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  1. 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:

  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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  7. 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

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  8. 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

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  9. 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

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  10. 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

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  11. 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

  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data,...

    Authors: Antoine Buetti-Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Francesco Delogu, Olga Ilie, Sören Bellenberg, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Ran Friedman and Mark Dopson

    Citation: BMC Bioinformatics 2020 21:23

    Content type: Research Article

    Published on:

    A Related Article has been published.

  17. Omics-profiling is a collection of increasingly prominent approaches that result in large-scale biological datasets, for instance capturing an organism’s behavior and response in an environment. It can be daun...

    Authors: Defne Surujon and Tim van Opijnen

    Citation: BMC Bioinformatics 2020 21:22

    Content type: Software

    Published on:

  18. Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analy...

    Authors: Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang and Xianming Shi

    Citation: BMC Bioinformatics 2020 21:20

    Content type: Software

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  19. In order to improve the accuracy of constraint-based metabolic models, several approaches have been developed which intend to integrate additional biological information. Two of these methods, MOMENT and GECKO...

    Authors: Pavlos Stephanos Bekiaris and Steffen Klamt

    Citation: BMC Bioinformatics 2020 21:19

    Content type: Methodology article

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  20. Integrating genome-wide gene expression patient profiles with regulatory knowledge is a challenging task because of the inherent heterogeneity, noise and incompleteness of biological data. From the computation...

    Authors: Maxime Folschette, Vincent Legagneux, Arnaud Poret, Lokmane Chebouba, Carito Guziolowski and Nathalie Théret

    Citation: BMC Bioinformatics 2020 21:18

    Content type: Research Article

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  21. MicroRNAs (miRNAs) play important roles in a variety of biological processes by regulating gene expression at the post-transcriptional level. So, the discovery of new miRNAs has become a popular task in biolog...

    Authors: Xueming Zheng, Xingli Fu, Kaicheng Wang and Meng Wang

    Citation: BMC Bioinformatics 2020 21:17

    Content type: Methodology article

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  22. Cell-type heterogeneity of tumors is a key factor in tumor progression and response to chemotherapy. Tumor cell-type heterogeneity, defined as the proportion of the various cell-types in a tumor, can be inferr...

    Authors: Clémentine Decamps, Florian Privé, Raphael Bacher, Daniel Jost, Arthur Waguet, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Michael G. B. Blum and Magali Richard

    Citation: BMC Bioinformatics 2020 21:16

    Content type: Methodology article

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  23. Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints an...

    Authors: Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen and Rolf Backofen

    Citation: BMC Bioinformatics 2020 21:15

    Content type: Research Article

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  24. The rapid growth of available knowledge on metabolic processes across thousands of species continues to expand the possibilities of producing chemicals by combining pathways found in different species. Several...

    Authors: Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett and Lydia E. Kavraki

    Citation: BMC Bioinformatics 2020 21:13

    Content type: Methodology Article

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  25. Cell nuclei segmentation is a fundamental task in microscopy image analysis, based on which multiple biological related analysis can be performed. Although deep learning (DL) based techniques have achieved sta...

    Authors: Feixiao Long

    Citation: BMC Bioinformatics 2020 21:8

    Content type: Methodology Article

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  26. The green microalga Dunaliella salina accumulates a high proportion of β-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, thi...

    Authors: Melanie Fachet, Carina Witte, Robert J. Flassig, Liisa K. Rihko-Struckmann, Zaid McKie-Krisberg, Jürgen E. W. Polle and Kai Sundmacher

    Citation: BMC Bioinformatics 2020 21:1

    Content type: Research Article

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