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  1. Using visual, biological, and electronic health records data as the sole input source, pretrained convolutional neural networks and conventional machine learning methods have been heavily employed for the iden...

    Authors: Mpho Mokoatle, Vukosi Marivate, Darlington Mapiye, Riana Bornman and Vanessa. M. Hayes
    Citation: BMC Bioinformatics 2023 24:112
  2. Antibiotic resistance has become a global concern. Vancomycin is known as the last line of antibiotics, but its treatment index is narrow. Therefore, clinical dosing decisions must be made with the utmost care...

    Authors: Wen-Hsien Ho, Tian-Hsiang Huang, Yenming J. Chen, Lang-Yin Zeng, Fen-Fen Liao and Yeong-Cheng Liou
    Citation: BMC Bioinformatics 2023 22(Suppl 5):637

    This article is part of a Supplement: Volume 22 Supplement 5

  3. Subcellular localization of messenger RNA (mRNAs) plays a pivotal role in the regulation of gene expression, cell migration as well as in cellular adaptation. Experiment techniques for pinpointing the subcellu...

    Authors: Saleh Musleh, Mohammad Tariqul Islam, Rizwan Qureshi, Nehad M. Alajez and Tanvir Alam
    Citation: BMC Bioinformatics 2023 24:109

    The Correction to this article has been published in BMC Bioinformatics 2023 24:156

  4. The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used...

    Authors: Ivo Henrique Provensi Vieira, Eduardo Buganemi Botelho, Thales Junior de Souza Gomes, Roger Kist, Rafael Andrade Caceres and Fernando Berton Zanchi
    Citation: BMC Bioinformatics 2023 24:107
  5. Renal carcinoma is a common malignant tumor of the urinary system. Advanced renal carcinoma has a low 5-year survival rate and a poor prognosis. More and more studies have confirmed that chromatin regulators (...

    Authors: Puyu Liu, Jihang Luo, Na Tan, Chengfang Li, Jieyu Xu and Xiaorong Yang
    Citation: BMC Bioinformatics 2023 24:104
  6. Colon cancer (CC) is a common tumor that causes significant harm to human health. Bacteria play a vital role in cancer biology, particularly the biology of CC. Genes related to bacterial response were seldom u...

    Authors: Zuming Xiong, Wenxin Li, Xiangrong Luo, Yirong Lin, Wei Huang and Sen Zhang
    Citation: BMC Bioinformatics 2023 24:103
  7. Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to id...

    Authors: Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl A. Keller, Elisabeth F. Heuston, Stacie M. Anderson, Martha Kirby, David Bodine, Yu Zhang and Ross C. Hardison
    Citation: BMC Bioinformatics 2023 24:102
  8. In single-cell transcriptomics and other omics technologies, large fractions of missing values commonly occur. Researchers often either consider only those features that were measured for each instance of thei...

    Authors: Yannis Schumann, Julia E. Neumann and Philipp Neumann
    Citation: BMC Bioinformatics 2023 24:101
  9. Presenting with a poor prognosis, gastric cancer (GC) remains one of the leading causes of disease and death worldwide. Long non-coding RNAs (lncRNAs) regulate tumor formation and have been long used to predic...

    Authors: Bin Zhao, Fang Fang, Yiqun Liao, Yuji Chen, Fei Wang, Yichao Ma, Chen Wei, Jiahao Zhao, Hao Ji, Daorong Wang and Dong Tang
    Citation: BMC Bioinformatics 2023 24:100
  10. Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit...

    Authors: Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti and Alex Graudenzi
    Citation: BMC Bioinformatics 2023 24:99
  11. Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms...

    Authors: Tim Dunn, David Blaauw, Reetuparna Das and Satish Narayanasamy
    Citation: BMC Bioinformatics 2023 24:98
  12. The research of biomarker-treatment interactions is commonly investigated in randomized clinical trials (RCT) for improving medicine precision. The hierarchical interaction constraint states that an interactio...

    Authors: Shaima Belhechmi, Gwénaël Le Teuff, Riccardo De Bin, Federico Rotolo and Stefan Michiels
    Citation: BMC Bioinformatics 2023 24:96
  13. Understanding the role and function of genetic variants is extremely important when analyzing and interpreting a myriad of human disease processes. For cancer in general, cell-specific genetic variants are ubi...

    Authors: Nahla AlKurabi, Ahad AlGahtani and Turki M. Sobahy
    Citation: BMC Bioinformatics 2023 24:95
  14. High-throughput Proteomics has been accelerated by (tandem) mass spectrometry. However, the slow speed of mass spectra analysis prevents the analysis results from being up-to-date. Tandem mass spectrometry dat...

    Authors: Yoonsung Joh, Kangbae Lee, Hyunwoo Kim and Heejin Park
    Citation: BMC Bioinformatics 2023 24:94
  15. In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has ...

    Authors: Luísa C. de Souza, Karolayne S. Azevedo, Jackson G. de Souza, Raquel de M. Barbosa and Marcelo A. C. Fernandes
    Citation: BMC Bioinformatics 2023 24:92
  16. Renal cell carcinoma (RCC), one of the top 10 causes of cancer death, is responsible for more than 90% of all cases of primary renal cancer worldwide. Follicular dendritic cell-secreted protein (FDC-SP) specif...

    Authors: Fan Chang, Jiang-Hui Zhang, Wen-Song Wu, Shuai Tang, Zheng lv and Fang-Min Chen
    Citation: BMC Bioinformatics 2023 24:91
  17. Hepatocellular carcinoma (HCC) has a high incidence and mortality worldwide, which seriously threatens people's physical and mental health. Coagulation is closely related to the occurrence and development of H...

    Authors: Wan-Xia Yang, Hong-Wei Gao, Jia-Bo Cui, An-An Zhang, Fang-Fang Wang, Jian-Qin Xie, Ming-Hua Lu and Chong-Ge You
    Citation: BMC Bioinformatics 2023 24:89
  18. Personalized oncology represents a shift in cancer treatment from conventional methods to target specific therapies where the decisions are made based on the patient specific tumor profile. Selection of the op...

    Authors: Mirjam Figaschewski, Bilge Sürün, Thorsten Tiede and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2023 24:88
  19. Variation in omics data due to intrinsic biological stochasticity is often viewed as a challenging and undesirable feature of complex systems analyses. In fact, numerous statistical methods are utilized to min...

    Authors: Katherine F. Steward, Mohammed Refai, William E. Dyer, Valérie Copié, Jennifer Lachowiec and Brian Bothner
    Citation: BMC Bioinformatics 2023 24:87
  20. We developed a novel approach to minimize batch effects when assigning samples to batches. Our algorithm selects a batch allocation, among all possible ways of assigning samples to batches, that minimizes diff...

    Authors: Patrick M. Carry, Tim Vigers, Lauren A. Vanderlinden, Carson Keeter, Fran Dong, Teresa Buckner, Elizabeth Litkowski, Ivana Yang, Jill M. Norris and Katerina Kechris
    Citation: BMC Bioinformatics 2023 24:86
  21. Recent studies have indicated that a special class of long non-coding RNAs (lncRNAs), namely Transcribed-Ultraconservative Regions are transcribed from specific DNA regions (T-UCRs), 100 ...

    Authors: Angelo Ciaramella, Emanuel Di Nardo, Daniela Terracciano, Lia Conte, Ferdinando Febbraio and Amelia Cimmino
    Citation: BMC Bioinformatics 2023 23(Suppl 6):569

    This article is part of a Supplement: Volume 23 Supplement 6

  22. A cell exhibits a variety of responses to internal and external cues. These responses are possible, in part, due to the presence of an elaborate gene regulatory network (GRN) in every single cell. In the past ...

    Authors: Lior I. Shachaf, Elijah Roberts, Patrick Cahan and Jie Xiao
    Citation: BMC Bioinformatics 2023 24:84
  23. Massive amounts of data are produced by combining next-generation sequencing with complex biochemistry techniques to characterize regulatory genomics profiles, such as protein–DNA interaction and chromatin acc...

    Authors: Zhijian Li, Chao-Chung Kuo, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo Gade Gusmao, Manuel Allhoff, Martin Manolov, Martin Zenke and Ivan G. Costa
    Citation: BMC Bioinformatics 2023 24:79
  24. Applying deep learning to digital histopathology is hindered by the scarcity of manually annotated datasets. While data augmentation can ameliorate this obstacle, its methods are far from standardized. Our aim...

    Authors: Yusra A. Ameen, Dalia M. Badary, Ahmad Elbadry I. Abonnoor, Khaled F. Hussain and Adel A. Sewisy
    Citation: BMC Bioinformatics 2023 24:75
  25. Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses....

    Authors: Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows and Harriet Alexander
    Citation: BMC Bioinformatics 2023 24:74

    The Correction to this article has been published in BMC Bioinformatics 2023 24:185

  26. DNA mismatch repair deficiency (dMMR) testing is crucial for detection of microsatellite unstable (MSI) tumors. MSI is detected by aberrant indel length distributions of microsatellite markers, either by visua...

    Authors: Koen Swaerts, Franceska Dedeurwaerdere, Dieter De Smet, Peter De Jaeger and Geert A. Martens
    Citation: BMC Bioinformatics 2023 24:73
  27. Two main subclasses of macrophages are found in almost all solid tissues: embryo-derived resident tissue macrophages and bone marrow-derived infiltrated macrophages. These macrophage subtypes show transcriptio...

    Authors: Xiangjun Ji, Junwei Cai, Lixin Liang, Tieliu Shi and Jinghua Liu
    Citation: BMC Bioinformatics 2023 24:72
  28. Allosteric transcription factor (aTF) based biosensors can be used to engineer genetic circuits for a wide range of applications. The literature and online databases contain hundreds of experimentally validate...

    Authors: Jonathan Tellechea-Luzardo, Hèctor Martín Lázaro, Raúl Moreno López and Pablo Carbonell
    Citation: BMC Bioinformatics 2023 24:71
  29. B cell receptor (BCR) genes exposed to an antigen undergo somatic hypermutations and Darwinian antigen selection, generating a large BCR-antibody diversity. This process, known as B cell affinity maturation, i...

    Authors: Nika Abdollahi, Lucile Jeusset, Anne de Septenville, Frederic Davi and Juliana Silva Bernardes
    Citation: BMC Bioinformatics 2023 24:70
  30. Information provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and their context. Sequence alignment is a bioinformatics approach to identify...

    Authors: Antonio Benítez-Hidalgo, José F. Aldana-Montes, Ismael Navas-Delgado and María del Mar Roldán-García
    Citation: BMC Bioinformatics 2023 24:69
  31. Although research on non-coding RNAs (ncRNAs) is a hot topic in life sciences, the functions of numerous ncRNAs remain unclear. In recent years, researchers have found that ncRNAs of the same family have simil...

    Authors: Kai Chen, Xiaodong Zhu, Jiahao Wang, Lei Hao, Zhen Liu and Yuanning Liu
    Citation: BMC Bioinformatics 2023 24:68
  32. Streptococcus pneumoniae (Pneumococcus) has remained a leading cause of fatal infections such as pneumonia, meningitis, and sepsis. Moreover, this pathogen plays a major role in bacterial co-infection in patients...

    Authors: Mona Shafaghi, Zohreh Bahadori, Hamid Madanchi, Mohammad Mehdi Ranjbar, Ali Akbar Shabani and Seyed Fazlollah Mousavi
    Citation: BMC Bioinformatics 2023 24:67
  33. Acute oral toxicity of drug candidates can lead to drug development failure; thus, predicting the acute oral toxicity of small compounds is important for successful drug development. However, evaluation of the...

    Authors: Jae Yong Ryu, Woo Dae Jang, Jidon Jang and Kwang-Seok Oh
    Citation: BMC Bioinformatics 2023 24:66
  34. It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus...

    Authors: Hamid Motamedi, Marzie Mahdizade Ari, Mohsen Shahlaei, Sajad Moradi, Parisa Farhadikia, Amirhoushang Alvandi and Ramin Abiri
    Citation: BMC Bioinformatics 2023 24:65

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