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  1. Imaging mass spectrometry (imaging MS) is an enabling technology for spatial metabolomics of tissue sections with rapidly growing areas of applications in biology and medicine. However, imaging MS data is poll...

    Authors: Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart and Theodore Alexandrov
    Citation: BMC Bioinformatics 2020 21:129
    Content type: Methodology article Published on:

  2. Accumulated evidence shows that the abnormal regulation of long non-coding RNA (lncRNA) is associated with various human diseases. Accurately identifying disease-associated lncRNAs is helpful to study the mech...

    Authors: Dengju Yao, Xiaojuan Zhan, Xiaorong Zhan, Chee Keong Kwoh, Peng Li and Jinke Wang
    Citation: BMC Bioinformatics 2020 21:126
    Content type: Methodology article Published on:

  3. Both intra- and inter-sentential semantic relations in biomedical texts provide valuable information for biomedical research. However, most existing methods either focus on extracting intra-sentential relation...

    Authors: Zhiheng Li, Zhihao Yang, Yang Xiang, Ling Luo, Yuanyuan Sun and Hongfei Lin
    Citation: BMC Bioinformatics 2020 21:125
    Content type: Methodology article Published on:

  4. The notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged. The broad spectrum of the effects of heme makes it important to i...

    Authors: Ajay Abisheck Paul George, Mauricio Lacerda, Benjamin Franz Syllwasschy, Marie-Thérèse Hopp, Amelie Wißbrock and Diana Imhof
    Citation: BMC Bioinformatics 2020 21:124
    Content type: Research article Published on:

  6. Feature selection in class-imbalance learning has gained increasing attention in recent years due to the massive growth of high-dimensional class-imbalanced data across many scientific fields. In addition to r...

    Authors: Guang-Hui Fu, Yuan-Jiao Wu, Min-Jie Zong and Jianxin Pan
    Citation: BMC Bioinformatics 2020 21:121
    Content type: Research Article Published on:

  7. In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering metho...

    Authors: Audrey Hulot, Julien Chiquet, Florence Jaffrézic and Guillem Rigaill
    Citation: BMC Bioinformatics 2020 21:120
    Content type: Methodology Article Published on:

  8. The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatu...

    Authors: Aaron M. Smith, Jonathan R. Walsh, John Long, Craig B. Davis, Peter Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek and Charles K. Fisher
    Citation: BMC Bioinformatics 2020 21:119
    Content type: Research Article Published on:

  9. mRNA interaction with other mRNAs and other signaling molecules determine different biological pathways and functions. Gene co-expression network analysis methods have been widely used to identify correlation ...

    Authors: Anna M. Nia, Tianlong Chen, Brooke L. Barnette, Kamil Khanipov, Robert L. Ullrich, Suresh K. Bhavnani and Mark R. Emmett
    Citation: BMC Bioinformatics 2020 21:118
    Content type: Methodology article Published on:

  11. After publication of the original article [1], we were notified that legends of Fig. 1 and Fig. 2 have been swapped.

    Authors: Monica J. Quinzo, Esther M. Lafuente, Pilar Zuluaga, Darren R. Flower and Pedro A. Reche
    Citation: BMC Bioinformatics 2020 21:116
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2019 20:476

  13. Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix by mechanical loa...

    Authors: Gianluca Ascolani, Timothy M. Skerry, Damien Lacroix, Enrico Dall’Ara and Aban Shuaib
    Citation: BMC Bioinformatics 2020 21:114
    Content type: Methodology article Published on:

  15. Lung cancer is the leading cause of cancer-related deaths in both men and women in the United States, and it has a much lower five-year survival rate than many other cancers. Accurate survival analysis is urge...

    Authors: Lei Cui, Hansheng Li, Wenli Hui, Sitong Chen, Lin Yang, Yuxin Kang, Qirong Bo and Jun Feng
    Citation: BMC Bioinformatics 2020 21:112
    Content type: Methodology Article Published on:

  17. With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq da...

    Authors: Xiaokang Zhang and Inge Jonassen
    Citation: BMC Bioinformatics 2020 21:110
    Content type: Software Published on:

  19. DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations wi...

    Authors: Joshua J. Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas and Brock C. Christensen
    Citation: BMC Bioinformatics 2020 21:108
    Content type: Methodology article Published on:

  21. Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysi...

    Authors: Du Zhang, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu and Fei Gao
    Citation: BMC Bioinformatics 2020 21:106
    Content type: Software Published on:

  22. Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are...

    Authors: Tsunglin Liu, Chen-Yu Chen, An Chen-Deng, Yi-Lin Chen, Jiu-Yao Wang, Yung-I Hou and Min-Ching Lin
    Citation: BMC Bioinformatics 2020 21:105
    Content type: Methodology article Published on:

  25. All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoi...

    Authors: Robin Kobus, José M. Abuín, André Müller, Sören Lukas Hellmann, Juan C. Pichel, Tomás F. Pena, Andreas Hildebrandt, Thomas Hankeln and Bertil Schmidt
    Citation: BMC Bioinformatics 2020 21:102
    Content type: Software Published on:

  27. Chronic diseases are becoming more widespread each year in developed countries, mainly due to increasing life expectancy. Among them, diabetes mellitus (DM) and essential hypertension (EH) are two of the most ...

    Authors: Cristina Soguero-Ruiz, Inmaculada Mora-Jiménez, Miguel A. Mohedano-Munoz, Manuel Rubio-Sanchez, Pablo de Miguel-Bohoyo and Alberto Sanchez
    Citation: BMC Bioinformatics 2020 21(Suppl 2):92
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  28. Screening programs use mammography as primary diagnostic tool for detecting breast cancer at an early stage. The diagnosis of some lesions, such as microcalcifications, is still difficult today for radiologist...

    Authors: Annarita Fanizzi, Teresa M. A. Basile, Liliana Losurdo, Roberto Bellotti, Ubaldo Bottigli, Rosalba Dentamaro, Vittorio Didonna, Alfonso Fausto, Raffaella Massafra, Marco Moschetta, Ondina Popescu, Pasquale Tamborra, Sabina Tangaro and Daniele La Forgia
    Citation: BMC Bioinformatics 2020 21(Suppl 2):91
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  29. For optimization of microfluidic devices for the analysis of blood samples, it is useful to simulate blood cells as elastic objects in flow of blood plasma. In such numerical models, we primarily need to take ...

    Authors: Hynek Bachratý, Katarína Bachratá, Michal Chovanec, Iveta Jančigová, Monika Smiešková and Kristína Kovalčíková
    Citation: BMC Bioinformatics 2020 21(Suppl 2):90
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  30. Phenotype prediction problems are usually considered ill-posed, as the amount of samples is very limited with respect to the scrutinized genetic probes. This fact complicates the sampling of the defective gene...

    Authors: Ana Cernea, Juan Luis Fernández-Martínez, Enrique J. deAndrés-Galiana, Francisco Javier Fernández-Ovies, Oscar Alvarez-Machancoses, Zulima Fernández-Muñiz, Leorey N. Saligan and Stephen T. Sonis
    Citation: BMC Bioinformatics 2020 21(Suppl 2):89
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  31. In biomedicine, infrared thermography is the most promising technique among other conventional methods for revealing the differences in skin temperature, resulting from the irregular temperature dispersion, wh...

    Authors: Ayca Kirimtat, Ondrej Krejcar, Ali Selamat and Enrique Herrera-Viedma
    Citation: BMC Bioinformatics 2020 21(Suppl 2):88
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  32. The actual task of electrocardiographic examinations is to increase the reliability of diagnosing the condition of the heart. Within the framework of this task, an important direction is the solution of the in...

    Authors: G. V. Zhikhareva, Mikhail N. Kramm, O. N. Bodin, Ralf Seepold, Natividad Martinez Madrid, A. I. Chernikov, Y. A. Kupriyanova and N. A. Zhuravleva
    Citation: BMC Bioinformatics 2020 21(Suppl 2):87
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  33. The current study’s purpose is to compare hip structural analysis variables in a group of postmenopausal women with sarcopenia and another group of postmenopausal women with normal skeletal muscle mass index. ...

    Authors: Hayman Saddik, Riad Nasr, Antonio Pinti, Eric Watelain, Ibrahim Fayad, Rafic Baddoura, Abdel-Jalil Berro, Nathalie Al Rassy, Eric Lespessailles, Hechmi Toumi and Rawad El Hage
    Citation: BMC Bioinformatics 2020 21(Suppl 2):86
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  34. In the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interacti...

    Authors: Renzo Angles, Mauricio Arenas-Salinas, Roberto García, Jose Antonio Reyes-Suarez and Ehmke Pohl
    Citation: BMC Bioinformatics 2020 21(Suppl 2):85
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  35. Melanoma results in the vast majority of skin cancer deaths during the last decades, even though this disease accounts for only one percent of all skin cancers’ instances. The survival rates of melanoma from e...

    Authors: Sara Nasiri, Julien Helsper, Matthias Jung and Madjid Fathi
    Citation: BMC Bioinformatics 2020 21(Suppl 2):84
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  36. Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is...

    Authors: Michael G. Sadovsky, Maria Yu Senashova and Andrew V. Malyshev
    Citation: BMC Bioinformatics 2020 21(Suppl 2):83
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  37. Genomic micro-satellites are the genomic regions that consist of short and repetitive DNA motifs. Estimating the length distribution and state of a micro-satellite region is an important computational step in ...

    Authors: Yixuan Wang, Xuanping Zhang, Xiao Xiao, Fei-Ran Zhang, Xinxing Yan, Xuan Feng, Zhongmeng Zhao, Yanfang Guan and Jiayin Wang
    Citation: BMC Bioinformatics 2020 21(Suppl 2):82
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  38. The identification of all matches of a large set of position weight matrices (PWMs) in long DNA sequences requires significant computational resources for which a number of efficient yet complex algorithms hav...

    Authors: Jan Fostier
    Citation: BMC Bioinformatics 2020 21(Suppl 2):81
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  39. Interactions between proteins and non-proteic small molecule ligands play important roles in the biological processes of living systems. Thus, the development of computational methods to support our understand...

    Authors: Vagner S. Ribeiro, Charles A. Santana, Alexandre V. Fassio, Fabio R. Cerqueira, Carlos H. da Silveira, João P. R. Romanelli, Adriana Patarroyo-Vargas, Maria G. A. Oliveira, Valdete Gonçalves-Almeida, Sandro C. Izidoro, Raquel C. de Melo-Minardi and Sabrina de A. Silveira
    Citation: BMC Bioinformatics 2020 21(Suppl 2):80
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  40. Disease gene prediction is a critical and challenging task. Many computational methods have been developed to predict disease genes, which can reduce the money and time used in the experimental validation. Sin...

    Authors: Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao and Fang-Xiang Wu
    Citation: BMC Bioinformatics 2020 21(Suppl 2):79
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  41. Finding the tumor location in the prostate is an essential pathological step for prostate cancer diagnosis and treatment. The location of the tumor – the laterality – can be unilateral (the tumor is affecting ...

    Authors: Osama Hamzeh, Abedalrhman Alkhateeb, Julia Zheng, Srinath Kandalam and Luis Rueda
    Citation: BMC Bioinformatics 2020 21(Suppl 2):78
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  42. In biomarker discovery, applying domain knowledge is an effective approach to eliminating false positive features, prioritizing functionally impactful markers and facilitating the interpretation of predictive ...

    Authors: Xin Guan, George Runger and Li Liu
    Citation: BMC Bioinformatics 2020 21(Suppl 2):77
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  43. Traditional selection in livestock and crops focuses on additive genetic values or breeding values of the individuals. While traditional selection utilizes variation between individuals, differences between ga...

    Authors: Daniel Jordan de Abreu Santos, John B. Cole, George E. Liu, Paul M. VanRaden and Li Ma
    Citation: BMC Bioinformatics 2020 21:100
    Content type: Software Published on:

  45. Cancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical and logistical issues, however, make it chall...

    Authors: David Soong, Jeran Stratford, Herve Avet-Loiseau, Nizar Bahlis, Faith Davies, Angela Dispenzieri, A. Kate Sasser, Jordan M. Schecter, Ming Qi, Chad Brown, Wendell Jones, Jonathan J. Keats, Daniel Auclair, Christopher Chiu, Jason Powers and Michael Schaffer
    Citation: BMC Bioinformatics 2020 21:98
    Content type: Methodology article Published on:

  47. Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original D...

    Authors: Nicholas Stoler, Barbara Arbeithuber, Gundula Povysil, Monika Heinzl, Renato Salazar, Kateryna D Makova, Irene Tiemann-Boege and Anton Nekrutenko
    Citation: BMC Bioinformatics 2020 21:96
    Content type: Methodology article Published on:

  48. Many cancers arise from mutations in cells within epithelial tissues. Mutations manifesting at the subcellular level influence the structure and function of the tissue resulting in cancer. Previous work has pr...

    Authors: Lotte B. Romijn, Axel A. Almet, Chin Wee Tan and James M. Osborne
    Citation: BMC Bioinformatics 2020 21:95
    Content type: Research Article Published on:

  49. The systems-scale analysis of cellular metabolites, “metabolomics,” provides data ideal for applications in metabolic engineering. However, many of the computational tools for strain design are built around Fl...

    Authors: Robert A. Dromms, Justin Y. Lee and Mark P. Styczynski
    Citation: BMC Bioinformatics 2020 21:93
    Content type: Methodology article Published on:

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