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  1. Enhancers play a crucial role in gene regulation, and some active enhancers produce noncoding RNAs known as enhancer RNAs (eRNAs) bi-directionally. The most commonly used method for detecting eRNAs is CAGE-seq...

    Authors: Ximei Luo, Qun Li, Yifan Tang, Yan Liu, Quan Zou, Jie Zheng, Ying Zhang and Lei Xu
    Citation: BMC Bioinformatics 2023 24:414
  2. During drug development, it is essential to gather information about the change of clinical exposure of a drug (object) due to the pharmacokinetic (PK) drug-drug interactions (DDIs) with another drug (precipit...

    Authors: Joel Zirkle, Xiaomei Han, Rebecca Racz, Mohammadreza Samieegohar, Anik Chaturbedi, John Mann, Shilpa Chakravartula and Zhihua Li
    Citation: BMC Bioinformatics 2023 24:413
  3. The PubMed archive contains more than 34 million articles; consequently, it is becoming increasingly difficult for a biomedical researcher to keep up-to-date with different knowledge domains. Computationally e...

    Authors: Robert J. Millikin, Kalpana Raja, John Steill, Cannon Lock, Xuancheng Tu, Ian Ross, Lam C. Tsoi, Finn Kuusisto, Zijian Ni, Miron Livny, Brian Bockelman, James Thomson and Ron Stewart
    Citation: BMC Bioinformatics 2023 24:412
  4. Identifying variants associated with complex traits is a challenging task in genetic association studies due to linkage disequilibrium (LD) between genetic variants and population stratification, unrelated to ...

    Authors: Aritra Bose, Myson Burch, Agniva Chowdhury, Peristera Paschou and Petros Drineas
    Citation: BMC Bioinformatics 2023 24:411
  5. LncRNA–protein interactions are ubiquitous in organisms and play a crucial role in a variety of biological processes and complex diseases. Many computational methods have been reported for lncRNA–protein inter...

    Authors: Guohao Lv, Yingchun Xia, Zhao Qi, Zihao Zhao, Lianggui Tang, Cheng Chen, Shuai Yang, Qingyong Wang and Lichuan Gu
    Citation: BMC Bioinformatics 2023 24:410
  6. A Raman spectroscopy method can quickly and accurately measure the concentration of ofloxacin in solution. This method has the advantages of accuracy and rapidity over traditional detection methods. However, t...

    Authors: Chenyu Ma, Yuanbo Shi, Yueyang Huang and Gongwei Dai
    Citation: BMC Bioinformatics 2023 24:409
  7. Gene-wise differential expression is usually the first major step in the statistical analysis of high-throughput data obtained from techniques such as microarrays or RNA-sequencing. The analysis at gene level ...

    Authors: Adrià Caballé-Mestres, Antoni Berenguer-Llergo and Camille Stephan-Otto Attolini
    Citation: BMC Bioinformatics 2023 24:408
  8. Dimension reduction, especially feature selection, is an important step in improving classification performance for high-dimensional data. Particularly in cancer research, when reducing the number of features,...

    Authors: Hatice Yağmur Zengin and Erdem Karabulut
    Citation: BMC Bioinformatics 2023 24:407
  9. The commercial adoption of BCI technologies for both clinical and non-clinical applications is drawing scientists to the creation of wearable devices for daily living. Emotions are essential to human existence...

    Authors: Awwab Mohammad, Farheen Siddiqui, M. Afshar Alam and Sheikh Mohammad Idrees
    Citation: BMC Bioinformatics 2023 24:406
  10. Extracting information from free texts using natural language processing (NLP) can save time and reduce the hassle of manually extracting large quantities of data from incredibly complex clinical notes of canc...

    Authors: Maryam Gholipour, Reza Khajouei, Parastoo Amiri, Sadrieh Hajesmaeel Gohari and Leila Ahmadian
    Citation: BMC Bioinformatics 2023 24:405
  11. High-throughput experiments provide deep insight into the molecular biology of different species, but more tools need to be developed to handle this type of data. At the transcriptomics level, quantitative Pol...

    Authors: Alexis Germán Murillo Carrasco, Tatiane Katsue Furuya, Miyuki Uno, Tharcisio Citrangulo Tortelli Jr and Roger Chammas
    Citation: BMC Bioinformatics 2023 24:402
  12. Recent advancements in computing power and state-of-the-art algorithms have helped in more accessible and accurate diagnosis of numerous diseases. In addition, the development of de novo areas in imaging scien...

    Authors: Sadam Hussain, Yareth Lafarga-Osuna, Mansoor Ali, Usman Naseem, Masroor Ahmed and Jose Gerardo Tamez-Peña
    Citation: BMC Bioinformatics 2023 24:401
  13. Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, ...

    Authors: Lore Depuydt, Luca Renders, Thomas Abeel and Jan Fostier
    Citation: BMC Bioinformatics 2023 24:400
  14. We consider two key problems in genomics involving multiple traits: multi-trait genome wide association studies (GWAS), where the goal is to detect genetic variants associated with the traits; and multi-trait ...

    Authors: Aurélie C. Lozano, Hantian Ding, Naoki Abe and Alexander E. Lipka
    Citation: BMC Bioinformatics 2023 24:399
  15. In this paper, we are interested in interactions between a high-dimensional -omics dataset and clinical covariates. The goal is to evaluate the relationship between a phenotype of interest and a high-dimension...

    Authors: Charlie M. Carpenter, Lucas Gillenwater, Russell Bowler, Katerina Kechris and Debashis Ghosh
    Citation: BMC Bioinformatics 2023 24:398
  16. Technical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. For a given sequence, we usually use smaller subsequences (anchors) to find possible candi...

    Authors: Valeriy Titarenko and Sofya Titarenko
    Citation: BMC Bioinformatics 2023 24:396
  17. Transcription factors (TF) play a crucial role in the regulation of gene transcription; alterations of their activity and binding to DNA areas are strongly involved in cancer and other disease onset and develo...

    Authors: Silvia Cascianelli, Gaia Ceddia, Alberto Marchesi and Marco Masseroli
    Citation: BMC Bioinformatics 2023 24:395
  18. The rapid development of omics acquisition techniques has induced the production of a large volume of heterogeneous and multi-level omics datasets, which require specific and sometimes complex analyses to obta...

    Authors: Élise Maigné, Céline Noirot, Julien Henry, Yaa Adu Kesewaah, Ludovic Badin, Sébastien Déjean, Camille Guilmineau, Arielle Krebs, Fanny Mathevet, Audrey Segalini, Laurent Thomassin, David Colongo, Christine Gaspin, Laurence Liaubet and Nathalie Vialaneix
    Citation: BMC Bioinformatics 2023 24:391
  19. This Supplement issue, presents five research articles which are distributed, mainly due to the subject they address, from the 8th International Work-Conference on Bioinformatics and Biomedical Engineering (IW...

    Authors: Olga Valenzuela, Mario Cannataro, Irena Rusur, Jianxin Wang, Zhongming Zhao and Ignacio Rojas
    Citation: BMC Bioinformatics 2023 24(Suppl 2):361

    This article is part of a Supplement: Volume 24 Supplement 2

  20. Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experienc...

    Authors: Dao-Feng Zhang, Wei He, Zongze Shao, Iftikhar Ahmed, Yuqin Zhang, Wen-Jun Li and Zhe Zhao
    Citation: BMC Bioinformatics 2023 24:390
  21. Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational too...

    Authors: Pasquale Claudio Africa, Roberto Piersanti, Francesco Regazzoni, Michele Bucelli, Matteo Salvador, Marco Fedele, Stefano Pagani, Luca Dede’ and Alfio Quarteroni
    Citation: BMC Bioinformatics 2023 24:389
  22. Image segmentation pipelines are commonly used in microscopy to identify cellular compartments like nucleus and cytoplasm, but there are few standards for comparing segmentation accuracy across pipelines. The ...

    Authors: Vishakha Goyal, Nick J. Schaub, Ty C. Voss and Nathan A. Hotaling
    Citation: BMC Bioinformatics 2023 24:388
  23. Metagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection. Recently, nanopore sequencing has been emerging as a highly potential to...

    Authors: Xu Zhu, Lili Zhao, Lihong Huang, Wenxian Yang, Liansheng Wang and Rongshan Yu
    Citation: BMC Bioinformatics 2023 24:387
  24. Melanoma is one of the deadliest tumors in the world. Early detection is critical for first-line therapy in this tumor pathology and it remains challenging due to the need for histological analysis to ensure c...

    Authors: Luigi Di Biasi, Fabiola De Marco, Alessia Auriemma Citarella, Modesto Castrillón-Santana, Paola Barra and Genoveffa Tortora
    Citation: BMC Bioinformatics 2023 24:386
  25. In cancer genomic medicine, finding driver mutations involved in cancer development and tumor growth is crucial. Machine-learning methods to predict driver missense mutations have been developed because varian...

    Authors: Narumi Hatano, Mayumi Kamada, Ryosuke Kojima and Yasushi Okuno
    Citation: BMC Bioinformatics 2023 24:383
  26. An abnormal growth or fatty mass of cells in the brain is called a tumor. They can be either healthy (normal) or become cancerous, depending on the structure of their cells. This can result in increased pressu...

    Authors: A. Rohini, Carol Praveen, Sandeep Kumar Mathivanan, V. Muthukumaran, Saurav Mallik, Mohammed S. Alqahtani, Amal Al-Rasheed and Ben Othman Soufiene
    Citation: BMC Bioinformatics 2023 24:382
  27. Identification of pleiotropic variants associated with multiple phenotypic traits has received increasing attention in genetic association studies. Overlapping genetic associations from multiple traits help to...

    Authors: Kipoong Kim, Tae-Hwan Jun, Bo-Keun Ha, Shuang Wang and Hokeun Sun
    Citation: BMC Bioinformatics 2023 24:381
  28. Despite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds of problems of eukaryotic genome assembly are so-called "haplotypic du...

    Authors: Mikhail I. Schelkunov
    Citation: BMC Bioinformatics 2023 24:377
  29. Protein methylation, a post-translational modification, is crucial in regulating various cellular functions. Arginine methylation is required to understand crucial biochemical activities and biological functio...

    Authors: Monika Khandelwal and Ranjeet Kumar Rout
    Citation: BMC Bioinformatics 2023 24:376
  30. Identifying drug–target interactions (DTIs) plays a key role in drug development. Traditional wet experiments to identify DTIs are costly and time consuming. Effective computational methods to predict DTIs are...

    Authors: Junjun Zhang and Minzhu Xie
    Citation: BMC Bioinformatics 2023 24:375
  31. Drug repurposing is an approach that holds promise for identifying new therapeutic uses for existing drugs. Recently, knowledge graphs have emerged as significant tools for addressing the challenges of drug re...

    Authors: Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Najmeh Salehi, Mohammad Akbari and Ali Masoudi-Nejad
    Citation: BMC Bioinformatics 2023 24:374
  32. The relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a foundational principle in biological science. Only recently has the comp...

    Authors: F. Adriaan Lategan, Caroline Schreiber and Hugh G. Patterton
    Citation: BMC Bioinformatics 2023 24:373
  33. The rising risk of diabetes, particularly in emerging countries, highlights the importance of early detection. Manual prediction can be a challenging task, leading to the need for automatic approaches. The maj...

    Authors: Kiran Kumar Patro, Jaya Prakash Allam, Umamaheswararao Sanapala, Chaitanya Kumar Marpu, Nagwan Abdel Samee, Maali Alabdulhafith and Pawel Plawiak
    Citation: BMC Bioinformatics 2023 24:372
  34. Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases,...

    Authors: Ignas Rumbavicius, Trine B. Rounge and Torbjørn Rognes
    Citation: BMC Bioinformatics 2023 24:371
  35. Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequenci...

    Authors: Eric Kofman, Brian Yee, Hugo C. Medina-Munoz and Gene W. Yeo
    Citation: BMC Bioinformatics 2023 24:370
  36. Liquid biopsy is a minimally-invasive method of sampling bodily fluids, capable of revealing evidence of cancer. The distribution of cell-free DNA (cfDNA) fragment lengths has been shown to differ between heal...

    Authors: Mathias Cardner, Francesco Marass, Erika Gedvilaite, Julie L. Yang, Dana W. Y. Tsui and Niko Beerenwinkel
    Citation: BMC Bioinformatics 2023 24:368
  37. Obtaining accurate drug–target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins...

    Authors: Haixia Zhai, Hongli Hou, Junwei Luo, Xiaoyan Liu, Zhengjiang Wu and Junfeng Wang
    Citation: BMC Bioinformatics 2023 24:367
  38. We consider the problem of finding an accurate representation of neuron shapes, extracting sub-cellular features, and classifying neurons based on neuron shapes. In neuroscience research, the skeleton represen...

    Authors: Jiaxiang Jiang, Michael Goebel, Cezar Borba, William Smith and B. S. Manjunath
    Citation: BMC Bioinformatics 2023 24:366

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