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  2. Content type: Methodology article

    The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as ...

    Authors: Zhongwang Yu, Yuangen Yao, Haiyou Deng and Ming Yi

    Citation: BMC Bioinformatics 2019 20:299

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  3. Content type: Research article

    Gene regulatory networks can be modelled in various ways depending on the level of detail required and biological questions addressed. One of the earliest formalisms used for modeling is a Boolean network, alt...

    Authors: Dace Ruklisa, Alvis Brazma, Karlis Cerans, Thomas Schlitt and Juris Viksna

    Citation: BMC Bioinformatics 2019 20:296

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  4. Content type: Methodology article

    The real-time quantitative polymerase chain reaction (qPCR) is routinely used for quantification of nucleic acids and is considered the gold standard in the field of relative nucleic acid measurements. The eff...

    Authors: Yulia Panina, Arno Germond, Brit G. David and Tomonobu M. Watanabe

    Citation: BMC Bioinformatics 2019 20:295

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  5. Content type: Research article

    Biochemical networks are often described through static or time-averaged measurements of the component macromolecules. Temporal variation in these components plays an important role in both describing the dyna...

    Authors: Maryam Masnadi-Shirazi, Mano R. Maurya, Gerald Pao, Eugene Ke, Inder M. Verma and Shankar Subramaniam

    Citation: BMC Bioinformatics 2019 20:294

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  7. Content type: Methodology article

    Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromat...

    Authors: Denise Thiel, Nataša Djurdjevac Conrad, Evgenia Ntini, Ria X. Peschutter, Heike Siebert and Annalisa Marsico

    Citation: BMC Bioinformatics 2019 20:292

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  9. Content type: Research

    Drug candidates often cause an unwanted blockage of the potassium ion channel of the human ether-a-go-go-related gene (hERG). The blockage leads to long QT syndrome (LQTS), which is a severe life-threatening c...

    Authors: Hyang-Mi Lee, Myeong-Sang Yu, Sayada Reemsha Kazmi, Seong Yun Oh, Ki-Hyeong Rhee, Myung-Ae Bae, Byung Ho Lee, Dae-Seop Shin, Kwang-Seok Oh, Hyithaek Ceong, Donghyun Lee and Dokyun Na

    Citation: BMC Bioinformatics 2019 20(Suppl 10):250

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    This article is part of a Supplement: Volume 20 Supplement 10

  10. Content type: Research

    Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and sh...

    Authors: Wonjin Yoon, Chan Ho So, Jinhyuk Lee and Jaewoo Kang

    Citation: BMC Bioinformatics 2019 20(Suppl 10):249

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    This article is part of a Supplement: Volume 20 Supplement 10

  11. Content type: Research

    Computational analysis of complex diseases involving multiple organs requires the integration of multiple different models into a unified model. Different models are often constructed in heterogeneous formats....

    Authors: Mijin Kwon, Soorin Yim, Gwangmin Kim, Saehwan Lee, Chungsun Jeong and Doheon Lee

    Citation: BMC Bioinformatics 2019 20(Suppl 10):248

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    This article is part of a Supplement: Volume 20 Supplement 10

  12. Content type: Research

    Drug repositioning, also known as drug repurposing, defines new indications for existing drugs and can be used as an alternative to drug development. In recent years, the accumulation of large volumes of infor...

    Authors: Eunyoung Kim, A-sol Choi and Hojung Nam

    Citation: BMC Bioinformatics 2019 20(Suppl 10):247

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    This article is part of a Supplement: Volume 20 Supplement 10

  13. Content type: Research

    Given the increasing amount of biomedical resources that are being annotated with concepts from more than one ontology and covering multiple domains of knowledge, it is important to devise mechanisms to compar...

    Authors: João D. Ferreira and Francisco M. Couto

    Citation: BMC Bioinformatics 2019 20(Suppl 10):246

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    This article is part of a Supplement: Volume 20 Supplement 10

  14. Content type: Research

    The selection of reference genes is essential for quantifying gene expression. Theoretically they should be expressed stably and not regulated by experimental or pathological conditions. However, identificatio...

    Authors: Jihoon Jo, Sunkyung Choi, Jooseong Oh, Sung-Gwon Lee, Song Yi Choi, Kee K. Kim and Chungoo Park

    Citation: BMC Bioinformatics 2019 20(Suppl 10):245

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    This article is part of a Supplement: Volume 20 Supplement 10

  15. Content type: Research

    Due to the advent of deep learning, the increasing number of studies in the biomedical domain has attracted much interest in feature extraction and classification tasks. In this research, we seek the best comb...

    Authors: Zolzaya Dashdorj and Min Song

    Citation: BMC Bioinformatics 2019 20(Suppl 10):244

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    This article is part of a Supplement: Volume 20 Supplement 10

  16. Content type: Methodology article

    Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide app...

    Authors: Bruno M. S. Wanderley, Daniel S. A. Araújo, María V. Quiroga, André M. Amado, Adrião D. D. Neto, Hugo Sarmento, Sebastián D. Metz and Fernando Unrein

    Citation: BMC Bioinformatics 2019 20:274

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  17. Content type: Methodology article

    Modern molecular profiling techniques are yielding vast amounts of data from patient samples that could be utilized with machine learning methods to provide important biological insights and improvements in pa...

    Authors: Heinrich Roder, Carlos Oliveira, Lelia Net, Benjamin Linstid, Maxim Tsypin and Joanna Roder

    Citation: BMC Bioinformatics 2019 20:273

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  18. Content type: Methodology article

    Establishment of telomere maintenance mechanisms is a universal step in tumor development to achieve replicative immortality. These processes leave molecular footprints in cancer genomes in the form of altered...

    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

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  21. Content type: Software

    Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For...

    Authors: Zhiguo Li, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew Allen and Kouros Owzar

    Citation: BMC Bioinformatics 2019 20:269

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  23. Content type: Research article

    The recent success of immunotherapy in treating tumors has attracted increasing interest in research related to the adaptive immune system in the tumor microenvironment. Recent advances in next-generation sequ...

    Authors: Hiroki Konishi, Daisuke Komura, Hiroto Katoh, Shinichiro Atsumi, Hirotomo Koda, Asami Yamamoto, Yasuyuki Seto, Masashi Fukayama, Rui Yamaguchi, Seiya Imoto and Shumpei Ishikawa

    Citation: BMC Bioinformatics 2019 20:267

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  25. Content type: Methodology article

    In standard high throughput sequencing analysis, genetic variants are not assigned to a homologous chromosome of origin. This process, called haplotype phasing, can reveal information important for understandi...

    Authors: Alexandra R. Buckley, Trey Ideker, Hannah Carter and Nicholas J. Schork

    Citation: BMC Bioinformatics 2019 20:265

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  26. Content type: Software

    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

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  27. Content type: Software

    The retrieval of plant-related information is a challenging task due to variations in species name mentions as well as spelling or typographical errors across data sources. Scalable solutions are needed for id...

    Authors: Vivekanand Sharma, Maria Isabel Restrepo and Indra Neil Sarkar

    Citation: BMC Bioinformatics 2019 20:263

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  28. Content type: Software

    Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platfo...

    Authors: Andreas Hofmann, Sarah Preston, Megan Cross, H. M. P. Dilrukshi Herath, Anne Simon and Robin B. Gasser

    Citation: BMC Bioinformatics 2019 20:262

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  29. Content type: Methodology article

    Pairwise alignment of short DNA sequences with affine-gap scoring is a common processing step performed in a range of bioinformatics analyses. Dynamic programming (i.e. Smith-Waterman algorithm) is widely used...

    Authors: Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic and Sri Parameswaran

    Citation: BMC Bioinformatics 2019 20:261

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  30. Content type: Research article

    Automatic extraction of chemical-disease relations (CDR) from unstructured text is of essential importance for disease treatment and drug development. Meanwhile, biomedical experts have built many highly-struc...

    Authors: Huiwei Zhou, Chengkun Lang, Zhuang Liu, Shixian Ning, Yingyu Lin and Lei Du

    Citation: BMC Bioinformatics 2019 20:260

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  32. Content type: Research article

    Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretati...

    Authors: Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres and Philipp Rescheneder

    Citation: BMC Bioinformatics 2019 20:258

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  33. Content type: Methodology article

    Set enrichment methods are commonly used to analyze high-dimensional molecular data and gain biological insight into molecular or clinical phenotypes. One important category of analysis methods employs an enri...

    Authors: Joanna Roder, Benjamin Linstid and Carlos Oliveira

    Citation: BMC Bioinformatics 2019 20:257

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  35. Content type: Database

    The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio reri...

    Authors: Joseph Brown, Aaron R. Phillips, David A. Lewis, Michael-Andres Mans, Yvonne Chang, Robert L. Tanguay, Elena S. Peterson, Katrina M. Waters and Susan C. Tilton

    Citation: BMC Bioinformatics 2019 20:255

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  36. Content type: Software

    Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribut...

    Authors: E. Mossotto, J. J. Ashton, L. O’Gorman, R. J. Pengelly, R. M. Beattie, B. D. MacArthur and S. Ennis

    Citation: BMC Bioinformatics 2019 20:254

    Published on:

  37. Content type: Methodology article

    The development of whole genome bisulfite sequencing has made it possible to identify methylation differences at single base resolution throughout an entire genome. However, a persistent challenge in DNA methy...

    Authors: Akanksha Srivastava, Yuliya V. Karpievitch, Steven R. Eichten, Justin O. Borevitz and Ryan Lister

    Citation: BMC Bioinformatics 2019 20:253

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  38. Content type: Correction

    After publication of this supplement article

    Authors: Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong and Huixiao Hong

    Citation: BMC Bioinformatics 2019 20:252

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:101

  39. Content type: Software

    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

    Published on:

  42. Content type: Software

    Large-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological da...

    Authors: Jaume Bonet, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck and Bruno E. Correia

    Citation: BMC Bioinformatics 2019 20:240

    Published on:

  43. Content type: Software

    With advancements in high-throughput technologies, the cost of obtaining expression profiles of both mRNA and microRNA in the same individual has substantially decreased. Integrated analysis of these profiles ...

    Authors: Ti-Tai Wang, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu and Eric Y. Chuang

    Citation: BMC Bioinformatics 2019 20:239

    Published on:

  44. Content type: Research article

    Cancer as a worldwide problem is driven by genomic alterations. With the advent of high-throughput sequencing technology, a huge amount of genomic data generates at every second which offer many valuable cance...

    Authors: Junrong Song, Wei Peng and Feng Wang

    Citation: BMC Bioinformatics 2019 20:238

    Published on:

  46. Content type: Software

    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

    Published on:

  47. Content type: Software

    A microRNA (miRNA) sponge is an RNA molecule with multiple tandem miRNA response elements that can sequester miRNAs from their target mRNAs. Despite growing appreciation of the importance of miRNA sponges, our...

    Authors: Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li and Thuc Duy Le

    Citation: BMC Bioinformatics 2019 20:235

    Published on:

  48. Content type: Software

    The Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.

    Authors: Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook and Carlos Flores

    Citation: BMC Bioinformatics 2019 20:234

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  49. Content type: Research article

    Living organisms need to allocate their limited resources in a manner that optimizes their overall fitness by simultaneously achieving several different biological objectives. Examination of these biological t...

    Authors: Ali Navid, Yongqin Jiao, Sergio Ernesto Wong and Jennifer Pett-Ridge

    Citation: BMC Bioinformatics 2019 20:233

    Published on:

  50. Content type: Methodology article

    Draft quality genomes for a multitude of organisms have become common due to the advancement of genome assemblers using long-read technologies with high error rates. Although current assemblies are substantial...

    Authors: Philipp Bongartz

    Citation: BMC Bioinformatics 2019 20:232

    Published on:

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