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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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:

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. Cancer stem cells (CSCs) have features such as the ability to self-renew, differentiate into defined progenies and initiate the tumor growth. Treatments of cancer include drugs, chemotherapy and radiotherapy o...

    Authors: Monalisa Mandal, Sanjeeb Kumar Sahoo, Priyadarsan Patra, Saurav Mallik and Zhongming Zhao

    Citation: BMC Bioinformatics 2020 21(Suppl 21):499

    Content type: Research

    Published on:

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

  31. 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

  32. Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools ...

    Authors: Munira Alballa and Gregory Butler

    Citation: BMC Bioinformatics 2020 21(Suppl 19):575

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 19

  33. RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different al...

    Authors: Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini and Maria Paola Martelli

    Citation: BMC Bioinformatics 2020 21(Suppl 19):574

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 19

  34. Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disorder...

    Authors: Yasaman Karami, Paul Saighi, Rémy Vanderhaegen, Denis Gerlier, Sonia Longhi, Elodie Laine and Alessandra Carbone

    Citation: BMC Bioinformatics 2020 21(Suppl 19):573

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 19

  35. Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published lit...

    Authors: Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen and Cecile Paris

    Citation: BMC Bioinformatics 2020 21(Suppl 19):572

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 19

  36. Biomedical research projects deal with data management requirements from multiple sources like funding agencies’ guidelines, publisher policies, discipline best practices, and their own users’ needs. We descri...

    Authors: M. Suhr, C. Lehmann, C. R. Bauer, T. Bender, C. Knopp, L. Freckmann, B. Öst Hansen, C. Henke, G. Aschenbrandt, L. K. Kühlborn, S. Rheinländer, L. Weber, B. Marzec, M. Hellkamp, P. Wieder, U. Sax…

    Citation: BMC Bioinformatics 2020 21:582

    Content type: Software

    Published on:

  37. Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. Existing computational approaches us...

    Authors: Yongzhuang Liu, Jian Liu and Yadong Wang

    Citation: BMC Bioinformatics 2020 21(Suppl 16):547

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

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