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  1. RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different sof...

    Authors: Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng and Tomáš Pluskal
    Citation: BMC Bioinformatics 2023 24:133
  2. EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). How...

    Authors: Christoffer Trier Maansson, Emma Roger Andersen, Maiken Parm Ulhoi, Peter Meldgaard and Boe Sandahl Sorensen
    Citation: BMC Bioinformatics 2023 24:131
  3. In the field of genomics and personalized medicine, it is a key issue to find biomarkers directly related to the diagnosis of specific diseases from high-throughput gene microarray data. Feature selection tech...

    Authors: Wei Li, Yuhuan Chi, Kun Yu and Weidong Xie
    Citation: BMC Bioinformatics 2023 24:130
  4. Identification of hot spots in protein–DNA binding interfaces is extremely important for understanding the underlying mechanisms of protein–DNA interactions and drug design. Since experimental methods for iden...

    Authors: Yu Sun, Hongwei Wu, Zhengrong Xu, Zhenyu Yue and Ke Li
    Citation: BMC Bioinformatics 2023 24:129
  5. The human microbiome plays a critical role in maintaining human health. Due to the recent advances in high-throughput sequencing technologies, the microbiome profiles present in the human body have become publ...

    Authors: K. Syama, J. Angel Arul Jothi and Namita Khanna
    Citation: BMC Bioinformatics 2023 24:126

    The Correction to this article has been published in BMC Bioinformatics 2023 24:307

  6. Cluster analysis is utilized frequently in scientific theory and applications to separate data into groups. A key assumption in many clustering algorithms is that the data was generated from a population consi...

    Authors: Jose Laborde, Paul A. Stewart, Zhihua Chen, Yian A. Chen and Naomi C. Brownstein
    Citation: BMC Bioinformatics 2023 24:125
  7. Automatic cell tracking methods enable practitioners to analyze cell behaviors efficiently. Notwithstanding the continuous development of relevant software, user-friendly visualization tools have room for furt...

    Authors: Changbeom Shim, Wooil Kim, Tran Thien Dat Nguyen, Du Yong Kim, Yu Suk Choi and Yon Dohn Chung
    Citation: BMC Bioinformatics 2023 24:124
  8. In recent years, advances in high-throughput sequencing technologies have enabled the use of genomic information in many fields, such as precision medicine, oncology, and food quality control. The amount of ge...

    Authors: Yeremia Gunawan Adhisantoso, Jan Voges, Christian Rohlfing, Viktor Tunev, Jens-Rainer Ohm and Jörn Ostermann
    Citation: BMC Bioinformatics 2023 24:121
  9. High-throughput and selective detection of organelles in immunofluorescence images is an important but demanding task in cell biology. The centriole organelle is critical for fundamental cellular processes, an...

    Authors: Léo Bürgy, Martin Weigert, Georgios Hatzopoulos, Matthias Minder, Adrien Journé, Sahand Jamal Rahi and Pierre Gönczy
    Citation: BMC Bioinformatics 2023 24:120
  10. Genomic structural variant detection is a significant and challenging issue in genome analysis. The existing long-read based structural variant detection methods still have space for improvement in detecting m...

    Authors: Huidong Ma, Cheng Zhong, Danyang Chen, Haofa He and Feng Yang
    Citation: BMC Bioinformatics 2023 24:119
  11. It has been discovered that tumor-infiltrating lymphocytes (TILs) are essential for the emergence of bladder cancer (BCa). This study aimed to research TIL-related genes (TILRGs) and create a gene model to pre...

    Authors: Canxuan Li and Weibin Xie
    Citation: BMC Bioinformatics 2023 24:118
  12. Biomedical researchers use alignments produced by BLAST (Basic Local Alignment Search Tool) to categorize their query sequences. Producing such alignments is an essential bioinformatics task that is well suite...

    Authors: Christiam Camacho, Grzegorz M. Boratyn, Victor Joukov, Roberto Vera Alvarez and Thomas L. Madden
    Citation: BMC Bioinformatics 2023 24:117
  13. Sequence verification is essential for plasmids used as critical reagents or therapeutic products. Typically, high-quality plasmid sequence is achieved through capillary-based Sanger sequencing, requiring cust...

    Authors: Scott D. Brown, Lisa Dreolini, Jessica F. Wilson, Miruna Balasundaram and Robert A. Holt
    Citation: BMC Bioinformatics 2023 24:116
  14. Using visual, biological, and electronic health records data as the sole input source, pretrained convolutional neural networks and conventional machine learning methods have been heavily employed for the iden...

    Authors: Mpho Mokoatle, Vukosi Marivate, Darlington Mapiye, Riana Bornman and Vanessa. M. Hayes
    Citation: BMC Bioinformatics 2023 24:112
  15. Synchronization (insertions–deletions) errors are still a major challenge for reliable information retrieval in DNA storage. Unlike traditional error correction codes (ECC) that add redundancy in the stored in...

    Authors: Ranze Xie, Xiangzhen Zan, Ling Chu, Yanqing Su, Peng Xu and Wenbin Liu
    Citation: BMC Bioinformatics 2023 24:111
  16. Drug‒drug interactions (DDIs) are reactions between two or more drugs, i.e., possible situations that occur when two or more drugs are used simultaneously. DDIs act as an important link in both drug developmen...

    Authors: Zihao Yang, Kuiyuan Tong, Shiyu Jin, Shiyan Wang, Chao Yang and Feng Jiang
    Citation: BMC Bioinformatics 2023 24:110
  17. Antibiotic resistance has become a global concern. Vancomycin is known as the last line of antibiotics, but its treatment index is narrow. Therefore, clinical dosing decisions must be made with the utmost care...

    Authors: Wen-Hsien Ho, Tian-Hsiang Huang, Yenming J. Chen, Lang-Yin Zeng, Fen-Fen Liao and Yeong-Cheng Liou
    Citation: BMC Bioinformatics 2023 22(Suppl 5):637

    This article is part of a Supplement: Volume 22 Supplement 5

  18. Subcellular localization of messenger RNA (mRNAs) plays a pivotal role in the regulation of gene expression, cell migration as well as in cellular adaptation. Experiment techniques for pinpointing the subcellu...

    Authors: Saleh Musleh, Mohammad Tariqul Islam, Rizwan Qureshi, Nehad M. Alajez and Tanvir Alam
    Citation: BMC Bioinformatics 2023 24:109

    The Correction to this article has been published in BMC Bioinformatics 2023 24:156

  19. The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used...

    Authors: Ivo Henrique Provensi Vieira, Eduardo Buganemi Botelho, Thales Junior de Souza Gomes, Roger Kist, Rafael Andrade Caceres and Fernando Berton Zanchi
    Citation: BMC Bioinformatics 2023 24:107
  20. Renal carcinoma is a common malignant tumor of the urinary system. Advanced renal carcinoma has a low 5-year survival rate and a poor prognosis. More and more studies have confirmed that chromatin regulators (...

    Authors: Puyu Liu, Jihang Luo, Na Tan, Chengfang Li, Jieyu Xu and Xiaorong Yang
    Citation: BMC Bioinformatics 2023 24:104
  21. Colon cancer (CC) is a common tumor that causes significant harm to human health. Bacteria play a vital role in cancer biology, particularly the biology of CC. Genes related to bacterial response were seldom u...

    Authors: Zuming Xiong, Wenxin Li, Xiangrong Luo, Yirong Lin, Wei Huang and Sen Zhang
    Citation: BMC Bioinformatics 2023 24:103
  22. Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to id...

    Authors: Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl A. Keller, Elisabeth F. Heuston, Stacie M. Anderson, Martha Kirby, David Bodine, Yu Zhang and Ross C. Hardison
    Citation: BMC Bioinformatics 2023 24:102
  23. In single-cell transcriptomics and other omics technologies, large fractions of missing values commonly occur. Researchers often either consider only those features that were measured for each instance of thei...

    Authors: Yannis Schumann, Julia E. Neumann and Philipp Neumann
    Citation: BMC Bioinformatics 2023 24:101
  24. Presenting with a poor prognosis, gastric cancer (GC) remains one of the leading causes of disease and death worldwide. Long non-coding RNAs (lncRNAs) regulate tumor formation and have been long used to predic...

    Authors: Bin Zhao, Fang Fang, Yiqun Liao, Yuji Chen, Fei Wang, Yichao Ma, Chen Wei, Jiahao Zhao, Hao Ji, Daorong Wang and Dong Tang
    Citation: BMC Bioinformatics 2023 24:100
  25. Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit...

    Authors: Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti and Alex Graudenzi
    Citation: BMC Bioinformatics 2023 24:99
  26. Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms...

    Authors: Tim Dunn, David Blaauw, Reetuparna Das and Satish Narayanasamy
    Citation: BMC Bioinformatics 2023 24:98
  27. The research of biomarker-treatment interactions is commonly investigated in randomized clinical trials (RCT) for improving medicine precision. The hierarchical interaction constraint states that an interactio...

    Authors: Shaima Belhechmi, Gwénaël Le Teuff, Riccardo De Bin, Federico Rotolo and Stefan Michiels
    Citation: BMC Bioinformatics 2023 24:96
  28. Understanding the role and function of genetic variants is extremely important when analyzing and interpreting a myriad of human disease processes. For cancer in general, cell-specific genetic variants are ubi...

    Authors: Nahla AlKurabi, Ahad AlGahtani and Turki M. Sobahy
    Citation: BMC Bioinformatics 2023 24:95
  29. High-throughput Proteomics has been accelerated by (tandem) mass spectrometry. However, the slow speed of mass spectra analysis prevents the analysis results from being up-to-date. Tandem mass spectrometry dat...

    Authors: Yoonsung Joh, Kangbae Lee, Hyunwoo Kim and Heejin Park
    Citation: BMC Bioinformatics 2023 24:94
  30. In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has ...

    Authors: Luísa C. de Souza, Karolayne S. Azevedo, Jackson G. de Souza, Raquel de M. Barbosa and Marcelo A. C. Fernandes
    Citation: BMC Bioinformatics 2023 24:92
  31. Renal cell carcinoma (RCC), one of the top 10 causes of cancer death, is responsible for more than 90% of all cases of primary renal cancer worldwide. Follicular dendritic cell-secreted protein (FDC-SP) specif...

    Authors: Fan Chang, Jiang-Hui Zhang, Wen-Song Wu, Shuai Tang, Zheng lv and Fang-Min Chen
    Citation: BMC Bioinformatics 2023 24:91
  32. 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
  33. 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
  34. 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
  35. 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

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