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  1. Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, thes...

    Authors: Maxwell Spadafore, Kayvan Najarian and Alan P. Boyle
    Citation: BMC Bioinformatics 2017 18:530
    Content type: Methodology Article Published on:

  2. ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions f...

    Authors: Curtis T. Rueden, Johannes Schindelin, Mark C. Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena and Kevin W. Eliceiri
    Citation: BMC Bioinformatics 2017 18:529
    Content type: Software Published on:

  4. Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e....

    Authors: Peter Bajcsy, Soweon Yoon, Stephen J. Florczyk, Nathan A. Hotaling, Mylene Simon, Piotr M. Szczypinski, Nicholas J. Schaub, Carl G. Simon Jr, Mary Brady and Ram D. Sriram
    Citation: BMC Bioinformatics 2017 18:526
    Content type: Research Article Published on:

  6. High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may r...

    Authors: Yao-Ting Huang and Yu-Wen Huang
    Citation: BMC Bioinformatics 2017 18:524
    Content type: Methodology Article Published on:

  7. Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent ...

    Authors: Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu and Kevin L. Childs
    Citation: BMC Bioinformatics 2017 18:522
    Content type: Methodology Article Published on:

  8. Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic...

    Authors: Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang and David Vocadlo
    Citation: BMC Bioinformatics 2017 18:521
    Content type: Software Published on:

  9. Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene thera...

    Authors: Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi and Eugenio Montini
    Citation: BMC Bioinformatics 2017 18:520
    Content type: Software Published on:

  10. Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in m...

    Authors: Levi D. Mcclenny, Mahdi Imani and Ulisses M. Braga-Neto
    Citation: BMC Bioinformatics 2017 18:519
    Content type: Software Published on:

  11. Mantle Cell Lymphoma (MCL) is a B cell aggressive neoplasia accounting for about the 6% of all lymphomas. The most common molecular marker of clonality in MCL, as in other B lymphoproliferative disorders, is t...

    Authors: Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele Calogero, Simone Ferrero and Francesca Cordero
    Citation: BMC Bioinformatics 2017 18:516
    Content type: Research Article Published on:

  12. With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such genetic maps, quantitative ...

    Authors: Fenxiang Liu, Chunfa Tong, Shentong Tao, Jiyan Wu, Yuhua Chen, Dan Yao, Huogen Li and Jisen Shi
    Citation: BMC Bioinformatics 2017 18:515
    Content type: Software Published on:

  14. Gene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologicall...

    Authors: Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan and Casey S. Greene
    Citation: BMC Bioinformatics 2017 18:512
    Content type: Methodology Article Published on:

  15. Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, whil...

    Authors: Kosai Al-Nakeeb, Thomas Nordahl Petersen and Thomas Sicheritz-Pontén
    Citation: BMC Bioinformatics 2017 18:510
    Content type: Software Published on:

  18. Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more ...

    Authors: Daniel Castillo, Juan Manuel Gálvez, Luis Javier Herrera, Belén San Román, Fernando Rojas and Ignacio Rojas
    Citation: BMC Bioinformatics 2017 18:506
    Content type: Research Article Published on:

  19. Brain disorders are one of the top causes of human death. Generally, neurologists analyze brain medical images for diagnosis. In the image analysis field, corners are one of the most important features, which ...

    Authors: Linlin Gao, Haiwei Pan, Qing Li, Xiaoqin Xie, Zhiqiang Zhang, Jinming Han and Xiao Zhai
    Citation: BMC Bioinformatics 2017 18:505
    Content type: Research Article Published on:

  20. The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix a...

    Authors: Nathan Sloat, Jui-Wen Liu and Susan J. Schroeder
    Citation: BMC Bioinformatics 2017 18:504
    Content type: Methodology Article Published on:

  22. ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a...

    Authors: Yomtov Almozlino, Nir Atias, Dana Silverbush and Roded Sharan
    Citation: BMC Bioinformatics 2017 18:495
    Content type: Software Published on:

  23. Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. The...

    Authors: Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng and Guangqin Fan
    Citation: BMC Bioinformatics 2017 18:494
    Content type: Database Published on:

  24. Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding...

    Authors: Sérgio E. D. Dias, Ana Mafalda Martins, Quoc T. Nguyen and Abel J. P. Gomes
    Citation: BMC Bioinformatics 2017 18:493
    Content type: Software Published on:

  25. After publication of this supplement [1], it was brought to our attention that the wrong year was used in the title of the supplement. The 16th Annual UT-KBRIN Bioinformatics Summit was held in 2017.

    Authors: Eric C. Rouchka, Julia L. Chariker, David Tieri and Juw W. Park
    Citation: BMC Bioinformatics 2017 18:490
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2017 18:377

  28. The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Me...

    Authors: Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular and Maja Jagodic
    Citation: BMC Bioinformatics 2017 18:486
    Content type: Methodology Article Published on:

  30. The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexe...

    Authors: Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo and Rui Zhang
    Citation: BMC Bioinformatics 2017 18:482
    Content type: Software Published on:

  31. Gene expression profiling has led to the definition of breast cancer molecular subtypes: Basal-like, HER2-enriched, LuminalA, LuminalB and Normal-like. Different subtypes exhibit diverse responses to treatment...

    Authors: Liying Yang, Yunyan Shen, Xiguo Yuan, Junying Zhang and Jianhua Wei
    Citation: BMC Bioinformatics 2017 18:481
    Content type: Research Article Published on:

  32. With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and c...

    Authors: Oluwatosin Oluwadare and Jianlin Cheng
    Citation: BMC Bioinformatics 2017 18:480
    Content type: Research Article Published on:

  33. MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, ...

    Authors: Duc-Hau Le, Lieven Verbeke, Le Hoang Son, Dinh-Toi Chu and Van-Huy Pham
    Citation: BMC Bioinformatics 2017 18:479
    Content type: Research Article Published on:

  34. Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. ...

    Authors: Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W. Eyre, Anthony Underwood, Derrick Crook and David H. Wyllie
    Citation: BMC Bioinformatics 2017 18:477
    Content type: Software Published on:

  36. Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly en...

    Authors: Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann and Peter W. Hildebrand
    Citation: BMC Bioinformatics 2017 18:475
    Content type: Methodology Article Published on:

  40. Artificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of ...

    Authors: Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda and Koji Tsuda
    Citation: BMC Bioinformatics 2017 18:468
    Content type: Methodology Article Published on:

  41. De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-mem...

    Authors: Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva and Kirk E. Jordan
    Citation: BMC Bioinformatics 2017 18:467
    Content type: Methodology Article Published on:

  43. Biomedical named entity recognition(BNER) is a crucial initial step of information extraction in biomedical domain. The task is typically modeled as a sequence labeling problem. Various machine learning algori...

    Authors: Chen Lyu, Bo Chen, Yafeng Ren and Donghong Ji
    Citation: BMC Bioinformatics 2017 18:462
    Content type: Research Article Published on:

  44. Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009...

    Authors: Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin and Premal Shah
    Citation: BMC Bioinformatics 2017 18:461
    Content type: Database Published on:

  45. Detection of important functional and/or structural elements and identification of their positions in a large eukaryotic genomic sequence are an active research area. Gene is an important functional and struct...

    Authors: Biswanath Chowdhury, Arnav Garai and Gautam Garai
    Citation: BMC Bioinformatics 2017 18:460
    Content type: Methodology Article Published on:

  47. Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accum...

    Authors: Yahya Bokhari and Tomasz Arodz
    Citation: BMC Bioinformatics 2017 18:458
    Content type: Methodology Article Published on:

  48. An organism’s protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally...

    Authors: R. Greg Stacey, Michael A. Skinnider, Nichollas E. Scott and Leonard J. Foster
    Citation: BMC Bioinformatics 2017 18:457
    Content type: Research Article Published on:

  49. In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the bas...

    Authors: Jakub Wiedemann, Tomasz Zok, Maciej Milostan and Marta Szachniuk
    Citation: BMC Bioinformatics 2017 18:456
    Content type: Research Article Published on:

  50. DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variatio...

    Authors: Chaitanya R. Acharya, Kouros Owzar and Andrew S. Allen
    Citation: BMC Bioinformatics 2017 18:455
    Content type: Methodology Article Published on:

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