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Results and data

This section incorporates novel results, useful tools, and methods using bioinformatics in new ways, including but not limited to: biological conclusions that are only supported by bioinformatics analyses.

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  1. Transcription factors (TFs) act downstream of the major signalling pathways functioning as master regulators of cell fate. Their activity is tightly regulated at the transcriptional, post-transcriptional and p...

    Authors: Gennaro Gambardella, Ivana Peluso, Sandro Montefusco, Mukesh Bansal, Diego L. Medina, Neil Lawrence and Diego di Bernardo

    Citation: BMC Bioinformatics 2015 16:279

    Content type: Methodology article

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  2. Testing dependence/correlation of two variables is one of the fundamental tasks in statistics. In this work, we proposed a new way of testing nonlinear dependence between two continuous variables (X and Y).

    Authors: Yi Wang, Yi Li, Hongbao Cao, Momiao Xiong, Yin Yao Shugart and Li Jin

    Citation: BMC Bioinformatics 2015 16:260

    Content type: Methodology article

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  3. Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS ...

    Authors: Mohammad R. Nezami Ranjbar, Cristina Di Poto, Yue Wang and Habtom W. Ressom

    Citation: BMC Bioinformatics 2015 16:259

    Content type: Software

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  4. Identifying periodically expressed genes across different processes (e.g. the cell and metabolic cycles, circadian rhythms, etc) is a central problem in computational biology. Biological time series may contai...

    Authors: Jose A. Perea, Anastasia Deckard, Steve B. Haase and John Harer

    Citation: BMC Bioinformatics 2015 16:257

    Content type: Methodology Article

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  5. The traditional method used to estimate tree biomass is allometry. In this method, models are tested and equations fitted by regression usually applying ordinary least squares, though other analogous methods a...

    Authors: Carlos R. Sanquetta, Jaime Wojciechowski, Ana P. Dalla Corte, Alexandre Behling, Sylvio Péllico Netto, Aurélio L. Rodrigues and Mateus N. I. Sanquetta

    Citation: BMC Bioinformatics 2015 16:247

    Content type: Research article

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  6. Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integrat...

    Authors: Jonah D. Hocum, Logan R. Battrell, Ryan Maynard, Jennifer E. Adair, Brian C. Beard, David J. Rawlings, Hans-Peter Kiem, Daniel G. Miller and Grant D. Trobridge

    Citation: BMC Bioinformatics 2015 16:212

    Content type: Software

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  7. DNA gyrase, an enzyme once thought to be unique to bacteria, is also found in some eukaryotic plastids including the apicoplast of Apicomplexa such as Plasmodium falciparum and Toxoplasma gondii which are importa...

    Authors: Soshichiro Nagano, Ting-Yu Lin, Jyotheeswara Reddy Edula and Jonathan Gardiner Heddle

    Citation: BMC Bioinformatics 2014 15:416

    Content type: Research article

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  8. According to Regulation (EU) No 619/2011, trace amounts of non-authorised genetically modified organisms (GMO) in feed are tolerated within the EU if certain prerequisites are met. Tolerable traces must not ex...

    Authors: Lars Gerdes, Ulrich Busch and Sven Pecoraro

    Citation: BMC Bioinformatics 2014 15:407

    Content type: Research article

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  9. Cancer immunotherapy has recently entered a remarkable renaissance phase with the approval of several agents for treatment. Cancer treatment platforms have demonstrated profound tumor regressions including com...

    Authors: Andreas Dander, Matthias Baldauf, Michael Sperk, Stephan Pabinger, Benjamin Hiltpolt and Zlatko Trajanoski

    Citation: BMC Bioinformatics 2014 15:306

    Content type: Software

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  10. Computational modeling transcription factor (TF) sequence specificity is an important research topic in regulatory genomics. A systematic comparison of 26 algorithms to learn TF-DNA binding specificity in in vitr...

    Authors: Junbai Wang

    Citation: BMC Bioinformatics 2014 15:289

    Content type: Research article

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  11. Human epidermal growth factor receptor 2 (HER2) has an important role in cancer aggressiveness and poor prognosis. HER2 has been used as a drug target for cancers. In particular, to effectively treat HER2-posi...

    Authors: Wannarat Yim-im, Orathai Sawatdichaikul, Suwanna Semsri, Natharinee Horata, Wanwimon Mokmak, Sissades Tongsima, Apichart Suksamrarn and Kiattawee Choowongkomon

    Citation: BMC Bioinformatics 2014 15:261

    Content type: Research article

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  12. It is important to accurately determine the performance of peptide:MHC binding predictions, as this enables users to compare and choose between different prediction methods and provides estimates of the expect...

    Authors: Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen and Bjoern Peters

    Citation: BMC Bioinformatics 2014 15:241

    Content type: Research article

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  13. Current research suggests that a small set of “driver” mutations are responsible for tumorigenesis while a larger body of “passenger” mutations occur in the tumor but do not progress the disease. Due to recent...

    Authors: Gregory A Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Robert D Bjornson, Daniel Zelterman, Yorgo Modis and Hongyu Zhao

    Citation: BMC Bioinformatics 2014 15:231

    Content type: Methodology article

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  14. Several regulators of programmed cell death (PCD) in plants encode proteins with putative lipid-binding domains. Among them, VAD1 is a regulator of PCD propagation harboring a GRAM putative lipid-binding domai...

    Authors: Mehdi Khafif, Ludovic Cottret, Claudine Balagué and Sylvain Raffaele

    Citation: BMC Bioinformatics 2014 15:222

    Content type: Research article

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  15. Meganucleases are important tools for genome engineering, providing an efficient way to generate DNA double-strand breaks at specific loci of interest. Numerous experimental efforts, ranging from in vivo selectio...

    Authors: Mikhail Zaslavskiy, Claudia Bertonati, Philippe Duchateau, Aymeric Duclert and George H Silva

    Citation: BMC Bioinformatics 2014 15:191

    Content type: Methodology article

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  16. In vitro generated dose-response curves of human cancer cell lines are widely used to develop new therapeutics. The curves are summarised by simplified statistics that ignore the conventionally used dose-response...

    Authors: Steffen Falgreen, Maria Bach Laursen, Julie Støve Bødker, Malene Krag Kjeldsen, Alexander Schmitz, Mette Nyegaard, Hans Erik Johnsen, Karen Dybkær and Martin Bøgsted

    Citation: BMC Bioinformatics 2014 15:168

    Content type: Methodology article

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  17. Coronaviruses are the diverse group of RNA virus. From 1960, six strains of human coronaviruses have emerged that includes SARS-CoV and the recent infection by deadly MERS-CoV which is now going to cause anoth...

    Authors: Refat Sharmin and Abul Bashar Mir Md Khademul Islam

    Citation: BMC Bioinformatics 2014 15:161

    Content type: Research article

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  18. Many variable selection techniques have been proposed for the clustering of gene expression data. While these methods tend to filter out irrelevant genes and identify informative genes that contribute to a clu...

    Authors: Zixing Wang, F Anthony San Lucas, Peng Qiu and Yin Liu

    Citation: BMC Bioinformatics 2014 15:153

    Content type: Research article

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  19. Array based methylation profiling is a cost-effective solution to study the association between genome methylation and human disease & development. Available tools to analyze the Illumina Infinium HumanMethyla...

    Authors: Martin A Rijlaarsdam, Yvonne G van der Zwan, Lambert CJ Dorssers and Leendert HJ Looijenga

    Citation: BMC Bioinformatics 2014 15:141

    Content type: Software

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  20. Studies involving the analysis of structural variation including Copy Number Variation (CNV) have recently exploded in the literature. Furthermore, CNVs have been associated with a number of complex diseases a...

    Authors: Christina A Castellani, Melkaye G Melka, Andrea E Wishart, M Elizabeth O Locke, Zain Awamleh, Richard L O’Reilly and Shiva M Singh

    Citation: BMC Bioinformatics 2014 15:114

    Content type: Research article

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  21. Measuring the impact of combinations of genetic or chemical perturbations on cellular fitness, sometimes referred to as synthetic lethal screening, is a powerful method for obtaining novel insights into gene f...

    Authors: Markus K Muellner, Gerhard Duernberger, Florian Ganglberger, Claudia Kerzendorfer, Iris Z Uras, Andreas Schoenegger, Klaudia Bagienski, Jacques Colinge and Sebastian MB Nijman

    Citation: BMC Bioinformatics 2014 15:98

    Content type: Software

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  22. High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history an...

    Authors: Wei Jiao, Shankar Vembu, Amit G Deshwar, Lincoln Stein and Quaid Morris

    Citation: BMC Bioinformatics 2014 15:35

    Content type: Methodology article

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  23. Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and ana...

    Authors: Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S Almeida, William J Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan and Raja Mazumder

    Citation: BMC Bioinformatics 2014 15:28

    Content type: Methodology article

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  24. The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation h...

    Authors: Eran Elhaik, Matteo Pellegrini and Tatiana V Tatarinova

    Citation: BMC Bioinformatics 2014 15:23

    Content type: Methodology article

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  25. RNA silencing is a process triggered by 21–24 small RNAs to repress gene expression. Many organisms including plants use RNA silencing to regulate development and physiology, and to maintain genome stability. ...

    Authors: Xiang Liu, Tao Lu, Yongchao Dou, Bin Yu and Chi Zhang

    Citation: BMC Bioinformatics 2014 15:4

    Content type: Research article

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  26. Amyloids are proteins capable of forming aberrant intramolecular contact sites, characteristic of beta zipper configuration. Amyloids can underlie serious health conditions, e.g. Alzheimer’s or Parkinson’s dis...

    Authors: Malgorzata Kotulska and Olgierd Unold

    Citation: BMC Bioinformatics 2013 14:351

    Content type: Correspondence

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  27. Gene expression in the Drosophila embryo is controlled by functional interactions between a large network of protein transcription factors (TFs) and specific sequences in DNA cis-regulatory modules (CRMs). The bi...

    Authors: Jessica L Stringham, Adam S Brown, Robert A Drewell and Jacqueline M Dresch

    Citation: BMC Bioinformatics 2013 14:298

    Content type: Research article

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  28. Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying seque...

    Authors: Penelope Coggill, Ruth Y Eberhardt, Robert D Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L Axelrod, L Aravind, Alexey G Murzin and Alex Bateman

    Citation: BMC Bioinformatics 2013 14:265

    Content type: Research article

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  29. Texture within biological specimens may reveal critical insights, while being very difficult to quantify. This is a particular problem in histological analysis. For example, cross-polar images of picrosirius s...

    Authors: Osman S Osman, Joanne L Selway, Parvathy E Harikumar, Claire J Stocker, Edward T Wargent, Michael A Cawthorne, Sabah Jassim and Kenneth Langlands

    Citation: BMC Bioinformatics 2013 14:260

    Content type: Methodology article

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  30. Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and...

    Authors: Annette Block, Frédéric Debode, Lutz Grohmann, Julie Hulin, Isabel Taverniers, Linda Kluga, Elodie Barbau-Piednoir, Sylvia Broeders, Ingrid Huber, Marc Van den Bulcke, Petra Heinze, Gilbert Berben, Ulrich Busch, Nancy Roosens, Eric Janssen, Jana Žel…

    Citation: BMC Bioinformatics 2013 14:256

    Content type: Database

    Published on:

  31. The emergence of high-throughput genomic datasets from different sources and platforms (e.g., gene expression, single nucleotide polymorphisms (SNP), and copy number variation (CNV)) has greatly enhanced our unde...

    Authors: Dongdong Lin, Jigang Zhang, Jingyao Li, Vince D Calhoun, Hong-Wen Deng and Yu-Ping Wang

    Citation: BMC Bioinformatics 2013 14:245

    Content type: Methodology article

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  32. Somatic mutation-calling based on DNA from matched tumor-normal patient samples is one of the key tasks carried by many cancer genome projects. One such large-scale project is The Cancer Genome Atlas (TCGA), w...

    Authors: Su Yeon Kim and Terence P Speed

    Citation: BMC Bioinformatics 2013 14:189

    Content type: Research article

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  33. Next-generation sequencing (NGS) has changed genomics significantly. More and more applications strive for sequencing with different platforms. Now, in 2012, after a decade of development and evolution, NGS ha...

    Authors: Norbert Niklas, Johannes Pröll, Martin Danzer, Stephanie Stabentheiner, Katja Hofer and Christian Gabriel

    Citation: BMC Bioinformatics 2013 14:176

    Content type: Research article

    Published on:

  34. Machine learning techniques are becoming useful as an alternative approach to conventional medical diagnosis or prognosis as they are good for handling noisy and incomplete data, and significant results can be...

    Authors: Siow-Wee Chang, Sameem Abdul-Kareem, Amir Feisal Merican and Rosnah Binti Zain

    Citation: BMC Bioinformatics 2013 14:170

    Content type: Research article

    Published on:

  35. Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed...

    Authors: Josh Eckels, Cory Nathe, Elizabeth K Nelson, Sara G Shoemaker, Elizabeth Van Nostrand, Nicole L Yates, Vicki C Ashley, Linda J Harris, Mark Bollenbeck, Youyi Fong, Georgia D Tomaras and Britt Piehler

    Citation: BMC Bioinformatics 2013 14:145

    Content type: Software

    Published on:

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2019 Journal Metrics

  • Citation Impact
    3.242 - 2-year Impact Factor
    3.213 - 5-year Impact Factor
    1.156 - Source Normalized Impact per Paper (SNIP)
    1.626 - SCImago Journal Rank (SJR)

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