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  1. 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:

  2. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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, Wenxing Li, Jingfei Huang and Wenzhong Xiao
    Citation: BMC Bioinformatics 2020 21:67
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2020 21:409

  10. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  23. 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:

  27. The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don’t code for proteins, yielding a need to infer evolutionary history of sequen...

    Authors: Kun Gao and Jonathan Miller
    Citation: BMC Bioinformatics 2020 21:48
    Content type: Methodology article Published on:

  29. During the last decade, with the aim to solve the challenge of post-genomic and transcriptomic data mining, a plethora of tools have been developed to create, edit and analyze metabolic pathways. In particular...

    Authors: Valentino Palombo, Marco Milanesi, Gabriella Sferra, Stefano Capomaccio, Sandy Sgorlon and Mariasilvia D’Andrea
    Citation: BMC Bioinformatics 2020 21:46
    Content type: Software Published on:

  30. Current popular variant calling pipelines rely on the mapping coordinates of each input read to a reference genome in order to detect variants. Since reads deriving from variant loci that diverge in sequence s...

    Authors: Izaak Coleman, Giacomo Corleone, James Arram, Ho-Cheung Ng, Luca Magnani and Wayne Luk
    Citation: BMC Bioinformatics 2020 21:45
    Content type: Software Published on:

  31. The localization of objects of interest is a key initial step in most image analysis workflows. For biomedical image data, classical image-segmentation methods like thresholding or edge detection are typically...

    Authors: Laurent S. V. Thomas and Jochen Gehrig
    Citation: BMC Bioinformatics 2020 21:44
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2022 23:3

  32. Various methods for differential expression analysis have been widely used to identify features which best distinguish between different categories of samples. Multiple hypothesis testing may leave out explana...

    Authors: Xudong Zhao, Qing Jiao, Hangyu Li, Yiming Wu, Hanxu Wang, Shan Huang and Guohua Wang
    Citation: BMC Bioinformatics 2020 21:43
    Content type: Software Published on:

  33. Glycans are complex sugar chains, crucial to many biological processes. By participating in binding interactions with proteins, glycans often play key roles in host–pathogen interactions. The specificities of ...

    Authors: Lachlan Coff, Jeffrey Chan, Paul A. Ramsland and Andrew J. Guy
    Citation: BMC Bioinformatics 2020 21:42
    Content type: Methodology Article Published on:

  34. Haplotyping reveals chromosome blocks inherited from parents to in vitro fertilized (IVF) embryos in preimplantation genetic diagnosis (PGD), enabling the observation of the transmission of disease alleles bet...

    Authors: Zhiqiang Yan, Xiaohui Zhu, Yuqian Wang, Yanli Nie, Shuo Guan, Ying Kuo, Di Chang, Rong Li, Jie Qiao and Liying Yan
    Citation: BMC Bioinformatics 2020 21:41
    Content type: Software Published on:

  37. Whole genome bisulfite sequencing (WGBS) also known as BS-seq has been widely used to measure the methylation of whole genome at single-base resolution. One of the key steps in the assay is converting unmethyl...

    Authors: Junhua Zhou, Minqiong Zhao, Zefang Sun, Feilong Wu, Yucong Liu, Xianghua Liu, Zuping He, Quanze He and Quanyuan He
    Citation: BMC Bioinformatics 2020 21:38
    Content type: Methodology article Published on:

  40. Automated biomedical named entity recognition and normalization serves as the basis for many downstream applications in information management. However, this task is challenging due to name variations and enti...

    Authors: Huiwei Zhou, Shixian Ning, Zhe Liu, Chengkun Lang, Zhuang Liu and Bizun Lei
    Citation: BMC Bioinformatics 2020 21:35
    Content type: Research article Published on:

  41. To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a potential...

    Authors: Mikołaj Rybiński, Simon Möller, Mikael Sunnåker, Claude Lormeau and Jörg Stelling
    Citation: BMC Bioinformatics 2020 21:34
    Content type: Software Published on:

  42. Studies using quantitative experimental methods have shown that intracellular spatial distribution of molecules plays a central role in many cellular systems. Spatially resolved computer simulations can integr...

    Authors: Satya N.V. Arjunan, Atsushi Miyauchi, Kazunari Iwamoto and Koichi Takahashi
    Citation: BMC Bioinformatics 2020 21:33
    Content type: Methodology Article Published on:

  43. After publication of this supplement article [1], it was brought to our attention that the Fig. 3 was incorrect. The correct Fig. 3 is as below:

    Authors: Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu, Taosheng Xu, Buu Truong, Jiuyong Li, Nini Rao and Thuc Duy Le
    Citation: BMC Bioinformatics 2020 21:32
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2019 20:613

  45. High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to b...

    Authors: Arran K. Turnbull, Cigdem Selli, Carlos Martinez-Perez, Anu Fernando, Lorna Renshaw, Jane Keys, Jonine D. Figueroa, Xiaping He, Maki Tanioka, Alison F. Munro, Lee Murphy, Angie Fawkes, Richard Clark, Audrey Coutts, Charles M. Perou, Lisa A. Carey…
    Citation: BMC Bioinformatics 2020 21:30
    Content type: Research article Published on:

  47. Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step i...

    Authors: Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich Maus, Thomas Illig and David S. DeLuca
    Citation: BMC Bioinformatics 2020 21:28
    Content type: Methodology Article Published on:

  48. Phosphorylated histone H2AX, also known as γH2AX, forms μm-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensit...

    Authors: Simon Memmel, Dmitri Sisario, Heiko Zimmermann, Markus Sauer, Vladimir L. Sukhorukov, Cholpon S. Djuzenova and Michael Flentje
    Citation: BMC Bioinformatics 2020 21:27
    Content type: Methodology article Published on:

  49. With modern methods in biotechnology, the search for biomarkers has advanced to a challenging statistical task exploring high dimensional data sets. Feature selection is a widely researched preprocessing step ...

    Authors: Rudolf Jagdhuber, Michel Lang, Arnulf Stenzl, Jochen Neuhaus and Jörg Rahnenführer
    Citation: BMC Bioinformatics 2020 21:26
    Content type: Methodology Article Published on:

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