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  1. The human body is inhabited by a diverse community of commensal non-pathogenic bacteria, many of which are essential for our health. By contrast, pathogenic bacteria have the ability to invade their hosts and ...

    Authors: Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein and Michal Ziv-Ukelson
    Citation: BMC Bioinformatics 2022 23:253
  2. Hepatocellular carcinoma (HCC) is a primary malignant tumor that accounts for approximately 90% of all cases of primary liver cancer worldwide. Microtubule alterations may contribute to the broad spectrum of r...

    Authors: Gang Chi, Jin-Hong Pei and Xue-Qing Li
    Citation: BMC Bioinformatics 2022 23:252
  3. Glioma is the most aggressive and dangerous primary brain tumor with a survival time of less than 14 months. Segmentation of tumors is a necessary task in the image processing of the gliomas and is important f...

    Authors: Zeeshan Shaukat, Qurat ul Ain Farooq, Shanshan Tu, Chuangbai Xiao and Saqib Ali
    Citation: BMC Bioinformatics 2022 23:251
  4. At present, the diagnostic ability of hepatocellular carcinoma (HCC) based on serum alpha-fetoprotein level is limited. Finding markers that can effectively distinguish cancer and non-cancerous tissues is impo...

    Authors: Binglin Cheng, Peitao Zhou and Yuhan Chen
    Citation: BMC Bioinformatics 2022 23:248
  5. Human protein kinases, the key players in phosphoryl signal transduction, have been actively investigated as drug targets for complex diseases such as cancer, immune disorders, and Alzheimer’s disease, with mo...

    Authors: Xiang-Yu Lin, Yu-Wei Huang, You-Wei Fan, Yun-Ti Chen, Nikhil Pathak, Yen-Chao Hsu and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2022 23(Suppl 4):247

    This article is part of a Supplement: Volume 23 Supplement 4

  6. De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read...

    Authors: Vladimir Nikolić, Amirhossein Afshinfard, Justin Chu, Johnathan Wong, Lauren Coombe, Ka Ming Nip, René L. Warren and Inanç Birol
    Citation: BMC Bioinformatics 2022 23:246
  7. Drug-target interactions (DTIs) are critical for drug repurposing and elucidation of drug mechanisms, and are manually curated by large databases, such as ChEMBL, BindingDB, DrugBank and DrugTargetCommons. How...

    Authors: Jehad Aldahdooh, Markus Vähä-Koskela, Jing Tang and Ziaurrehman Tanoli
    Citation: BMC Bioinformatics 2022 23:245
  8. There is a growing body of evidence from biological experiments suggesting that microRNAs (miRNAs) play a significant regulatory role in both diverse cellular activities and pathological processes. Exploring m...

    Authors: Guanghui Li, Tao Fang, Yuejin Zhang, Cheng Liang, Qiu Xiao and Jiawei Luo
    Citation: BMC Bioinformatics 2022 23:244
  9. While it has been known that human protein kinases mediate most signal transductions in cells and their dysfunction can result in inflammatory diseases and cancers, it remains a challenge to find effective kin...

    Authors: You-Wei Fan, Wan-Hsin Liu, Yun-Ti Chen, Yen-Chao Hsu, Nikhil Pathak, Yu-Wei Huang and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2022 23(Suppl 4):242

    This article is part of a Supplement: Volume 23 Supplement 4

  10. The biological relevance and accuracy of gene expression data depend on the adequacy of data normalization. This is both due to its role in resolving and accounting for technical variation and errors, and its ...

    Authors: Yusuf Khan, Daniel Hammarström, Stian Ellefsen and Rafi Ahmad
    Citation: BMC Bioinformatics 2022 23:241
  11. This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outpu...

    Authors: Sofia Persson, Christina Larsson, Magnus Simonsson and Patrik Ellström
    Citation: BMC Bioinformatics 2022 23:239
  12. Several computational advances have been achieved in the drug discovery field, promoting the identification of novel drug–target interactions and new leads. However, most of these methodologies have been overl...

    Authors: Nelson R. C. Monteiro, Carlos J. V. Simões, Henrique V. Ávila, Maryam Abbasi, José L. Oliveira and Joel P. Arrais
    Citation: BMC Bioinformatics 2022 23:237
  13. Protein–protein interaction (PPI) plays an important role in regulating cells and signals. Despite the ongoing efforts of the bioassay group, continued incomplete data limits our ability to understand the mole...

    Authors: Xiao-Rui Su, Lun Hu, Zhu-Hong You, Peng-Wei Hu and Bo-Wei Zhao
    Citation: BMC Bioinformatics 2022 23:234
  14. The Open Targets (OT) Platform integrates a wide range of data sources on target-disease associations to facilitate identification of potential therapeutic drug targets to treat human diseases. However, due to...

    Authors: Yingnan Han, Katherine Klinger, Deepak K. Rajpal, Cheng Zhu and Erin Teeple
    Citation: BMC Bioinformatics 2022 23:232
  15. Distinct gene expression patterns within cells are foundational for the diversity of functions and unique characteristics observed in specific contexts, such as human tissues and cell types. Though some biolog...

    Authors: Rebeca Queiroz Figueiredo, Sara Díaz del Ser, Tamara Raschka, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Sarah Mubeen and Daniel Domingo-Fernández
    Citation: BMC Bioinformatics 2022 23:231
  16. Abundant datasets generated from various big science projects on diseases have presented great challenges and opportunities, which contributed to unfolding the complexity of diseases. The discovery of disease-...

    Authors: Yu Zhang, Xiao Chang, Jie Xia, Yanhong Huang, Shaoyan Sun, Luonan Chen and Xiaoping Liu
    Citation: BMC Bioinformatics 2022 23:230
  17. Many wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and acc...

    Authors: Verena E. Kutschera, Marcin Kierczak, Tom van der Valk, Johanna von Seth, Nicolas Dussex, Edana Lord, Marianne Dehasque, David W. G. Stanton, Payam Emami Khoonsari, Björn Nystedt, Love Dalén and David Díez-del-Molino
    Citation: BMC Bioinformatics 2022 23:228
  18. Elucidating cellular metabolism led to many breakthroughs in biotechnology, synthetic biology, and health sciences. To date, deriving metabolic fluxes by 13C tracer experiments is the most prominent approach for ...

    Authors: Kulwadee Thanamit, Franziska Hoerhold, Marcus Oswald and Rainer Koenig
    Citation: BMC Bioinformatics 2022 23:226
  19. An important initial phase of arguably most homology search and alignment methods such as required for genome alignments is seed finding. The seed finding step is crucial to curb the runtime as potential alignmen...

    Authors: Matthis Ebel, Giovanna Migliorelli and Mario Stanke
    Citation: BMC Bioinformatics 2022 23:225
  20. Drug-Drug interactions (DDIs) are a challenging problem in drug research. Drug combination therapy is an effective solution to treat diseases, but it can also cause serious side effects. Therefore, DDIs predic...

    Authors: Changxiang He, Yuru Liu, Hao Li, Hui Zhang, Yaping Mao, Xiaofei Qin, Lele Liu and Xuedian Zhang
    Citation: BMC Bioinformatics 2022 23:224
  21. Precision medicine for cancer treatment relies on an accurate pathological diagnosis. The number of known tumor classes has increased rapidly, and reliance on traditional methods of histopathologic classificat...

    Authors: Quynh T. Tran, Md Zahangir Alom and Brent A. Orr
    Citation: BMC Bioinformatics 2022 23:223
  22. Computer-aided drug design provides an effective method of identifying lead compounds. However, success rates are significantly bottlenecked by the lack of accurate and reliable scoring functions needed to eva...

    Authors: Yu Wang, Zhengxiao Wei and Lei Xi
    Citation: BMC Bioinformatics 2022 23:222
  23. Due to their diverse bioactivity, natural product (NP)s have been developed as commercial products in the pharmaceutical, food and cosmetic sectors as natural compound (NC)s and in the form of extracts. Follow...

    Authors: Seo Hyun Shin, Seung Man Oh, Jung Han Yoon Park, Ki Won Lee and Hee Yang
    Citation: BMC Bioinformatics 2022 23:218
  24. Myocardial infarction can lead to malignant arrhythmia, heart failure, and sudden death. Clinical studies have shown that early identification of and timely intervention for acute MI can significantly reduce m...

    Authors: Ran Liu, Miye Wang, Tao Zheng, Rui Zhang, Nan Li, Zhongxiu Chen, Hongmei Yan and Qingke Shi
    Citation: BMC Bioinformatics 2022 23:217
  25. The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected b...

    Authors: Tristan Dubos, Axel Poulet, Geoffrey Thomson, Emilie Péry, Frédéric Chausse, Christophe Tatout, Sophie Desset, Josien C. van Wolfswinkel and Yannick Jacob
    Citation: BMC Bioinformatics 2022 23:216
  26. Modern sequencing technologies have generated low-cost microbiome survey datasets, across sample sites, conditions, and treatments, on an unprecedented scale and throughput. These datasets often come with a ph...

    Authors: Tiantian Liu, Chao Zhou, Huimin Wang, Hongyu Zhao and Tao Wang
    Citation: BMC Bioinformatics 2022 23:213
  27. Nested and overlapping events are particularly frequent and informative structures in biomedical event extraction. However, state-of-the-art neural models either neglect those structures during learning or use...

    Authors: Kurt Espinosa, Panagiotis Georgiadis, Fenia Christopoulou, Meizhi Ju, Makoto Miwa and Sophia Ananiadou
    Citation: BMC Bioinformatics 2022 23:211
  28. Bioinformatics investigators often gain insights by combining information across multiple and disparate data sets. Merging data from multiple sources frequently results in data sets that are incomplete or cont...

    Authors: Zachary R. McCaw, Hugues Aschard and Hanna Julienne
    Citation: BMC Bioinformatics 2022 23:208
  29. In integrative bioinformatic analyses, it is of great interest to stablish the equivalence between gene or (more in general) feature lists, up to a given level and in terms of their annotations in the Gene Ont...

    Authors: Pablo Flores, Miquel Salicrú, Alex Sánchez-Pla and Jordi Ocaña
    Citation: BMC Bioinformatics 2022 23:207
  30. The zone adjacent to a transcription start site (TSS), namely, the promoter, is primarily involved in the process of DNA transcription initiation and regulation. As a result, proper promoter identification is ...

    Authors: Ying Wang, Qinke Peng, Xu Mou, Xinyuan Wang, Haozhou Li, Tian Han, Zhao Sun and Xiao Wang
    Citation: BMC Bioinformatics 2022 23(Suppl 1):206

    This article is part of a Supplement: Volume 23 Supplement 1

  31. Cluster algorithms are gaining in popularity in biomedical research due to their compelling ability to identify discrete subgroups in data, and their increasing accessibility in mainstream software. While guid...

    Authors: Edwin S. Dalmaijer, Camilla L. Nord and Duncan E. Astle
    Citation: BMC Bioinformatics 2022 23:205
  32. Molecular gene signatures are useful tools to characterize the physiological state of cell populations, but most have developed under a narrow range of conditions and cell types and are often restricted to a s...

    Authors: Laura Puente-Santamaría, Lucia Sanchez-Gonzalez, Ricardo Ramos-Ruiz and Luis del Peso
    Citation: BMC Bioinformatics 2022 23:204

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