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  1. Biclustering of biologically meaningful binary information is essential in many applications related to drug discovery, like protein–protein interactions and gene expressions. However, for robust performance i...

    Authors: Brijesh K. Sriwastava, Anup Kumar Halder, Subhadip Basu and Tapabrata Chakraborti
    Citation: BMC Bioinformatics 2023 24:435
  2. Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estima...

    Authors: Orly Avraham, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban and Ora Schueler-Furman
    Citation: BMC Bioinformatics 2023 24:433
  3. Deep generative models naturally become nonlinear dimension reduction tools to visualize large-scale datasets such as single-cell RNA sequencing datasets for revealing latent grouping patterns or identifying o...

    Authors: Gwangwoo Kim and Hyonho Chun
    Citation: BMC Bioinformatics 2023 24:432
  4. Liquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis scenarios, features of each run are aligned into consensus features by feature...

    Authors: Ruimin Wang, Miaoshan Lu, Shaowei An, Jinyin Wang and Changbin Yu
    Citation: BMC Bioinformatics 2023 24:431
  5. Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments....

    Authors: Rongyuan Li, Jingli Wu, Gaoshi Li, Jiafei Liu, Junbo Xuan and Qi Zhu
    Citation: BMC Bioinformatics 2023 24:427
  6. Computational methods of predicting protein stability changes upon missense mutations are invaluable tools in high-throughput studies involving a large number of protein variants. However, they are limited by ...

    Authors: Yesol Sapozhnikov, Jagdish Suresh Patel, F. Marty Ytreberg and Craig R. Miller
    Citation: BMC Bioinformatics 2023 24:426
  7. Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical As...

    Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny
    Citation: BMC Bioinformatics 2023 24:425
  8. The causes of many complex human diseases are still largely unknown. Genetics plays an important role in uncovering the molecular mechanisms of complex human diseases. A key step to characterize the genetics o...

    Authors: Yixin Zhang, Wei Liu and Weiliang Qiu
    Citation: BMC Bioinformatics 2023 24:423
  9. Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial ...

    Authors: Thomas Binet, Séverine Padiolleau-Lefèvre, Stéphane Octave, Bérangère Avalle and Irene Maffucci
    Citation: BMC Bioinformatics 2023 24:422
  10. In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a ...

    Authors: Grégoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella, Mélisande Blein-Nicolas, Virginie Lollier, Emile Benoist, Géraldine Jean, Guillaume Fertin, Hélène Rogniaux and Dominique Tessier
    Citation: BMC Bioinformatics 2023 24:421
  11. The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentrat...

    Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny
    Citation: BMC Bioinformatics 2023 24:418
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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

  31. 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
  32. 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
  33. 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

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