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  1. 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:

  2. 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:

  3. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  10. 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

  12. 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:

  14. 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:

  16. 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:

  18. 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:

  20. 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:

  21. 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:

  24. 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:

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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:

  44. 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:

  46. 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:

  47. 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:

  48. 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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