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  4. Identification of the cancer subtype plays a crucial role to provide an accurate diagnosis and proper treatment to improve the clinical outcomes of patients. Recent studies have shown that DNA methylation is o...

    Authors: Joung Min Choi, Chaelin Park and Heejoon Chae
    Citation: BMC Bioinformatics 2023 24:168
    Content type: Research Published on:

  5. CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted comp...

    Authors: Ho-min Park, Jongbum Won, Yunseol Park, Esla Timothy Anzaku, Joris Vankerschaver, Arnout Van Messem, Wesley De Neve and Hyunjin Shim
    Citation: BMC Bioinformatics 2023 24:167
    Content type: Software Published on:

  6. Wound healing involves careful coordination among various cell types carrying out unique or even multifaceted functions. The abstraction of this complex dynamic process into four primary wound stages is essent...

    Authors: Ksenia Zlobina, Eric Malekos, Han Chen and Marcella Gomez
    Citation: BMC Bioinformatics 2023 24:166
    Content type: Research Published on:

  10. 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
    Content type: Research Published on:

  12. 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
    Content type: Review Published on:

  13. 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
    Content type: Software Published on:

  14. 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
    Content type: Research Published on:

  17. 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
    Content type: Research Published on:

  18. 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
    Content type: Research Published on:

  19. 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
    Content type: Software Published on:

  20. 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
    Content type: Database Published on:

  23. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  26. 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
    Content type: Research Published on:

  27. 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
    Content type: Research Published on:

  29. 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
    Content type: Software Published on:

  30. 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
    Content type: Research Published on:

  31. 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
    Content type: Research Published on:

  32. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  34. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  37. 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
    Content type: Research Published on:

  39. 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
    Content type: Software Published on:

  40. 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
    Content type: Software Published on:

  41. 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
    Content type: Research Published on:

  42. 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
    Content type: Research Published on:

  43. 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
    Content type: Research Published on:

  46. 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
    Content type: Research Published on:

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

  47. 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
    Content type: Research article Published on:

  48. 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
    Content type: Software Published on:

  50. 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
    Content type: Software Published on:

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