Software Published on:

  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
    Content type: Research Published on:

    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
    Content type: Research Published on:

  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
    Content type: Research Published on:

  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
    Content type: Research Published on:

  39. 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
    Content type: Research Published on:

  40. Whole genome sequencing using the long-read Oxford Nanopore Technologies (ONT) MinION sequencer provides a cost-effective option for structural variant (SV) detection in clinical applications. Despite the adva...

    Authors: Yekai Zhou, Amy Wing-Sze Leung, Syed Shakeel Ahmed, Tak-Wah Lam and Ruibang Luo
    Citation: BMC Bioinformatics 2022 23:465
    Content type: Software Published on:

  41. In recent years, huge improvements have been made in the context of sequencing genomic data under what is called Next Generation Sequencing (NGS). However, the DNA reads generated by current NGS platforms are ...

    Authors: Roberto R. Expósito, Marco Martínez-Sánchez and Juan Touriño
    Citation: BMC Bioinformatics 2022 23:464
    Content type: Software Published on:

  42. Chromosome conformation capture and its derivatives have provided substantial genetic data for understanding how chromatin self-organizes. These techniques have identified regions of high intrasequence interac...

    Authors: Sean Higgins, Victor Akpokiro, Allen Westcott and Oluwatosin Oluwadare
    Citation: BMC Bioinformatics 2022 23:463
    Content type: Software Published on:

  44. Adaptor proteins play a key role in intercellular signal transduction, and dysfunctional adaptor proteins result in diseases. Understanding its structure is the first step to tackling the associated conditions...

    Authors: Sylwan Rahardja, Mou Wang, Binh P. Nguyen, Pasi Fränti and Susanto Rahardja
    Citation: BMC Bioinformatics 2022 23:461
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2023 24:15

  45. Single-cell RNA sequencing (scRNA-seq) technology has contributed significantly to diverse research areas in biology, from cancer to development. Since scRNA-seq data is high-dimensional, a common strategy is ...

    Authors: Hui Li, Davis J. McCarthy, Heejung Shim and Susan Wei
    Citation: BMC Bioinformatics 2022 23:460
    Content type: Research Published on:

  48. Cancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon b...

    Authors: Ta-Chun Liu, Peter N. Kalugin, Jennifer L. Wilding and Walter F. Bodmer
    Citation: BMC Bioinformatics 2022 23:457
    Content type: Research Published on:

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