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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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

  6. 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
  7. 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
  8. 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
  9. 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

  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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

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

  34. 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

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

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