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  1. The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration...

    Authors: Atul Kamboj, Claus V. Hallwirth, Ian E. Alexander, Geoffrey B. McCowage and Belinda Kramer
    Citation: BMC Bioinformatics 2017 18:305
    Content type: Software Published on:

  2. Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify...

    Authors: Kolja Stahl, Michael Schneider and Oliver Brock
    Citation: BMC Bioinformatics 2017 18:303
    Content type: Research Article Published on:

  4. The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-s...

    Authors: Stephen J. Bush, Mary E. B. McCulloch, Kim M. Summers, David A. Hume and Emily L. Clark
    Citation: BMC Bioinformatics 2017 18:301
    Content type: Methodology Article Published on:

  5. DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding p...

    Authors: Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu and Keliang Li
    Citation: BMC Bioinformatics 2017 18:300
    Content type: Research article Published on:

  7. The low success rate and high cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. The Anatomical Therapeutic Chemical (ATC) Code System is a World Healt...

    Authors: Thomas Olson and Rahul Singh
    Citation: BMC Bioinformatics 2017 18(Suppl 8):266
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  8. Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytome...

    Authors: Sunny Raj, Faraz Hussain, Zubir Husein, Neslisah Torosdagli, Damla Turgut, Narsingh Deo, Sumanta Pattanaik, Chung-Che (Jeff) Chang and Sumit Kumar Jha
    Citation: BMC Bioinformatics 2017 18(Suppl 8):245
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  9. For fighting cancer, earlier detection is crucial. Circulating auto-antibodies produced by the patient’s own immune system after exposure to cancer proteins are promising bio-markers for the early detection of...

    Authors: Ekaterina Gerasimov, Alex Zelikovsky, Ion Măndoiu and Yurij Ionov
    Citation: BMC Bioinformatics 2017 18(Suppl 8):244
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  10. The notion of centrality is used to identify “important” nodes in social networks. Importance of nodes is not well-defined, and many different notions exist in the literature. The challenge of defining centrality...

    Authors: Trevor Cickovski, Eli Peake, Vanessa Aguiar-Pulido and Giri Narasimhan
    Citation: BMC Bioinformatics 2017 18(Suppl 8):239
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  11. Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer base...

    Authors: Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan and Srinivas Aluru
    Citation: BMC Bioinformatics 2017 18(Suppl 8):238
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  13. CRISPR is a versatile gene editing tool which has revolutionized genetic research in the past few years. Optimizing sgRNA design to improve the efficiency of target/DNA cleavage is critical to ensure the succe...

    Authors: Pei Fen Kuan, Scott Powers, Shuyao He, Kaiqiao Li, Xiaoyu Zhao and Bo Huang
    Citation: BMC Bioinformatics 2017 18:297
    Content type: Research Article Published on:

  14. Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipeli...

    Authors: Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta and Marcos J. Araúzo-Bravo
    Citation: BMC Bioinformatics 2017 18:296
    Content type: Software Published on:

  15. Despite advances in the gene-set enrichment analysis methods; inadequate definitions of gene-sets cause a major limitation in the discovery of novel biological processes from the transcriptomic datasets. Typic...

    Authors: Atif Khan, Dejan Katanic and Juilee Thakar
    Citation: BMC Bioinformatics 2017 18:295
    Content type: Research Article Published on:

  16. Global scale brain research collaborations such as the ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis) consortium are beginning to collect data in large quantity and to conduct meta-analyses us...

    Authors: Guohao Zhang, Peter Kochunov, Elliot Hong, Sinead Kelly, Christopher Whelan, Neda Jahanshad, Paul Thompson and Jian Chen
    Citation: BMC Bioinformatics 2017 18(Suppl 6):253
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  17. There exists a need for effective and easy-to-use software tools supporting the analysis of complex Electrocorticography (ECoG) data. Understanding how epileptic seizures develop or identifying diagnostic indi...

    Authors: Sugeerth Murugesan, Kristofer Bouchard, Edward Chang, Max Dougherty, Bernd Hamann and Gunther H. Weber
    Citation: BMC Bioinformatics 2017 18(Suppl 6):236
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  18. Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area...

    Authors: Marianna Milano, Pietro Hiram Guzzi, Olga Tymofieva, Duan Xu, Christofer Hess, Pierangelo Veltri and Mario Cannataro
    Citation: BMC Bioinformatics 2017 18(Suppl 6):235
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  20. Detecting homologous protein sequences and computing multiple sequence alignments (MSA) are fundamental tasks in molecular bioinformatics. These tasks usually require a substitution matrix for modeling evoluti...

    Authors: Frank Keul, Martin Hess, Michael Goesele and Kay Hamacher
    Citation: BMC Bioinformatics 2017 18:293
    Content type: Research Article Published on:

  21. In phylogenetics, we often seek to reconcile gene trees with species trees within the framework of an evolutionary model. While the most popular models for eukaryotic species allow for only gene duplication an...

    Authors: Jennifer Rogers, Andrew Fishberg, Nora Youngs and Yi-Chieh Wu
    Citation: BMC Bioinformatics 2017 18:292
    Content type: Methodology Article Published on:

  22. Dictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of ne...

    Authors: Miha Stajdohar, Rafael D. Rosengarten, Janez Kokosar, Luka Jeran, Domen Blenkus, Gad Shaulsky and Blaz Zupan
    Citation: BMC Bioinformatics 2017 18:291
    Content type: Software Published on:

  23. RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maxi...

    Authors: Marek Palkowski and Wlodzimierz Bielecki
    Citation: BMC Bioinformatics 2017 18:290
    Content type: Research Article Published on:

  27. Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have creat...

    Authors: Fatima Zare, Michelle Dow, Nicholas Monteleone, Abdelrahman Hosny and Sheida Nabavi
    Citation: BMC Bioinformatics 2017 18:286
    Content type: Research article Published on:

  28. Transcription factor (TF) networks play a key role in controlling the transfer of genetic information from gene to mRNA. Much progress has been made on understanding and reverse-engineering TF network topologi...

    Authors: Namshik Han, Harry A. Noyes and Andy Brass
    Citation: BMC Bioinformatics 2017 18(Suppl 7):260
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 7

  29. Genomic analysis of drug response can provide unique insights into therapies that can be used to match the “right drug to the right patient.” However, the process of discovering such therapeutic insights using...

    Authors: Hai Joey Tran, Gil Speyer, Jeff Kiefer and Seungchan Kim
    Citation: BMC Bioinformatics 2017 18(Suppl 7):252
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 7

  30. Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented wi...

    Authors: Go Eun Heo, Keun Young Kang, Min Song and Jeong-Hoon Lee
    Citation: BMC Bioinformatics 2017 18(Suppl 7):251
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 7

  31. Pandemic is a typical spreading phenomenon that can be observed in the human society and is dependent on the structure of the social network. The Susceptible-Infective-Recovered (SIR) model describes spreading...

    Authors: Kiseong Kim, Sangyeon Lee, Doheon Lee and Kwang Hyung Lee
    Citation: BMC Bioinformatics 2017 18(Suppl 7):250
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 7

  33. Computational approaches in the identification of drug targets are expected to reduce time and effort in drug development. Advances in genomics and proteomics provide the opportunity to uncover properties of d...

    Authors: Baeksoo Kim, Jihoon Jo, Jonghyun Han, Chungoo Park and Hyunju Lee
    Citation: BMC Bioinformatics 2017 18(Suppl 7):248
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 7

  34. Drug-induced liver injury (DILI) is a critical issue in drug development because DILI causes failures in clinical trials and the withdrawal of approved drugs from the market. There have been many attempts to p...

    Authors: Eunyoung Kim and Hojung Nam
    Citation: BMC Bioinformatics 2017 18(Suppl 7):227
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 7

  35. Recently, the metabolite-likeness of the drug space has emerged and has opened a new possibility for exploring human metabolite-like candidates in drug discovery. However, the applicability of metabolite-liken...

    Authors: Yoon Hyeok Lee, Hojae Choi, Seongyong Park, Boah Lee and Gwan-Su Yi
    Citation: BMC Bioinformatics 2017 18(Suppl 7):226
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 7

  36. Survival analysis is an important element of reasoning from data. Applied in a number of fields, it has become particularly useful in medicine to estimate the survival rate of patients on the basis of their co...

    Authors: Łukasz Wróbel, Adam Gudyś and Marek Sikora
    Citation: BMC Bioinformatics 2017 18:285
    Content type: Research Article Published on:

  37. Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic ste...

    Authors: Christian Schäfer, Alexander H. Schmidt and Jürgen Sauter
    Citation: BMC Bioinformatics 2017 18:284
    Content type: Software Published on:

  38. Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data. Here we e...

    Authors: Jonathan L. Golob, Elisa Margolis, Noah G. Hoffman and David N. Fredricks
    Citation: BMC Bioinformatics 2017 18:283
    Content type: Research Article Published on:

  40. Histopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the work...

    Authors: Yan Xu, Zhipeng Jia, Liang-Bo Wang, Yuqing Ai, Fang Zhang, Maode Lai and Eric I-Chao Chang
    Citation: BMC Bioinformatics 2017 18:281
    Content type: Methodology Article Published on:

  41. Image segmentation and registration techniques have enabled biologists to place large amounts of volume data from fluorescence microscopy, morphed three-dimensionally, onto a common spatial frame. Existing too...

    Authors: Yong Wan, Hideo Otsuna, Holly A. Holman, Brig Bagley, Masayoshi Ito, A. Kelsey Lewis, Mary Colasanto, Gabrielle Kardon, Kei Ito and Charles Hansen
    Citation: BMC Bioinformatics 2017 18:280
    Content type: Software Published on:

  45. Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantit...

    Authors: Špela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe-Novak and Kristina Gruden
    Citation: BMC Bioinformatics 2017 18:276
    Content type: Software Published on:

  48. Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes....

    Authors: Marijke Van Moerbeke, Adetayo Kasim, Willem Talloen, Joke Reumers, Hinrick W. H. Göhlmann and Ziv Shkedy
    Citation: BMC Bioinformatics 2017 18:273
    Content type: Methodology Article Published on:

  49. In neuroscience research, mouse models are valuable tools to understand the genetic mechanisms that advance evidence-based discovery. In this context, large-scale studies emphasize the need for automated high-...

    Authors: Jakob Unger, Mike Mansour, Marcin Kopaczka, Nina Gronloh, Marc Spehr and Dorit Merhof
    Citation: BMC Bioinformatics 2017 18:272
    Content type: Methodology Article Published on:

  50. Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two...

    Authors: Charles C. David, Ettayapuram Ramaprasad Azhagiya Singam and Donald J. Jacobs
    Citation: BMC Bioinformatics 2017 18:271
    Content type: Software Published on:

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