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  1. As an important task in bioinformatics, clustering analysis plays a critical role in understanding the functional mechanisms of many complex biological systems, which can be modeled as biological networks. The...

    Authors: Dong-Xu Li, Peng Zhou, Bo-Wei Zhao, Xiao-Rui Su, Guo-Dong Li, Jun Zhang, Peng-Wei Hu and Lun Hu
    Citation: BMC Bioinformatics 2023 24:451
  2. Acute myeloid leukaemia (AML) is characterised by the malignant accumulation of myeloid progenitors with a high recurrence rate after chemotherapy. Blasts (leukaemia cells) exhibit a complete myeloid different...

    Authors: Nan Shao, Chenshuo Ren, Tianyuan Hu, Dianbing Wang, Xiaofan Zhu, Min Li, Tao Cheng, Yingchi Zhang and Xian-En Zhang
    Citation: BMC Bioinformatics 2023 24:450
  3. Protein ubiquitination is a critical post-translational modification (PTMs) involved in numerous cellular processes. Identifying ubiquitination sites (Ubi-sites) on proteins offers valuable insights into their...

    Authors: Mahdi Pourmirzaei, Shahin Ramazi, Farzaneh Esmaili, Seyedehsamaneh Shojaeilangari and Abdollah Allahvardi
    Citation: BMC Bioinformatics 2023 24:449
  4. The discovery of anticancer drug combinations is a crucial work of anticancer treatment. In recent years, pre-screening drug combinations with synergistic effects in a large-scale search space adopting computa...

    Authors: Danyi Chen, Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Qi Liu and Qin Liu
    Citation: BMC Bioinformatics 2023 24:448
  5. Aptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as next-generation materials, particularly for drug discovery. The systematic evo...

    Authors: Incheol Shin, Keumseok Kang, Juseong Kim, Sanghun Sel, Jeonghoon Choi, Jae-Wook Lee, Ho Young Kang and Giltae Song
    Citation: BMC Bioinformatics 2023 24:447
  6. Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a col...

    Authors: Anup Kumar, Björn Grüning and Rolf Backofen
    Citation: BMC Bioinformatics 2023 24:446
  7. Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such t...

    Authors: Valentina Nale, Alice Chiodi, Noemi Di Nanni, Ingrid Cifola, Marco Moscatelli, Cinzia Cocola, Matteo Gnocchi, Eleonora Piscitelli, Ada Sula, Ileana Zucchi, Rolland Reinbold, Luciano Milanesi, Alessandra Mezzelani, Paride Pelucchi and Ettore Mosca
    Citation: BMC Bioinformatics 2023 24:445
  8. For ligand binding prediction, it is crucial for molecular docking programs to integrate template-based modeling with a precise scoring function. Here, we proposed the CoDock-Ligand docking method that combine...

    Authors: Mingwei Pang, Wangqiu He, Xufeng Lu, Yuting She, Liangxu Xie, Ren Kong and Shan Chang
    Citation: BMC Bioinformatics 2023 24:444
  9. Drug repurposing is an exciting field of research toward recognizing a new FDA-approved drug target for the treatment of a specific disease. It has received extensive attention regarding the tedious, time-cons...

    Authors: Ramin Amiri, Jafar Razmara, Sepideh Parvizpour and Habib Izadkhah
    Citation: BMC Bioinformatics 2023 24:442
  10. Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when com...

    Authors: Cullen Roth, Vrinda Venu, Vanessa Job, Nicholas Lubbers, Karissa Y. Sanbonmatsu, Christina R. Steadman and Shawn R. Starkenburg
    Citation: BMC Bioinformatics 2023 24:441
  11. Single-cell RNA sequencing (scRNA-seq) is a powerful tool for investigating cell abundance changes during tissue regeneration and remodeling processes. Differential cell abundance supports the initial clusteri...

    Authors: Juan Domingo, Oleksandra Kutsyr-Kolesnyk, Teresa Leon, Raul Perez-Moraga, Guillermo Ayala and Beatriz Roson
    Citation: BMC Bioinformatics 2023 24:440
  12. Cancer is a collection of diseases caused by the deregulation of cell processes, which is triggered by somatic mutations. The search for patterns in somatic mutations, known as mutational signatures, is a grow...

    Authors: Rodrigo D. Drummond, Alexandre Defelicibus, Mathilde Meyenberg, Renan Valieris, Emmanuel Dias-Neto, Rafael A. Rosales and Israel Tojal da Silva
    Citation: BMC Bioinformatics 2023 24:439
  13. Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce t...

    Authors: Jakob P. Pettersen, Sandra Castillo, Paula Jouhten and Eivind Almaas
    Citation: BMC Bioinformatics 2023 24:438
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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

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