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  2. 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
    Content type: Research Published on:

  3. 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
    Content type: Research Published on:

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

  4. 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
    Content type: Research Published on:

  5. 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
    Content type: Research Published on:

  6. 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
    Content type: Research Published on:

  7. 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
    Content type: Research Published on:

  8. 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
    Content type: Research Published on:

  9. 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
    Content type: Research Published on:

  10. 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
    Content type: Research Published on:

  11. 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
    Content type: Research Published on:

  12. 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
    Content type: Research Published on:

  15. Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD f...

    Authors: Sungyoung Lee, Choong-Hyun Sun, Heejun Jang, Daeyoon Kim, Sung-Soo Yoon, Youngil Koh, Seung Chan Na, Sung Im Cho, Man Jin Kim, Moon-Woo Seong, Ja Min Byun and Hongseok Yun
    Citation: BMC Bioinformatics 2023 24:62
    Content type: Research Published on:

  16. Current clinical routines rely more and more on “omics” data such as flow cytometry data from host and microbiota. Cohorts variability in addition to patients’ heterogeneity and huge dimensions make it difficu...

    Authors: Elie-Julien El Hachem, Nataliya Sokolovska and Hedi Soula
    Citation: BMC Bioinformatics 2023 24:61
    Content type: Research Published on:

  17. Cell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these netwo...

    Authors: Malik Yousef, Fatma Ozdemir, Amhar Jaber, Jens Allmer and Burcu Bakir-Gungor
    Citation: BMC Bioinformatics 2023 24:60
    Content type: Research article Published on:

  20. The growing amount of high dimensional biomolecular data has spawned new statistical and computational models for risk prediction and disease classification. Yet, many of these methods do not yield biologicall...

    Authors: Brian Kwan, Tobias Fuhrer, Daniel Montemayor, Jeffery C. Fink, Jiang He, Chi-yuan Hsu, Karen Messer, Robert G. Nelson, Minya Pu, Ana C. Ricardo, Hernan Rincon-Choles, Vallabh O. Shah, Hongping Ye, Jing Zhang, Kumar Sharma and Loki Natarajan
    Citation: BMC Bioinformatics 2023 24:57
    Content type: Research Published on:

  21. Sudden sensorineural hearing loss is a common and frequently occurring condition in otolaryngology. Existing studies have shown that sudden sensorineural hearing loss is closely associated with mutations in ge...

    Authors: Xiao Liu, Li Teng, Wenqi Zuo, Shixun Zhong, Yuqiao Xu and Jing Sun
    Citation: BMC Bioinformatics 2023 24:56
    Content type: Research Published on:

  22. The advance in single-cell RNA sequencing technology has enhanced the analysis of cell development by profiling heterogeneous cells in individual cell resolution. In recent years, many trajectory inference met...

    Authors: Yifan Zhang, Duc Tran, Tin Nguyen, Sergiu M. Dascalu and Frederick C. Harris Jr.
    Citation: BMC Bioinformatics 2023 24:55
    Content type: Research Published on:

  23. Invasion and metastasis of hepatocellular carcinoma (HCC) is still an important reason for poor prognosis. LincRNA ZNF529-AS1 is a recently identified tumour-associated molecule that is differentially expresse...

    Authors: Yang Ma, Wan-liang Sun, Shuo Shuo Ma, Guanru Zhao, Zhong Liu, Zheng Lu and Dengyong Zhang
    Citation: BMC Bioinformatics 2023 24:54
    Content type: Research Published on:

  24. Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing o...

    Authors: Anna-Maria Liebhoff, Kevin Menden, Alena Laschtowitz, Andre Franke, Christoph Schramm and Stefan Bonn
    Citation: BMC Bioinformatics 2023 24:53
    Content type: Research Published on:

  25. Due to the high resource consumption of introducing a new drug, drug repurposing plays an essential role in drug discovery. To do this, researchers examine the current drug-target interaction (DTI) to predict ...

    Authors: S. Morteza Hashemi, Arash Zabihian, Mohsen Hooshmand and Sajjad Gharaghani
    Citation: BMC Bioinformatics 2023 24:52
    Content type: Research Published on:

  27. Mitochondrial respiration is central to cellular and organismal health in eukaryotes. In baker’s yeast, however, respiration is dispensable under fermentation conditions. Because yeast are tolerant of this mit...

    Authors: Christopher J. Nunn, Eugene Klyshko and Sidhartha Goyal
    Citation: BMC Bioinformatics 2023 24:50
    Content type: Research Published on:

  28. A wide range of tools are available for the detection of copy number variants (CNVs) from whole-genome sequencing (WGS) data. However, none of them focus on clinically-relevant CNVs, such as those that are ass...

    Authors: Mikhail Gudkov, Loïc Thibaut, Matloob Khushi, Gillian M. Blue, David S. Winlaw, Sally L. Dunwoodie and Eleni Giannoulatou
    Citation: BMC Bioinformatics 2023 24:49
    Content type: Software Published on:

  31. Finding a globally optimal Bayesian Network using exhaustive search is a problem with super-exponential complexity, which severely restricts the number of variables that can feasibly be included. We implement ...

    Authors: Nand Sharma and Joshua Millstein
    Citation: BMC Bioinformatics 2023 24:46
    Content type: Research Published on:

  32. Recent years have seen a surge of novel neural network architectures for the integration of multi-omics data for prediction. Most of the architectures include either encoders alone or encoders and decoders, i....

    Authors: Tony Hauptmann and Stefan Kramer
    Citation: BMC Bioinformatics 2023 24:45
    Content type: Research Published on:

  33. XRCC4 is a NHEJ factor identified recently that plays a vital role in repairing DNA double-stranded breaks. Studies have reported the associations between abnormal expression of XRCC4 and tumor susceptibility ...

    Authors: Yang Yu, Yanyan Sun, Zhaoxian Li, Jiang Li and Dazhi Tian
    Citation: BMC Bioinformatics 2023 24:44
    Content type: Research Published on:

  34. It remains an important challenge to predict the functional consequences or clinical impacts of genetic variants in human diseases, such as cancer. An increasing number of genetic variants in cancer have been ...

    Authors: Zilin Ren, Quan Li, Kajia Cao, Marilyn M. Li, Yunyun Zhou and Kai Wang
    Citation: BMC Bioinformatics 2023 24:43
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2023 23:572

  36. Protein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signa...

    Authors: Pawel Pratyush, Suresh Pokharel, Hiroto Saigo and Dukka B. KC
    Citation: BMC Bioinformatics 2023 24:41
    Content type: Research Published on:

  37. Distance functions are fundamental for evaluating the differences between gene expression profiles. Such a function would output a low value if the profiles are strongly correlated—either negatively or positiv...

    Authors: Jiaxing Chen, Yen Kaow Ng, Lu Lin, Xianglilan Zhang and Shuaicheng Li
    Citation: BMC Bioinformatics 2023 24:40
    Content type: Methodology Published on:

    The Correction to this article has been published in BMC Bioinformatics 2023 23:571

  38. Lung cancer is the leading cause of cancer-related deaths worldwide. The majority of lung cancers are non-small cell lung cancer (NSCLC), accounting for approximately 85% of all lung cancer types. The Cox prop...

    Authors: Seungwon Oh, Sae-Ryung Kang, In-Jae Oh and Min-Soo Kim
    Citation: BMC Bioinformatics 2023 24:39
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2023 23:573

  39. The experimental verification of a drug discovery process is expensive and time-consuming. Therefore, efficiently and effectively identifying drug–target interactions (DTIs) has been the focus of research. At ...

    Authors: Lingzhi Hu, Chengzhou Fu, Zhonglu Ren, Yongming Cai, Jin Yang, Siwen Xu, Wenhua Xu and Deyu Tang
    Citation: BMC Bioinformatics 2023 24:38
    Content type: Research Published on:

  41. CRISPR screens provide large-scale assessment of cellular gene functions. Pooled libraries typically consist of several single guide RNAs (sgRNAs) per gene, for a large number of genes, which are transduced in...

    Authors: Renaud L. M. Tissier, Janne J. M. van Schie, Rob M. F. Wolthuis, Job de Lange and Renée de Menezes
    Citation: BMC Bioinformatics 2023 24:36
    Content type: Research Published on:

  42. As new drug targets, human microbes are proven to be closely related to human health. Effective computational methods for inferring potential microbe-drug associations can provide a useful complement to conven...

    Authors: Qing Ma, Yaqin Tan and Lei Wang
    Citation: BMC Bioinformatics 2023 24:35
    Content type: Research Published on:

  43. As one of the fundamental problems in bioinformatics, the double digest problem (DDP) focuses on reordering genetic fragments in a proper sequence. Although many algorithms for dealing with the DDP problem wer...

    Authors: Jingwen Suo, Lize Gu, Xingyu Yan, Sijia Yang, Xiaoya Hu and Licheng Wang
    Citation: BMC Bioinformatics 2023 24:34
    Content type: Research Published on:

  44. Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique f...

    Authors: Qun-ting Lin, Wei Yang, Xin Zhang, Qi-gang Li, Yong-feng Liu, Qin Yan and Lei Sun
    Citation: BMC Bioinformatics 2023 24:33
    Content type: Research Published on:

  45. In the global effort to discover biomarkers for cancer prognosis, prediction tools have become essential resources. TCR (T cell receptor) repertoires contain important features that differentiate healthy contr...

    Authors: Dhiego Souto Andrade, Patrick Terrematte, César Rennó-Costa, Alona Zilberberg and Sol Efroni
    Citation: BMC Bioinformatics 2023 24:32
    Content type: Software Published on:

  46. Nanopore sequencing allows selective sequencing, the ability to programmatically reject unwanted reads in a sample. Selective sequencing has many present and future applications in genomics research and the cl...

    Authors: Anjana Senanayake, Hasindu Gamaarachchi, Damayanthi Herath and Roshan Ragel
    Citation: BMC Bioinformatics 2023 24:31
    Content type: Research Published on:

  48. The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spati...

    Authors: Frédéric Pont, Juan Pablo Cerapio, Pauline Gravelle, Laetitia Ligat, Carine Valle, Emeline Sarot, Marion Perrier, Frédéric Lopez, Camille Laurent, Jean Jacques Fournié and Marie Tosolini
    Citation: BMC Bioinformatics 2023 24:30
    Content type: Software Published on:

  49. Rhodopsin is a seven-transmembrane protein covalently linked with retinal chromophore that absorbs photons for energy conversion and intracellular signaling in eukaryotes, bacteria, and archaea. Haloarchaeal r...

    Authors: Muthu Krishnan Selvaraj, Anamika Thakur, Manoj Kumar, Anil Kumar Pinnaka, Chander Raman Suri, Busi Siddhardha and Senthil Prasad Elumalai
    Citation: BMC Bioinformatics 2023 24:29
    Content type: Research Published on:

  50. In individuals or animals suffering from genetic or acquired diseases, it is important to identify which clinical or phenotypic variables can be used to discriminate between disease and non-disease states, the...

    Authors: Maria del Mar Muñiz Moreno, Claire Gavériaux-Ruff and Yann Herault
    Citation: BMC Bioinformatics 2023 24:28
    Content type: Software Published on:

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