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  1. Genes implicated in tumorigenesis often exhibit diverse sets of genomic variants in the tumor cohorts within which they are frequently mutated. For many genes, neither the transcriptomic effects of these varia...

    Authors: Michal R. Grzadkowski, Hannah D. Holly, Julia Somers and Emek Demir

    Citation: BMC Bioinformatics 2021 22:233

    Content type: Research article

    Published on:

  2. Epitope prediction is a useful approach in cancer immunology and immunotherapy. Many computational methods, including machine learning and network analysis, have been developed quickly for such purposes. Howev...

    Authors: Xiaoyun Yang, Liyuan Zhao, Fang Wei and Jing Li

    Citation: BMC Bioinformatics 2021 22:231

    Content type: Methodology article

    Published on:

  3. The identification of gene–gene and gene–environment interactions in genome-wide association studies is challenging due to the unknown nature of the interactions and the overwhelmingly large number of possible...

    Authors: Pål V. Johnsen, Signe Riemer-Sørensen, Andrew Thomas DeWan, Megan E. Cahill and Mette Langaas

    Citation: BMC Bioinformatics 2021 22:230

    Content type: Methodology article

    Published on:

  4. Leveraging previously identified viral interactions with human host proteins, we apply a machine learning-based approach to connect SARS-CoV-2 viral proteins to relevant host biological functions, diseases, an...

    Authors: Andreas Krämer, Jean-Noël Billaud, Stuart Tugendreich, Dan Shiffman, Martin Jones and Jeff Green

    Citation: BMC Bioinformatics 2021 22:229

    Content type: Software

    Published on:

  5. Statistical geneticists employ simulation to estimate the power of proposed studies, test new analysis tools, and evaluate properties of causal models. Although there are existing trait simulators, there is am...

    Authors: Sarah S. Ji, Christopher A. German, Kenneth Lange, Janet S. Sinsheimer, Hua Zhou, Jin Zhou and Eric M. Sobel

    Citation: BMC Bioinformatics 2021 22:228

    Content type: Software

    Published on:

  6. In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such a...

    Authors: Ben Bettisworth and Alexandros Stamatakis

    Citation: BMC Bioinformatics 2021 22:225

    Content type: Software

    Published on:

  7. RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps a researcher must perform ...

    Authors: Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe and Leonardo Collado-Torres

    Citation: BMC Bioinformatics 2021 22:224

    Content type: Software

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:381

  8. Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to ...

    Authors: Jin Li, Wenjie Liu, Huang Li, Feng Chen, Haoran Luo, Peihua Bao, Yanzhao Li, Hailong Jiang, Yue Gao, Hong Liang and Shiaofen Fang

    Citation: BMC Bioinformatics 2021 22:223

    Content type: Research article

    Published on:

  9. Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite the lack of clear sequence homology. They are hard to detect in large sequence databases eith...

    Authors: Witold Dyrka, Marlena Gąsior-Głogowska, Monika Szefczyk and Natalia Szulc

    Citation: BMC Bioinformatics 2021 22:222

    Content type: Methodology article

    Published on:

  10. Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow ...

    Authors: Maria Zanti, Kyriaki Michailidou, Maria A. Loizidou, Christina Machattou, Panagiota Pirpa, Kyproula Christodoulou, George M. Spyrou, Kyriacos Kyriacou and Andreas Hadjisavvas

    Citation: BMC Bioinformatics 2021 22:218

    Content type: Research

    Published on:

  11. lncRNA may be involved in the occurrence, metastasis, and chemical reaction of hepatocellular carcinoma (HCC) through various pathways associated with autophagy. Therefore, it is urgent to reveal more autophag...

    Authors: Shiming Yang, Yaping Zhou, Xiangxin Zhang, Lu Wang, Jianfeng Fu, Xiaotong Zhao and Liu Yang

    Citation: BMC Bioinformatics 2021 22:217

    Content type: Research

    Published on:

  12. Carbonylation is a non-enzymatic irreversible protein post-translational modification, and refers to the side chain of amino acid residues being attacked by reactive oxygen species and finally converted into c...

    Authors: Yun Zuo, Jianyuan Lin, Xiangxiang Zeng, Quan Zou and Xiangrong Liu

    Citation: BMC Bioinformatics 2021 22:216

    Content type: Methodology article

    Published on:

  13. Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomiRs. Some isomiRs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variab...

    Authors: Jose Francisco Sanchez Herrero, Raquel Pluvinet, Antonio Luna de Haro and Lauro Sumoy

    Citation: BMC Bioinformatics 2021 22:215

    Content type: Research article

    Published on:

  14. Area-proportional Euler diagrams are frequently used to visualize data from Microarray experiments, but are also applied to a wide variety of other data from biosciences, social networks and other domains.

    Authors: Michael Wybrow, Peter Rodgers and Fadi K. Dib

    Citation: BMC Bioinformatics 2021 22:214

    Content type: Software

    Published on:

  15. Linear regression models are important tools for learning regulatory networks from gene expression time series. A conventional assumption for non-homogeneous regulatory processes on a short time scale is that ...

    Authors: Mahdi Shafiee Kamalabad and Marco Grzegorczyk

    Citation: BMC Bioinformatics 2021 22(Suppl 2):196

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  16. Genome-wide reconstructions of metabolism opened the way to thorough investigations of cell metabolism for health care and industrial purposes. However, the predictions offered by Flux Balance Analysis (FBA) c...

    Authors: Marco S. Nobile, Vasco Coelho, Dario Pescini and Chiara Damiani

    Citation: BMC Bioinformatics 2021 22(Suppl 2):78

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  17. Mass spectrometry remains the privileged method to characterize proteins. Nevertheless, most of the spectra generated by an experiment remain unidentified after their analysis, mostly because of the modificati...

    Authors: Albane Lysiak, Guillaume Fertin, Géraldine Jean and Dominique Tessier

    Citation: BMC Bioinformatics 2021 22(Suppl 2):65

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  18. Tremor severity assessment is an important step for the diagnosis and treatment decision-making of essential tremor (ET) patients. Traditionally, tremor severity is assessed by using questionnaires (e.g., ETRS...

    Authors: Caro Fuchs, Marco S. Nobile, Guillaume Zamora, Aurélie Degeneffe, Pieter Kubben and Uzay Kaymak

    Citation: BMC Bioinformatics 2021 22(Suppl 2):57

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  19. High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices descri...

    Authors: Daniele D’Agostino, Pietro Liò, Marco Aldinucci and Ivan Merelli

    Citation: BMC Bioinformatics 2021 22(Suppl 2):43

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  20. Unsupervised learning can discover various unseen abnormalities, relying on large-scale unannotated medical images of healthy subjects. Towards this, unsupervised methods reconstruct a 2D/3D single medical ima...

    Authors: Changhee Han, Leonardo Rundo, Kohei Murao, Tomoyuki Noguchi, Yuki Shimahara, Zoltán Ádám Milacski, Saori Koshino, Evis Sala, Hideki Nakayama and Shin’ichi Satoh

    Citation: BMC Bioinformatics 2021 22(Suppl 2):31

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  21. In this research, an astute system has been developed by using machine learning and data mining approach to predict the risk level of cervical and ovarian cancer in association to stress.

    Authors: Sayed Asaduzzaman, Md. Raihan Ahmed, Hasin Rehana, Setu Chakraborty, Md. Shariful Islam and Touhid Bhuiyan

    Citation: BMC Bioinformatics 2021 22:213

    Content type: Research

    Published on:

  22. Mutation-induced variations in the functional architecture of the NaV1.7 channel protein are causally related to a broad spectrum of human pain disorders. Predicting in silico the phenotype of NaV1.7 variant i...

    Authors: Makros N. Xenakis, Dimos Kapetis, Yang Yang, Monique M. Gerrits, Jordi Heijman, Stephen G. Waxman, Giuseppe Lauria, Catharina G. Faber, Ronald L. Westra, Patrick J. Lindsey and Hubert J. Smeets

    Citation: BMC Bioinformatics 2021 22:212

    Content type: Research article

    Published on:

  23. Single-cell RNA sequencing (scRNA-seq) is the most widely used technique to obtain gene expression profiles from complex tissues. Cell subsets and developmental states are often identified via differential gen...

    Authors: Zechuan Chen, Zeruo Yang, Xiaojun Yuan, Xiaoming Zhang and Pei Hao

    Citation: BMC Bioinformatics 2021 22:211

    Content type: Research

    Published on:

  24. Mutations in an enzyme target are one of the most common mechanisms whereby antibiotic resistance arises. Identification of the resistance mutations in bacteria is essential for understanding the structural ba...

    Authors: Qing Ning, Dali Wang, Fei Cheng, Yuheng Zhong, Qi Ding and Jing You

    Citation: BMC Bioinformatics 2021 22:210

    Content type: Research

    Published on:

  25. Graphs are mathematical structures widely used for expressing relationships among elements when representing biomedical and biological information. On top of these representations, several analyses are perform...

    Authors: Nicola Licheri, Vincenzo Bonnici, Marco Beccuti and Rosalba Giugno

    Citation: BMC Bioinformatics 2021 22:209

    Content type: Methodology article

    Published on:

  26. The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualizat...

    Authors: Suzanne Paley and Peter D. Karp

    Citation: BMC Bioinformatics 2021 22:208

    Content type: Software

    Published on:

  27. Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping ...

    Authors: Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z. Sen, Roger P. Wise and Carson M. Andorf

    Citation: BMC Bioinformatics 2021 22:205

    Content type: Software

    Published on:

  28. Drug–target interaction (DTI) plays a vital role in drug discovery. Identifying drug–target interactions related to wet-lab experiments are costly, laborious, and time-consuming. Therefore, computational metho...

    Authors: Seyedeh Zahra Sajadi, Mohammad Ali Zare Chahooki, Sajjad Gharaghani and Karim Abbasi

    Citation: BMC Bioinformatics 2021 22:204

    Content type: Research

    Published on:

  29. Genetic testing is widely used in evaluating a patient’s predisposition to hereditary diseases. In the case of cancer, when a functionally impactful mutation (i.e. genetic variant) is identified in a disease-r...

    Authors: Jesse T. Chao, Calvin D. Roskelley and Christopher J. R. Loewen

    Citation: BMC Bioinformatics 2021 22:202

    Content type: Methodology article

    Published on:

  30. A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this ch...

    Authors: An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren and Melissa Gymrek

    Citation: BMC Bioinformatics 2021 22:201

    Content type: Software

    Published on:

  31. Genotype–phenotype predictions are of great importance in genetics. These predictions can help to find genetic mutations causing variations in human beings. There are many approaches for finding the associatio...

    Authors: Muhammad Muneeb and Andreas Henschel

    Citation: BMC Bioinformatics 2021 22:198

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:319

  32. Recent clinical advances in cancer immuno-therapeutics underscore the need for improved understanding of the complex relationship between cancer and the multiple, multi-functional, inter-dependent, cellular an...

    Authors: Harold P. Frisch, Allan Sprau, Virginia F. McElroy, James D. Turner, Laura R. E. Becher, Wendy K. Nevala, Alexey A. Leontovich and Svetomir N. Markovic

    Citation: BMC Bioinformatics 2021 22:197

    Content type: Research article

    Published on:

  33. ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and a...

    Authors: Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan

    Citation: BMC Bioinformatics 2021 22:193

    Content type: Methodology article

    Published on:

  34. The Cox proportional hazards model is commonly used to predict hazard ratio, which is the risk or probability of occurrence of an event of interest. However, the Cox proportional hazard model cannot directly g...

    Authors: Eu-Tteum Baek, Hyung Jeong Yang, Soo Hyung Kim, Guee Sang Lee, In-Jae Oh, Sae-Ryung Kang and Jung-Joon Min

    Citation: BMC Bioinformatics 2021 22:192

    Content type: Methodology article

    Published on:

  35. Harmonin Homogy Domains (HHD) are recently identified orphan domains of about 70 residues folded in a compact five alpha-helix bundle that proved to be versatile in terms of function, allowing for direct bindi...

    Authors: Baptiste Colcombet-Cazenave, Karen Druart, Crystel Bonnet, Christine Petit, Olivier Spérandio, Julien Guglielmini and Nicolas Wolff

    Citation: BMC Bioinformatics 2021 22:190

    Content type: Research article

    Published on:

  36. We previously developed TANTIGEN, a comprehensive online database cataloging more than 1000 T cell epitopes and HLA ligands from 292 tumor antigens. In TANTIGEN 2.0, we significantly expanded coverage in both ...

    Authors: Guanglan Zhang, Lou Chitkushev, Lars Rønn Olsen, Derin B. Keskin and Vladimir Brusic

    Citation: BMC Bioinformatics 2021 22(Suppl 8):40

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 8

  37. Despite the importance of alternative poly-adenylation and 3′ UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data.

    Authors: Stefan Gerber, Gerhard Schratt and Pierre-Luc Germain

    Citation: BMC Bioinformatics 2021 22:189

    Content type: Methodology article

    Published on:

  38. The genomics data analysis has been widely used to study disease genes and drug targets. However, the existence of missing values in genomics datasets poses a significant problem, which severely hinders the us...

    Authors: Xinshan Zhu, Jiayu Wang, Biao Sun, Chao Ren, Ting Yang and Jie Ding

    Citation: BMC Bioinformatics 2021 22:188

    Content type: Methodology article

    Published on:

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