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  2. Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction. Currently, most of the distance prediction ...

    Authors: Tianqi Wu, Zhiye Guo, Jie Hou and Jianlin Cheng
    Citation: BMC Bioinformatics 2021 22:30
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:354

  4. Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost eff...

    Authors: Tamer N. Jarada, Jon G. Rokne and Reda Alhajj
    Citation: BMC Bioinformatics 2021 22:28
    Content type: Research article Published on:

  5. Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-e...

    Authors: Lingpeng Kong, Yuanyuan Chen, Fengjiao Xu, Mingmin Xu, Zutan Li, Jingya Fang, Liangyun Zhang and Cong Pian
    Citation: BMC Bioinformatics 2021 22:27
    Content type: Methodology article Published on:

  6. Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a ...

    Authors: Mehrdad Kashefi and Mohammad Reza Daliri
    Citation: BMC Bioinformatics 2021 22:26
    Content type: Research article Published on:

  7. Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structur...

    Authors: Eliza Dhungel, Yassin Mreyoud, Ho-Jin Gwak, Ahmad Rajeh, Mina Rho and Tae-Hyuk Ahn
    Citation: BMC Bioinformatics 2021 22:25
    Content type: Software Published on:

  8. Long non-coding RNAs (lncRNAs) regulate diverse biological processes via interactions with proteins. Since the experimental methods to identify these interactions are expensive and time-consuming, many computa...

    Authors: Dipan Shaw, Hao Chen, Minzhu Xie and Tao Jiang
    Citation: BMC Bioinformatics 2021 22:24
    Content type: Methodology article Published on:

  9. Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data...

    Authors: Xinping Fan, Guanghao Luo and Yu S. Huang
    Citation: BMC Bioinformatics 2021 22:23
    Content type: Methodology article Published on:

  10. In this study, we demonstrate that our modified Gene Set Enrichment Analysis (GSEA) method, drug perturbation GSEA (dpGSEA), can detect phenotypically relevant drug targets through a unique transcriptomic enri...

    Authors: Mike Fang, Brian Richardson, Cheryl M. Cameron, Jean-Eudes Dazard and Mark J. Cameron
    Citation: BMC Bioinformatics 2021 22:22
    Content type: Methodology article Published on:

  15. Querying drug-induced gene expression profiles with machine learning method is an effective way for revealing drug mechanism of actions (MOAs), which is strongly supported by the growth of large scale and high...

    Authors: Shengqiao Gao, Lu Han, Dan Luo, Gang Liu, Zhiyong Xiao, Guangcun Shan, Yongxiang Zhang and Wenxia Zhou
    Citation: BMC Bioinformatics 2021 22:17
    Content type: Research article Published on:

  17. One of the current directions of precision medicine is the use of computational methods to aid in the diagnosis, prognosis, and treatment of disease based on data driven approaches. For instance, in oncology, ...

    Authors: Joshua D. Mannheimer, Ashok Prasad and Daniel L. Gustafson
    Citation: BMC Bioinformatics 2021 22:15
    Content type: Research article Published on:

  20. Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessmen...

    Authors: Bing Song, August E. Woerner and John Planz
    Citation: BMC Bioinformatics 2021 22:12
    Content type: Methodology article Published on:

  21. High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelin...

    Authors: Carlos A. Ruiz-Perez, Roth E. Conrad and Konstantinos T. Konstantinidis
    Citation: BMC Bioinformatics 2021 22:11
    Content type: Software Published on:

  22. Circular RNA (circRNA) is a novel type of RNA with a closed-loop structure. Increasing numbers of circRNAs are being identified in plants and animals, and recent studies have shown that circRNAs play an import...

    Authors: Shuwei Yin, Xiao Tian, Jingjing Zhang, Peisen Sun and Guanglin Li
    Citation: BMC Bioinformatics 2021 22:10
    Content type: Software Published on:

  23. Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent hi...

    Authors: Edwin A. Solares, Yuan Tao, Anthony D. Long and Brandon S. Gaut
    Citation: BMC Bioinformatics 2021 22:9
    Content type: Methodology article Published on:

  24. Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binne...

    Authors: Badri Adhikari, Bikash Shrestha, Matthew Bernardini, Jie Hou and Jamie Lea
    Citation: BMC Bioinformatics 2021 22:8
    Content type: Software Published on:

  25. Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools de...

    Authors: Yilin Ye, Jian Wang, Yunwan Xu, Yi Wang, Youdong Pan, Qi Song, Xing Liu and Ji Wan
    Citation: BMC Bioinformatics 2021 22:7
    Content type: Research article Published on:

  26. Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characte...

    Authors: Johanna Zoppi, Jean-François Guillaume, Michel Neunlist and Samuel Chaffron
    Citation: BMC Bioinformatics 2021 22:6
    Content type: Software Published on:

  28. Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein–protein interaction (PPI) ...

    Authors: Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes and Baldo Oliva
    Citation: BMC Bioinformatics 2021 22:4
    Content type: Software Published on:

  29. Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanog...

    Authors: Nick W. Smith, Paul R. Shorten, Eric Altermann, Nicole C. Roy and Warren C. McNabb
    Citation: BMC Bioinformatics 2021 22:3
    Content type: Research article Published on:

  31. Protein–peptide interactions play a fundamental role in a wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized ...

    Authors: Pedro M. Martins, Lucianna H. Santos, Diego Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de S. Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina A. Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira and Raquel C. de Melo-Minardi
    Citation: BMC Bioinformatics 2021 22:1
    Content type: Database Published on:

  32. As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate ana...

    Authors: Noel-Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard Meindl, Gemma Casadesus and Helen Piontkivska
    Citation: BMC Bioinformatics 2020 21(Suppl 18):578
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 18

  33. Addiction to drugs and alcohol constitutes one of the significant factors underlying the decline in life expectancy in the US. Several context-specific reasons influence drug use and recovery. In particular em...

    Authors: Deeptanshu Jha and Rahul Singh
    Citation: BMC Bioinformatics 2020 21(Suppl 18):554
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 18

  34. Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in...

    Authors: Elham Sherafat, Jordan Force and Ion I. Măndoiu
    Citation: BMC Bioinformatics 2020 21(Suppl 18):498
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 18

  35. Drug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice...

    Authors: Dhara Shah, Christopher Freas, Irene T. Weber and Robert W. Harrison
    Citation: BMC Bioinformatics 2020 21(Suppl 18):497
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 18

  36. In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene ...

    Authors: Sudipta Acharya, Laizhong Cui and Yi Pan
    Citation: BMC Bioinformatics 2020 21(Suppl 18):483
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 18

  37. In molecular epidemiology, comparison of intra-host viral variants among infected persons is frequently used for tracing transmissions in human population and detecting viral infection outbreaks. Application o...

    Authors: David S. Campo and Yury Khudyakov
    Citation: BMC Bioinformatics 2020 21(Suppl 18):482
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 18

  38. Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promi...

    Authors: Rodrigo Ochoa, Mikhail Magnitov, Roman A. Laskowski, Pilar Cossio and Janet M. Thornton
    Citation: BMC Bioinformatics 2020 21:586
    Content type: Methodology article Published on:

  39. Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years, Universal Dependencies (UD) has emerged as the leading fo...

    Authors: Jenna Kanerva, Filip Ginter and Sampo Pyysalo
    Citation: BMC Bioinformatics 2020 21(Suppl 23):580
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 23

  40. Entity normalization is an important information extraction task which has gained renewed attention in the last decade, particularly in the biomedical and life science domains. In these domains, and more gener...

    Authors: Arnaud Ferré, Louise Deléger, Robert Bossy, Pierre Zweigenbaum and Claire Nédellec
    Citation: BMC Bioinformatics 2020 21(Suppl 23):579
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 23

  42. The estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challe...

    Authors: Min Jin Ha, Junghi Kim, Jessica Galloway-Peña, Kim-Anh Do and Christine B. Peterson
    Citation: BMC Bioinformatics 2020 21(Suppl 21):581
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

  43. Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing...

    Authors: Zicheng Zhao, Yingxiao Zhou, Shuai Wang, Xiuqing Zhang, Changfa Wang and Shuaicheng Li
    Citation: BMC Bioinformatics 2020 21(Suppl 21):570
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

  44. The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Inte...

    Authors: Yan Guo, Li Shen, Xinghua Shi, Kai Wang, Yulin Dai and Zhongming Zhao
    Citation: BMC Bioinformatics 2020 21(Suppl 21):563
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

  45. In genomics, we often assume that continuous data, such as gene expression, follow a specific kind of distribution. However we rarely stop to question the validity of this assumption, or consider how broadly a...

    Authors: Laurence de Torrenté, Samuel Zimmerman, Masako Suzuki, Maximilian Christopeit, John M. Greally and Jessica C. Mar
    Citation: BMC Bioinformatics 2020 21(Suppl 21):562
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

  46. Short tandem repeat (STR), or “microsatellite”, is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific r...

    Authors: Qian Liu, Yao Tong and Kai Wang
    Citation: BMC Bioinformatics 2020 21(Suppl 21):542
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

  47. Although genetic risk factors and network-level neuroimaging abnormalities have shown effects on cognitive performance and brain atrophy in Alzheimer’s disease (AD), little is understood about how apolipoprote...

    Authors: Jin Li, Chenyuan Bian, Dandan Chen, Xianglian Meng, Haoran Luo, Hong Liang and Li Shen
    Citation: BMC Bioinformatics 2020 21(Suppl 21):535
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

  48. Cryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D ...

    Authors: Adil Al-Azzawi, Anes Ouadou, Ye Duan and Jianlin Cheng
    Citation: BMC Bioinformatics 2020 21(Suppl 21):534
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

    The Correction to this article has been published in BMC Bioinformatics 2022 23:92

  49. Fingerprint biometrics play an essential role in authentication. It remains a challenge to match fingerprints with the minutiae or ridges missing. Many fingerprints failed to match their targets due to the inc...

    Authors: Yanglin Tu, Zengwei Yao, Jiao Xu, Yilin Liu and Zhe Zhang
    Citation: BMC Bioinformatics 2020 21(Suppl 21):514
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

  50. Alzheimer’s disease (AD) is the most common type of dementia, typically characterized by memory loss followed by progressive cognitive decline and functional impairment. Many clinical trials of potential thera...

    Authors: Taeho Jo, Kwangsik Nho, Shannon L. Risacher and Andrew J. Saykin
    Citation: BMC Bioinformatics 2020 21(Suppl 21):496
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 21

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