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438 result(s) for 'Software' within Volume 20 of BMC Bioinformatics

Page 2 of 9

  1. High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track cons...

    Authors: Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev and Ivan V. Kulakovskiy
    Citation: BMC Bioinformatics 2019 20:113
  2. With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI ...

    Authors: Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin and Alexander L. Greninger
    Citation: BMC Bioinformatics 2019 20:48
  3. COMMAND>_ facilitates the creation of local datasets of gene expression data coming from both microarray and RNA-seq experiments and may be a more efficient tool to build integrated gene expression compendia. COM...

    Authors: Marco Moretto, Paolo Sonego, Ana B. Villaseñor-Altamirano and Kristof Engelen
    Citation: BMC Bioinformatics 2019 20:54
  4. With an ontology that represents patient-centric dialogue to communicate health information, we have an application-driven model that formalizes the structure for the communication of health information, and a re...

    Authors: Muhammad Amith, Kirk Roberts and Cui Tao
    Citation: BMC Bioinformatics 2019 20(Suppl 21):706

    This article is part of a Supplement: Volume 20 Supplement 21

  5. De novo assembling of large genomes, such as in conifers (~ 12–30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assemb...

    Authors: Dmitry A. Kuzmin, Sergey I. Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Yuliya A. Putintseva, Natalya V. Oreshkova and Konstantin V. Krutovsky
    Citation: BMC Bioinformatics 2019 20(Suppl 1):37

    This article is part of a Supplement: Volume 20 Supplement 1

  6. Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations,...

    Authors: Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki and Dario Greco
    Citation: BMC Bioinformatics 2019 20:79
  7. Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and req...

    Authors: Lang Yang, Xia Zhang, Yuqi Liu, Hao Li, Shaofu Qiu, Peng Li and Hongbin Song
    Citation: BMC Bioinformatics 2019 20:215
  8. Molecular simulations are used to provide insight into protein structure and dynamics, and have the potential to provide important context when predicting the impact of sequence variation on protein function. In ...

    Authors: Matthew D. McCoy, Vikram Shivakumar, Sridhar Nimmagadda, Mohsin Saleet Jafri and Subha Madhavan
    Citation: BMC Bioinformatics 2019 20:171
  9. The development of sequencing techniques and statistical methods provides great opportunities for identifying the impact of rare genetic variation on complex traits. However, there is a lack of knowledge on th...

    Authors: Xinyuan Zhang, Anna O. Basile, Sarah A. Pendergrass and Marylyn D. Ritchie
    Citation: BMC Bioinformatics 2019 20:46
  10. Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, ...

    Authors: Ryan O. Schenck, Eszter Lakatos, Chandler Gatenbee, Trevor A. Graham and Alexander R.A. Anderson
    Citation: BMC Bioinformatics 2019 20:264
  11. The Chinese National Infrastructure of Cell Line stores and distributes cell lines for biomedical research in China. This study aims to represent and integrate the information of NICR cell lines into the commu...

    Authors: Hongjie Pan, Xiaocui Bian, Sheng Yang, Yongqun He, Xiaolin Yang and Yuqin Liu
    Citation: BMC Bioinformatics 2019 20(Suppl 5):179

    This article is part of a Supplement: Volume 20 Supplement 5

  12. Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed s...

    Authors: Xikang Feng, Zishuai Wang, Hechen Li and Shuai Cheng Li
    Citation: BMC Bioinformatics 2019 20(Suppl 24):596

    This article is part of a Supplement: Volume 20 Supplement 24

  13. Bisulfite sequencing allows base-pair resolution profiling of DNA methylation and has recently been adapted for use in single-cells. Analyzing these data, including making comparisons with existing data, remai...

    Authors: Divy Kangeyan, Andrew Dunford, Sowmya Iyer, Chip Stewart, Megan Hanna, Gad Getz and Martin J. Aryee
    Citation: BMC Bioinformatics 2019 20:160
  14. Existing tools for the aggregation and visualization of differential expression data have discrete functionality and require that end-users rely on multiple software packages with complex dependencies or manually...

    Authors: Adam Price, Adrian Caciula, Cheng Guo, Bohyun Lee, Juliet Morrison, Angela Rasmussen, W. Ian Lipkin and Komal Jain
    Citation: BMC Bioinformatics 2019 20:110
  15. Researchers commonly analyze lists of differentially expressed entities (DEEs), such as differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and differentially methylated positions/...

    Authors: Stanislav A. Listopad and Trina M. Norden-Krichmar
    Citation: BMC Bioinformatics 2019 20:595
  16. Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well...

    Authors: Yu Xu, Zhe Lin, Chong Tang, Yujing Tang, Yue Cai, Hongbin Zhong, Xuebin Wang, Wenwei Zhang, Chongjun Xu, Jingjing Wang, Jian Wang, Huanming Yang, Linfeng Yang and Qiang Gao
    Citation: BMC Bioinformatics 2019 20:153
  17. Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extrac...

    Authors: Rebecca C. Jackson, James P. Balhoff, Eric Douglass, Nomi L. Harris, Christopher J. Mungall and James A. Overton
    Citation: BMC Bioinformatics 2019 20:407
  18. We here present TelomereHunter, a software for the detailed characterization of telomere maintenance...

    Authors: Lars Feuerbach, Lina Sieverling, Katharina I. Deeg, Philip Ginsbach, Barbara Hutter, Ivo Buchhalter, Paul A. Northcott, Sadaf S. Mughal, Priya Chudasama, Hanno Glimm, Claudia Scholl, Peter Lichter, Stefan Fröhling, Stefan M. Pfister, David T. W. Jones, Karsten Rippe…
    Citation: BMC Bioinformatics 2019 20:272
  19. We developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined...

    Authors: Kaining Hu, Kai Xu, Jing Wen, Bin Yi, Jinxiong Shen, Chaozhi Ma, Tingdong Fu, Yidan Ouyang and Jinxing Tu
    Citation: BMC Bioinformatics 2019 20:354
  20. The complexity of representing biological systems is compounded by an ever-expanding body of knowledge emerging from multi-omics experiments. A number of pathway databases have facilitated pathway-centric appr...

    Authors: Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt and Martin Hofmann-Apitius
    Citation: BMC Bioinformatics 2019 20:243
  21. High throughput sequencing technologies have been increasingly used in basic genetic research as well as in clinical applications. More and more variants underlying Mendelian and complex diseases are being dis...

    Authors: Mohammad Zia, Paul Spurgeon, Adrian Levesque, Thomas Furlani and Jianxin Wang
    Citation: BMC Bioinformatics 2019 20:61
  22. Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in dev...

    Authors: Konrad Zych, Gerrit Gort, Chris A. Maliepaard, Ritsert C. Jansen and Roeland E. Voorrips
    Citation: BMC Bioinformatics 2019 20:148
  23. A crucial task in metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and search...

    Authors: Cuncong Zhong, Youngik Yang and Shibu Yooseph
    Citation: BMC Bioinformatics 2019 20(Suppl 11):276

    This article is part of a Supplement: Volume 20 Supplement 11

  24. Recent comparative studies have brought to our attention how somatic mutation detection from next-generation sequencing data is still an open issue in bioinformatics, because different pipelines result in a low c...

    Authors: Noemi Di Nanni, Marco Moscatelli, Matteo Gnocchi, Luciano Milanesi and Ettore Mosca
    Citation: BMC Bioinformatics 2019 20:107
  25. Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data access...

    Authors: Daniel Perez-Gil, Francisco J. Lopez, Joaquin Dopazo, Pablo Marin-Garcia, Augusto Rendon and Ignacio Medina
    Citation: BMC Bioinformatics 2019 20:159
  26. High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population un...

    Authors: Chandler D. Gatenbee, Ryan O. Schenck, Rafael R. Bravo and Alexander R. A. Anderson
    Citation: BMC Bioinformatics 2019 20:710
  27. Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate d...

    Authors: Salvatore Alaimo, Antonio Di Maria, Dennis Shasha, Alfredo Ferro and Alfredo Pulvirenti
    Citation: BMC Bioinformatics 2019 20(Suppl 9):366

    This article is part of a Supplement: Volume 20 Supplement 9

  28. With the widespread use of multiple amplicon-sequencing (MAS) in genetic variation detection, an efficient tool is required to remove primer sequences from short reads to ensure the reliability of downstream a...

    Authors: Xiaolong Zhang, Yanyan Shao, Jichao Tian, Yuwei Liao, Peiying Li, Yu Zhang, Jun Chen and Zhiguang Li
    Citation: BMC Bioinformatics 2019 20:236
  29. R-loops are three-stranded nucleic acid structures that usually form during transcription and that may lead to gene regulation or genome instability. DRIP (DNA:RNA Immunoprecipitation)-seq techniques are widel...

    Authors: Marco Russo, Bruno De Lucca, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi and Giovanni Capranico
    Citation: BMC Bioinformatics 2019 20:414
  30. Between June 9–11, 2019, the International Conference on Intelligent Biology and Medicine (ICIBM 2019) was held in Columbus, Ohio, USA. The conference included 12 scientific sessions, five tutorials or worksho...

    Authors: Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy Mathé, Lai Wei and Kai Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 24):676

    This article is part of a Supplement: Volume 20 Supplement 24

    The Correction to this article has been published in BMC Bioinformatics 2020 21:148

  31. Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questi...

    Authors: Joshua R. Williams, Ruoting Yang, John L. Clifford, Daniel Watson, Ross Campbell, Derese Getnet, Raina Kumar, Rasha Hammamieh and Marti Jett
    Citation: BMC Bioinformatics 2019 20:81
  32. Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with D...

    Authors: Min Li, Li Tang, Fang-Xiang Wu, Yi Pan and Jianxin Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 15):515

    This article is part of a Supplement: Volume 20 Supplement 15

  33. The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification ...

    Authors: Jungmin Ha, Ho Hwi Jeon, Dong U. Woo, Yejin Lee, Halim Park, Joohyeong Lee and Yang Jae Kang
    Citation: BMC Bioinformatics 2019 20(Suppl 13):384

    This article is part of a Supplement: Volume 20 Supplement 13

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