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  1. 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:

  2. 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:

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. MicroRNA (miRNA) regulation is associated with several diseases, including neurodegenerative diseases. Several approaches can be used for modeling miRNA regulation. However, their precision may be limited for ...

    Authors: Lucile Mégret, Satish Sasidharan Nair, Julia Dancourt, Jeff Aaronson, Jim Rosinski and Christian Neri

    Citation: BMC Bioinformatics 2020 21:75

    Content type: Research article

    Published on:

  25. Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, sho...

    Authors: Michelle L. Treiber, Diana H. Taft, Ian Korf, David A. Mills and Danielle G. Lemay

    Citation: BMC Bioinformatics 2020 21:74

    Content type: Research article

    Published on:

  26. The transitions between epithelial (E) and mesenchymal (M) cell phenotypes are essential in many biological processes like tissue development and cancer metastasis. Previous studies, both modeling and experime...

    Authors: Ying Xin, Bree Cummins and Tomáš Gedeon

    Citation: BMC Bioinformatics 2020 21:71

    Content type: Research Article

    Published on:

  27. The study of functional associations between ncRNAs and human diseases is a pivotal task of modern research to develop new and more effective therapeutic approaches. Nevertheless, it is not a trivial task sinc...

    Authors: Emanuele Pio Barracchia, Gianvito Pio, Domenica D’Elia and Michelangelo Ceci

    Citation: BMC Bioinformatics 2020 21:70

    Content type: Methodology Article

    Published on:

  28. In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we prop...

    Authors: Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira and Susana Vinga

    Citation: BMC Bioinformatics 2020 21:69

    Content type: Software

    Published on:

  29. Genome-wide association studies (GWAS) provide a powerful means to identify associations between genetic variants and phenotypes. However, GWAS techniques for detecting epistasis, the interactions between gene...

    Authors: Yu-Chuan Chang, June-Tai Wu, Ming-Yi Hong, Yi-An Tung, Ping-Han Hsieh, Sook Wah Yee, Kathleen M. Giacomini, Yen-Jen Oyang and Chien-Yu Chen

    Citation: BMC Bioinformatics 2020 21:68

    Content type: Software

    Published on:

  30. Constraint-based metabolic modeling has been applied to understand metabolism related disease mechanisms, to predict potential new drug targets and anti-metabolites, and to identify biomarkers of complex disea...

    Authors: Gong-Hua Li, Shaoxing Dai, Feifei Han, Wenxin Li, Jingfei Huang and Wenzhong Xiao

    Citation: BMC Bioinformatics 2020 21:67

    Content type: Software

    Published on:

  31. Advances in whole genome sequencing strategies have provided the opportunity for genomic and comparative genomic analysis of a vast variety of organisms. The analysis results are highly dependent on the qualit...

    Authors: Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt and Torbjørn Rognes

    Citation: BMC Bioinformatics 2020 21:66

    Content type: Software

    Published on:

  32. Single-cell RNA sequencing (scRNA-seq) is an emerging technology that can assess the function of an individual cell and cell-to-cell variability at the single cell level in an unbiased manner. Dimensionality r...

    Authors: Eugene Lin, Sudipto Mukherjee and Sreeram Kannan

    Citation: BMC Bioinformatics 2020 21:64

    Content type: Methodology article

    Published on:

  33. Key aspects of microbiome research are the accurate identification of taxa and the profiling of their functionality. Amplicon profiling based on the 16S ribosomal DNA sequence is a ubiquitous technique to iden...

    Authors: Mrinmoy Das, Tarini Shankar Ghosh and Ian B. Jeffery

    Citation: BMC Bioinformatics 2020 21:62

    Content type: Methodology article

    Published on:

  34. The aberrant expression of microRNAs is closely connected to the occurrence and development of a great deal of human diseases. To study human diseases, numerous effective computational models that are valuable...

    Authors: Zhen Gao, Yu-Tian Wang, Qing-Wen Wu, Jian-Cheng Ni and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2020 21:61

    Content type: Methodology article

    Published on:

  35. The interactions between non-coding RNAs (ncRNA) and proteins play an essential role in many biological processes. Several high-throughput experimental methods have been applied to detect ncRNA-protein interac...

    Authors: Hai-Cheng Yi, Zhu-Hong You, Mei-Neng Wang, Zhen-Hao Guo, Yan-Bin Wang and Ji-Ren Zhou

    Citation: BMC Bioinformatics 2020 21:60

    Content type: Methodology article

    Published on:

  36. To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been in...

    Authors: Celine Everaert, Pieter-Jan Volders, Annelien Morlion, Olivier Thas and Pieter Mestdagh

    Citation: BMC Bioinformatics 2020 21:58

    Content type: Methodology article

    Published on:

  37. The maintenance of protein structural stability requires the cooperativity among spatially neighboring residues. Previous studies have shown that conserved residues tend to occur clustered together within enzy...

    Authors: Zhen Yang, Xueqing Deng, Yang Liu, Weikang Gong and Chunhua Li

    Citation: BMC Bioinformatics 2020 21:57

    Content type: Research article

    Published on:

  38. Quality Control in any high-throughput sequencing technology is a critical step, which if overlooked can compromise an experiment and the resulting conclusions. A number of methods exist to identify biases dur...

    Authors: Gaurav Kumar, Adam Ertel, George Feldman, Joan Kupper and Paolo Fortina

    Citation: BMC Bioinformatics 2020 21:56

    Content type: Software

    Published on:

  39. Epigenetic regulation is essential in regulating gene expression across a variety of biological processes. Many high-throughput sequencing technologies have been widely used to generate epigenetic data, such a...

    Authors: Jia Li, Yue Yin, Mutian Zhang, Jie Cui, Zhenhai Zhang, Zhiyong Zhang and Deqiang Sun

    Citation: BMC Bioinformatics 2020 21:55

    Content type: Software

    Published on:

  40. Feature selection is a crucial step in machine learning analysis. Currently, many feature selection approaches do not ensure satisfying results, in terms of accuracy and computational time, when the amount of ...

    Authors: Mattia Chiesa, Giada Maioli, Gualtiero I. Colombo and Luca Piacentini

    Citation: BMC Bioinformatics 2020 21:54

    Content type: Software

    Published on:

  41. HIV/AIDS is responsible for the deaths of one million people every year. Although mathematical modeling has provided many insights into the dynamics of HIV infection, there is still a lack of accessible tools ...

    Authors: Sinead E Morris, Luise Dziobek-Garrett, Andrew J Yates and in collaboration with the EPIICAL Consortium

    Citation: BMC Bioinformatics 2020 21:52

    Content type: Software

    Published on:

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