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  1. Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the ...

    Authors: Michael Olbrich, Axel Künstner and Hauke Busch
    Citation: BMC Bioinformatics 2023 24:182
  2. Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) ...

    Authors: Matthias van den Belt, Cameron Gilchrist, Thomas J. Booth, Yit-Heng Chooi, Marnix H. Medema and Mohammad Alanjary
    Citation: BMC Bioinformatics 2023 24:181
  3. Large-scale multi-ethnic DNA sequencing data is increasingly available owing to decreasing cost of modern sequencing technologies. Inference of the population structure with such sequencing data is fundamental...

    Authors: Jinghan Yang, Yuyang Xu, Minhao Yao, Gao Wang and Zhonghua Liu
    Citation: BMC Bioinformatics 2023 24:180
  4. The prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailo...

    Authors: Nassim Versbraegen, Barbara Gravel, Charlotte Nachtegael, Alexandre Renaux, Emma Verkinderen, Ann Nowé, Tom Lenaerts and Sofia Papadimitriou
    Citation: BMC Bioinformatics 2023 24:179
  5. The field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, rese...

    Authors: Trevor Doherty, Emma Dempster, Eilis Hannon, Jonathan Mill, Richie Poulton, David Corcoran, Karen Sugden, Ben Williams, Avshalom Caspi, Terrie E. Moffitt, Sarah Jane Delany and Therese M. Murphy
    Citation: BMC Bioinformatics 2023 24:178
  6. Pyroptosis is closely related to cancer prognosis. In this study, we tried to construct an individualized prognostic risk model for hepatocellular carcinoma (HCC) based on within-sample relative expression ord...

    Authors: Tong Wu, Na Li, Fengyuan Luo, Zhihong Chen, Liyuan Ma, Tao Hu, Guini Hong and Hongdong Li
    Citation: BMC Bioinformatics 2023 24:176
  7. Complex diseases such as neurodevelopmental disorders (NDDs) exhibit multiple etiologies. The multi-etiological nature of complex-diseases emerges from distinct but functionally similar group of genes. Differe...

    Authors: Muhammad Asif, Hugo F. M. C. Martiniano, Andre Lamurias, Samina Kausar and Francisco M. Couto
    Citation: BMC Bioinformatics 2023 24:171
  8. Genome-wide tests, including genome-wide association studies (GWAS) of germ-line genetic variants, driver tests of cancer somatic mutations, and transcriptome-wide association tests of RNAseq data, carry a hig...

    Authors: Jitong Cai, Jianan Zhan, Dan E. Arking and Joel S. Bader
    Citation: BMC Bioinformatics 2023 24:170
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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

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