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  1. The identification of disease-related genes is of great significance for the diagnosis and treatment of human disease. Most studies have focused on developing efficient and accurate computational methods to pr...

    Authors: Linlin Zhang, Dianrong Lu, Xuehua Bi, Kai Zhao, Guanglei Yu and Na Quan
    Citation: BMC Bioinformatics 2023 24:162
  2. Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both increased the capacity and decreased the cost of storing info...

    Authors: Golam Md Mortuza, Jorge Guerrero, Shoshanna Llewellyn, Michael D. Tobiason, George D. Dickinson, William L. Hughes, Reza Zadegan and Tim Andersen
    Citation: BMC Bioinformatics 2023 24:160
  3. Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible t...

    Authors: Marco A. Cano, Ginger Tsueng, Xinghua Zhou, Jiwen Xin, Laura D. Hughes, Julia L. Mullen, Andrew I. Su and Chunlei Wu
    Citation: BMC Bioinformatics 2023 24:159
  4. Accurate somatic variant calling from next-generation sequencing data is one most important tasks in personalised cancer therapy. The sophistication of the available technologies is ever-increasing, yet, manua...

    Authors: Marc Vaisband, Maria Schubert, Franz Josef Gassner, Roland Geisberger, Richard Greil, Nadja Zaborsky and Jan Hasenauer
    Citation: BMC Bioinformatics 2023 24:158
  5. The TP53 tumor suppressor gene is one of the most mutated genes in lung adenocarcinoma (LUAD) and plays a vital role in regulating the occurrence and progression of cancer. We aimed to elucidate the association b...

    Authors: He Li, Lei Yang, Yuanyuan Wang, Lingchan Wang, Gang Chen, Li Zhang and Dongchang Wang
    Citation: BMC Bioinformatics 2023 24:155
  6. Elucidating compound mechanism of action (MoA) is beneficial to drug discovery, but in practice often represents a significant challenge. Causal Reasoning approaches aim to address this situation by inferring ...

    Authors: Layla Hosseini-Gerami, Ixavier Alonzo Higgins, David A. Collier, Emma Laing, David Evans, Howard Broughton and Andreas Bender
    Citation: BMC Bioinformatics 2023 24:154
  7. Construction of kinship matrices among individuals is an important step for both association studies and prediction studies based on different levels of omic data. Methods for constructing kinship matrices are...

    Authors: Wei Zhao, Qamar Raza Qadri, Zhenyang Zhang, Zhen Wang, Yuchun Pan, Qishan Wang and Zhe Zhang
    Citation: BMC Bioinformatics 2023 24:153
  8. The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool ret...

    Authors: Pengli Cai, Sheng Liu, Dachuan Zhang, Huadong Xing, Mengying Han, Dongliang Liu, Linlin Gong and Qian-Nan Hu
    Citation: BMC Bioinformatics 2023 24:152
  9. It has been observed that high levels of enhancer of zeste homolog 2 (EZH2) expression are associated with unsatisfactory prognoses and can be found in a wide range of malignancies. However, the effects of EZH...

    Authors: Kui Fan, Bo-hui Zhang, Deng Han and Yun-chuan Sun
    Citation: BMC Bioinformatics 2023 24:149
  10. Concurrent existence of lncRNA and circular RNA at both nucleus and cytosol within a cell at different proportions is well reported. Previous studies showed that circular RNAs are synthesized in nucleus follow...

    Authors: Rajnish Kumar, Rajkrishna Mondal, Tapobrata Lahiri and Manoj Kumar Pal
    Citation: BMC Bioinformatics 2023 24:148
  11. Gastric cancer (GC) is one of the most common causes of cancer-related fatalities worldwide, and its progression is associated with RNA modifications. Here, using RNA modification-related genes (RNAMRGs), we a...

    Authors: Airexiati Tuhongjiang, Feng Wang, Chengrong Zhang, Sisi Pang, Yujiang Qu, Bo Feng and Gulimire Amuti
    Citation: BMC Bioinformatics 2023 24:147
  12. The aim was to develop a personalized survival prediction deep learning model for cervical adenocarcinoma patients and process personalized survival prediction.

    Authors: Ruowen Li, Wenjie Qu, Qingqing Liu, Yilin Tan, Wenjing Zhang, Yiping Hao, Nan Jiang, Zhonghao Mao, Jinwen Ye, Jun Jiao, Qun Gao, Baoxia Cui and Taotao Dong
    Citation: BMC Bioinformatics 2023 24:146
  13. Compositional heterogeneity—when the proportions of nucleotides and amino acids are not broadly similar across the dataset—is a cause of a great number of phylogenetic artefacts. Whilst a variety of methods ca...

    Authors: James F. Fleming and Torsten H. Struck
    Citation: BMC Bioinformatics 2023 24:145
  14. Modeling the whole cardiac function involves the solution of several complex multi-physics and multi-scale models that are highly computationally demanding, which call for simpler yet accurate, high-performanc...

    Authors: Pasquale Claudio Africa, Roberto Piersanti, Marco Fedele, Luca Dede’ and Alfio Quarteroni
    Citation: BMC Bioinformatics 2023 24:143
  15. Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that is highly phenotypically and genetically heterogeneous. With the accumulation of biological sequencing data, more and more studies s...

    Authors: Junjie Zhang, Guoli Ji, Xilin Gao and Jinting Guan
    Citation: BMC Bioinformatics 2023 24:142
  16. Inflammatory mediators play havoc in several diseases including the novel Coronavirus disease 2019 (COVID-19) and generally correlate with the severity of the disease. Interleukin-13 (IL-13), is a pleiotropic ...

    Authors: Pooja Arora, Neha Periwal, Yash Goyal, Vikas Sood and Baljeet Kaur
    Citation: BMC Bioinformatics 2023 24:141
  17. Different machine learning techniques have been proposed to classify a wide range of biological/clinical data. Given the practicability of these approaches accordingly, various software packages have been also...

    Authors: Negar Hossein-Nezhad Daneshvar, Yosef Masoudi-Sobhanzadeh and Yadollah Omidi
    Citation: BMC Bioinformatics 2023 24:140
  18. Microarray data have been widely utilized for cancer classification. The main characteristic of microarray data is “large p and small n” in that data contain a small number of subjects but a large number of ge...

    Authors: Zixuan Wang, Yi Zhou, Tatsuya Takagi, Jiangning Song, Yu-Shi Tian and Tetsuo Shibuya
    Citation: BMC Bioinformatics 2023 24:139
  19. For detecting genotype-phenotype association from case–control single nucleotide polymorphism (SNP) data, one class of methods relies on testing each genomic variant site individually. However, this approach i...

    Authors: Jin Du, Chaojie Wang, Lijun Wang, Shanjun Mao, Bencong Zhu, Zheng Li and Xiaodan Fan
    Citation: BMC Bioinformatics 2023 24:138
  20. Bistable systems, i.e., systems that exhibit two stable steady states, are of particular interest in biology. They can implement binary cellular decision making, e.g., in pathways for cellular differentiation ...

    Authors: Vandana Sreedharan, Upinder S. Bhalla and Naren Ramakrishnan
    Citation: BMC Bioinformatics 2023 24:136
  21. Population structure and cryptic relatedness between individuals (samples) are two major factors affecting false positives in genome-wide association studies (GWAS). In addition, population stratification and ...

    Authors: Elena Solovieva and Hiroaki Sakai
    Citation: BMC Bioinformatics 2023 24:135
  22. 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
  23. In protein sequences—as there are 61 sense codons but only 20 standard amino acids—most amino acids are encoded by more than one codon. Although such synonymous codons do not alter the encoded amino acid seque...

    Authors: Rishab Jain, Aditya Jain, Elizabeth Mauro, Kevin LeShane and Douglas Densmore
    Citation: BMC Bioinformatics 2023 24:132
  24. 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
  25. 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
  26. 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
  27. 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

  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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

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